101
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Urban JM, Foulk MS, Bliss JE, Coleman CM, Lu N, Mazloom R, Brown SJ, Spradling AC, Gerbi SA. High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing. BMC Genomics 2021; 22:643. [PMID: 34488624 PMCID: PMC8419958 DOI: 10.1186/s12864-021-07926-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 08/08/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features that challenge the rule of genome DNA constancy. For example, Sciara undergoes paternal chromosome elimination and maternal X chromosome nondisjunction during spermatogenesis, paternal X elimination during embryogenesis, intrachromosomal DNA amplification of DNA puff loci during larval development, and germline-limited chromosome elimination from all somatic cells. Paternal chromosome elimination in Sciara was the first observation of imprinting, though the mechanism remains a mystery. Here, we present the first draft genome sequence for Sciara coprophila to take a large step forward in addressing these features. RESULTS We assembled the Sciara genome using PacBio, Nanopore, and Illumina sequencing. To find an optimal assembly using these datasets, we generated 44 short-read and 50 long-read assemblies. We ranked assemblies using 27 metrics assessing contiguity, gene content, and dataset concordance. The highest-ranking assemblies were scaffolded using BioNano optical maps. RNA-seq datasets from multiple life stages and both sexes facilitated genome annotation. A set of 66 metrics was used to select the first draft assembly for Sciara. Nearly half of the Sciara genome sequence was anchored into chromosomes, and all scaffolds were classified as X-linked or autosomal by coverage. CONCLUSIONS We determined that X-linked genes in Sciara males undergo dosage compensation. An entire bacterial genome from the Rickettsia genus, a group known to be endosymbionts in insects, was co-assembled with the Sciara genome, opening the possibility that Rickettsia may function in sex determination in Sciara. Finally, the signal level of the PacBio and Nanopore data support the presence of cytosine and adenine modifications in the Sciara genome, consistent with a possible role in imprinting.
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Affiliation(s)
- John M Urban
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall for Life Sciences, 185 Meeting Street, Providence, RI, 02912, USA.
- Department of Embryology, Carnegie Institution for Science, Howard Hughes Medical Institute Research Laboratories, 3520 San Martin Drive, Baltimore, MD, 21218, USA.
| | - Michael S Foulk
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall for Life Sciences, 185 Meeting Street, Providence, RI, 02912, USA
- Present Address: Department of Biology, Mercyhurst University, Erie, PA, 16546, USA
| | - Jacob E Bliss
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall for Life Sciences, 185 Meeting Street, Providence, RI, 02912, USA
| | - C Michelle Coleman
- KSU Bioinformatics Center, Kansas State University Division of Biology, Ackert Hall, Manhattan, Kansas, 66502, USA
| | - Nanyan Lu
- KSU Bioinformatics Center, Kansas State University Division of Biology, Ackert Hall, Manhattan, Kansas, 66502, USA
| | - Reza Mazloom
- KSU Bioinformatics Center, Kansas State University Division of Biology, Ackert Hall, Manhattan, Kansas, 66502, USA
| | - Susan J Brown
- KSU Bioinformatics Center, Kansas State University Division of Biology, Ackert Hall, Manhattan, Kansas, 66502, USA
| | - Allan C Spradling
- Department of Embryology, Carnegie Institution for Science, Howard Hughes Medical Institute Research Laboratories, 3520 San Martin Drive, Baltimore, MD, 21218, USA
| | - Susan A Gerbi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall for Life Sciences, 185 Meeting Street, Providence, RI, 02912, USA.
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102
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Kaskinova M, Yunusbayev B, Altinbaev R, Raffiudin R, Carpenter MH, Kwon HW, Nikolenko A, Harpur BA, Yunusbaev U. Improved Apis mellifera reference genome based on the alternative long-read-based assemblies. G3-GENES GENOMES GENETICS 2021; 11:6317671. [PMID: 34544128 PMCID: PMC8661400 DOI: 10.1093/g3journal/jkab223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/20/2021] [Indexed: 11/14/2022]
Abstract
Apis mellifera L., the western honey bee is a major crop pollinator that plays a key role in beekeeping and serves as an important model organism in social behavior studies. Recent efforts have improved on the quality of the honey bee reference genome and developed a chromosome-level assembly of 16 chromosomes, two of which are gapless. However, the rest suffer from 51 gaps, 160 unplaced/unlocalized scaffolds, and the lack of 2 distal telomeres. The gaps are located at the hard-to-assemble extended highly repetitive chromosomal regions that may contain functional genomic elements. Here, we use de novo re-assemblies from the most recent reference genome Amel_HAv_3.1 raw reads and other long-read-based assemblies (INRA_AMelMel_1.0, ASM1384120v1, and ASM1384124v1) of the honey bee genome to resolve 13 gaps, five unplaced/unlocalized scaffolds and, the lacking telomeres of the Amel_HAv_3.1. The total length of the resolved gaps is 848,747 bp. The accuracy of the corrected assembly was validated by mapping PacBio reads and performing gene annotation assessment. Comparative analysis suggests that the PacBio-reads-based assemblies of the honey bee genomes failed in the same highly repetitive extended regions of the chromosomes, especially on chromosome 10. To fully resolve these extended repetitive regions, further work using ultra-long Nanopore sequencing would be needed. Our updated assembly facilitates more accurate reference-guided scaffolding and marker/sequence mapping in honey bee genomics studies.
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Affiliation(s)
- Milyausha Kaskinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of Russian Academy of Sciences, Ufa 450054, Russia
| | - Bayazit Yunusbayev
- SCAMT Institute, ITMO University, Saint-Petersburg 191002, Russia.,Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Radick Altinbaev
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, Moscow 117485, Russia
| | - Rika Raffiudin
- Department of Biology, Faculty of Mathematics and Natural Sciences, IPB University, Bogor 16680, Indonesia
| | | | - Hyung Wook Kwon
- Division of Life Sciences & Convergence Research Center for Insect Vectors, Incheon National University, Incheon 22012, Republic of Korea
| | - Alexey Nikolenko
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of Russian Academy of Sciences, Ufa 450054, Russia
| | - Brock A Harpur
- Department of Entomology, Purdue University, West Lafayette, IN 47907, USA
| | - Ural Yunusbaev
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of Russian Academy of Sciences, Ufa 450054, Russia.,Division of Life Sciences & Convergence Research Center for Insect Vectors, Incheon National University, Incheon 22012, Republic of Korea
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103
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Morales-Cruz A, Aguirre-Liguori JA, Zhou Y, Minio A, Riaz S, Walker AM, Cantu D, Gaut BS. Introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation. Genome Biol 2021; 22:254. [PMID: 34479604 PMCID: PMC8414701 DOI: 10.1186/s13059-021-02467-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 08/12/2021] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Introgressive hybridization can reassort genetic variants into beneficial combinations, permitting adaptation to new ecological niches. To evaluate evolutionary patterns and dynamics that contribute to introgression, we investigate six wild Vitis species that are native to the Southwestern United States and useful for breeding grapevine (V. vinifera) rootstocks. RESULTS By creating a reference genome assembly from one wild species, V. arizonica, and by resequencing 130 accessions, we focus on identifying putatively introgressed regions (pIRs) between species. We find six species pairs with signals of introgression between them, comprising up to ~ 8% of the extant genome for some pairs. The pIRs tend to be gene poor, located in regions of high recombination and enriched for genes implicated in disease resistance functions. To assess potential pIR function, we explore SNP associations to bioclimatic variables and to bacterial levels after infection with the causative agent of Pierce's disease (Xylella fastidiosa). pIRs are enriched for SNPs associated with both climate and bacterial levels, suggesting that introgression is driven by adaptation to biotic and abiotic stressors. CONCLUSIONS Altogether, this study yields insights into the genomic extent of introgression, potential pressures that shape adaptive introgression, and the evolutionary history of economically important wild relatives of a critical crop.
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Affiliation(s)
- Abraham Morales-Cruz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA USA
| | | | - Yongfeng Zhou
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA USA
| | - Andrea Minio
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Summaira Riaz
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Andrew M. Walker
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Brandon S. Gaut
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA USA
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104
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Arastehfar A, Marcet-Houben M, Daneshnia F, Taj-Aldeen S, Batra D, Lockhart S, Shor E, Gabaldón T, Perlin D. Comparative genomic analysis of clinical Candida glabrata isolates identifies multiple polymorphic loci that can improve existing multilocus sequence typing strategy. Stud Mycol 2021; 100:100133. [PMID: 34909054 PMCID: PMC8640552 DOI: 10.1016/j.simyco.2021.100133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Candida glabrata is the second leading cause of candidemia in many countries and is one of the most concerning yeast species of nosocomial importance due to its increasing rate of antifungal drug resistance and emerging multidrug-resistant isolates. Application of multilocus sequence typing (MLST) to clinical C. glabrata isolates revealed an association of certain sequence types (STs) with drug resistance and mortality. The current C. glabrata MLST scheme is based on single nucleotide polymorphisms (SNPs) at six loci and is therefore relatively laborious and costly. Furthermore, only a few high-quality C. glabrata reference genomes are available, limiting rapid analysis of clinical isolates by whole genome sequencing. In this study we provide long-read based assemblies for seven additional clinical strains belonging to three different STs and use this information to simplify the C. glabrata MLST scheme. Specifically, a comparison of these genomes identified highly polymorphic loci (HPL) defined by frequent insertions and deletions (indels), two of which proved to be highly resolutive for ST. When challenged with 53 additional isolates, a combination of TRP1 (a component of the current MLST scheme) with either of the two HPL fully recapitulated ST identification. Therefore, our comparative genomic analysis identified a new typing approach combining SNPs and indels and based on only two loci, thus significantly simplifying ST identification in C. glabrata. Because typing tools are instrumental in addressing numerous clinical and biological questions, our new MLST scheme can be used for high throughput typing of C. glabrata in clinical and research settings.
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Affiliation(s)
- A. Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - M. Marcet-Houben
- Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona 29, 08034, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - F. Daneshnia
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | | | - D. Batra
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - S.R. Lockhart
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - E. Shor
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
- Hackensack Meridian Health School of Medicine, Nutley, NJ, 07710, USA
| | - T. Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona 29, 08034, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - D.S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
- Hackensack Meridian Health School of Medicine, Nutley, NJ, 07710, USA
- Georgetown University Lombardi Comprehensive Cancer Center, Department of Microbiology and Immunology, Washington, DC, 20057, USA
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105
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Zhang YD, Zhang YY, Chen JY, Huang JQ, Zhang J, Liu L, Wang D, Zhao J, Song J, Li R, Yang L, Kong ZQ, Klosterman SJ, Subbarao KV, Dai XF, Zhang DD. Genome Sequence Data of MAT1-1 and MAT1-2 Idiomorphs from Verticillium dahliae. PHYTOPATHOLOGY 2021; 111:1686-1691. [PMID: 33673752 DOI: 10.1094/phyto-01-21-0012-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Though Verticillium dahliae is an asexually reproducing fungus, it is considered heterothallic owing to the presence of only one of the two mating-type idiomorphs (MAT1-1 or MAT1-2) in individual isolates. But sexual reproduction has never been observed either in nature or in the laboratory. All of the genomic information in the literature thus far has therefore come from studies on isolates carrying only the MAT1-2 idiomorph. Herein, we sequenced and compared high-quality reference genomes of MAT1-1 strain S011 and MAT1-2 strain S023 obtained from the same sunflower field. The two genomic sequences displayed high synteny, and encoded similar number genes, a similarity especially notable among pathogenicity-related genes. Homolog analysis between these two genomes revealed that 80% of encoded genes are highly conserved (95% identity and coverage), but only 20% of the single copy genes were identical. These novel genome resources will support the analysis of the structure and function of the two idiomorphs and provide valuable tools to elucidate the evolution and potential mechanisms of sexual reproduction in V. dahliae.
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Affiliation(s)
- Ya-Duo Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yuan-Yuan Zhang
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Jie-Yin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | | | - Jian Zhang
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Lin Liu
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Dan Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jun Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Jian Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ran Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lin Yang
- BGI-Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhi-Qiang Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Steven J Klosterman
- U.S. Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA, U.S.A
| | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, Salinas, CA, U.S.A
| | - Xiao-Feng Dai
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Dan-Dan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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106
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Kang L, Qian L, Zheng M, Chen L, Chen H, Yang L, You L, Yang B, Yan M, Gu Y, Wang T, Schiessl SV, An H, Blischak P, Liu X, Lu H, Zhang D, Rao Y, Jia D, Zhou D, Xiao H, Wang Y, Xiong X, Mason AS, Chris Pires J, Snowdon RJ, Hua W, Liu Z. Genomic insights into the origin, domestication and diversification of Brassica juncea. Nat Genet 2021; 53:1392-1402. [PMID: 34493868 PMCID: PMC8423626 DOI: 10.1038/s41588-021-00922-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 07/23/2021] [Indexed: 02/07/2023]
Abstract
Despite early domestication around 3000 BC, the evolutionary history of the ancient allotetraploid species Brassica juncea (L.) Czern & Coss remains uncertain. Here, we report a chromosome-scale de novo assembly of a yellow-seeded B. juncea genome by integrating long-read and short-read sequencing, optical mapping and Hi-C technologies. Nuclear and organelle phylogenies of 480 accessions worldwide supported that B. juncea is most likely a single origin in West Asia, 8,000-14,000 years ago, via natural interspecific hybridization. Subsequently, new crop types evolved through spontaneous gene mutations and introgressions along three independent routes of eastward expansion. Selective sweeps, genome-wide trait associations and tissue-specific RNA-sequencing analysis shed light on the domestication history of flowering time and seed weight, and on human selection for morphological diversification in this versatile species. Our data provide a comprehensive insight into the origin and domestication and a foundation for genomics-based breeding of B. juncea.
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Affiliation(s)
- Lei Kang
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Lunwen Qian
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, China
| | - Ming Zheng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Liyang Chen
- Novogene Bioinformatics Institute, Beijing, China
| | - Hao Chen
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Liu Yang
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Liang You
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Bin Yang
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Guizhou Institute of Oil Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Mingli Yan
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life Science, Hunan University of Science and Technology, Xiangtan, China
| | - Yuanguo Gu
- Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Tianyi Wang
- Novogene Bioinformatics Institute, Beijing, China
| | | | - Hong An
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Paul Blischak
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Xianjun Liu
- College of Life Sciences, Resources and Environment Sciences, Yichun University, Yichun, China
| | - Hongfeng Lu
- Novogene Bioinformatics Institute, Beijing, China
| | - Dawei Zhang
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life Science, Hunan University of Science and Technology, Xiangtan, China
| | - Yong Rao
- Guizhou Institute of Oil Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Donghai Jia
- Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Dinggang Zhou
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life Science, Hunan University of Science and Technology, Xiangtan, China
| | - Huagui Xiao
- Guizhou Institute of Oil Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yonggang Wang
- Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Xinghua Xiong
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Annaliese S Mason
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
- Plant Breeding Department, University of Bonn, Bonn, Germany
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Wei Hua
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China.
| | - Zhongsong Liu
- College of Agronomy, Hunan Agricultural University, Changsha, China.
