201
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Guan DL, Hao XQ, Mi D, Peng J, Li Y, Xie JY, Huang H, Xu SQ. Draft Genome of a Blister Beetle Mylabris aulica. Front Genet 2020; 10:1281. [PMID: 32010178 PMCID: PMC6972506 DOI: 10.3389/fgene.2019.01281] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/21/2019] [Indexed: 11/13/2022] Open
Abstract
Mylabris aulica is a widely distributed blister beetle of the Meloidae family. It has the ability to synthesize a potent defensive secretion that includes cantharidin, a toxic compound used to treat many major illnesses. However, owing to the lack of genetic studies on cantharidin biosynthesis in M. aulica, the commercial use of this species is less extensive than that of other blister beetle species in China. This study reports a draft assembly and possible genes and pathways related to cantharidin biosynthesis for the M. aulica blister beetle using nanopore sequencing data. The draft genome assembly size was 288.5 Mb with a 467.8 Kb N50, and a repeat content of 50.62%. An integrated gene finding pipeline performed for assembly obtained 16,500 protein coding genes. Benchmarking universal single-copy orthologs assessment showed that this gene set included 94.4% complete Insecta universal single-copy orthologs. Over 99% of these genes were assigned functional annotations in the gene ontology, Kyoto Encyclopedia of Genes and Genomes, or Genbank non-redundant databases. Comparative genomic analysis showed that the completeness and continuity of our assembly was better than those of Hycleus cichorii and Hycleus phaleratus blister beetle genomes. The analysis of homologous orthologous genes and inference from evolutionary history imply that the Mylabris and Hycleus genera are genetically close, have a similar genetic background, and have differentiated within one million years. This M. aulica genome assembly provides a valuable resource for future blister beetle studies and will contribute to cantharidin biosynthesis.
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Affiliation(s)
- De-Long Guan
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Xiao-Qian Hao
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Da Mi
- NextOmics Biosciences Institute, Wuhan, China
| | - Jiong Peng
- NextOmics Biosciences Institute, Wuhan, China
| | - Yuan Li
- NextOmics Biosciences Institute, Wuhan, China
| | - Juan-Ying Xie
- College of Computer Science, Shaanxi Normal University, Xi’an, China
| | - Huateng Huang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Sheng-Quan Xu
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
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202
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Ibarra Caballero JR, Ata JP, Leddy KA, Glenn TC, Kieran TJ, Klopfenstein NB, Kim MS, Stewart JE. Genome comparison and transcriptome analysis of the invasive brown root rot pathogen, Phellinus noxius, from different geographic regions reveals potential enzymes associated with degradation of different wood substrates. Fungal Biol 2020; 124:144-154. [PMID: 32008755 DOI: 10.1016/j.funbio.2019.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/11/2019] [Accepted: 12/18/2019] [Indexed: 11/25/2022]
Abstract
Phellinus noxius is a root-decay pathogen with a pan-tropical/subtropical distribution that attacks a wide range of tree hosts. For this study, genomic sequencing was conducted on P. noxius isolate P919-02W.7 from Federated States of Micronesia (Pohnpei), and its gene expression profile was analyzed using different host wood (Acer, Pinus, Prunus, and Salix) substrates. The assembled genome was 33.92 Mbp with 2954 contigs and 9389 predicted genes. Only small differences were observed in size and gene content in comparison with two other P. noxius genome assemblies (isolates OVT-YTM/97 from Hong Kong, China and FFPRI411160 from Japan, respectively). Genome analysis of P. noxius isolate P919-02W.7 revealed 488 genes encoding proteins related to carbohydrate and lignin metabolism, many of these enzymes are associated with degradation of plant cell wall components. Most of the transcripts expressed by P. noxius isolate P919-02W.7 were similar regardless of wood substrates. This study highlights the vast suite of decomposing enzymes produced by P. noxius, which suggests potential for degrading diverse wood substrates, even from temperate host trees. This information contributes to our understanding of pathogen ecology, mechanisms of wood decomposition, and pathogenic/saprophytic lifestyle.
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Affiliation(s)
- Jorge R Ibarra Caballero
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | - Jessa P Ata
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA; Department of Forest Biological Sciences, University of the Philippines Los Baños, Laguna 4031, Philippines
| | - K A Leddy
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Troy J Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Ned B Klopfenstein
- USDA Forest Service, Rocky Mountain Research Station, Moscow, ID 83843, USA
| | - Mee-Sook Kim
- USDA Forest Service, Pacific Northwest Research Station, Corvallis, OR 97331, USA.
| | - Jane E Stewart
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA.
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203
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Long-read sequencing reveals genomic structural variations that underlie creation of quality protein maize. Nat Commun 2020; 11:17. [PMID: 31911615 PMCID: PMC6946643 DOI: 10.1038/s41467-019-14023-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/12/2019] [Indexed: 02/05/2023] Open
Abstract
Mutation of o2 doubles maize endosperm lysine content, but it causes an inferior kernel phenotype. Developing quality protein maize (QPM) by introgressing o2 modifiers (Mo2s) into the o2 mutant benefits millions of people in developing countries where maize is a primary protein source. Here, we report genome sequence and annotation of a South African QPM line K0326Y, which is assembled from single-molecule, real-time shotgun sequencing reads collinear with an optical map. We achieve a N50 contig length of 7.7 million bases (Mb) directly from long-read assembly, compared to those of 1.04 Mb for B73 and 1.48 Mb for Mo17. To characterize Mo2s, we map QTLs to chromosomes 1, 6, 7, and 9 using an F2 population derived from crossing K0326Y and W64Ao2. RNA-seq analysis of QPM and o2 endosperms reveals a group of differentially expressed genes that coincide with Mo2 QTLs, suggesting a potential role in vitreous endosperm formation. The South African quality protein maize (QPM) cultivars have the desired high lysine content and kernel hardness due to o2 mutation and the introgression of modifiers of o2 (Mo2) QTLs, respectively. Here, the authors assemble the genome of a QPM line and identify candidate genes underlying Mo2 QTLs.
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204
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Wey B, Heavner ME, Wittmeyer KT, Briese T, Hopper KR, Govind S. Immune Suppressive Extracellular Vesicle Proteins of Leptopilina heterotoma Are Encoded in the Wasp Genome. G3 (BETHESDA, MD.) 2020; 10:1-12. [PMID: 31676506 PMCID: PMC6945029 DOI: 10.1534/g3.119.400349] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 10/22/2019] [Indexed: 12/29/2022]
Abstract
Leptopilina heterotoma are obligate parasitoid wasps that develop in the body of their Drosophila hosts. During oviposition, female wasps introduce venom into the larval hosts' body cavity. The venom contains discrete, 300 nm-wide, mixed-strategy extracellular vesicles (MSEVs), until recently referred to as virus-like particles. While the crucial immune suppressive functions of L. heterotoma MSEVs have remained undisputed, their biotic nature and origin still remain controversial. In recent proteomics analyses of L. heterotoma MSEVs, we identified 161 proteins in three classes: conserved eukaryotic proteins, infection and immunity related proteins, and proteins without clear annotation. Here we report 246 additional proteins from the L. heterotoma MSEV proteome. An enrichment analysis of the entire proteome supports vesicular nature of these structures. Sequences for more than 90% of these proteins are present in the whole-body transcriptome. Sequencing and de novo assembly of the 460 Mb-sized L. heterotoma genome revealed 90% of MSEV proteins have coding regions within the genomic scaffolds. Altogether, these results explain the stable association of MSEVs with their wasps, and like other wasp structures, their vertical inheritance. While our results do not rule out a viral origin of MSEVs, they suggest that a similar strategy for co-opting cellular machinery for immune suppression may be shared by other wasps to gain advantage over their hosts. These results are relevant to our understanding of the evolution of figitid and related wasp species.