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107
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Haas M, Kono T, Macchietto M, Millas R, McGilp L, Shao M, Duquette J, Qiu Y, Hirsch CN, Kimball J. Whole-genome assembly and annotation of northern wild rice, Zizania palustris L., supports a whole-genome duplication in the Zizania genus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1802-1818. [PMID: 34310794 DOI: 10.1111/tpj.15419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 06/16/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Zizania palustris L. (northern wild rice, NWR) is an aquatic grass native to North America that is notable for its nutritious grain. This is an important species with ecological, cultural and agricultural significance, specifically in the Great Lakes region of the USA. Using flow cytometry, we first estimated the NWR genome size to be 1.8 Gb. Using long- and short-range sequencing, Hi-C scaffolding and RNA-seq data from eight tissues, we generated an annotated whole-genome de novo assembly of NWR. The assembly was 1.29 Gb in length, highly repetitive (approx. 76.0%) and contained 46 421 putative protein-coding genes. The expansion of retrotransposons within the genome and a whole-genome duplication (WGD) after the Zizania-Oryza speciation event have both led to an increase in the genome size of NWR in comparison with Oryza sativa L. and Zizania latifolia. Both events depict a genome rapidly undergoing change over a short evolutionary time. Comparative analyses revealed the conservation of large syntenic blocks between NWR and O. sativa, which were used to identify putative seed-shattering genes. Estimates of divergence times revealed that the Zizania genus diverged from Oryza approximately 26-30 million years ago (26-30 MYA), whereas NWR and Z. latifolia diverged from one another approximately 6-8 MYA. Comparative genomics confirmed evidence of a WGD in the Zizania genus and provided support that the event occurred prior to the NWR-Z. latifolia speciation event. This genome assembly and annotation provides a valuable resource for comparative genomics in the Oryzeae tribe and provides an important resource for future conservation and breeding efforts of NWR.
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Affiliation(s)
- Matthew Haas
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Thomas Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Marissa Macchietto
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Reneth Millas
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Lillian McGilp
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Mingqin Shao
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Jacques Duquette
- North Central Research and Outreach Center, University of Minnesota, Grand Rapids, MN, 55744, USA
| | - Yinjie Qiu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Jennifer Kimball
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
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108
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Gainett G, González VL, Ballesteros JA, Setton EVW, Baker CM, Barolo Gargiulo L, Santibáñez-López CE, Coddington JA, Sharma PP. The genome of a daddy-long-legs (Opiliones) illuminates the evolution of arachnid appendages. Proc Biol Sci 2021; 288:20211168. [PMID: 34344178 PMCID: PMC8334856 DOI: 10.1098/rspb.2021.1168] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/14/2021] [Indexed: 12/24/2022] Open
Abstract
Chelicerate arthropods exhibit dynamic genome evolution, with ancient whole-genome duplication (WGD) events affecting several orders. Yet, genomes remain unavailable for a number of poorly studied orders, such as Opiliones (daddy-long-legs), which has hindered comparative study. We assembled the first harvestman draft genome for the species Phalangium opilio, which bears elongate, prehensile appendages, made possible by numerous distal articles called tarsomeres. Here, we show that the genome of P. opilio exhibits a single Hox cluster and no evidence of WGD. To investigate the developmental genetic basis for the quintessential trait of this group-the elongate legs-we interrogated the function of the Hox genes Deformed (Dfd) and Sex combs reduced (Scr), and a homologue of Epidermal growth factor receptor (Egfr). Knockdown of Dfd incurred homeotic transformation of two pairs of legs into pedipalps, with dramatic shortening of leg segments in the longest leg pair, whereas homeosis in L3 is only achieved upon double Dfd + Scr knockdown. Knockdown of Egfr incurred shortened appendages and the loss of tarsomeres. The similarity of Egfr loss-of-function phenotypic spectra in insects and this arachnid suggest that repeated cooption of EGFR signalling underlies the independent gains of supernumerary tarsomeres across the arthropod tree of life.
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Affiliation(s)
- Guilherme Gainett
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, 53706 WI, USA
| | - Vanessa L. González
- Global Genome Initiative, Smithsonian Institution, National Museum of Natural History, 10th and Constitution, NW, Washington, DC 20560-0105, USA
| | - Jesús A. Ballesteros
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, 53706 WI, USA
| | - Emily V. W. Setton
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, 53706 WI, USA
| | - Caitlin M. Baker
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, 53706 WI, USA
| | | | - Carlos E. Santibáñez-López
- Department of Biological and Environmental Sciences, Western Connecticut State University, 181 White St, Danbury, CT 06810, USA
| | - Jonathan A. Coddington
- Global Genome Initiative, Smithsonian Institution, National Museum of Natural History, 10th and Constitution, NW, Washington, DC 20560-0105, USA
| | - Prashant P. Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, 53706 WI, USA
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109
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Yuan XL, Zhang CS, Kong FY, Zhang ZF, Wang FL. Genome Analysis of Phytophthora nicotianae JM01 Provides Insights into Its Pathogenicity Mechanisms. PLANTS 2021; 10:plants10081620. [PMID: 34451665 PMCID: PMC8400872 DOI: 10.3390/plants10081620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/01/2021] [Accepted: 08/04/2021] [Indexed: 12/21/2022]
Abstract
Phytophthora nicotianae is a widely distributed plant pathogen that can cause serious disease and cause significant economic losses to various crops, including tomatoes, tobacco, onions, and strawberries. To understand its pathogenic mechanisms and explore strategies for controlling diseases caused by this pathogen, we sequenced and analyzed the whole genome of Ph. nicotianae JM01. The Ph. nicotianae JM01 genome was assembled using a combination of approaches including shotgun sequencing, single-molecule sequencing, and the Hi-C technique. The assembled Ph. nicotianae JM01 genome is about 95.32 Mb, with contig and scaffold N50 54.23 kb and 113.15 kb, respectively. The average GC content of the whole-genome is about 49.02%, encoding 23,275 genes. In addition, we identified 19.15% of interspersed elements and 0.95% of tandem elements in the whole genome. A genome-wide phylogenetic tree indicated that Phytophthora diverged from Pythium approximately 156.32 Ma. Meanwhile, we found that 252 and 285 gene families showed expansion and contraction in Phytophthora when compared to gene families in Pythium. To determine the pathogenic mechanisms Ph. nicotianae JM01, we analyzed a suite of proteins involved in plant-pathogen interactions. The results revealed that gene duplication contributed to the expansion of Cell Wall Degrading Enzymes (CWDEs) such as glycoside hydrolases, and effectors such as Arg-Xaa-Leu-Arg (RXLR) effectors. In addition, transient expression was performed on Nicotiana benthamiana by infiltrating with Agrobacterium tumefaciens cells containing a cysteine-rich (SCR) protein. The results indicated that SCR can cause symptoms of hypersensitive response. Moreover, we also conducted comparative genome analysis among four Ph. nicotianae genomes. The completion of the Ph. nicotianae JM01 genome can not only help us understand its genomic characteristics, but also help us discover genes involved in infection and then help us understand its pathogenic mechanisms.
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Affiliation(s)
- Xiao-Long Yuan
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (X.-L.Y.); (F.-Y.K.); (Z.-F.Z.)
- Special Crops Research Center of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Cheng-Sheng Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (X.-L.Y.); (F.-Y.K.); (Z.-F.Z.)
- Special Crops Research Center of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
- Correspondence: (C.-S.Z.); (F.-L.W.); Tel.: +86-532-88701035 (C.-S.Z. & F.-L.W.)
| | - Fan-Yu Kong
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (X.-L.Y.); (F.-Y.K.); (Z.-F.Z.)
- Special Crops Research Center of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Zhong-Feng Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (X.-L.Y.); (F.-Y.K.); (Z.-F.Z.)
- Special Crops Research Center of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Feng-Long Wang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (X.-L.Y.); (F.-Y.K.); (Z.-F.Z.)
- Special Crops Research Center of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
- Correspondence: (C.-S.Z.); (F.-L.W.); Tel.: +86-532-88701035 (C.-S.Z. & F.-L.W.)
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110
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Smith SR, Normandeau E, Djambazian H, Nawarathna PM, Berube P, Muir AM, Ragoussis J, Penney CM, Scribner KT, Luikart G, Wilson CC, Bernatchez L. A chromosome-anchored genome assembly for Lake Trout (Salvelinus namaycush). Mol Ecol Resour 2021; 22:679-694. [PMID: 34351050 PMCID: PMC9291852 DOI: 10.1111/1755-0998.13483] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/25/2021] [Accepted: 07/28/2021] [Indexed: 01/23/2023]
Abstract
Here, we present an annotated, chromosome‐anchored, genome assembly for Lake Trout (Salvelinus namaycush) – a highly diverse salmonid species of notable conservation concern and an excellent model for research on adaptation and speciation. We leveraged Pacific Biosciences long‐read sequencing, paired‐end Illumina sequencing, proximity ligation (Hi‐C) sequencing, and a previously published linkage map to produce a highly contiguous assembly composed of 7378 contigs (contig N50 = 1.8 Mb) assigned to 4120 scaffolds (scaffold N50 = 44.975 Mb). Long read sequencing data were generated using DNA from a female double haploid individual. 84.7% of the genome was assigned to 42 chromosome‐sized scaffolds and 93.2% of Benchmarking Universal Single Copy Orthologues were recovered, putting this assembly on par with the best currently available salmonid genomes. Estimates of genome size based on k‐mer frequency analysis were highly similar to the total size of the finished genome, suggesting that the entirety of the genome was recovered. A mitochondrial genome assembly was also produced. Self‐versus‐self synteny analysis allowed us to identify homeologs resulting from the salmonid specific autotetraploid event (Ss4R) as well as regions exhibiting delayed rediploidization. Alignment with three other salmonid genomes and the Northern Pike (Esox lucius) genome also allowed us to identify homologous chromosomes in related taxa. We also generated multiple resources useful for future genomic research on Lake Trout, including a repeat library and a sex‐averaged recombination map. A novel RNA sequencing data set for liver tissue was also generated in order to produce a publicly available set of annotations for 49,668 genes and pseudogenes. Potential applications of these resources to population genetics and the conservation of native populations are discussed.
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Affiliation(s)
- Seth R Smith
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA.,Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada
| | - Haig Djambazian
- McGill Genome Centre, Department of Human Genetics, Montreal, QC, Canada
| | - Pubudu M Nawarathna
- Department of Human Genetics, Canadian Centre for Computational Genomics (C3G, McGill University, Montréal, QC, Canada
| | - Pierre Berube
- McGill Genome Centre, Department of Human Genetics, Montreal, QC, Canada
| | | | - Jiannis Ragoussis
- McGill Genome Centre, Department of Human Genetics, Montreal, QC, Canada
| | - Chantelle M Penney
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
| | - Kim T Scribner
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA.,Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA.,Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Gordon Luikart
- Fish and Wildlife Genomics Group, University of Montana, Missoula, MT, USA.,Flathead Lake Biological Station, Division of Biological Sciences, University of Montana, Polson, MT, USA
| | - Chris C Wilson
- Aquatic Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, ON, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada
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111
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Galvez LC, Koh RBL, Barbosa CFC, Asunto JC, Catalla JL, Atienza RG, Costales KT, Aquino VM, Zhang D. Sequencing and de Novo Assembly of Abaca ( Musa textilis Née) var. Abuab Genome. Genes (Basel) 2021; 12:genes12081202. [PMID: 34440376 PMCID: PMC8392402 DOI: 10.3390/genes12081202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/02/2021] [Accepted: 07/01/2021] [Indexed: 01/14/2023] Open
Abstract
Abaca (Musa textilis Née), an indigenous crop to the Philippines, is known to be the source of the strongest natural fiber. Despite its huge economic contributions, research on crop improvement is limited due to the lack of genomic data. In this study, the whole genome of the abaca var. Abuab was sequenced using Illumina Novaseq 6000 and Pacific Biosciences Single-Molecule Real-Time Sequel. The genome size of Abuab was estimated to be 616 Mbp based on total k-mer number and volume peak. Its genome was assembled at 65× depth, mapping 95.28% of the estimated genome size. BUSCO analysis recovered 78.2% complete BUSCO genes. A total of 33,277 gene structures were predicted which is comparable to the number of predicted genes from recently assembled Musa spp. genomes. A total of 330 Mbp repetitive elements were also mined, accounting to 53.6% of the genome length. Here we report the sequencing and genome assembly of the abaca var. Abuab that will facilitate gene discovery for crop improvement and an indispensable source for genetic diversity studies in Musa.
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Affiliation(s)
- Leny Calano Galvez
- Philippine Fiber Industry Development Authority (PhilFIDA), PCAF Bldg, DA Compound, Diliman, Quezon City 1101, Philippines; (C.F.C.B.); (J.C.A.); (J.L.C.); (R.G.A.); (K.T.C.)
- Correspondence:
| | - Rhosener Bhea Lu Koh
- National Institute of Molecular Biology and Biotechnology, University of the Philippines Diliman, Quezon City 1101, Philippines; (R.B.L.K.); (V.M.A.)
| | - Cris Francis Cortez Barbosa
- Philippine Fiber Industry Development Authority (PhilFIDA), PCAF Bldg, DA Compound, Diliman, Quezon City 1101, Philippines; (C.F.C.B.); (J.C.A.); (J.L.C.); (R.G.A.); (K.T.C.)
| | - Jayson Calundre Asunto
- Philippine Fiber Industry Development Authority (PhilFIDA), PCAF Bldg, DA Compound, Diliman, Quezon City 1101, Philippines; (C.F.C.B.); (J.C.A.); (J.L.C.); (R.G.A.); (K.T.C.)
| | - Jose Leonido Catalla
- Philippine Fiber Industry Development Authority (PhilFIDA), PCAF Bldg, DA Compound, Diliman, Quezon City 1101, Philippines; (C.F.C.B.); (J.C.A.); (J.L.C.); (R.G.A.); (K.T.C.)
| | - Robert Gomez Atienza
- Philippine Fiber Industry Development Authority (PhilFIDA), PCAF Bldg, DA Compound, Diliman, Quezon City 1101, Philippines; (C.F.C.B.); (J.C.A.); (J.L.C.); (R.G.A.); (K.T.C.)
| | - Kennedy Trinidad Costales
- Philippine Fiber Industry Development Authority (PhilFIDA), PCAF Bldg, DA Compound, Diliman, Quezon City 1101, Philippines; (C.F.C.B.); (J.C.A.); (J.L.C.); (R.G.A.); (K.T.C.)
| | - Vermando Masinsin Aquino
- National Institute of Molecular Biology and Biotechnology, University of the Philippines Diliman, Quezon City 1101, Philippines; (R.B.L.K.); (V.M.A.)
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, USDA-ARS, Beltsville, MD 20705, USA;
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112
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Sharma T, Sharma NK, Kumar P, Panzade G, Rana T, Swarnkar MK, Singh AK, Singh D, Shankar R, Kumar S. The first draft genome of Picrorhiza kurrooa, an endangered medicinal herb from Himalayas. Sci Rep 2021; 11:14944. [PMID: 34294764 PMCID: PMC8298464 DOI: 10.1038/s41598-021-93495-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 06/24/2021] [Indexed: 11/23/2022] Open
Abstract
Picrorhiza kurrooa is an endangered medicinal herb which is distributed across the Himalayan region at an altitude between 3000–5000 m above mean sea level. The medicinal properties of P. kurrooa are attributed to monoterpenoid picrosides present in leaf, rhizome and root of the plant. However, no genomic information is currently available for P. kurrooa, which limits our understanding about its molecular systems and associated responses. The present study brings the first assembled draft genome of P. kurrooa by using 227 Gb of raw data generated by Illumina and PacBio RS II sequencing platforms. The assembled genome has a size of n = ~ 1.7 Gb with 12,924 scaffolds. Four pronged assembly quality validations studies, including experimentally reported ESTs mapping and directed sequencing of the assembled contigs, confirmed high reliability of the assembly. About 76% of the genome is covered by complex repeats alone. Annotation revealed 24,798 protein coding and 9789 non-coding genes. Using the assembled genome, a total of 710 miRNAs were discovered, many of which were found responsible for molecular response against temperature changes. The miRNAs and targets were validated experimentally. The availability of draft genome sequence will aid in genetic improvement and conservation of P. kurrooa. Also, this study provided an efficient approach for assembling complex genomes while dealing with repeats when regular assemblers failed to progress due to repeats.
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Affiliation(s)
- Tanvi Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Nitesh Kumar Sharma
- Studio of Computational Biology and Bioinformatics, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Prakash Kumar
- Studio of Computational Biology and Bioinformatics, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Ganesh Panzade
- Studio of Computational Biology and Bioinformatics, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Tanuja Rana
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India
| | - Mohit Kumar Swarnkar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India
| | - Anil Kumar Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India.,ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834 003, India
| | - Dharam Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Ravi Shankar
- Studio of Computational Biology and Bioinformatics, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
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113
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Saremi NF, Oppenheimer J, Vollmers C, O'Connell B, Milne SA, Byrne A, Yu L, Ryder OA, Green RE, Shapiro B. An Annotated Draft Genome for the Andean Bear, Tremarctos ornatus. J Hered 2021; 112:377-384. [PMID: 33882130 PMCID: PMC8280923 DOI: 10.1093/jhered/esab021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/20/2021] [Indexed: 12/18/2022] Open
Abstract
The Andean bear is the only extant member of the Tremarctine subfamily and the only extant ursid species to inhabit South America. Here, we present an annotated de novo assembly of a nuclear genome from a captive-born female Andean bear, Mischief, generated using a combination of short and long DNA and RNA reads. Our final assembly has a length of 2.23 Gb, and a scaffold N50 of 21.12 Mb, contig N50 of 23.5 kb, and BUSCO score of 88%. The Andean bear genome will be a useful resource for exploring the complex phylogenetic history of extinct and extant bear species and for future population genetics studies of Andean bears.
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Affiliation(s)
- Nedda F Saremi
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Jonas Oppenheimer
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Christopher Vollmers
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Brendan O'Connell
- Department of Medical and Molecular Genetics, Oregon Health & Science University, Portland, OR
| | - Shard A Milne
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Ashley Byrne
- Department of Molecular, Cellular, Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | | | - Richard E Green
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA
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114
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Shenton M, Kobayashi M, Terashima S, Ohyanagi H, Copetti D, Hernández-Hernández T, Zhang J, Ohmido N, Fujita M, Toyoda A, Ikawa H, Fujiyama A, Furuumi H, Miyabayashi T, Kubo T, Kudrna D, Wing R, Yano K, Nonomura KI, Sato Y, Kurata N. Evolution and Diversity of the Wild Rice Oryza officinalis Complex, across Continents, Genome Types, and Ploidy Levels. Genome Biol Evol 2021; 12:413-428. [PMID: 32125373 PMCID: PMC7531200 DOI: 10.1093/gbe/evaa037] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2020] [Indexed: 12/15/2022] Open
Abstract
The Oryza officinalis complex is the largest species group in
Oryza, with more than nine species from four continents, and is a
tertiary gene pool that can be exploited in breeding programs for the improvement of
cultivated rice. Most diploid and tetraploid members of this group have a C genome. Using
a new reference C genome for the diploid species O. officinalis, and
draft genomes for two other C genome diploid species Oryza eichingeri and
Oryza rhizomatis, we examine the influence of transposable elements on
genome structure and provide a detailed phylogeny and evolutionary history of the
Oryza C genomes. The O. officinalis genome is 1.6
times larger than the A genome of cultivated Oryza sativa, mostly due to
proliferation of Gypsy type long-terminal repeat transposable elements,
but overall syntenic relationships are maintained with other Oryza
genomes (A, B, and F). Draft genome assemblies of the two other C genome diploid species,
Oryza eichingeri and Oryza rhizomatis, and short-read
resequencing of a series of other C genome species and accessions reveal that after the
divergence of the C genome progenitor, there was still a substantial degree of variation
within the C genome species through proliferation and loss of both DNA and long-terminal
repeat transposable elements. We provide a detailed phylogeny and evolutionary history of
the Oryza C genomes and a genomic resource for the exploitation of the
Oryza tertiary gene pool.
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Affiliation(s)
| | | | | | - Hajime Ohyanagi
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Dario Copetti
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona.,T.T. Chang Genetic Resources Center, International Rice Research Institute, Los Baños, Philippines
| | | | - Jianwei Zhang
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona
| | - Nobuko Ohmido
- Division of the Living Environment, Kobe University, Japan
| | | | | | | | | | | | | | - Takahiko Kubo
- National Institute of Genetics, Mishima, Japan.,Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - David Kudrna
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona
| | - Rod Wing
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona.,T.T. Chang Genetic Resources Center, International Rice Research Institute, Los Baños, Philippines.,Biological and Environment Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Kentaro Yano
- School of Agriculture, Meiji University, Tokyo, Japan
| | | | - Yutaka Sato
- National Institute of Genetics, Mishima, Japan
| | - Nori Kurata
- National Institute of Genetics, Mishima, Japan
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115
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Tsuchiya MTN, Dikow RB, Cassin-Sackett L. First Genome Sequence of the Gunnison's Prairie Dog (Cynomys gunnisoni), a Keystone Species and Player in the Transmission of Sylvatic Plague. Genome Biol Evol 2021; 12:618-625. [PMID: 32277812 PMCID: PMC7250503 DOI: 10.1093/gbe/evaa069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2020] [Indexed: 12/30/2022] Open
Abstract
Prairie dogs (genus Cynomys) are a charismatic symbol of the American West. Their large social aggregations and complex vocalizations have been the subject of scientific and popular interest for decades. A large body of literature has documented their role as keystone species of western North America's grasslands: They generate habitat for other vertebrates, increase nutrient availability for plants, and act as a food source for mammalian, squamate, and avian predators. An additional keystone role lies in their extreme susceptibility to sylvatic plague (caused by Yersinia pestis), which results in periodic population extinctions, thereby generating spatiotemporal heterogeneity in both biotic communities and ecological processes. Here, we report the first Cynomys genome for a Gunnison's prairie dog (C. gunnisoni gunnisoni) from Telluride, Colorado (USA). The genome was constructed using a hybrid assembly of PacBio and Illumina reads and assembled with MaSuRCA and PBJelly, which resulted in a scaffold N50 of 824 kb. Total genome size was 2.67 Gb, with 32.46% of the bases occurring in repeat regions. We recovered 94.9% (91% complete) of the single copy orthologs using the mammalian Benchmarking Universal Single-Copy Orthologs database and detected 49,377 gene models (332,141 coding regions). Pairwise Sequentially Markovian Coalescent showed support for long-term stable population size followed by a steady decline beginning near the end of the Pleistocene, as well as a recent population reduction. The genome will aid in studies of mammalian evolution, disease resistance, and the genomic basis of life history traits in ground squirrels.
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Affiliation(s)
- Mirian T N Tsuchiya
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia
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116
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Zhu B, Hu L, Qian F, Gao Z, Gan C, Liu Z, Du X, Wang H. Chloroplast genome features of Moricandia arvensis (Brassicaceae), a C3-C4 intermediate photosynthetic species. PLoS One 2021; 16:e0254109. [PMID: 34237086 PMCID: PMC8266105 DOI: 10.1371/journal.pone.0254109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/20/2021] [Indexed: 11/18/2022] Open
Abstract
Moricandia arvensis, a plant species originating from the Mediterranean, has been classified as a rare C3-C4 intermediate species, and it is a possible bridge during the evolutionary process from C3 to C4 plant photosynthesis in the family Brassicaceae. Understanding the genomic structure, gene order, and gene content of chloroplasts (cp) of such species can provide a glimpse into the evolution of photosynthesis. In the present study, we obtained a well-annotated cp genome of M. arvensis using long PacBio and short Illumina reads with a de novo assembly strategy. The M. arvensis cp genome was a quadripartite circular molecule with the length of 153,312 bp, including two inverted repeats (IR) regions of 26,196 bp, divided by a small single copy (SSC) region of 17,786 bp and a large single copy (LSC) region of 83,134 bp. We detected 112 unigenes in this genome, comprising 79 protein-coding genes, 29 tRNAs, and four rRNAs. Forty-nine long repeat sequences and 51 simple sequence repeat (SSR) loci of 15 repeat types were identified. The analysis of Ks (synonymous) and Ka (non-synonymous) substitution rates indicated that the genes associated with “subunits of ATP synthase” (atpB), “subunits of NADH-dehydrogenase” (ndhG and ndhE), and “self-replication” (rps12 and rpl16) showed relatively higher Ka/Ks values than those of the other genes. The gene content, gene order, and LSC/IR/SSC boundaries and adjacent genes of the M. arvensis cp genome were highly conserved compared to those in related C3 species. Our phylogenetic analysis demonstrated that M. arvensis was clustered into a subclade with cultivated Brassica species and Raphanus sativus, indicating that M. arvensis was not involved in an independent evolutionary origin event. These results will open the way for further studies on the evolutionary process from C3 to C4 photosynthesis and hopefully provide guidance for utilizing M. arvensis as a resource for improvinng photosynthesis efficiency in cultivated Brassica species.
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Affiliation(s)
- Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Lijuan Hu
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Fang Qian
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Zuomin Gao
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Chenchen Gan
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Zhaochao Liu
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Xuye Du
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Hongcheng Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, People’s Republic of China
- * E-mail:
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117
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Strijk JS, Hinsinger DD, Roeder MM, Chatrou LW, Couvreur TLP, Erkens RHJ, Sauquet H, Pirie MD, Thomas DC, Cao K. Chromosome-level reference genome of the soursop (Annona muricata): A new resource for Magnoliid research and tropical pomology. Mol Ecol Resour 2021; 21:1608-1619. [PMID: 33569882 PMCID: PMC8251617 DOI: 10.1111/1755-0998.13353] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 11/27/2022]
Abstract
The flowering plant family Annonaceae includes important commercially grown tropical crops, but development of promising species is hindered by a lack of genomic resources to build breeding programs. Annonaceae are part of the magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades remain unclear. To provide resources to breeders and evolutionary researchers, we report a chromosome-level genome assembly of the soursop (Annona muricata). We assembled the genome using 444.32 Gb of DNA sequences (676× sequencing depth) from PacBio and Illumina short-reads, in combination with 10× Genomics and Bionano data (v1). A total of 949 scaffolds were assembled to a final size of 656.77 Mb, with a scaffold N50 of 3.43 Mb (v1), and then further improved to seven pseudo-chromosomes using Hi-C sequencing data (v2; scaffold N50: 93.2 Mb, total size in chromosomes: 639.6 Mb). Heterozygosity was very low (0.06%), while repeat sequences accounted for 54.87% of the genome, and 23,375 protein-coding genes with an average of 4.79 exons per gene were annotated using de novo, RNA-seq and homology-based approaches. Reconstruction of the historical population size showed a slow continuous contraction, probably related to Cenozoic climate changes. The soursop is the first genome assembled in Annonaceae, supporting further studies of floral evolution in magnoliids, providing an essential resource for delineating relationships of ancient angiosperm lineages. Both genome-assisted improvement and conservation efforts will be strengthened by the availability of the soursop genome. As a community resource, this assembly will further strengthen the role of Annonaceae as model species for research on the ecology, evolution and domestication potential of tropical species in pomology and agroforestry.
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Affiliation(s)
- Joeri S. Strijk
- Institute for Biodiversity and Environmental ResearchUniversiti Brunei DarussalamJalan Tungku LinkBrunei Darussalam
- Alliance for Conservation Tree GenomicsPha Tad Ke Botanical GardenLuang PrabangLaos
- Guangxi Key Laboratory of Forest Ecology and ConservationBiodiversity Genomics TeamNanningGuangxiChina
| | - Damien D. Hinsinger
- Alliance for Conservation Tree GenomicsPha Tad Ke Botanical GardenLuang PrabangLaos
- Génomique Métabolique, GenoscopeInstitut de Biologie François JacobCommissariat à l′Énergie Atomique (CEA), CNRSUniversité ÉvryUniversité Paris‐SaclayÉvryFrance
| | - Mareike M. Roeder
- Community Ecology and Conservation GroupXishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglun, MenglaYunnanChina
- AueninstitutInstitute for Geography and GeoecologyKarlsruhe Institute of TechnologyRastattGermany
| | - Lars W. Chatrou
- Systematic and Evolutionary Botany LaboratoryGhent UniversityGhentBelgium
| | | | - Roy H. J. Erkens
- Maastricht Science ProgrammeMaastricht UniversityMaastrichtThe Netherlands
| | - Hervé Sauquet
- National Herbarium of New South Wales (NSW)Royal Botanic Gardens and Domain TrustSydneyNSWAustralia
| | - Michael D. Pirie
- Department of Natural HistoryUniversity MuseumUniversity of BergenBergenNorway
| | | | - Kunfang Cao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesGuangxi UniversityNanningGuangxiChina
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118
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Wang R, Yang Y, Jing Y, Segar ST, Zhang Y, Wang G, Chen J, Liu QF, Chen S, Chen Y, Cruaud A, Ding YY, Dunn DW, Gao Q, Gilmartin PM, Jiang K, Kjellberg F, Li HQ, Li YY, Liu JQ, Liu M, Machado CA, Ming R, Rasplus JY, Tong X, Wen P, Yang HM, Yang JJ, Yin Y, Zhang XT, Zhang YY, Yu H, Yue Z, Compton SG, Chen XY. Molecular mechanisms of mutualistic and antagonistic interactions in a plant-pollinator association. Nat Ecol Evol 2021; 5:974-986. [PMID: 34002050 DOI: 10.1038/s41559-021-01469-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/20/2021] [Indexed: 02/06/2023]
Abstract
Many insects metamorphose from antagonistic larvae into mutualistic adult pollinators, with reciprocal adaptation leading to specialized insect-plant associations. It remains unknown how such interactions are established at molecular level. Here we assemble high-quality genomes of a fig species, Ficus pumila var. pumila, and its specific pollinating wasp, Wiebesia pumilae. We combine multi-omics with validation experiments to reveal molecular mechanisms underlying this specialized interaction. In the plant, we identify the specific compound attracting pollinators and validate the function of several key genes regulating its biosynthesis. In the pollinator, we find a highly reduced number of odorant-binding protein genes and an odorant-binding protein mainly binding the attractant. During antagonistic interaction, we find similar chemical profiles and turnovers throughout the development of galled ovules and seeds, and a significant contraction of detoxification-related gene families in the pollinator. Our study identifies some key genes bridging coevolved mutualists, establishing expectations for more diffuse insect-pollinator systems.