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Affiliation(s)
- Brian Wey
- Biology Department, The City College of New York, 160 Convent Avenue, New York, 10031
- PhD Program in Biology, The Graduate Center of the City University of New York
| | - Mary Ellen Heavner
- Biology Department, The City College of New York, 160 Convent Avenue, New York, 10031
- PhD Program in Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, 10016
- Laboratory of Host-Pathogen Biology, Rockefeller University, 1230 York Ave, New York, 10065
| | - Kameron T Wittmeyer
- USDA-ARS, Beneficial Insect Introductions Research Unit, Newark, DE 19713, and
| | - Thomas Briese
- Center of Infection and Immunity, and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, 10032
| | - Keith R Hopper
- USDA-ARS, Beneficial Insect Introductions Research Unit, Newark, DE 19713, and
| | - Shubha Govind
- Biology Department, The City College of New York, 160 Convent Avenue, New York, 10031,
- PhD Program in Biology, The Graduate Center of the City University of New York
- PhD Program in Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, 10016
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205
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Wang C, Ulloa M, Nichols RL, Roberts PA. Sequence Composition of Bacterial Chromosome Clones in a Transgressive Root-Knot Nematode Resistance Chromosome Region in Tetraploid Cotton. FRONTIERS IN PLANT SCIENCE 2020; 11:574486. [PMID: 33381129 PMCID: PMC7767830 DOI: 10.3389/fpls.2020.574486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/15/2020] [Indexed: 05/08/2023]
Abstract
Plants evolve innate immunity including resistance genes to defend against pest and pathogen attack. Our previous studies in cotton (Gossypium spp.) revealed that one telomeric segment on chromosome (Chr) 11 in G. hirsutum cv. Acala NemX (rkn1 locus) contributed to transgressive resistance to the plant parasitic nematode Meloidogyne incognita, but the highly homologous segment on homoeologous Chr 21 had no resistance contribution. To better understand the resistance mechanism, a bacterial chromosome (BAC) library of Acala N901 (Acala NemX resistance source) was used to select, sequence, and analyze BAC clones associated with SSR markers in the complex rkn1 resistance region. Sequence alignment with the susceptible G. hirsutum cv. TM-1 genome indicated that 23 BACs mapped to TM-1-Chr11 and 18 BACs mapped to TM-1-Chr 21. Genetic and physical mapping confirmed less BAC sequence (53-84%) mapped with the TM-1 genome in the rkn1 region on Chr 11 than to the homologous region (>89%) on Chr 21. A 3.1-cM genetic distance between the rkn1 flanking markers CIR316 and CIR069 was mapped in a Pima S-7 × Acala NemX RIL population with a physical distance ∼1 Mbp in TM-1. NCBI Blast and Gene annotation indicated that both Chr 11 and Chr 21 harbor resistance gene-rich cluster regions, but more multiple homologous copies of Resistance (R) proteins and of adjacent transposable elements (TE) are present within Chr 11 than within Chr 21. (CC)-NB-LRR type R proteins were found in the rkn1 region close to CIR316, and (TIR)-NB-LRR type R proteins were identified in another resistance rich region 10 cM from CIR 316 (∼3.1 Mbp in the TM-1 genome). The identified unique insertion/deletion in NB-ARC domain, different copies of LRR domain, multiple copies or duplication of R proteins, adjacent protein kinases, or TE in the rkn1 region on Chr 11 might be major factors contributing to complex recombination and transgressive resistance.
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Affiliation(s)
- Congli Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Department of Nematology, University of California, Riverside, Riverside, CA, United States
| | - Mauricio Ulloa
- United States Department of Agriculture-Agricultural Research Service, Plains Area, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research, Lubbock, TX, United States
| | | | - Philip A. Roberts
- Department of Nematology, University of California, Riverside, Riverside, CA, United States
- *Correspondence: Philip A. Roberts,
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206
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Oppenheim S, Cao X, Rueppel O, Krongdang S, Phokasem P, DeSalle R, Goodwin S, Xing J, Chantawannakul P, Rosenfeld JA. Whole Genome Sequencing and Assembly of the Asian Honey Bee Apis dorsata. Genome Biol Evol 2020; 12:3677-3683. [PMID: 31860080 PMCID: PMC6953811 DOI: 10.1093/gbe/evz277] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2019] [Indexed: 12/16/2022] Open
Abstract
The Asian honey bee (Apis dorsata) is distinct from its more widely distributed cousin Apis mellifera by a few key characteristics. Most prominently, A. dorsata, nest in the open by forming a colony clustered around the honeycomb, whereas A. mellifera nest in concealed cavities. Additionally, the worker and reproductive castes are all of the same size in A. dorsata. In order to investigate these differences, we performed whole genome sequencing of A. dorsata using a hybrid Oxford Nanopore and Illumina approach. The 223 Mb genome has an N50 of 35 kb with the largest scaffold of 302 kb. We have found that there are many genes in the dorsata genome that are distinct from other hymenoptera and also large amounts of transposable elements, and we suggest some candidate genes for A. dorsata's exceptional level of defensive aggression.
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Affiliation(s)
- Sara Oppenheim
- Sackler Institute for Comparative Genomics, American Museum of Natural History
| | - Xiaolong Cao
- Department of Genetics, Human Genetic Institute of New Jersey, Rutgers, The State University of New Jersey
| | - Olav Rueppel
- Biology Department, University of North Carolina at Greensboro
| | - Sasiprapa Krongdang
- Department of Biology & Environmental Science Research Center (ESRC), Faculty of Science, Chiang Mai University, Thailand
| | - Patcharin Phokasem
- Department of Biology & Environmental Science Research Center (ESRC), Faculty of Science, Chiang Mai University, Thailand
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History
| | | | - Jinchuan Xing
- Department of Genetics, Human Genetic Institute of New Jersey, Rutgers, The State University of New Jersey
| | - Panuwan Chantawannakul
- Department of Biology & Environmental Science Research Center (ESRC), Faculty of Science, Chiang Mai University, Thailand
| | - Jeffrey A Rosenfeld
- Sackler Institute for Comparative Genomics, American Museum of Natural History
- Rutgers Cancer Institute of New Jersey
- Department of Pathology, Robert Wood Johnson Medical School
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207
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Haag KL, Pombert JF, Sun Y, de Albuquerque NRM, Batliner B, Fields P, Lopes TF, Ebert D. Microsporidia with Vertical Transmission Were Likely Shaped by Nonadaptive Processes. Genome Biol Evol 2020; 12:3599-3614. [PMID: 31825473 PMCID: PMC6944219 DOI: 10.1093/gbe/evz270] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2019] [Indexed: 12/14/2022] Open
Abstract
Microsporidia have the leanest genomes among eukaryotes, and their physiological and genomic simplicity has been attributed to their intracellular, obligate parasitic life-style. However, not all microsporidia genomes are small or lean, with the largest dwarfing the smallest ones by at least an order of magnitude. To better understand the evolutionary mechanisms behind this genomic diversification, we explore here two clades of microsporidia with distinct life histories, Ordospora and Hamiltosporidium, parasitizing the same host species, Daphnia magna. Based on seven newly assembled genomes, we show that mixed-mode transmission (the combination of horizontal and vertical transmission), which occurs in Hamiltosporidium, is found to be associated with larger and AT-biased genomes, more genes, and longer intergenic regions, as compared with the exclusively horizontally transmitted Ordospora. Furthermore, the Hamiltosporidium genome assemblies contain a variety of repetitive elements and long segmental duplications. We show that there is an excess of nonsynonymous substitutions in the microsporidia with mixed-mode transmission, which cannot be solely attributed to the lack of recombination, suggesting that bursts of genome size in these microsporidia result primarily from genetic drift. Overall, these findings suggest that the switch from a horizontal-only to a mixed mode of transmission likely produces population bottlenecks in Hamiltosporidium species, therefore reducing the effectiveness of natural selection, and allowing their genomic features to be largely shaped by nonadaptive processes.