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Affiliation(s)
- Rong Wang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China.,Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China
| | - Yang Yang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Yi Jing
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Simon T Segar
- Agriculture and Environment Department, Harper Adams University, Newport, UK
| | - Yu Zhang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Gang Wang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Jin Chen
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | | | - Shan Chen
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Yan Chen
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | | | - Yuan-Yuan Ding
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Derek W Dunn
- College of Life Sciences, Northwest University, Xi'an, China
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Philip M Gilmartin
- Department of Biological and Marine Science, University of Hull, Hull, UK
| | - Kai Jiang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Finn Kjellberg
- CEFE, CNRS, University of Montpellier, Paul Valéry University Montpellier, EPHE, IRD, Montpellier, France
| | - Hong-Qing Li
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Yuan-Yuan Li
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Jian-Quan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Min Liu
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Carlos A Machado
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Xin Tong
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Ping Wen
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | | | - Jing-Jun Yang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Ye Yin
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Xing-Tan Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Hui Yu
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China. .,School of Life Sciences, Qufu Normal University, Qufu, China.
| | - Zhen Yue
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.
| | | | - Xiao-Yong Chen
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China. .,Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China.
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119
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Herpin A, Schartl M, Depincé A, Guiguen Y, Bobe J, Hua-Van A, Hayman ES, Octavera A, Yoshizaki G, Nichols KM, Goetz GW, Luckenbach JA. Allelic diversification after transposable element exaptation promoted gsdf as the master sex determining gene of sablefish. Genome Res 2021; 31:1366-1380. [PMID: 34183453 PMCID: PMC8327909 DOI: 10.1101/gr.274266.120] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 06/22/2021] [Indexed: 11/24/2022]
Abstract
Concepts of evolutionary biology suggest that morphological change may occur by rare punctual but rather large changes, or by more steady and gradual transformations. It can therefore be asked whether genetic changes underlying morphological, physiological, and/or behavioral innovations during evolution occur in a punctual manner, whereby a single mutational event has prominent phenotypic consequences, or if many consecutive alterations in the DNA over longer time periods lead to phenotypic divergence. In the marine teleost, sablefish (Anoplopoma fimbria), complementary genomic and genetic studies led to the identification of a sex locus on the Y Chromosome. Further characterization of this locus resulted in identification of the transforming growth factor, beta receptor 1a (tgfbr1a) gene, gonadal somatic cell derived factor (gsdf), as the main candidate for fulfilling the master sex determining (MSD) function. The presence of different X and Y Chromosome copies of this gene indicated that the male heterogametic (XY) system of sex determination in sablefish arose by allelic diversification. The gsdfY gene has a spatio-temporal expression profile characteristic of a male MSD gene. We provide experimental evidence demonstrating a pivotal role of a transposable element (TE) for the divergent function of gsdfY. By insertion within the gsdfY promoter region, this TE generated allelic diversification by bringing cis-regulatory modules that led to transcriptional rewiring and thus creation of a new MSD gene. This points out, for the first time in the scenario of MSD gene evolution by allelic diversification, a single, punctual molecular event in the appearance of a new trigger for male development.
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Affiliation(s)
- Amaury Herpin
- INRAE, LPGP, 35000, Rennes, France.,State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China
| | - Manfred Schartl
- University of Wuerzburg, Developmental Biochemistry, Biocenter, 97074 Wuerzburg, Germany.,Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
| | | | | | | | - Aurélie Hua-Van
- Laboratoire Evolution, Génomes Comportement, Ecologie, CNRS Université Paris-Saclay, UMR 9191, IRD UMR 247, F-91198 Gif-sur-Yvette, France
| | - Edward S Hayman
- Ocean Associates Incorporated, under contract to Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington 98112, USA
| | - Anna Octavera
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Goro Yoshizaki
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Krista M Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington 98112, USA
| | - Giles W Goetz
- Cooperative Institutes for Climate, Ocean, and Environmental Sciences, University of Washington, Seattle, Washington 98112, USA
| | - J Adam Luckenbach
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington 98112, USA.,Center for Reproductive Biology, Washington State University, Pullman, Washington 99164, USA
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120
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Hu Y, Yu L, Fan H, Huang G, Wu Q, Nie Y, Liu S, Yan L, Wei F. Genomic Signatures of Coevolution between Nonmodel Mammals and Parasitic Roundworms. Mol Biol Evol 2021; 38:531-544. [PMID: 32960966 PMCID: PMC7826172 DOI: 10.1093/molbev/msaa243] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Antagonistic coevolution between host and parasite drives species evolution. However, most of the studies only focus on parasitism adaptation and do not explore the coevolution mechanisms from the perspective of both host and parasite. Here, through the de novo sequencing and assembly of the genomes of giant panda roundworm, red panda roundworm, and lion roundworm parasitic on tiger, we investigated the genomic mechanisms of coevolution between nonmodel mammals and their parasitic roundworms and those of roundworm parasitism in general. The genome-wide phylogeny revealed that these parasitic roundworms have not phylogenetically coevolved with their hosts. The CTSZ and prolyl 4-hydroxylase subunit beta (P4HB) immunoregulatory proteins played a central role in protein interaction between mammals and parasitic roundworms. The gene tree comparison identified that seven pairs of interactive proteins had consistent phylogenetic topology, suggesting their coevolution during host–parasite interaction. These coevolutionary proteins were particularly relevant to immune response. In addition, we found that the roundworms of both pandas exhibited higher proportions of metallopeptidase genes, and some positively selected genes were highly related to their larvae’s fast development. Our findings provide novel insights into the genetic mechanisms of coevolution between nonmodel mammals and parasites and offer the valuable genomic resources for scientific ascariasis prevention in both pandas.
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Affiliation(s)
- Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Lijun Yu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Huizhong Fan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Guangping Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qi Wu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yonggang Nie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Shuai Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Li Yan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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121
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Yang Y, Huang L, Xu C, Qi L, Wu Z, Li J, Chen H, Wu Y, Fu T, Zhu H, Saand MA, Li J, Liu L, Fan H, Zhou H, Qin W. Chromosome-scale genome assembly of areca palm (Areca catechu). Mol Ecol Resour 2021; 21:2504-2519. [PMID: 34133844 DOI: 10.1111/1755-0998.13446] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 11/28/2022]
Abstract
Areca palm (Areca catechu L.; family Arecaceae) is an important tropical medicinal crop and is also used for masticatory and religious purposes in Asia. Improvements to areca properties made by traditional breeding tools have been very slow, and further advances in its cultivation and practical use require genomic information, which is still unavailable. Here, we present a chromosome-scale reference genome assembly for areca by combining Illumina and PacBio data with Hi-C mapping technologies, covering the predicted A. catechu genome length (2.59 Gb, variety "Reyan#1") to an estimated 240× read depth. The assembly was 2.51 Gb in length with a scaffold N50 of 1.7Mb. The scaffolds were then further assembled into 16 pseudochromosomes, with an N50 of 172 Mb. Transposable elements comprised 80.37% of the areca genome, and 68.68% of them were long-terminal repeat retrotransposon elements. The areca palm genome was predicted to harbour 31,571 protein-coding genes and overall, 92.92% of genes were functionally annotated, including enriched and expanded families of genes responsible for biosynthesis of flavonoid, anthocyanin, monoterpenoid and their derivatives. Comparative analyses indicated that A. catechu probably diverged from its close relatives Elaeis guineensis and Cocos nucifera approximately 50.3 million years ago (Ma). Two whole genome duplication events in areca palm were found to be shared by palms and monocots, respectively. This genome assembly and associated resources represents an important addition to the palm genomics community and will be a valuable resource that will facilitate areca palm breeding and improve our understanding of areca palm biology and evolution.
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Affiliation(s)
- Yaodong Yang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Liyun Huang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Chunyan Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Lan Qi
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | | | - Jia Li
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | | | - Yi Wu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Tao Fu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Hui Zhu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Mumtaz Ali Saand
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Jing Li
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Liyun Liu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Haikou Fan
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Huanqi Zhou
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Weiquan Qin
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
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122
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Insights into the genomic evolution of insects from cricket genomes. Commun Biol 2021; 4:733. [PMID: 34127782 PMCID: PMC8203789 DOI: 10.1038/s42003-021-02197-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 04/16/2021] [Indexed: 12/14/2022] Open
Abstract
Most of our knowledge of insect genomes comes from Holometabolous species, which undergo complete metamorphosis and have genomes typically under 2 Gb with little signs of DNA methylation. In contrast, Hemimetabolous insects undergo the presumed ancestral process of incomplete metamorphosis, and have larger genomes with high levels of DNA methylation. Hemimetabolous species from the Orthopteran order (grasshoppers and crickets) have some of the largest known insect genomes. What drives the evolution of these unusual insect genome sizes, remains unknown. Here we report the sequencing, assembly and annotation of the 1.66-Gb genome of the Mediterranean field cricket Gryllus bimaculatus, and the annotation of the 1.60-Gb genome of the Hawaiian cricket Laupala kohalensis. We compare these two cricket genomes with those of 14 additional insects and find evidence that hemimetabolous genomes expanded due to transposable element activity. Based on the ratio of observed to expected CpG sites, we find higher conservation and stronger purifying selection of methylated genes than non-methylated genes. Finally, our analysis suggests an expansion of the pickpocket class V gene family in crickets, which we speculate might play a role in the evolution of cricket courtship, including their characteristic chirping. Ylla, Extavour et al. use genomic data from crickets to investigate the evolution of large genome sizes and DNA methylation events in insects. Their findings indicate that transposable element activity drove genome expansion in hemimetabolous insects, such as crickets and grasshoppers, and that DNA methylation is predominant in conserved genes.
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123
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Panibe JP, Wang L, Li J, Li MY, Lee YC, Wang CS, Ku MSB, Lu MYJ, Li WH. Chromosomal-level genome assembly of the semi-dwarf rice Taichung Native 1, an initiator of Green Revolution. Genomics 2021; 113:2656-2674. [PMID: 34111524 DOI: 10.1016/j.ygeno.2021.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 10/21/2022]
Abstract
Here we report the 409.5 Mb chromosome-level assembly of the first bred semi-dwarf rice, the Taichung Native 1 (TN1), which served as the template for the development of the Green Revolution (GR) cultivar IR8 "miracle rice". We sequenced the TN1 genome utilizing multiple platforms and produced PacBio long reads, Illumina paired-end reads, Illumina mate-pair reads and 10x Genomics linked reads. We used a hybrid approach to assemble the 226× coverage of sequences by a combination of de novo and reference-guided approaches. The assembled TN1 genome has an N50 scaffold size of 33.1 Mb with the longest measuring 45.5 Mb. We annotated 37,526 genes, in which 24,102 (64.23%) were assigned Blast2GO annotations. The genome has 4672 or 95.4% complete BUSCOs and a repeat content of 51.52%. We developed our own method of creating a GR pangenome using the orthologous relationships of the proteins of TN1, IR8, MH63 and IR64, identifying 16,999 core orthologue groups of Green Revolution. From the pangenome, we identified a set of shared and unique gene ontology terms for the accessory clusters, characterizing TN1, IR8, MH63 and IR64. This TN1 genome assembly and GR pangenome will be a resource for new genomic discoveries about Green Revolution, and for improving the disease and insect resistances and the yield of rice.
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Affiliation(s)
- Jerome P Panibe
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan; Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023 Nanjing, China
| | - Jengyi Li
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Meng-Yun Li
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yi-Chen Lee
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chang-Sheng Wang
- Department of Agronomy, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Maurice S B Ku
- Department of Bioagricultutral Sciences, National Chiayi University, Chiayi 60004, Taiwan; School of Biological Sciences, Washington State University, Pullman 99164, WA, USA
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Wen-Hsiung Li
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan; Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan; Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.
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124
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Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome. Genes (Basel) 2021; 12:genes12060847. [PMID: 34070911 PMCID: PMC8228171 DOI: 10.3390/genes12060847] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/21/2021] [Accepted: 05/27/2021] [Indexed: 12/27/2022] Open
Abstract
The domestic dog has evolved to be an important biomedical model for studies regarding the genetic basis of disease, morphology and behavior. Genetic studies in the dog have relied on a draft reference genome of a purebred female boxer dog named "Tasha" initially published in 2005. Derived from a Sanger whole genome shotgun sequencing approach coupled with limited clone-based sequencing, the initial assembly and subsequent updates have served as the predominant resource for canine genetics for 15 years. While the initial assembly produced a good-quality draft, as with all assemblies produced at the time, it contained gaps, assembly errors and missing sequences, particularly in GC-rich regions, which are found at many promoters and in the first exons of protein-coding genes. Here, we present Dog10K_Boxer_Tasha_1.0, an improved chromosome-level highly contiguous genome assembly of Tasha created with long-read technologies that increases sequence contiguity >100-fold, closes >23,000 gaps of the CanFam3.1 reference assembly and improves gene annotation by identifying >1200 new protein-coding transcripts. The assembly and annotation are available at NCBI under the accession GCF_000002285.5.
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125
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Liu H, Chen C, Lv M, Liu N, Hu Y, Zhang H, Enbody ED, Gao Z, Andersson L, Wang W. A chromosome-level assembly of blunt snout bream (Megalobrama amblycephala) reveals an expansion of olfactory receptor genes in freshwater fish. Mol Biol Evol 2021; 38:4238-4251. [PMID: 34003267 PMCID: PMC8476165 DOI: 10.1093/molbev/msab152] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The number of olfactory receptor genes (ORs), which are responsible for detecting diverse odor molecules varies extensively among mammals as a result of frequent gene gains and losses that contribute to olfactory specialization. However, how OR expansions/contractions in fish are influenced by habitat and feeding habit and which OR subfamilies are important in each ecological niche is unknown. Here, we report a major OR expansion in a freshwater herbivorous fish, Megalobrama amblycephala, using a highly contiguous, chromosome-level assembly. We evaluate the possible contribution of OR expansion to habitat and feeding specialization by comparing the OR repertoire in 28 phylogenetically and ecologically diverse teleosts. In total, we analyzed > 4,000 ORs including 3,253 intact, 122 truncated, and 913 pseudogenes. The number of intact ORs is highly variable ranging from 20 to 279. We estimate that the most recent common ancestor of Osteichthyes had 62 intact ORs, which declined in most lineages except the freshwater Otophysa clade that has a substantial expansion in subfamily β and ε ORs. Across teleosts, we found a strong association between duplications of β and ε ORs and freshwater habitat. Nearly, all ORs were expressed in the olfactory epithelium (OE) in three tested fish species. Specifically, all the expanded β and ε ORs were highly expressed in OE of M. amblycephala. Together, we provide molecular and functional evidence for how OR repertoires in fish have undergone gain and loss with respect to ecological factors and highlight the role of β and ε OR in freshwater adaptation.
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Affiliation(s)
- Han Liu
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China.,Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Wuhan, 430070, China
| | - Chunhai Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Maolin Lv
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ning Liu
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yafei Hu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hailin Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Erik D Enbody
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE75237, Sweden
| | - Zexia Gao
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China.,Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Wuhan, 430070, China
| | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE75237, Sweden.,Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, USA.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Weimin Wang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
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126
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Mu Y, Bian C, Liu R, Wang Y, Shao G, Li J, Qiu Y, He T, Li W, Ao J, Shi Q, Chen X. Whole genome sequencing of a snailfish from the Yap Trench (~7,000 m) clarifies the molecular mechanisms underlying adaptation to the deep sea. PLoS Genet 2021; 17:e1009530. [PMID: 33983934 PMCID: PMC8118300 DOI: 10.1371/journal.pgen.1009530] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 04/05/2021] [Indexed: 11/25/2022] Open
Abstract
Hadal environments (depths below 6,000 m) are characterized by extremely high hydrostatic pressures, low temperatures, a scarce food supply, and little light. The evolutionary adaptations that allow vertebrates to survive in this extreme environment are poorly understood. Here, we constructed a high-quality reference genome for Yap hadal snailfish (YHS), which was captured at a depth of ~7,000 m in the Yap Trench. The final YHS genome assembly was 731.75 Mb, with a contig N50 of 0.75 Mb and a scaffold N50 of 1.26 Mb. We predicted 24,329 protein-coding genes in the YHS genome, and 24,265 of these genes were successfully functionally annotated. Phylogenetic analyses suggested that YHS diverged from a Mariana Trench snailfish approximately 0.92 million years ago. Many genes associated with DNA repair show evidence of positive selection and have expanded copy numbers in the YHS genome, possibly helping to maintain the integrity of DNA under increased hydrostatic pressure. The levels of trimethylamine N-oxide (TMAO), a potent protein stabilizer, are much higher in the muscles of YHS than in those of shallow-water fish. This difference is perhaps due to the five copies of the TMAO-generating enzyme flavin-containing monooxygenase-3 gene (fmo3) in the YHS genome and the abundance of trimethylamine (TMA)-generating bacteria in the YHS gut. Thus, the high TMAO content might help YHS adapt to high hydrostatic pressure by improving protein stability. Additionally, the evolutionary features of the YHS genes encoding sensory-related proteins are consistent with the scarce food supply and darkness in the hadal environments. These results clarify the molecular mechanisms underlying the adaptation of hadal organisms to the deep-sea environment and provide valuable genomic resources for in-depth investigations of hadal biology. Hadal environments (depths below 6,000 m) are characterized by extremely high hydrostatic pressures, low temperatures, a scarce food supply, and little light. Fish are the only vertebrates inhabiting the hadal zone, and hadal snailfishes have been found in at least five geographically separated marine trenches. However, the genetic mechanisms that allow vertebrates to live in such extreme conditions are not well understood. Here, we constructed a high-quality reference genome for Yap hadal snailfish (YHS) captured at a depth of ~7,000 m in the Yap Trench, using long reads obtained by Pacific Biosciences Sequel sequencing. Comparative genomic analyses revealed that many genes associated with DNA repair show evidence of positive selection and have expanded copy numbers in the YHS genome, which potentially reflect the difficulty of maintaining DNA integrity under high hydrostatic pressure. Moreover, the five copies of the trimethylamine N-oxide (TMAO)-generating enzyme flavin-containing monooxygenase-3 gene (fmo3) and the abundance of trimethylamine (TMA)-generating bacteria in the YHS gut could provide enough TMAO to improve protein stability under hadal conditions. In addition, characteristics of the YHS sensory system genes were consistent with the scarce food supply and darkness in the hadal zone. Our results provide new insights into the molecular mechanisms underlying the adaptation of hadal organisms to the deep-sea environment and valuable genomic resources that will help further clarify hadal adaptations.
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Affiliation(s)
- Yinnan Mu
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong, China
| | - Ruoyu Liu
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuguang Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Guangming Shao
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jia Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong, China
| | - Ying Qiu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong, China
| | - Tianliang He
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Wanru Li
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jingqun Ao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong, China
- * E-mail: (QS); (XC)
| | - Xinhua Chen
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
- * E-mail: (QS); (XC)
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127
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Zhou X, Dou Q, Fan G, Zhang Q, Sanderford M, Kaya A, Johnson J, Karlsson EK, Tian X, Mikhalchenko A, Kumar S, Seluanov A, Zhang ZD, Gorbunova V, Liu X, Gladyshev VN. Beaver and Naked Mole Rat Genomes Reveal Common Paths to Longevity. Cell Rep 2021; 32:107949. [PMID: 32726638 DOI: 10.1016/j.celrep.2020.107949] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 02/20/2020] [Accepted: 07/02/2020] [Indexed: 11/29/2022] Open
Abstract
Long-lived rodents have become an attractive model for the studies on aging. To understand evolutionary paths to long life, we prepare chromosome-level genome assemblies of the two longest-lived rodents, Canadian beaver (Castor canadensis) and naked mole rat (NMR, Heterocephalus glaber), which were scaffolded with in vitro proximity ligation and chromosome conformation capture data and complemented with long-read sequencing. Our comparative genomic analyses reveal that amino acid substitutions at "disease-causing" sites are widespread in the rodent genomes and that identical substitutions in long-lived rodents are associated with common adaptive phenotypes, e.g., enhanced resistance to DNA damage and cellular stress. By employing a newly developed substitution model and likelihood ratio test, we find that energy and fatty acid metabolism pathways are enriched for signals of positive selection in both long-lived rodents. Thus, the high-quality genome resource of long-lived rodents can assist in the discovery of genetic factors that control longevity and adaptive evolution.
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Affiliation(s)
- Xuming Zhou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, Massachusetts, MA 02142, USA
| | - Qianhui Dou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Quanwei Zhang
- Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Maxwell Sanderford
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
| | - Alaattin Kaya
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, Massachusetts, MA 02142, USA; Department of Biology, Virginia Commonwealth University, Richmond, VA 23284 USA
| | - Jeremy Johnson
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, MA 02142, USA
| | - Elinor K Karlsson
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, MA 02142, USA; University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Xiao Tian
- Department of Biology, University of Rochester, Rochester, NY 14627, USA; Department of Medicine, University of Rochester, Rochester, NY 14627, USA
| | - Aleksei Mikhalchenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY 14627, USA; Department of Medicine, University of Rochester, Rochester, NY 14627, USA
| | | | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA; Department of Medicine, University of Rochester, Rochester, NY 14627, USA
| | - Xin Liu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, Massachusetts, MA 02142, USA.
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128
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Szövényi P, Gunadi A, Li FW. Charting the genomic landscape of seed-free plants. NATURE PLANTS 2021; 7:554-565. [PMID: 33820965 DOI: 10.1038/s41477-021-00888-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 02/25/2021] [Indexed: 05/02/2023]
Abstract
During the past few years several high-quality genomes has been published from Charophyte algae, bryophytes, lycophytes and ferns. These genomes have not only elucidated the origin and evolution of early land plants, but have also provided important insights into the biology of the seed-free lineages. However, critical gaps across the phylogeny remain and many new questions have been raised through comparing seed-free and seed plant genomes. Here, we review the reference genomes available and identify those that are missing in the seed-free lineages. We compare patterns of various levels of genome and epigenomic organization found in seed-free plants to those of seed plants. Some genomic features appear to be fundamentally different. For instance, hornworts, Selaginella and most liverworts are devoid of whole-genome duplication, in stark contrast to other land plants. In addition, the distribution of genes and repeats appear to be less structured in seed-free genomes than in other plants, and the levels of gene body methylation appear to be much lower. Finally, we highlight the currently available (or needed) model systems, which are crucial to further our understanding about how changes in genes translate into evolutionary novelties.
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Affiliation(s)
- Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich and Zurich-Basel Plant Science Center, Zurich, Switzerland.
| | | | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
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129
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Seferbekova Z, Zabelkin A, Yakovleva Y, Afasizhev R, Dranenko NO, Alexeev N, Gelfand MS, Bochkareva OO. High Rates of Genome Rearrangements and Pathogenicity of Shigella spp. Front Microbiol 2021; 12:628622. [PMID: 33912145 PMCID: PMC8072062 DOI: 10.3389/fmicb.2021.628622] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/22/2021] [Indexed: 02/01/2023] Open
Abstract
Shigella are pathogens originating within the Escherichia lineage but frequently classified as a separate genus. Shigella genomes contain numerous insertion sequences (ISs) that lead to pseudogenisation of affected genes and an increase of non-homologous recombination. Here, we study 414 genomes of E. coli and Shigella strains to assess the contribution of genomic rearrangements to Shigella evolution. We found that Shigella experienced exceptionally high rates of intragenomic rearrangements and had a decreased rate of homologous recombination compared to pathogenic and non-pathogenic E. coli. The high rearrangement rate resulted in independent disruption of syntenic regions and parallel rearrangements in different Shigella lineages. Specifically, we identified two types of chromosomally encoded E3 ubiquitin-protein ligases acquired independently by all Shigella strains that also showed a high level of sequence conservation in the promoter and further in the 5′-intergenic region. In the only available enteroinvasive E. coli (EIEC) strain, which is a pathogenic E. coli with a phenotype intermediate between Shigella and non-pathogenic E. coli, we found a rate of genome rearrangements comparable to those in other E. coli and no functional copies of the two Shigella-specific E3 ubiquitin ligases. These data indicate that the accumulation of ISs influenced many aspects of genome evolution and played an important role in the evolution of intracellular pathogens. Our research demonstrates the power of comparative genomics-based on synteny block composition and an important role of non-coding regions in the evolution of genomic islands.
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Affiliation(s)
- Zaira Seferbekova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Institute for Information Transmission Problems (The Kharkevich Institute, RAS), Moscow, Russia
| | - Alexey Zabelkin
- Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russia.,JetBrains Research, Saint Petersburg, Russia.,Bioinformatics Institute, Saint Petersburg, Russia
| | - Yulia Yakovleva
- Bioinformatics Institute, Saint Petersburg, Russia.,Department of Cytology and Histology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Robert Afasizhev
- Institute for Information Transmission Problems (The Kharkevich Institute, RAS), Moscow, Russia
| | - Natalia O Dranenko
- Institute for Information Transmission Problems (The Kharkevich Institute, RAS), Moscow, Russia
| | - Nikita Alexeev
- Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russia
| | - Mikhail S Gelfand
- Institute for Information Transmission Problems (The Kharkevich Institute, RAS), Moscow, Russia.,Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Olga O Bochkareva
- Institute for Information Transmission Problems (The Kharkevich Institute, RAS), Moscow, Russia.,Institute of Science and Technology (IST Austria), Klosterneuburg, Austria
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130
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Kronenberg ZN, Rhie A, Koren S, Concepcion GT, Peluso P, Munson KM, Porubsky D, Kuhn K, Mueller KA, Low WY, Hiendleder S, Fedrigo O, Liachko I, Hall RJ, Phillippy AM, Eichler EE, Williams JL, Smith TPL, Jarvis ED, Sullivan ST, Kingan SB. Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C. Nat Commun 2021; 12:1935. [PMID: 33911078 PMCID: PMC8081726 DOI: 10.1038/s41467-020-20536-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 11/12/2020] [Indexed: 01/27/2023] Open
Abstract
Haplotype-resolved genome assemblies are important for understanding how combinations of variants impact phenotypes. To date, these assemblies have been best created with complex protocols, such as cultured cells that contain a single-haplotype (haploid) genome, single cells where haplotypes are separated, or co-sequencing of parental genomes in a trio-based approach. These approaches are impractical in most situations. To address this issue, we present FALCON-Phase, a phasing tool that uses ultra-long-range Hi-C chromatin interaction data to extend phase blocks of partially-phased diploid assembles to chromosome or scaffold scale. FALCON-Phase uses the inherent phasing information in Hi-C reads, skipping variant calling, and reduces the computational complexity of phasing. Our method is validated on three benchmark datasets generated as part of the Vertebrate Genomes Project (VGP), including human, cow, and zebra finch, for which high-quality, fully haplotype-resolved assemblies are available using the trio-based approach. FALCON-Phase is accurate without having parental data and performance is better in samples with higher heterozygosity. For cow and zebra finch the accuracy is 97% compared to 80-91% for human. FALCON-Phase is applicable to any draft assembly that contains long primary contigs and phased associate contigs.
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Affiliation(s)
- Zev N Kronenberg
- Phase Genomics, Seattle, WA, USA.
- Pacific Biosciences, Menlo Park, CA, USA.
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | | | | | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Kristen Kuhn
- US Meat Animal Research Center, ARS USDA, Clay Center, NE, USA
| | | | - Wai Yee Low
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Stefan Hiendleder
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Olivier Fedrigo
- Vertebrate Genomes Laboratory, The Rockefeller University, New York, NY, USA
| | | | | | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, 29122, Piacenza, Italy
| | | | - Erich D Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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131
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Engelbrecht J, Duong TA, Prabhu SA, Seedat M, van den Berg N. Genome of the destructive oomycete Phytophthora cinnamomi provides insights into its pathogenicity and adaptive potential. BMC Genomics 2021; 22:302. [PMID: 33902447 PMCID: PMC8074420 DOI: 10.1186/s12864-021-07552-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 03/24/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Phytophthora cinnamomi is an oomycete pathogen of global relevance. It is considered as one of the most invasive species, which has caused irreversible damage to natural ecosystems and horticultural crops. There is currently a lack of a high-quality reference genome for this species despite several attempts that have been made towards sequencing its genome. The lack of a good quality genome sequence has been a setback for various genetic and genomic research to be done on this species. As a consequence, little is known regarding its genome characteristics and how these contribute to its pathogenicity and invasiveness. RESULTS In this work we generated a high-quality genome sequence and annotation for P. cinnamomi using a combination of Oxford Nanopore and Illumina sequencing technologies. The annotation was done using RNA-Seq data as supporting gene evidence. The final assembly consisted of 133 scaffolds, with an estimated genome size of 109.7 Mb, N50 of 1.18 Mb, and BUSCO completeness score of 97.5%. Genome partitioning analysis revealed that P. cinnamomi has a two-speed genome characteristic, similar to that of other oomycetes and fungal plant pathogens. In planta gene expression analysis revealed up-regulation of pathogenicity-related genes, suggesting their important roles during infection and host degradation. CONCLUSION This study has provided a high-quality reference genome and annotation for P. cinnamomi. This is among the best assembled genomes for any Phytophthora species assembled to date and thus resulted in improved identification and characterization of pathogenicity-related genes, some of which were undetected in previous versions of genome assemblies. Phytophthora cinnamomi harbours a large number of effector genes which are located in the gene-poor regions of the genome. This unique genomic partitioning provides P. cinnamomi with a high level of adaptability and could contribute to its success as a highly invasive species. Finally, the genome sequence, its annotation and the pathogenicity effectors identified in this study will serve as an important resource that will enable future studies to better understand and mitigate the impact of this important pathogen.