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Affiliation(s)
- Karen L Haag
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Yukun Sun
- Department of Biology, Illinois Institute of Technology
| | - Nathalia Rammé M de Albuquerque
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Peter Fields
- Department of Environmental Sciences, Zoology, Basel University, Switzerland
| | - Tiago Falcon Lopes
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, Basel University, Switzerland
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208
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Marsh JT, Jayasena S, Gaskin F, Baumert JL, Johnson P. Thermal processing of peanut impacts detection by current analytical techniques. Food Chem 2019; 313:126019. [PMID: 31931421 DOI: 10.1016/j.foodchem.2019.126019] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/02/2019] [Accepted: 12/03/2019] [Indexed: 11/17/2022]
Abstract
Recalls of spice containing products due to undeclared peanut have highlighted the importance of analytical methods in these foods. We examined the performance of peanut detection methods in cumin and garlic, focusing on quantitative ELISA. Although suitable for qualitative detection, accurate quantitation proved difficult. Roasting of peanut contaminants influenced ELISA results, with raw peanut over-detected (3.9-fold) and roasted peanut under-detected (3.5-fold). Further investigation demonstrated the importance of protein targets for ELISA. The kit which gave the least variable results was based on detection of 2S albumin proteins. Additionally, we show that these proteins are more efficiently extracted from roasted peanut. We conclude that current methods are largely suitable for the qualitative detection of peanut in cumin and garlic. Quantitation relies on assumptions as to the state of thermal processing of peanut. We suggest that analytical method providers address robust detection by target selection, including identifying targets by MS.
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Affiliation(s)
- Justin T Marsh
- Department of Food Science & Technology, Food Allergy Research & Resource Program, University of Nebraska-Lincoln, Food Innovation Center, 1901 North 21st Street Lincoln, NE 68588-6205, United States.
| | - Shyamali Jayasena
- Department of Food Science & Technology, Food Allergy Research & Resource Program, University of Nebraska-Lincoln, Food Innovation Center, 1901 North 21st Street Lincoln, NE 68588-6205, United States
| | - Ferdelie Gaskin
- Department of Food Science & Technology, Food Allergy Research & Resource Program, University of Nebraska-Lincoln, Food Innovation Center, 1901 North 21st Street Lincoln, NE 68588-6205, United States
| | - Joseph L Baumert
- Department of Food Science & Technology, Food Allergy Research & Resource Program, University of Nebraska-Lincoln, Food Innovation Center, 1901 North 21st Street Lincoln, NE 68588-6205, United States
| | - Philip Johnson
- Department of Food Science & Technology, Food Allergy Research & Resource Program, University of Nebraska-Lincoln, Food Innovation Center, 1901 North 21st Street Lincoln, NE 68588-6205, United States.
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209
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Pan B, Chen X, Hou L, Zhang Q, Qu Z, Warren A, Miao M. Comparative Genomics Analysis of Ciliates Provides Insights on the Evolutionary History Within "Nassophorea-Synhymenia-Phyllopharyngea" Assemblage. Front Microbiol 2019; 10:2819. [PMID: 31921016 PMCID: PMC6920121 DOI: 10.3389/fmicb.2019.02819] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/20/2019] [Indexed: 11/13/2022] Open
Abstract
Ciliated protists (ciliates) are widely used for investigating evolution, mostly due to their successful radiation after their early evolutionary branching. In this study, we employed high-throughput sequencing technology to reveal the phylogenetic position of Synhymenia, as well as two classes Nassophorea and Phyllopharyngea, which have been a long-standing puzzle in the field of ciliate systematics and evolution. We obtained genomic and transcriptomic data from single cells of one synhymenian (Chilodontopsis depressa) and six other species of phyllopharyngeans (Chilodochona sp., Dysteria derouxi, Hartmannula sinica, Trithigmostoma cucullulus, Trochilia petrani, and Trochilia sp.). Phylogenomic analysis based on 157 orthologous genes comprising 173,835 amino acid residues revealed the affiliation of C. depressa within the class Phyllopharyngea, and the monophyly of Nassophorea, which strongly support the assignment of Synhymenia as a subclass within the class Phyllopharyngea. Comparative genomic analyses further revealed that C. depressa shares more orthologous genes with the class Nassophorea than with Phyllopharyngea, and the stop codon usage in C. depressa resembles that of Phyllopharyngea. Functional enrichment analysis demonstrated that biological pathways in C. depressa are more similar to Phyllopharyngea than Nassophorea. These results suggest that genomic and transcriptomic data can be used to provide insights into the evolutionary relationships within the "Nassophorea-Synhymenia-Phyllopharyngea" assemblage.
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Affiliation(s)
- Bo Pan
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, United States
| | - Lina Hou
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Qianqian Zhang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Zhishuai Qu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.,Ecology Group, Technical University of Kaiserslautern, Kaiserslautern, Germany
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Miao Miao
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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210
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Soza VL, Lindsley D, Waalkes A, Ramage E, Patwardhan RP, Burton JN, Adey A, Kumar A, Qiu R, Shendure J, Hall B. The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae). Genome Biol Evol 2019; 11:3353-3371. [PMID: 31702783 PMCID: PMC6907397 DOI: 10.1093/gbe/evz245] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2019] [Indexed: 02/06/2023] Open
Abstract
The genus Rhododendron (Ericaceae), which includes horticulturally important plants such as azaleas, is a highly diverse and widely distributed genus of >1,000 species. Here, we report the chromosome-scale de novo assembly and genome annotation of Rhododendron williamsianum as a basis for continued study of this large genus. We created multiple short fragment genomic libraries, which were assembled using ALLPATHS-LG. This was followed by contiguity preserving transposase sequencing (CPT-seq) and fragScaff scaffolding of a large fragment library, which improved the assembly by decreasing the number of scaffolds and increasing scaffold length. Chromosome-scale scaffolding was performed by proximity-guided assembly (LACHESIS) using chromatin conformation capture (Hi-C) data. Chromosome-scale scaffolding was further refined and linkage groups defined by restriction-site associated DNA (RAD) sequencing of the parents and progeny of a genetic cross. The resulting linkage map confirmed the LACHESIS clustering and ordering of scaffolds onto chromosomes and rectified large-scale inversions. Assessments of the R. williamsianum genome assembly and gene annotation estimate them to be 89% and 79% complete, respectively. Predicted coding sequences from genome annotation were used in syntenic analyses and for generating age distributions of synonymous substitutions/site between paralgous gene pairs, which identified whole-genome duplications (WGDs) in R. williamsianum. We then analyzed other publicly available Ericaceae genomes for shared WGDs. Based on our spatial and temporal analyses of paralogous gene pairs, we find evidence for two shared, ancient WGDs in Rhododendron and Vaccinium (cranberry/blueberry) members that predate the Ericaceae family and, in one case, the Ericales order.