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Affiliation(s)
- Juanita Engelbrecht
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa.
| | - Tuan A Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - S Ashok Prabhu
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Mohamed Seedat
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Noëlani van den Berg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
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132
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Xu W, Wu D, Yang T, Sun C, Wang Z, Han B, Wu S, Yu A, Chapman MA, Muraguri S, Tan Q, Wang W, Bao Z, Liu A, Li DZ. Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean. Genome Biol 2021; 22:113. [PMID: 33874982 PMCID: PMC8056531 DOI: 10.1186/s13059-021-02333-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/29/2021] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Castor bean (Ricinus communis L.) is an important oil crop, which belongs to the Euphorbiaceae family. The seed oil of castor bean is currently the only commercial source of ricinoleic acid that can be used for producing about 2000 industrial products. However, it remains largely unknown regarding the origin, domestication, and the genetic basis of key traits of castor bean. RESULTS Here we perform a de novo chromosome-level genome assembly of the wild progenitor of castor bean. By resequencing and analyzing 505 worldwide accessions, we reveal that the accessions from East Africa are the extant wild progenitors of castor bean, and the domestication occurs ~ 3200 years ago. We demonstrate that significant genetic differentiation between wild populations in Kenya and Ethiopia is associated with past climate fluctuation in the Turkana depression ~ 7000 years ago. This dramatic change in climate may have caused the genetic bottleneck in wild castor bean populations. By a genome-wide association study, combined with quantitative trait locus analysis, we identify important candidate genes associated with plant architecture and seed size. CONCLUSIONS This study provides novel insights of domestication and genome evolution of castor bean, which facilitates genomics-based breeding of this important oilseed crop and potentially other tree-like crops in future.
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Affiliation(s)
- Wei Xu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Di Wu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Tianquan Yang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Chao Sun
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zaiqing Wang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Bing Han
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Shibo Wu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Anmin Yu
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Mark A Chapman
- Biological Sciences and Centre for Underutilised Crops, University of Southampton, Southampton, SO17 1BJ, UK
| | - Sammy Muraguri
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Qing Tan
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Wenbo Wang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhigui Bao
- Shanghai OE Biotech Co., Ltd, Shanghai, 201114, China
| | - Aizhong Liu
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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Raharimalala N, Rombauts S, McCarthy A, Garavito A, Orozco-Arias S, Bellanger L, Morales-Correa AY, Froger S, Michaux S, Berry V, Metairon S, Fournier C, Lepelley M, Mueller L, Couturon E, Hamon P, Rakotomalala JJ, Descombes P, Guyot R, Crouzillat D. The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago. Sci Rep 2021; 11:8119. [PMID: 33854089 PMCID: PMC8046976 DOI: 10.1038/s41598-021-87419-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/23/2021] [Indexed: 02/02/2023] Open
Abstract
Caffeine is the most consumed alkaloid stimulant in the world. It is synthesized through the activity of three known N-methyltransferase proteins. Here we are reporting on the 422-Mb chromosome-level assembly of the Coffea humblotiana genome, a wild and endangered, naturally caffeine-free, species from the Comoro archipelago. We predicted 32,874 genes and anchored 88.7% of the sequence onto the 11 chromosomes. Comparative analyses with the African Robusta coffee genome (C. canephora) revealed an extensive genome conservation, despite an estimated 11 million years of divergence and a broad diversity of genome sizes within the Coffea genus. In this genome, the absence of caffeine is likely due to the absence of the caffeine synthase gene which converts theobromine into caffeine through an illegitimate recombination mechanism. These findings pave the way for further characterization of caffeine-free species in the Coffea genus and will guide research towards naturally-decaffeinated coffee drinks for consumers.
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Affiliation(s)
- Nathalie Raharimalala
- grid.433118.c0000 0001 2302 6762Centre National de Recherche Appliquée au Développement Rural, BP 1444, 101 Ambatobe, Antananarivo Madagascar
| | - Stephane Rombauts
- grid.5342.00000 0001 2069 7798Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium ,grid.11486.3a0000000104788040VIB Center for Plant Systems Biology, 9052 Gent, Belgium
| | - Andrew McCarthy
- grid.418923.50000 0004 0638 528XEuropean Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Andréa Garavito
- grid.7779.e0000 0001 2290 6370Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia ,Centro de Bioinformática y biología computacional de Colombia – BIOS, Ecoparque los Yarumos, Manizales, Caldas, Colombia
| | - Simon Orozco-Arias
- grid.7779.e0000 0001 2290 6370Department of Systems and Informatics, Universidad de Caldas, Manizales, Colombia ,grid.441739.c0000 0004 0486 2919Universidad Autónoma de Manizales, Manizales, Colombia
| | - Laurence Bellanger
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Alexa Yadira Morales-Correa
- grid.7779.e0000 0001 2290 6370Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia
| | - Solène Froger
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Stéphane Michaux
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Victoria Berry
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Sylviane Metairon
- grid.419905.00000 0001 0066 4948Nestle Research, Société des Produits Nestlé SA, 1015 Lausanne, Switzerland
| | - Coralie Fournier
- grid.419905.00000 0001 0066 4948Nestle Research, Société des Produits Nestlé SA, 1015 Lausanne, Switzerland ,grid.8591.50000 0001 2322 4988Present Address: University of Geneva, CMU-Décanat, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Maud Lepelley
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Lukas Mueller
- grid.5386.8000000041936877XBoyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853 USA
| | - Emmanuel Couturon
- grid.121334.60000 0001 2097 0141Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Perla Hamon
- grid.121334.60000 0001 2097 0141Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Jean-Jacques Rakotomalala
- grid.433118.c0000 0001 2302 6762Centre National de Recherche Appliquée au Développement Rural, BP 1444, 101 Ambatobe, Antananarivo Madagascar
| | - Patrick Descombes
- grid.419905.00000 0001 0066 4948Nestle Research, Société des Produits Nestlé SA, 1015 Lausanne, Switzerland
| | - Romain Guyot
- grid.441739.c0000 0004 0486 2919Universidad Autónoma de Manizales, Manizales, Colombia ,grid.121334.60000 0001 2097 0141Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Dominique Crouzillat
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
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134
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Henry PM, Pincot DD, Jenner BN, Borrero C, Aviles M, Nam M, Epstein L, Knapp SJ, Gordon TR. Horizontal chromosome transfer and independent evolution drive diversification in Fusarium oxysporum f. sp. fragariae. THE NEW PHYTOLOGIST 2021; 230:327-340. [PMID: 33616938 PMCID: PMC7986148 DOI: 10.1111/nph.17141] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/02/2020] [Indexed: 05/13/2023]
Abstract
The genes required for host-specific pathogenicity in Fusarium oxysporum can be acquired through horizontal chromosome transfer (HCT). However, it is unknown if HCT commonly contributes to the diversification of pathotypes. Using comparative genomics and pathogenicity phenotyping, we explored the role of HCT in the evolution of F. oxysporum f. sp. fragariae, the cause of Fusarium wilt of strawberry, with isolates from four continents. We observed two distinct syndromes: one included chlorosis ('yellows-fragariae') and the other did not ('wilt-fragariae'). All yellows-fragariae isolates carried a predicted pathogenicity chromosome, 'chrY-frag ', that was horizontally transferred at least four times. chrY-frag was associated with virulence on specific cultivars and encoded predicted effectors that were highly upregulated during infection. chrY-frag was not present in wilt-fragariae; isolates causing this syndrome evolved pathogenicity independently. All origins of F. oxysporum f. sp. fragariae occurred outside of the host's native range. Our data support the conclusion that HCT is widespread in F. oxysporum, but pathogenicity can also evolve independently. The absence of chrY-frag in wilt-fragariae suggests that multiple, distinct pathogenicity chromosomes can confer the same host specificity. The wild progenitors of cultivated strawberry (Fragaria × ananassa) did not co-evolve with this pathogen, yet we discovered several sources of genetic resistance.
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Affiliation(s)
- Peter M. Henry
- United States Department of AgricultureAgricultural Research Service1636 E. Alisal St.SalinasCA93905USA
| | - Dominique D.A. Pincot
- Department of Plant SciencesUniversity of CaliforniaOne Shields AvenueDavisCA95616USA
| | - Bradley N. Jenner
- Department of Plant PathologyUniversity of CaliforniaOne Shields AvenueDavisCA95616USA
| | - Celia Borrero
- Department of Ciencias AgroforestalesEscuela Técnica Superior de Ingeniería AgronómicaUniversidad de SevillaCtra. Utrera km 1Sevilla41013Spain
| | - Manuel Aviles
- Department of Ciencias AgroforestalesEscuela Técnica Superior de Ingeniería AgronómicaUniversidad de SevillaCtra. Utrera km 1Sevilla41013Spain
| | - Myeong‐Hyeon Nam
- Strawberry Research InstituteChungcheongnam‐do Agricultural Research & Extension ServicesNonsan32914Korea
| | - Lynn Epstein
- Department of Plant PathologyUniversity of CaliforniaOne Shields AvenueDavisCA95616USA
| | - Steven J. Knapp
- Department of Plant SciencesUniversity of CaliforniaOne Shields AvenueDavisCA95616USA
| | - Thomas R. Gordon
- Department of Plant PathologyUniversity of CaliforniaOne Shields AvenueDavisCA95616USA
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135
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Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Bista I, Smith M, Haase B, Mountcastle J, Winkler S, Paez S, Howard J, Vernes SC, Lama TM, Grutzner F, Warren WC, Balakrishnan CN, Burt D, George JM, Biegler MT, Iorns D, Digby A, Eason D, Robertson B, Edwards T, Wilkinson M, Turner G, Meyer A, Kautt AF, Franchini P, Detrich HW, Svardal H, Wagner M, Naylor GJP, Pippel M, Malinsky M, Mooney M, Simbirsky M, Hannigan BT, Pesout T, Houck M, Misuraca A, Kingan SB, Hall R, Kronenberg Z, Sović I, Dunn C, Ning Z, Hastie A, Lee J, Selvaraj S, Green RE, Putnam NH, Gut I, Ghurye J, Garrison E, Sims Y, Collins J, Pelan S, Torrance J, Tracey A, Wood J, Dagnew RE, Guan D, London SE, Clayton DF, Mello CV, Friedrich SR, Lovell PV, Osipova E, Al-Ajli FO, Secomandi S, Kim H, Theofanopoulou C, Hiller M, Zhou Y, Harris RS, Makova KD, Medvedev P, Hoffman J, Masterson P, Clark K, Martin F, Howe K, Flicek P, Walenz BP, Kwak W, Clawson H, Diekhans M, Nassar L, Paten B, Kraus RHS, Crawford AJ, Gilbert MTP, Zhang G, Venkatesh B, Murphy RW, Koepfli KP, Shapiro B, Johnson WE, Di Palma F, Marques-Bonet T, Teeling EC, Warnow T, Graves JM, Ryder OA, Haussler D, O'Brien SJ, Korlach J, Lewin HA, Howe K, Myers EW, Durbin R, Phillippy AM, Jarvis ED. Towards complete and error-free genome assemblies of all vertebrate species. Nature 2021; 592:737-746. [PMID: 33911273 PMCID: PMC8081667 DOI: 10.1038/s41586-021-03451-0] [Citation(s) in RCA: 752] [Impact Index Per Article: 250.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 03/12/2021] [Indexed: 02/02/2023]
Abstract
High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.
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Affiliation(s)
- Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shane A McCarthy
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | - Joana Damas
- The Genome Center, University of California Davis, Davis, CA, USA
| | - Giulio Formenti
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marcela Uliano-Silva
- Leibniz Institute for Zoo and Wildlife Research, Department of Evolutionary Genetics, Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | | | | | - Juwan Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Chul Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Byung June Ko
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Mark Chaisson
- University of Southern California, Los Angeles, CA, USA
| | - Gregory L Gedman
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Lindsey J Cantin
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Iliana Bista
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | | | - Bettina Haase
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | | | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- DRESDEN-concept Genome Center, Dresden, Germany
| | - Sadye Paez
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | | | - Sonja C Vernes
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
- School of Biology, University of St Andrews, St Andrews, UK
| | - Tanya M Lama
- University of Massachusetts Cooperative Fish and Wildlife Research Unit, Amherst, MA, USA
| | - Frank Grutzner
- School of Biological Science, The Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Wesley C Warren
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | | | - Dave Burt
- UQ Genomics, University of Queensland, Brisbane, Queensland, Australia
| | - Julia M George
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Matthew T Biegler
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - David Iorns
- The Genetic Rescue Foundation, Wellington, New Zealand
| | - Andrew Digby
- Kākāpō Recovery, Department of Conservation, Invercargill, New Zealand
| | - Daryl Eason
- Kākāpō Recovery, Department of Conservation, Invercargill, New Zealand
| | - Bruce Robertson
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | | | - Mark Wilkinson
- Department of Life Sciences, Natural History Museum, London, UK
| | - George Turner
- School of Natural Sciences, Bangor University, Gwynedd, UK
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Andreas F Kautt
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - H William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, USA
| | - Hannes Svardal
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Maximilian Wagner
- Institute of Biology, Karl-Franzens University of Graz, Graz, Austria
| | - Gavin J P Naylor
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology, Dresden, Germany
| | - Milan Malinsky
- Wellcome Sanger Institute, Cambridge, UK
- Zoological Institute, University of Basel, Basel, Switzerland
| | | | | | | | - Trevor Pesout
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | | | | | | | | | | | - Ivan Sović
- Pacific Biosciences, Menlo Park, CA, USA
- Digital BioLogic, Ivanić-Grad, Croatia
| | | | - Zemin Ning
- Wellcome Sanger Institute, Cambridge, UK
| | | | - Joyce Lee
- Bionano Genomics, San Diego, CA, USA
| | | | - Richard E Green
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
- Dovetail Genomics, Santa Cruz, CA, USA
| | | | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Jay Ghurye
- Dovetail Genomics, Santa Cruz, CA, USA
- Department of Computer Science, University of Maryland College Park, College Park, MD, USA
| | - Erik Garrison
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Ying Sims
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | | | | | | | | | - Dengfeng Guan
- Department of Genetics, University of Cambridge, Cambridge, UK
- School of Computer Science and Technology, Center for Bioinformatics, Harbin Institute of Technology, Harbin, China
| | - Sarah E London
- Department of Psychology, Institute for Mind and Biology, University of Chicago, Chicago, IL, USA
| | - David F Clayton
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Samantha R Friedrich
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Ekaterina Osipova
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Farooq O Al-Ajli
- Monash University Malaysia Genomics Facility, School of Science, Selangor Darul Ehsan, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Selangor Darul Ehsan, Malaysia
- Qatar Falcon Genome Project, Doha, Qatar
| | | | - Heebal Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc., Seoul, Republic of Korea
| | | | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany
- Senckenberg Research Institute, Frankfurt, Germany
- Goethe-University, Faculty of Biosciences, Frankfurt, Germany
| | | | - Robert S Harris
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Kateryna D Makova
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Center for Medical Genomics, Pennsylvania State University, University Park, PA, USA
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA
| | - Paul Medvedev
- Center for Medical Genomics, Pennsylvania State University, University Park, PA, USA
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA
- Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Jinna Hoffman
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Patrick Masterson
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Karen Clark
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Fergal Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Kevin Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Brian P Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Woori Kwak
- eGnome, Inc., Seoul, Republic of Korea
- Hoonygen, Seoul, Korea
| | - Hiram Clawson
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Luis Nassar
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Robert H S Kraus
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Guojie Zhang
- China National Genebank, BGI-Shenzhen, Shenzhen, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore
| | - Robert W Murphy
- Centre for Biodiversity, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
- The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD, USA
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Federica Di Palma
- Department of Biological Sciences, Earlham Institute, University of East Anglia, Norwich, UK
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Tandy Warnow
- Department of Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Oliver A Ryder
- San Diego Zoo Global, Escondido, CA, USA
- Department of Evolution, Behavior, and Ecology, University of California San Diego, La Jolla, CA, USA
| | - David Haussler
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Stephen J O'Brien
- Laboratory of Genomics Diversity-Center for Computer Technologies, ITMO University, St. Petersburg, Russian Federation
- Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, FL, USA
| | | | - Harris A Lewin
- The Genome Center, University of California Davis, Davis, CA, USA
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
- John Muir Institute for the Environment, University of California Davis, Davis, CA, USA
| | | | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Center for Systems Biology, Dresden, Germany.
- Faculty of Computer Science, Technical University Dresden, Dresden, Germany.
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Cambridge, UK.
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Erich D Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA.
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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136
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Peñaloza C, Gutierrez AP, Eöry L, Wang S, Guo X, Archibald AL, Bean TP, Houston RD. A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas. Gigascience 2021; 10:6187865. [PMID: 33764468 PMCID: PMC7992393 DOI: 10.1093/gigascience/giab020] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/10/2021] [Accepted: 03/03/2021] [Indexed: 02/06/2023] Open
Abstract
Background The Pacific oyster (Crassostrea gigas) is a bivalve mollusc with vital roles in coastal ecosystems and aquaculture globally. While extensive genomic tools are available for C. gigas, highly contiguous reference genomes are required to support both fundamental and applied research. Herein we report the creation and annotation of a chromosome-level assembly for C. gigas. Findings High-coverage long- and short-read sequence data generated on Pacific Biosciences and Illumina platforms were used to generate an initial assembly, which was then scaffolded into 10 pseudo-chromosomes using both Hi-C sequencing and a high-density linkage map. The assembly has a scaffold N50 of 58.4 Mb and a contig N50 of 1.8 Mb, representing a step advance on the previously published C. gigas assembly. Annotation based on Pacific Biosciences Iso-Seq and Illumina RNA-Seq resulted in identification of ∼30,000 putative protein-coding genes. Annotation of putative repeat elements highlighted an enrichment of Helitron rolling-circle transposable elements, suggesting their potential role in shaping the evolution of the C. gigas genome. Conclusions This new chromosome-level assembly will be an enabling resource for genetics and genomics studies to support fundamental insight into bivalve biology, as well as for selective breeding of C. gigas in aquaculture.
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Affiliation(s)
- Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Alejandro P Gutierrez
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Lél Eöry
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Shan Wang
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ 08349, USA
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ 08349, USA
| | - Alan L Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Tim P Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
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137
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Liu Z, Zhang L, Yan Z, Ren Z, Han F, Tan X, Xiang Z, Dong F, Yang Z, Liu G, Wang Z, Zhang J, Que T, Tang C, Li Y, Wang S, Wu J, Li L, Huang C, Roos C, Li M. Genomic Mechanisms of Physiological and Morphological Adaptations of Limestone Langurs to Karst Habitats. Mol Biol Evol 2021; 37:952-968. [PMID: 31846031 DOI: 10.1093/molbev/msz301] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Knowledge of the physiological and morphological evolution and adaptation of nonhuman primates is critical to understand hominin origins, physiological ecology, morphological evolution, and applications in biomedicine. Particularly, limestone langurs represent a direct example of adaptations to the challenges of exploiting a high calcium and harsh environment. Here, we report a de novo genome assembly (Tfra_2.0) of a male François's langur (Trachypithecus francoisi) with contig N50 of 16.3 Mb and resequencing data of 23 individuals representing five limestone and four forest langur species. Comparative genomics reveals evidence for functional evolution in genes and gene families related to calcium signaling in the limestone langur genome, probably as an adaptation to naturally occurring high calcium levels present in water and plant resources in karst habitats. The genomic and functional analyses suggest that a single point mutation (Lys1905Arg) in the α1c subunit of the L-type voltage-gated calcium channel Cav1.2 (CACNA1C) attenuates the inward calcium current into the cells in vitro. Population genomic analyses and RNA-sequencing indicate that EDNRB is less expressed in white tail hair follicles of the white-headed langur (T. leucocephalus) compared with the black-colored François's langur and hence might be responsible for species-specific differences in body coloration. Our findings contribute to a new understanding of gene-environment interactions and physiomorphological adaptative mechanisms in ecologically specialized primate taxa.
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Affiliation(s)
- Zhijin Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.,Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Liye Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongze Yan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.,Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Zhijie Ren
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Fengming Han
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Xinxin Tan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiyuan Xiang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Dong
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.,Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Zuomin Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.,School of Life Sciences, Qufu Normal University, Qufu 273165, Shandong, China
| | - Guangjian Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China
| | - Ziming Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiali Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China
| | - Tengcheng Que
- Guangxi Zhuang Autonomous Region Terrestrial Wildlife Medical-Aid Monitoring Epidemic Diseases Research Center, Nanning 530001, Guangxi Province, China
| | - Chaohui Tang
- Wuzhou Langur Breeding and Research Center, Wuzhou 543002, Guangxi Province, China
| | - Yifeng Li
- Wuzhou Langur Breeding and Research Center, Wuzhou 543002, Guangxi Province, China
| | - Song Wang
- Nanning Zoo, Nanning 530000, Guangxi Province, China
| | - Junyi Wu
- Nanning Zoo, Nanning 530000, Guangxi Province, China
| | - Legong Li
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Chengming Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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138
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Edwards RJ, Field MA, Ferguson JM, Dudchenko O, Keilwagen J, Rosen BD, Johnson GS, Rice ES, Hillier LD, Hammond JM, Towarnicki SG, Omer A, Khan R, Skvortsova K, Bogdanovic O, Zammit RA, Aiden EL, Warren WC, Ballard JWO. Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome. BMC Genomics 2021; 22:188. [PMID: 33726677 PMCID: PMC7962210 DOI: 10.1186/s12864-021-07493-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/28/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. RESULTS Here, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three dog breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative dog breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. CONCLUSIONS The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific dog breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies.
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Affiliation(s)
- Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Matt A. Field
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878 Australia
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600 Australia
| | - James M. Ferguson
- Kinghorn Center for Clinical Genomics, Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010 Australia
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Computer Science, Rice University, Houston, TX USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX USA
| | - Jens Keilwagen
- Julius Kühn-Institut, Erwin-Baur-Str, 27 06484 Quedlinburg, Germany
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Beltsville, MD 20705 USA
| | - Gary S. Johnson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211 USA
| | - Edward S. Rice
- Department of Surgery, University of Missouri, Columbia, MO 65211 USA
| | | | - Jillian M. Hammond
- Kinghorn Center for Clinical Genomics, Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010 Australia
| | - Samuel G. Towarnicki
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Arina Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Computer Science, Rice University, Houston, TX USA
| | - Ruqayya Khan
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Computer Science, Rice University, Houston, TX USA
| | - Ksenia Skvortsova
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010 Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2010 Australia
| | - Ozren Bogdanovic
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010 Australia
| | - Robert A. Zammit
- Vineyard Veterinary Hospital, 703 Windsor Rd, Vineyard, NSW 2765 Australia
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Computer Science, Rice University, Houston, TX USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX USA
- Faculty of Science, UWA School of Agriculture and Environment, University of Western Australia, Perth, WA 6009 Australia
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Wesley C. Warren
- Department of Animal Sciences, University of Missouri, Columbia, MO 65211 Australia
| | - J. William O. Ballard
- Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria 3086 Australia
- School of Biosciences, University of Melbourne, Parkville, Victoria 3052 Australia
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139
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Zhu B, Qian F, Hou Y, Yang W, Cai M, Wu X. Complete chloroplast genome features and phylogenetic analysis of Eruca sativa (Brassicaceae). PLoS One 2021; 16:e0248556. [PMID: 33711072 PMCID: PMC7954331 DOI: 10.1371/journal.pone.0248556] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/01/2021] [Indexed: 12/05/2022] Open
Abstract
Eruca sativa Mill. (Brassicaceae) is an important edible vegetable and a potential medicinal plant due to the antibacterial activity of its seed oil. Here, the complete chloroplast (cp) genome of E. sativa was de novo assembled with a combination of long PacBio reads and short Illumina reads. The E. sativa cp genome had a quadripartite structure that was 153,522 bp in size, consisting of one large single-copy region of 83,320 bp and one small single-copy region of 17,786 bp which were separated by two inverted repeat (IRa and IRb) regions of 26,208 bp. This complete cp genome harbored 113 unique genes: 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Forty-nine long repetitive sequences and 69 simple sequence repeats were identified in the E. sativa cp genome. A codon usage analysis of the E. sativa cp genome showed a bias toward codons ending in A/T. The E. sativa cp genome was similar in size, gene composition, and linearity of the structural region when compared with other Brassicaceae cp genomes. Moreover, the analysis of the synonymous (Ks) and non-synonymous (Ka) substitution rates demonstrated that protein-coding genes generally underwent purifying selection pressure, expect ycf1, ycf2, and rps12. A phylogenetic analysis determined that E. sativa is evolutionarily close to important Brassica species, indicating that it may be possible to transfer favorable E. sativa alleles into other Brassica species. Our results will be helpful to advance genetic improvement and breeding of E. sativa, and will provide valuable information for utilizing E. sativa as an important resource to improve other Brassica species.
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Affiliation(s)
- Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Fang Qian
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yunfeng Hou
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Weicheng Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Mengxian Cai
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Xiaoming Wu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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140
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A Comparative Genomic Study of Attenuated and Virulent Strains of Babesia bigemina. Pathogens 2021; 10:pathogens10030318. [PMID: 33800466 PMCID: PMC7999288 DOI: 10.3390/pathogens10030318] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/23/2021] [Accepted: 03/06/2021] [Indexed: 11/17/2022] Open
Abstract
Cattle babesiosis is a socio-economically important tick-borne disease caused by Apicomplexa protozoa of the genus Babesia that are obligate intraerythrocytic parasites. The pathogenicity of Babesia parasites for cattle is determined by the interaction with the host immune system and the presence of the parasite’s virulence genes. A Babesia bigemina strain that has been maintained under a microaerophilic stationary phase in in vitro culture conditions for several years in the laboratory lost virulence for the bovine host and the capacity for being transmitted by the tick vector. In this study, we compared the virulome of the in vitro culture attenuated Babesia bigemina strain (S) and the virulent tick transmitted parental Mexican B. bigemina strain (M). Preliminary results obtained by using the Basic Local Alignment Search Tool (BLAST) showed that out of 27 virulence genes described and analyzed in the B. bigemina virulent tick transmitted strain, only five were fully identified in the attenuated laboratory strain. In all cases, the identity and coverture of the identified genes of the wildtype strain were higher than those of the laboratory strain. This finding is putatively associated with the continuous partial loss of virulence genes in the laboratory strain after several passages of the parasite population under optimal in vitro growth conditions. The loss of virulence factors might be reflected in the absence of symptoms of the disease in cattle inoculated with the attenuated strain despite the presence of infection in the bovine host cells.
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141
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Qin X, Zhang Z, Lou Q, Xia L, Li J, Li M, Zhou J, Zhao X, Xu Y, Li Q, Yang S, Yu X, Cheng C, Huang S, Chen J. Chromosome-scale genome assembly of Cucumis hystrix-a wild species interspecifically cross-compatible with cultivated cucumber. HORTICULTURE RESEARCH 2021; 8:40. [PMID: 33642577 PMCID: PMC7917098 DOI: 10.1038/s41438-021-00475-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/30/2020] [Accepted: 01/07/2021] [Indexed: 05/06/2023]
Abstract
Cucumis hystrix Chakr. (2n = 2x = 24) is a wild species that can hybridize with cultivated cucumber (C. sativus L., 2n = 2x = 14), a globally important vegetable crop. However, cucumber breeding is hindered by its narrow genetic base. Therefore, introgression from C. hystrix has been anticipated to bring a breakthrough in cucumber improvement. Here, we report the chromosome-scale assembly of C. hystrix genome (289 Mb). Scaffold N50 reached 14.1 Mb. Over 90% of the sequences were anchored onto 12 chromosomes. A total of 23,864 genes were annotated using a hybrid method. Further, we conducted a comprehensive comparative genomic analysis of cucumber, C. hystrix, and melon (C. melo L., 2n = 2x = 24). Whole-genome comparisons revealed that C. hystrix is phylogenetically closer to cucumber than to melon, providing a molecular basis for the success of its hybridization with cucumber. Moreover, expanded gene families of C. hystrix were significantly enriched in "defense response," and C. hystrix harbored 104 nucleotide-binding site-encoding disease resistance gene analogs. Furthermore, 121 genes were positively selected, and 12 (9.9%) of these were involved in responses to biotic stimuli, which might explain the high disease resistance of C. hystrix. The alignment of whole C. hystrix genome with cucumber genome and self-alignment revealed 45,417 chromosome-specific sequences evenly distributed on C. hystrix chromosomes. Finally, we developed four cucumber-C. hystrix alien addition lines and identified the exact introgressed chromosome using molecular and cytological methods. The assembled C. hystrix genome can serve as a valuable resource for studies on Cucumis evolution and interspecific introgression breeding of cucumber.
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Affiliation(s)
- Xiaodong Qin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhonghua Zhang
- College of Horticulture, Qingdao Agricultural University, 266109, Qingdao, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Lei Xia
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Ji Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Mengxue Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Junguo Zhou
- College of Horticulture and Landscape, Henan Institute of Science and Technology, 453003, Xinxiang, China
| | - Xiaokun Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Yuanchao Xu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Qing Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Shuqiong Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Xiaqing Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Chunyan Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Sanwen Huang
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China.
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.
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142
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Luo J, Wei Y, Lyu M, Wu Z, Liu X, Luo H, Yan C. A comprehensive review of scaffolding methods in genome assembly. Brief Bioinform 2021; 22:6149347. [PMID: 33634311 DOI: 10.1093/bib/bbab033] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/20/2022] Open
Abstract
In the field of genome assembly, scaffolding methods make it possible to obtain a more complete and contiguous reference genome, which is the cornerstone of genomic research. Scaffolding methods typically utilize the alignments between contigs and sequencing data (reads) to determine the orientation and order among contigs and to produce longer scaffolds, which are helpful for genomic downstream analysis. With the rapid development of high-throughput sequencing technologies, diverse types of reads have emerged over the past decade, especially in long-range sequencing, which have greatly enhanced the assembly quality of scaffolding methods. As the number of scaffolding methods increases, biology and bioinformatics researchers need to perform in-depth analyses of state-of-the-art scaffolding methods. In this article, we focus on the difficulties in scaffolding, the differences in characteristics among various kinds of reads, the methods by which current scaffolding methods address these difficulties, and future research opportunities. We hope this work will benefit the design of new scaffolding methods and the selection of appropriate scaffolding methods for specific biological studies.