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Affiliation(s)
- Valerie L Soza
- Department of Biology, University of Washington, Seattle, WA
| | - Dale Lindsley
- Department of Biology, University of Washington, Seattle, WA
- Retired
| | - Adam Waalkes
- Department of Biology, University of Washington, Seattle, WA
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | | | | | - Joshua N Burton
- Department of Genome Sciences, University of Washington, Seattle, WA
- Adaptive Biotechnologies, Seattle, WA
| | - Andrew Adey
- Department of Genome Sciences, University of Washington, Seattle, WA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR
| | - Akash Kumar
- Department of Genome Sciences, University of Washington, Seattle, WA
- Department of Pediatrics, Stanford University, Palo Alto, CA
| | - Ruolan Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA
- Retired
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA
- Brotman Baty Institute for Precision Medicine, Seattle, WA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA
| | - Benjamin Hall
- Department of Biology, University of Washington, Seattle, WA
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211
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Souza GM, Van Sluys MA, Lembke CG, Lee H, Margarido GRA, Hotta CT, Gaiarsa JW, Diniz AL, Oliveira MDM, Ferreira SDS, Nishiyama MY, ten-Caten F, Ragagnin GT, Andrade PDM, de Souza RF, Nicastro GG, Pandya R, Kim C, Guo H, Durham AM, Carneiro MS, Zhang J, Zhang X, Zhang Q, Ming R, Schatz MC, Davidson B, Paterson AH, Heckerman D. Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop. Gigascience 2019; 8:giz129. [PMID: 31782791 PMCID: PMC6884061 DOI: 10.1093/gigascience/giz129] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 05/23/2019] [Accepted: 10/08/2019] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Sugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically with 10-13 sets of chromosomes from 2 Saccharum species. The ploidy, hybridity, and size of the genome, estimated to have >10 Gb, pose a challenge for sequencing. RESULTS Here we present a gene space assembly of SP80-3280, including 373,869 putative genes and their potential regulatory regions. The alignment of single-copy genes in diploid grasses to the putative genes indicates that we could resolve 2-6 (up to 15) putative homo(eo)logs that are 99.1% identical within their coding sequences. Dissimilarities increase in their regulatory regions, and gene promoter analysis shows differences in regulatory elements within gene families that are expressed in a species-specific manner. We exemplify these differences for sucrose synthase (SuSy) and phenylalanine ammonia-lyase (PAL), 2 gene families central to carbon partitioning. SP80-3280 has particular regulatory elements involved in sucrose synthesis not found in the ancestor Saccharum spontaneum. PAL regulatory elements are found in co-expressed genes related to fiber synthesis within gene networks defined during plant growth and maturation. Comparison with sorghum reveals predominantly bi-allelic variations in sugarcane, consistent with the formation of 2 "subgenomes" after their divergence ∼3.8-4.6 million years ago and reveals single-nucleotide variants that may underlie their differences. CONCLUSIONS This assembly represents a large step towards a whole-genome assembly of a commercial sugarcane cultivar. It includes a rich diversity of genes and homo(eo)logous resolution for a representative fraction of the gene space, relevant to improve biomass and food production.
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Affiliation(s)
- Glaucia Mendes Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, SP 05508-090, Brazil
| | - Carolina Gimiliani Lembke
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Hayan Lee
- Cold Spring Harbor Laboratory, One Bungtown Road, Koch Building #1119, Cold Spring Harbor, NY11724, United States of America
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CACA94598, United States of America
| | - Gabriel Rodrigues Alves Margarido
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias, 11, Piracicaba, SP 13418-900, Brazil
| | - Carlos Takeshi Hotta
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Jonas Weissmann Gaiarsa
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, SP 05508-090, Brazil
| | - Augusto Lima Diniz
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Mauro de Medeiros Oliveira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Sávio de Siqueira Ferreira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, SP 05508-090, Brazil
| | - Milton Yutaka Nishiyama
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, Av. Vital Brasil, 1500, São Paulo, SP05503-900, Brazil
| | - Felipe ten-Caten
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Geovani Tolfo Ragagnin
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, SP 05508-090, Brazil
| | - Pablo de Morais Andrade
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Robson Francisco de Souza
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av.Professor Lineu Prestes, 1734, São Paulo, SP 05508-900, Brazil
| | - Gianlucca Gonçalves Nicastro
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av.Professor Lineu Prestes, 1734, São Paulo, SP 05508-900, Brazil
| | - Ravi Pandya
- Microsoft Research, One Microsoft Way, Redmond, WA 98052, United States of America
| | - Changsoo Kim
- Plant Genome Mapping Laboratory, University of Georgia, 120 Green Street, Athens, GA 30602-7223,United States of America
- Department of Crop Science, Chungnam National University, 99 Daehak Ro Yuseong Gu, Deajeon,34134, South Korea
| | - Hui Guo
- Plant Genome Mapping Laboratory, University of Georgia, 120 Green Street, Athens, GA 30602-7223,United States of America
| | - Alan Mitchell Durham
- Departamento de Ciências da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo, Rua do Matão, 1010, São Paulo, SP 05508-090, Brazil
| | - Monalisa Sampaio Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Washington Luis km 235, Araras, SP 13.565-905, Brazil
| | - Jisen Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Shangxiadian Road, Fuzhou 350002, Fujian, China
| | - Xingtan Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Shangxiadian Road, Fuzhou 350002, Fujian, China
| | - Qing Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Shangxiadian Road, Fuzhou 350002, Fujian, China
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Shangxiadian Road, Fuzhou 350002, Fujian, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 201 W. Gregory Dr. Urbana, Urbana, Illinois 61801, United States of America
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, One Bungtown Road, Koch Building #1119, Cold Spring Harbor, NY11724, United States of America
- Departments of Computer Science and Biology, Johns Hopkins University, 3400 North Charles Street,Baltimore, MD 21218-2608, United States of America
| | - Bob Davidson
- Microsoft Research, One Microsoft Way, Redmond, WA 98052, United States of America
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, 120 Green Street, Athens, GA 30602-7223,United States of America
| | - David Heckerman
- Microsoft Research, One Microsoft Way, Redmond, WA 98052, United States of America
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212
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Dudin O, Ondracka A, Grau-Bové X, Haraldsen AA, Toyoda A, Suga H, Bråte J, Ruiz-Trillo I. A unicellular relative of animals generates a layer of polarized cells by actomyosin-dependent cellularization. eLife 2019; 8:49801. [PMID: 31647412 PMCID: PMC6855841 DOI: 10.7554/elife.49801] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 10/23/2019] [Indexed: 12/30/2022] Open
Abstract
In animals, cellularization of a coenocyte is a specialized form of cytokinesis that results in the formation of a polarized epithelium during early embryonic development. It is characterized by coordinated assembly of an actomyosin network, which drives inward membrane invaginations. However, whether coordinated cellularization driven by membrane invagination exists outside animals is not known. To that end, we investigate cellularization in the ichthyosporean Sphaeroforma arctica, a close unicellular relative of animals. We show that the process of cellularization involves coordinated inward plasma membrane invaginations dependent on an actomyosin network and reveal the temporal order of its assembly. This leads to the formation of a polarized layer of cells resembling an epithelium. We show that this stage is associated with tightly regulated transcriptional activation of genes involved in cell adhesion. Hereby we demonstrate the presence of a self-organized, clonally-generated, polarized layer of cells in a unicellular relative of animals.