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Affiliation(s)
- Junwei Luo
- College of Computer Science and Technology, Henan Polytechnic University, Jiaozuo, China
| | - Yawei Wei
- College of Computer Science and Technology, Henan Polytechnic University, Jiaozuo, China
| | - Mengna Lyu
- College of Computer Science and Technology, Henan Polytechnic University, Jiaozuo, China
| | - Zhengjiang Wu
- College of Computer Science and Technology, Henan Polytechnic University, Jiaozuo, China
| | - Xiaoyan Liu
- College of Computer Science and Technology, Henan Polytechnic University, Jiaozuo, China
| | - Huimin Luo
- School of Computer and Information Engineering, Henan University, Kaifeng, China
| | - Chaokun Yan
- School of Computer and Information Engineering, Henan University, Kaifeng, China
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143
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Fischer C, Koblmüller S, Börger C, Michelitsch G, Trajanoski S, Schlötterer C, Guelly C, Thallinger GG, Sturmbauer C. Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco-morphologically divergent cichlid fishes endemic to Lake Tanganyika. Sci Rep 2021; 11:4309. [PMID: 33619328 PMCID: PMC7900123 DOI: 10.1038/s41598-021-81030-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 12/28/2020] [Indexed: 01/01/2023] Open
Abstract
With more than 1000 species, East African cichlid fishes represent the fastest and most species-rich vertebrate radiation known, providing an ideal model to tackle molecular mechanisms underlying recurrent adaptive diversification. We add high-quality genome reconstructions for two phylogenetic key species of a lineage that diverged about ~ 3-9 million years ago (mya), representing the earliest split of the so-called modern haplochromines that seeded additional radiations such as those in Lake Malawi and Victoria. Along with the annotated genomes we analysed discriminating genomic features of the study species, each representing an extreme trophic morphology, one being an algae browser and the other an algae grazer. The genomes of Tropheus moorii (TM) and Petrochromis trewavasae (PT) comprise 911 and 918 Mbp with 40,300 and 39,600 predicted genes, respectively. Our DNA sequence data are based on 5 and 6 individuals of TM and PT, and the transcriptomic sequences of one individual per species and sex, respectively. Concerning variation, on average we observed 1 variant per 220 bp (interspecific), and 1 variant per 2540 bp (PT vs PT)/1561 bp (TM vs TM) (intraspecific). GO enrichment analysis of gene regions affected by variants revealed several candidates which may influence phenotype modifications related to facial and jaw morphology, such as genes belonging to the Hedgehog pathway (SHH, SMO, WNT9A) and the BMP and GLI families.
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Affiliation(s)
- C Fischer
- Institute of Biology, University of Graz, Graz, Austria
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria
| | - S Koblmüller
- Institute of Biology, University of Graz, Graz, Austria
| | - C Börger
- Institute of Biology, University of Graz, Graz, Austria
| | - G Michelitsch
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - S Trajanoski
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - C Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - C Guelly
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - G G Thallinger
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
| | - C Sturmbauer
- Institute of Biology, University of Graz, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
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144
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Wang C, Wallerman O, Arendt ML, Sundström E, Karlsson Å, Nordin J, Mäkeläinen S, Pielberg GR, Hanson J, Ohlsson Å, Saellström S, Rönnberg H, Ljungvall I, Häggström J, Bergström TF, Hedhammar Å, Meadows JRS, Lindblad-Toh K. A novel canine reference genome resolves genomic architecture and uncovers transcript complexity. Commun Biol 2021; 4:185. [PMID: 33568770 PMCID: PMC7875987 DOI: 10.1038/s42003-021-01698-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/17/2020] [Indexed: 12/13/2022] Open
Abstract
We present GSD_1.0, a high-quality domestic dog reference genome with chromosome length scaffolds and contiguity increased 55-fold over CanFam3.1. Annotation with generated and existing long and short read RNA-seq, miRNA-seq and ATAC-seq, revealed that 32.1% of lifted over CanFam3.1 gaps harboured previously hidden functional elements, including promoters, genes and miRNAs in GSD_1.0. A catalogue of canine "dark" regions was made to facilitate mapping rescue. Alignment in these regions is difficult, but we demonstrate that they harbour trait-associated variation. Key genomic regions were completed, including the Dog Leucocyte Antigen (DLA), T Cell Receptor (TCR) and 366 COSMIC cancer genes. 10x linked-read sequencing of 27 dogs (19 breeds) uncovered 22.1 million SNPs, indels and larger structural variants. Subsequent intersection with protein coding genes showed that 1.4% of these could directly influence gene products, and so provide a source of normal or aberrant phenotypic modifications.
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Affiliation(s)
- Chao Wang
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| | - Ola Wallerman
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Maja-Louise Arendt
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Veterinary Clinical Sciences, University of Copenhagen, Frederiksberg D, Denmark
| | - Elisabeth Sundström
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Åsa Karlsson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jessika Nordin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Suvi Mäkeläinen
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gerli Rosengren Pielberg
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jeanette Hanson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Åsa Ohlsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Saellström
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Henrik Rönnberg
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ingrid Ljungvall
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jens Häggström
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Tomas F Bergström
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Åke Hedhammar
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jennifer R S Meadows
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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145
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Burley JT, Kellner JR, Hubbell SP, Faircloth BC. Genome assemblies for two Neotropical trees: Jacaranda copaia and Handroanthus guayacan. G3 (BETHESDA, MD.) 2021; 11:jkab010. [PMID: 33693604 PMCID: PMC8034707 DOI: 10.1093/g3journal/jkab010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/22/2020] [Indexed: 12/01/2022]
Abstract
The lack of genomic resources for tropical canopy trees is impeding several research avenues in tropical forest biology. We present genome assemblies for two Neotropical hardwood species, Jacaranda copaia and Handroanthus (formerly Tabebuia) guayacan, that are model systems for research on tropical tree demography and flowering phenology. For each species, we combined Illumina short-read data with in vitro proximity-ligation (Chicago) libraries to generate an assembly. For Jacaranda copaia, we obtained 104X physical coverage and produced an assembly with N50/N90 scaffold lengths of 1.020/0.277 Mbp. For H. guayacan, we obtained 129X coverage and produced an assembly with N50/N90 scaffold lengths of 0.795/0.165 Mbp. J. copaia and H. guayacan assemblies contained 95.8% and 87.9% of benchmarking orthologs, although they constituted only 77.1% and 66.7% of the estimated genome sizes of 799 and 512 Mbp, respectively. These differences were potentially due to high repetitive sequence content (>59.31% and 45.59%) and high heterozygosity (0.5% and 0.8%) in each species. Finally, we compared each new assembly to a previously sequenced genome for Handroanthus impetiginosus using whole-genome alignment. This analysis indicated extensive gene duplication in H. impetiginosus since its divergence from H. guayacan.
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Affiliation(s)
- John T Burley
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
- Institute at Brown for Environment and Society, Brown University, Providence, RI 02912, USA
| | - James R Kellner
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
- Institute at Brown for Environment and Society, Brown University, Providence, RI 02912, USA
| | - Stephen P Hubbell
- Department of Ecology and Evolutionary Biology, University of California—Los Angeles, Los Angeles, CA 90095, USA
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
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146
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Liao Y, Zhang X, Chakraborty M, Emerson JJ. Topologically associating domains and their role in the evolution of genome structure and function in Drosophila. Genome Res 2021; 31:397-410. [PMID: 33563719 PMCID: PMC7919452 DOI: 10.1101/gr.266130.120] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 12/24/2020] [Indexed: 12/18/2022]
Abstract
Topologically associating domains (TADs) were recently identified as fundamental units of three-dimensional eukaryotic genomic organization, although our knowledge of the influence of TADs on genome evolution remains preliminary. To study the molecular evolution of TADs in Drosophila species, we constructed a new reference-grade genome assembly and accompanying high-resolution TAD map for D. pseudoobscura Comparison of D. pseudoobscura and D. melanogaster, which are separated by ∼49 million years of divergence, showed that ∼30%-40% of their genomes retain conserved TADs. Comparative genomic analysis of 17 Drosophila species revealed that chromosomal rearrangement breakpoints are enriched at TAD boundaries but depleted within TADs. Additionally, genes within conserved TADs show lower expression divergence than those located in nonconserved TADs. Furthermore, we found that a substantial proportion of long genes (>50 kbp) in D. melanogaster (42%) and D. pseudoobscura (26%) constitute their own TADs, implying transcript structure may be one of the deterministic factors for TAD formation. By using structural variants (SVs) identified from 14 D. melanogaster strains, its three closest sibling species from the D. simulans species complex, and two obscura clade species, we uncovered evidence of selection acting on SVs at TAD boundaries, but with the nature of selection differing between SV types. Deletions are depleted at TAD boundaries in both divergent and polymorphic SVs, suggesting purifying selection, whereas divergent tandem duplications are enriched at TAD boundaries relative to polymorphism, suggesting they are adaptive. Our findings highlight how important TADs are in shaping the acquisition and retention of structural mutations that fundamentally alter genome organization.
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Affiliation(s)
- Yi Liao
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA
| | - Xinwen Zhang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA
| | - Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA
| | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA.,Center for Complex Biological Systems, University of California, Irvine, California 92697, USA
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147
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Worthington M, Perez JG, Mussurova S, Silva-Cordoba A, Castiblanco V, Cardoso Arango JA, Jones C, Fernandez-Fuentes N, Skot L, Dyer S, Tohme J, Di Palma F, Arango J, Armstead I, De Vega JJ. A new genome allows the identification of genes associated with natural variation in aluminium tolerance in Brachiaria grasses. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:302-319. [PMID: 33064149 PMCID: PMC7853602 DOI: 10.1093/jxb/eraa469] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 10/12/2020] [Indexed: 05/08/2023]
Abstract
Toxic concentrations of aluminium cations and low phosphorus availability are the main yield-limiting factors in acidic soils, which represent half of the potentially available arable land. Brachiaria grasses, which are commonly sown as forage in the tropics because of their resilience and low demand for nutrients, show greater tolerance to high concentrations of aluminium cations (Al3+) than most other grass crops. In this work, we explored the natural variation in tolerance to Al3+ between high and low tolerant Brachiaria species and characterized their transcriptional differences during stress. We identified three QTLs (quantitative trait loci) associated with root vigour during Al3+ stress in their hybrid progeny. By integrating these results with a new Brachiaria reference genome, we identified 30 genes putatively responsible for Al3+ tolerance in Brachiaria. We observed differential expression during stress of genes involved in RNA translation, response signalling, cell wall composition, and vesicle location homologous to aluminium-induced proteins involved in limiting uptake or localizing the toxin. However, there was limited regulation of malate transporters in Brachiaria, which suggests that exudation of organic acids and other external tolerance mechanisms, common in other grasses, might not be relevant in Brachiaria. The contrasting regulation of RNA translation and response signalling suggests that response timing is critical in high Al3+-tolerant Brachiaria.
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Affiliation(s)
- Margaret Worthington
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
- Present address: Department of Horticulture, University of Arkansas, 306 Plant Sciences Bldg, Fayetteville, AR 72701, USA
| | | | | | | | | | | | - Charlotte Jones
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, UK
| | - Narcis Fernandez-Fuentes
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, UK
| | - Leif Skot
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, UK
| | - Sarah Dyer
- Earlham Institute, Norwich Research Park, Norwich, UK
- Present address: NIAB, Huntingdon Road, Cambridge CB3 0LE, UK
| | - Joe Tohme
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | | | - Jacobo Arango
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Ian Armstead
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, UK
| | - Jose J De Vega
- Earlham Institute, Norwich Research Park, Norwich, UK
- Correspondence:
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148
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Yu F, Zhang W, Wang S, Wang H, Yu L, Zeng X, Fei Z, Li J. Genome Sequence of Fusarium oxysporum f. sp. conglutinans, the Etiological Agent of Cabbage Fusarium Wilt. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:210-213. [PMID: 33054566 DOI: 10.1094/mpmi-08-20-0245-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Fusarium oxysporum f. sp. conglutinans is the causal agent of Fusarium wilt of cabbage (Brassica oleracea var. capitata L.), which results in severe yield loss. Here, we report a high-quality genome sequence of a race 1 strain (IVC-1) of F. oxysporum f. sp. conglutinans, which was assembled using a combination of PacBio long-read and Illumina short-read sequences. The assembled IVC-1 genome has a total size of 71.18 Mb, with a contig N50 length of 4.59 Mb, and encodes 23,374 predicted protein-coding genes. The high-quality genome of IVC-1 provides a valuable resource for facilitating our understanding of F. oxysporum f. sp. conglutinans-cabbage interaction.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Fangwei Yu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Wei Zhang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Shenyun Wang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Hong Wang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Li Yu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xiaoping Zeng
- Jiangsu Agricultural Technology Extension Station, Nanjing 210036, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, U.S.A
| | - Jianbin Li
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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149
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Amynthas corticis genome reveals molecular mechanisms behind global distribution. Commun Biol 2021; 4:135. [PMID: 33514865 PMCID: PMC7846840 DOI: 10.1038/s42003-021-01659-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 01/05/2021] [Indexed: 01/30/2023] Open
Abstract
Earthworms (Annelida: Crassiclitellata) are widely distributed around the world due to their ancient origination as well as adaptation and invasion after introduction into new habitats over the past few centuries. Herein, we report a 1.2 Gb complete genome assembly of the earthworm Amynthas corticis based on a strategy combining third-generation long-read sequencing and Hi-C mapping. A total of 29,256 protein-coding genes are annotated in this genome. Analysis of resequencing data indicates that this earthworm is a triploid species. Furthermore, gene family evolution analysis shows that comprehensive expansion of gene families in the Amynthas corticis genome has produced more defensive functions compared with other species in Annelida. Quantitative proteomic iTRAQ analysis shows that expression of 147 proteins changed in the body of Amynthas corticis and 16 S rDNA sequencing shows that abundance of 28 microorganisms changed in the gut of Amynthas corticis when the earthworm was incubated with pathogenic Escherichia coli O157:H7. Our genome assembly provides abundant and valuable resources for the earthworm research community, serving as a first step toward uncovering the mysteries of this species, and may provide molecular level indicators of its powerful defensive functions, adaptation to complex environments and invasion ability.
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150
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Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis. Nat Commun 2021; 12:405. [PMID: 33452249 PMCID: PMC7810986 DOI: 10.1038/s41467-020-20508-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/07/2020] [Indexed: 01/29/2023] Open
Abstract
Plant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly of Ophiorrhiza pumila, a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb, Ophiorrhiza genome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as the origin of MIA evolution. The emergence of strictosidine biosynthesis-catalyzing enzymes precede downstream enzymes' evolution post γ whole-genome triplication, which occurred approximately 110 Mya in O. pumila, and before the whole-genome duplication in Camptotheca acuminata identified here. Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, we propose a working model for MIA evolution, and a pangenome for MIA biosynthesis, which will help in establishing a sustainable supply of camptothecin.
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