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Affiliation(s)
- Omaya Dudin
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Andrej Ondracka
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Xavier Grau-Bové
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.,Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Arthur Ab Haraldsen
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
| | - Hiroshi Suga
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Hiroshima, Japan
| | - Jon Bråte
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.,Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain.,ICREA, Barcelona, Spain
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213
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Wang C, Becker K, Pfütze S, Kuhnert E, Stadler M, Cox RJ, Skellam E. Investigating the Function of Cryptic Cytochalasan Cytochrome P450 Monooxygenases Using Combinatorial Biosynthesis. Org Lett 2019; 21:8756-8760. [PMID: 31644300 DOI: 10.1021/acs.orglett.9b03372] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tailoring enzymes in cytochalasan biosynthesis are relatively promiscuous. Exploiting this property, we deduced the function of four cryptic cytochrome P450 monooxygenases via heterologous expression of six cytochrome P450-encoding genes, originating from Hypoxylon fragiforme and Pyricularia oryzae, in pyrichalasin H ΔP450 strains. Three cryptic cytochrome P450 enzymes (HffD, HffG, and CYP1) restored pyrichalasin H production in mutant strains, while CYP3 catalyzed a site-selective epoxidation leading to the isolation of three novel cytochalasans.
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Affiliation(s)
- Chongqing Wang
- Institute for Organic Chemistry and Centre for Biomolecular Drug Research , Leibniz University Hannover , Schneiderberg 38 , Hannover 30167 , Germany
| | - Kevin Becker
- Department Microbial Drugs , Helmholtz Centre for Infection Research (HZI) , Inhoffenstraße 7 , 38124 Braunschweig , Germany
| | - Sebastian Pfütze
- Department Microbial Drugs , Helmholtz Centre for Infection Research (HZI) , Inhoffenstraße 7 , 38124 Braunschweig , Germany
| | - Eric Kuhnert
- Institute for Organic Chemistry and Centre for Biomolecular Drug Research , Leibniz University Hannover , Schneiderberg 38 , Hannover 30167 , Germany
| | - Marc Stadler
- Department Microbial Drugs , Helmholtz Centre for Infection Research (HZI) , Inhoffenstraße 7 , 38124 Braunschweig , Germany
| | - Russell J Cox
- Institute for Organic Chemistry and Centre for Biomolecular Drug Research , Leibniz University Hannover , Schneiderberg 38 , Hannover 30167 , Germany
| | - Elizabeth Skellam
- Institute for Organic Chemistry and Centre for Biomolecular Drug Research , Leibniz University Hannover , Schneiderberg 38 , Hannover 30167 , Germany
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214
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Kourelis J, Kaschani F, Grosse-Holz FM, Homma F, Kaiser M, van der Hoorn RAL. A homology-guided, genome-based proteome for improved proteomics in the alloploid Nicotiana benthamiana. BMC Genomics 2019; 20:722. [PMID: 31585525 PMCID: PMC6778390 DOI: 10.1186/s12864-019-6058-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 08/22/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Nicotiana benthamiana is an important model organism of the Solanaceae (Nightshade) family. Several draft assemblies of the N. benthamiana genome have been generated, but many of the gene-models in these draft assemblies appear incorrect. RESULTS Here we present an improved proteome based on the Niben1.0.1 draft genome assembly guided by gene models from other Nicotiana species. Due to the fragmented nature of the Niben1.0.1 draft genome, many protein-encoding genes are missing or partial. We complement these missing proteins by similarly annotating other draft genome assemblies. This approach overcomes problems caused by mis-annotated exon-intron boundaries and mis-assigned short read transcripts to homeologs in polyploid genomes. With an estimated 98.1% completeness; only 53,411 protein-encoding genes; and improved protein lengths and functional annotations, this new predicted proteome is better in assigning spectra than the preceding proteome annotations. This dataset is more sensitive and accurate in proteomics applications, clarifying the detection by activity-based proteomics of proteins that were previously predicted to be inactive. Phylogenetic analysis of the subtilase family of hydrolases reveal inactivation of likely homeologs, associated with a contraction of the functional genome in this alloploid plant species. Finally, we use this new proteome annotation to characterize the extracellular proteome as compared to a total leaf proteome, which highlights the enrichment of hydrolases in the apoplast. CONCLUSIONS This proteome annotation provides the community working with Nicotiana benthamiana with an important new resource for functional proteomics.
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Affiliation(s)
- Jiorgos Kourelis
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Farnusch Kaschani
- Chemische Biologie, Zentrum fur Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Essen, Germany
| | - Friederike M Grosse-Holz
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Felix Homma
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Markus Kaiser
- Chemische Biologie, Zentrum fur Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Essen, Germany
| | - Renier A L van der Hoorn
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
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215
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Martin SL, Parent JS, Laforest M, Page E, Kreiner JM, James T. Population Genomic Approaches for Weed Science. PLANTS (BASEL, SWITZERLAND) 2019; 8:E354. [PMID: 31546893 PMCID: PMC6783936 DOI: 10.3390/plants8090354] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/12/2019] [Accepted: 09/14/2019] [Indexed: 12/16/2022]
Abstract
Genomic approaches are opening avenues for understanding all aspects of biological life, especially as they begin to be applied to multiple individuals and populations. However, these approaches typically depend on the availability of a sequenced genome for the species of interest. While the number of genomes being sequenced is exploding, one group that has lagged behind are weeds. Although the power of genomic approaches for weed science has been recognized, what is needed to implement these approaches is unfamiliar to many weed scientists. In this review we attempt to address this problem by providing a primer on genome sequencing and provide examples of how genomics can help answer key questions in weed science such as: (1) Where do agricultural weeds come from; (2) what genes underlie herbicide resistance; and, more speculatively, (3) can we alter weed populations to make them easier to control? This review is intended as an introduction to orient weed scientists who are thinking about initiating genome sequencing projects to better understand weed populations, to highlight recent publications that illustrate the potential for these methods, and to provide direction to key tools and literature that will facilitate the development and execution of weed genomic projects.
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Affiliation(s)
- Sara L Martin
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Jean-Sebastien Parent
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Martin Laforest
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada.
| | - Eric Page
- Harrow Research and Development Centre, Agriculture and Agri-Food Canada, Harrow, ON N0R 1G0, Canada.
| | - Julia M Kreiner
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
| | - Tracey James
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
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216
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Kreplak J, Madoui MA, Cápal P, Novák P, Labadie K, Aubert G, Bayer PE, Gali KK, Syme RA, Main D, Klein A, Bérard A, Vrbová I, Fournier C, d'Agata L, Belser C, Berrabah W, Toegelová H, Milec Z, Vrána J, Lee H, Kougbeadjo A, Térézol M, Huneau C, Turo CJ, Mohellibi N, Neumann P, Falque M, Gallardo K, McGee R, Tar'an B, Bendahmane A, Aury JM, Batley J, Le Paslier MC, Ellis N, Warkentin TD, Coyne CJ, Salse J, Edwards D, Lichtenzveig J, Macas J, Doležel J, Wincker P, Burstin J. A reference genome for pea provides insight into legume genome evolution. Nat Genet 2019; 51:1411-1422. [PMID: 31477930 DOI: 10.1038/s41588-019-0480-1] [Citation(s) in RCA: 238] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 07/10/2019] [Indexed: 02/03/2023]
Abstract
We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel's original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from its sister tribes. During Pisum evolution, translocation and transposition differentially occurred across lineages. This reference sequence will accelerate our understanding of the molecular basis of agronomically important traits and support crop improvement.
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Affiliation(s)
- Jonathan Kreplak
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Mohammed-Amin Madoui
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Petr Cápal
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Petr Novák
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Grégoire Aubert
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
| | - Krishna K Gali
- Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Robert A Syme
- Centre for Crop and Disease Management, Curtin University, Bentley, Western Australia, Australia
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Anthony Klein
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Aurélie Bérard
- Etude du Polymorphisme des Génomes Végétaux, INRA, Université Paris-Saclay, Evry, France
| | - Iva Vrbová
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Cyril Fournier
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Leo d'Agata
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Caroline Belser
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Wahiba Berrabah
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Helena Toegelová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Zbyněk Milec
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - HueyTyng Lee
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Ayité Kougbeadjo
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Morgane Térézol
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Cécile Huneau
- UMR 1095 Génétique, Diversité, Ecophysiologie des Céréales, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Chala J Turo
- Centre for Crop and Disease Management, School of Molecular and Life Science, Curtin University, Bentley, Western Australia, Australia
| | | | - Pavel Neumann
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Matthieu Falque
- GQE-Le Moulon, INRA, University of Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Karine Gallardo
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Rebecca McGee
- USDA Agricultural Research Service, Pullman, WA, USA
| | - Bunyamin Tar'an
- Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay, INRA, CNRS, University of Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Orsay, France
| | - Jean-Marc Aury
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
| | | | - Noel Ellis
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Thomas D Warkentin
- Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | | | - Jérome Salse
- UMR 1095 Génétique, Diversité, Ecophysiologie des Céréales, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
| | - Judith Lichtenzveig
- School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Jiří Macas
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Judith Burstin
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France.
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Stortz JF, Del Rosario M, Singer M, Wilkes JM, Meissner M, Das S. Formin-2 drives polymerisation of actin filaments enabling segregation of apicoplasts and cytokinesis in Plasmodium falciparum. eLife 2019; 8:e49030. [PMID: 31322501 PMCID: PMC6688858 DOI: 10.7554/elife.49030] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 07/17/2019] [Indexed: 12/16/2022] Open
Abstract
In addition to its role in erythrocyte invasion, Plasmodium falciparum actin is implicated in endocytosis, cytokinesis and inheritance of the chloroplast-like organelle called the apicoplast. Previously, the inability to visualise filamentous actin (F-actin) dynamics had restricted the characterisation of both F-actin and actin regulatory proteins, a limitation we recently overcame for Toxoplasma (Periz et al, 2017). Here, we have expressed and validated actin-binding chromobodies as F-actin-sensors in Plasmodium falciparum and characterised in-vivo actin dynamics. F-actin could be chemically modulated, and genetically disrupted upon conditionally deleting actin-1. In a comparative approach, we demonstrate that Formin-2, a predicted nucleator of F-actin, is responsible for apicoplast inheritance in both Plasmodium and Toxoplasma, and additionally mediates efficient cytokinesis in Plasmodium. Finally, time-averaged local intensity measurements of F-actin in Toxoplasma conditional mutants revealed molecular determinants of spatiotemporally regulated F-actin flow. Together, our data indicate that Formin-2 is the primary F-actin nucleator during apicomplexan intracellular growth, mediating multiple essential functions.
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Affiliation(s)
- Johannes Felix Stortz
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity & InflammationUniversity of GlasgowGlasgowUnited Kingdom
| | - Mario Del Rosario
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity & InflammationUniversity of GlasgowGlasgowUnited Kingdom
| | - Mirko Singer
- Faculty of Veterinary Medicine, Experimental ParasitologyLudwig Maximilian UniversityMunichGermany
| | - Jonathan M Wilkes
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity & InflammationUniversity of GlasgowGlasgowUnited Kingdom
| | - Markus Meissner
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity & InflammationUniversity of GlasgowGlasgowUnited Kingdom
- Faculty of Veterinary Medicine, Experimental ParasitologyLudwig Maximilian UniversityMunichGermany
| | - Sujaan Das
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity & InflammationUniversity of GlasgowGlasgowUnited Kingdom
- Faculty of Veterinary Medicine, Experimental ParasitologyLudwig Maximilian UniversityMunichGermany
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218
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Abstract
As in any endeavor, the strategy applied to a genome project can mean the difference between success and failure. This is especially important when limited funding often means only a single approach may be tried at a given time. Although the advance of all areas of genomics and transcriptomics in recent years has led to an embarrassment of riches, methods in the field have not quite reached the turn-key production status for all species, despite being closer than ever. Here I contrast and compare the technical approaches to genome projects in the hope of enabling strategy choices with higher probabilities of success. Finally, I review the new technologies that are not yet widely distributed which are revolutionizing the future of genomics.
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Affiliation(s)
- Stephen Richards
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
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219
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Seasonal adaptations of the hypothalamo-neurohypophyseal system of the dromedary camel. PLoS One 2019; 14:e0216679. [PMID: 31211771 PMCID: PMC6581255 DOI: 10.1371/journal.pone.0216679] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 04/24/2019] [Indexed: 12/12/2022] Open
Abstract
The “ship” of the Arabian and North African deserts, the one-humped dromedary camel (Camelus dromedarius) has a remarkable capacity to survive in conditions of extreme heat without needing to drink water. One of the ways that this is achieved is through the actions of the antidiuretic hormone arginine vasopressin (AVP), which is made in a specialised part of the brain called the hypothalamo-neurohypophyseal system (HNS), but exerts its effects at the level of the kidney to provoke water conservation. Interestingly, our electron microscopy studies have shown that the ultrastructure of the dromedary HNS changes according to season, suggesting that in the arid conditions of summer the HNS is in an activated state, in preparation for the likely prospect of water deprivation. Based on our dromedary genome sequence, we have carried out an RNAseq analysis of the dromedary HNS in summer and winter. Amongst the 171 transcripts found to be significantly differentially regulated (>2 fold change, p value <0.05) there is a significant over-representation of neuropeptide encoding genes, including that encoding AVP, the expression of which appeared to increase in summer. Identification of neuropeptides in the HNS and analysis of neuropeptide profiles in extracts from individual camels using mass spectrometry indicates that overall AVP peptide levels decreased in the HNS during summer compared to winter, perhaps due to increased release during periods of dehydration in the dry season.
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220
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Pucker B, Holtgräwe D, Stadermann KB, Frey K, Huettel B, Reinhardt R, Weisshaar B. A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set. PLoS One 2019; 14:e0216233. [PMID: 31112551 PMCID: PMC6529160 DOI: 10.1371/journal.pone.0216233] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/16/2019] [Indexed: 01/27/2023] Open
Abstract
In addition to the BAC-based reference sequence of the accession Columbia-0 from the year 2000, several short read assemblies of THE plant model organism Arabidopsis thaliana were published during the last years. Also, a SMRT-based assembly of Landsberg erecta has been generated that identified translocation and inversion polymorphisms between two genotypes of the species. Here we provide a chromosome-arm level assembly of the A. thaliana accession Niederzenz-1 (AthNd-1_v2c) based on SMRT sequencing data. The best assembly comprises 69 nucleome sequences and displays a contig length of up to 16 Mbp. Compared to an earlier Illumina short read-based NGS assembly (AthNd-1_v1), a 75 fold increase in contiguity was observed for AthNd-1_v2c. To assign contig locations independent from the Col-0 gold standard reference sequence, we used genetic anchoring to generate a de novo assembly. In addition, we assembled the chondrome and plastome sequences. Detailed analyses of AthNd-1_v2c allowed reliable identification of large genomic rearrangements between A. thaliana accessions contributing to differences in the gene sets that distinguish the genotypes. One of the differences detected identified a gene that is lacking from the Col-0 gold standard sequence. This de novo assembly extends the known proportion of the A. thaliana pan-genome.
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Affiliation(s)
- Boas Pucker
- Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
| | - Daniela Holtgräwe
- Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
| | - Kai Bernd Stadermann
- Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
| | - Katharina Frey
- Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Richard Reinhardt
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Bernd Weisshaar
- Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
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221
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Sforça DA, Vautrin S, Cardoso-Silva CB, Mancini MC, Romero-da Cruz MV, Pereira GDS, Conte M, Bellec A, Dahmer N, Fourment J, Rodde N, Van Sluys MA, Vicentini R, Garcia AAF, Forni-Martins ER, Carneiro MS, Hoffmann HP, Pinto LR, Landell MGDA, Vincentz M, Berges H, de Souza AP. Gene Duplication in the Sugarcane Genome: A Case Study of Allele Interactions and Evolutionary Patterns in Two Genic Regions. FRONTIERS IN PLANT SCIENCE 2019; 10:553. [PMID: 31134109 PMCID: PMC6514446 DOI: 10.3389/fpls.2019.00553] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/11/2019] [Indexed: 05/25/2023]
Abstract
Sugarcane (Saccharum spp.) is highly polyploid and aneuploid. Modern cultivars are derived from hybridization between S. officinarum and S. spontaneum. This combination results in a genome exhibiting variable ploidy among different loci, a huge genome size (~10 Gb) and a high content of repetitive regions. An approach using genomic, transcriptomic, and genetic mapping can improve our knowledge of the behavior of genetics in sugarcane. The hypothetical HP600 and Centromere Protein C (CENP-C) genes from sugarcane were used to elucidate the allelic expression and genomic and genetic behaviors of this complex polyploid. The physically linked side-by-side genes HP600 and CENP-C were found in two different homeologous chromosome groups with ploidies of eight and ten. The first region (Region01) was a Sorghum bicolor ortholog region with all haplotypes of HP600 and CENP-C expressed, but HP600 exhibited an unbalanced haplotype expression. The second region (Region02) was a scrambled sugarcane sequence formed from different noncollinear genes containing partial duplications of HP600 and CENP-C (paralogs). This duplication resulted in a non-expressed HP600 pseudogene and a recombined fusion version of CENP-C and the orthologous gene Sobic.003G299500 with at least two chimeric gene haplotypes expressed. It was also determined that it occurred before Saccharum genus formation and after the separation of sorghum and sugarcane. A linkage map was constructed using markers from nonduplicated Region01 and for the duplication (Region01 and Region02). We compare the physical and linkage maps, demonstrating the possibility of mapping markers located in duplicated regions with markers in nonduplicated region. Our results contribute directly to the improvement of linkage mapping in complex polyploids and improve the integration of physical and genetic data for sugarcane breeding programs. Thus, we describe the complexity involved in sugarcane genetics and genomics and allelic dynamics, which can be useful for understanding complex polyploid genomes.
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Affiliation(s)
| | - Sonia Vautrin
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | | | | | | | | | - Mônica Conte
- Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Arnaud Bellec
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | - Nair Dahmer
- Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Joelle Fourment
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | - Nathalie Rodde
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | | | | | | | | | | | - Hermann Paulo Hoffmann
- Centro de Ciências Agrárias, Universidade Federal de São Carlos (UFSCAR), Araras, Brazil
| | | | | | - Michel Vincentz
- Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Helene Berges
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
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222
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Isolation and Characterization of Live Yeast Cells from Ancient Vessels as a Tool in Bio-Archaeology. mBio 2019; 10:mBio.00388-19. [PMID: 31040238 PMCID: PMC6495373 DOI: 10.1128/mbio.00388-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
So far, most of the study of ancient organisms has been based mainly on the analysis of ancient DNA. Here we show that it is possible to isolate and study microorganisms—yeast in this case—from ancient pottery vessels used for fermentation. We demonstrate that it is highly likely that these cells are descendants of the original yeast strains that participated in the fermentation process and were absorbed into the clay matrix of the pottery vessels. Moreover, we characterized the isolated yeast strains, their genomes, and the beer they produced. These results open new and exciting avenues in the study of domesticated microorganisms and contribute significantly to the fields of bio- and experimental archaeology that aim to reconstruct ancient artifacts and products. Ancient fermented food has been studied based on recipes, residue analysis, and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach based on our hypothesis that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and their descendants could be isolated and studied today. We developed a pipeline of yeast isolation from clay vessels and screened for yeast cells in beverage-related and non-beverage-related ancient vessels and sediments from several archaeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. The findings that genotypically the isolated yeasts are similar to those found in traditional African beverages and phenotypically they grow similar to modern beer-producing yeast strongly suggest that they are descendants of the original fermenting yeast. These results demonstrate that modern microorganisms can serve as a new tool in bio-archaeology research.
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223
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Stevens L, Félix M, Beltran T, Braendle C, Caurcel C, Fausett S, Fitch D, Frézal L, Gosse C, Kaur T, Kiontke K, Newton MD, Noble LM, Richaud A, Rockman MV, Sudhaus W, Blaxter M. Comparative genomics of 10 new Caenorhabditis species. Evol Lett 2019; 3:217-236. [PMID: 31007946 PMCID: PMC6457397 DOI: 10.1002/evl3.110] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 02/08/2019] [Accepted: 02/25/2019] [Indexed: 01/29/2023] Open
Abstract
The nematode Caenorhabditis elegans has been central to the understanding of metazoan biology. However, C. elegans is but one species among millions and the significance of this important model organism will only be fully revealed if it is placed in a rich evolutionary context. Global sampling efforts have led to the discovery of over 50 putative species from the genus Caenorhabditis, many of which await formal species description. Here, we present species descriptions for 10 new Caenorhabditis species. We also present draft genome sequences for nine of these new species, along with a transcriptome assembly for one. We exploit these whole-genome data to reconstruct the Caenorhabditis phylogeny and use this phylogenetic tree to dissect the evolution of morphology in the genus. We reveal extensive variation in genome size and investigate the molecular processes that underlie this variation. We show unexpected complexity in the evolutionary history of key developmental pathway genes. These new species and the associated genomic resources will be essential in our attempts to understand the evolutionary origins of the C. elegans model.
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Affiliation(s)
- Lewis Stevens
- Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3JTUnited Kingdom
| | - Marie‐Anne Félix
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, École Normale SupérieureParis Sciences et Lettres75005ParisFrance
| | - Toni Beltran
- MRC London Institute of Medical SciencesLondonW12 0NNUnited Kingdom
| | - Christian Braendle
- Université Côte d'Azur, Centre National de la Recherche Scientifique, InsermInstitute of Biology Valrose06108NiceFrance
| | - Carlos Caurcel
- Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3JTUnited Kingdom
| | - Sarah Fausett
- Université Côte d'Azur, Centre National de la Recherche Scientifique, InsermInstitute of Biology Valrose06108NiceFrance
| | - David Fitch
- Department of BiologyNew York UniversityNew YorkNew York10003
| | - Lise Frézal
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, École Normale SupérieureParis Sciences et Lettres75005ParisFrance
| | - Charlie Gosse
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, École Normale SupérieureParis Sciences et Lettres75005ParisFrance
| | - Taniya Kaur
- Center for Genomics and Systems Biology, Department of BiologyNew York UniversityNew YorkNew York10003
| | - Karin Kiontke
- Department of BiologyNew York UniversityNew YorkNew York10003
| | - Matthew D. Newton
- MRC London Institute of Medical SciencesLondonW12 0NNUnited Kingdom
- Molecular Virology, Department of MedicineImperial College LondonDu Cane RoadLondonW12 0NNUnited Kingdom
| | - Luke M. Noble
- Center for Genomics and Systems Biology, Department of BiologyNew York UniversityNew YorkNew York10003
| | - Aurélien Richaud
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, École Normale SupérieureParis Sciences et Lettres75005ParisFrance
| | - Matthew V. Rockman
- Center for Genomics and Systems Biology, Department of BiologyNew York UniversityNew YorkNew York10003
| | - Walter Sudhaus
- Institut für Biologie/ZoologieFreie Universität BerlinBerlinD‐14195Germany
| | - Mark Blaxter
- Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3JTUnited Kingdom
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224
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Yao G, Peng C, Zhu Y, Fan C, Jiang H, Chen J, Cao Y, Shi Q. High-Throughput Identification and Analysis of Novel Conotoxins from Three Vermivorous Cone Snails by Transcriptome Sequencing. Mar Drugs 2019; 17:md17030193. [PMID: 30917600 PMCID: PMC6471451 DOI: 10.3390/md17030193] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/19/2019] [Accepted: 03/25/2019] [Indexed: 12/13/2022] Open
Abstract
The venom of each Conus species consists of a diverse array of neurophysiologically active peptides, which are mostly unique to the examined species. In this study, we performed high-throughput transcriptome sequencing to extract and analyze putative conotoxin transcripts from the venom ducts of 3 vermivorous cone snails (C. caracteristicus, C. generalis, and C. quercinus), which are resident in offshore waters of the South China Sea. In total, 118, 61, and 48 putative conotoxins (across 22 superfamilies) were identified from the 3 Conus species, respectively; most of them are novel, and some possess new cysteine patterns. Interestingly, a series of 45 unassigned conotoxins presented with a new framework of C-C-C-C-C-C, and their mature regions were sufficiently distinct from any other known conotoxins, most likely representing a new superfamily. O- and M-superfamily conotoxins were the most abundant in transcript number and transcription level, suggesting their critical roles in the venom functions of these vermivorous cone snails. In addition, we identified numerous functional proteins with potential involvement in the biosynthesis, modification, and delivery process of conotoxins, which may shed light on the fundamental mechanisms for the generation of these important conotoxins within the venom duct of cone snails.
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Affiliation(s)
- Ge Yao
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Chao Peng
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Yabing Zhu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China.
| | - Chongxu Fan
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Hui Jiang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Jisheng Chen
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Ying Cao
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
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225
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Dale AL, Feau N, Everhart SE, Dhillon B, Wong B, Sheppard J, Bilodeau GJ, Brar A, Tabima JF, Shen D, Brasier CM, Tyler BM, Grünwald NJ, Hamelin RC. Mitotic Recombination and Rapid Genome Evolution in the Invasive Forest Pathogen Phytophthora ramorum. mBio 2019; 10:e02452-18. [PMID: 30862749 PMCID: PMC6414701 DOI: 10.1128/mbio.02452-18] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/29/2019] [Indexed: 12/21/2022] Open
Abstract
Invasive alien species often have reduced genetic diversity and must adapt to new environments. Given the success of many invasions, this is sometimes called the genetic paradox of invasion. Phytophthora ramorum is invasive, limited to asexual reproduction within four lineages, and presumed clonal. It is responsible for sudden oak death in the United States, sudden larch death in Europe, and ramorum blight in North America and Europe. We sequenced the genomes of 107 isolates to determine how this pathogen can overcome the invasion paradox. Mitotic recombination (MR) associated with transposons and low gene density has generated runs of homozygosity (ROH) affecting 2,698 genes, resulting in novel genotypic diversity within the lineages. One ROH enriched in effectors was fixed in the NA1 lineage. An independent ROH affected the same scaffold in the EU1 lineage, suggesting an MR hot spot and a selection target. Differences in host infection between EU1 isolates with and without the ROH suggest that they may differ in aggressiveness. Non-core regions (not shared by all lineages) had signatures of accelerated evolution and were enriched in putative pathogenicity genes and transposons. There was a striking pattern of gene loss, including all effectors, in the non-core EU2 genome. Positive selection was observed in 8.0% of RxLR and 18.8% of Crinkler effector genes compared with 0.9% of the core eukaryotic gene set. We conclude that the P. ramorum lineages are diverging via a rapidly evolving non-core genome and that the invasive asexual lineages are not clonal, but display genotypic diversity caused by MR.IMPORTANCE Alien species are often successful invaders in new environments, despite the introduction of a few isolates with a reduced genetic pool. This is called the genetic paradox of invasion. We found two mechanisms by which the invasive forest pathogen causing sudden oak and sudden larch death can evolve. Extensive mitotic recombination producing runs of homozygosity generates genotypic diversity even in the absence of sexual reproduction, and rapid turnover of genes in the non-core, or nonessential portion of genome not shared by all isolates, allows pathogenicity genes to evolve rapidly or be eliminated while retaining essential genes. Mitotic recombination events occur in genomic hot spots, resulting in similar ROH patterns in different isolates or groups; one ROH, independently generated in two different groups, was enriched in pathogenicity genes and may be a target for selection. This provides important insights into the evolution of invasive alien pathogens and their potential for adaptation and future persistence.
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Affiliation(s)
- Angela L Dale
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- GC-New Construction Materials, FPInnovations, Vancouver, British Columbia, Canada
| | - Nicolas Feau
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sydney E Everhart
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, USA
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Braham Dhillon
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Barbara Wong
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Faculté de Foresterie et Géomatique, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada
| | - Julie Sheppard
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Guillaume J Bilodeau
- Ottawa Plant Laboratory, Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Avneet Brar
- Ottawa Plant Laboratory, Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Javier F Tabima
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Clive M Brasier
- Forest Research, Alice Holt Lodge, Farnham, Surrey, United Kingdom
| | - Brett M Tyler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA
| | - Niklaus J Grünwald
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon, USA
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Faculté de Foresterie et Géomatique, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada
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226
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Leonard G, Labarre A, Milner DS, Monier A, Soanes D, Wideman JG, Maguire F, Stevens S, Sain D, Grau-Bové X, Sebé-Pedrós A, Stajich JE, Paszkiewicz K, Brown MW, Hall N, Wickstead B, Richards TA. Comparative genomic analysis of the 'pseudofungus' Hyphochytrium catenoides. Open Biol 2019; 8:rsob.170184. [PMID: 29321239 PMCID: PMC5795050 DOI: 10.1098/rsob.170184] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 12/01/2017] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic microbes have three primary mechanisms for obtaining nutrients and energy: phagotrophy, photosynthesis and osmotrophy. Traits associated with the latter two functions arose independently multiple times in the eukaryotes. The Fungi successfully coupled osmotrophy with filamentous growth, and similar traits are also manifested in the Pseudofungi (oomycetes and hyphochytriomycetes). Both the Fungi and the Pseudofungi encompass a diversity of plant and animal parasites. Genome-sequencing efforts have focused on host-associated microbes (mutualistic symbionts or parasites), providing limited comparisons with free-living relatives. Here we report the first draft genome sequence of a hyphochytriomycete ‘pseudofungus’; Hyphochytrium catenoides. Using phylogenomic approaches, we identify genes of recent viral ancestry, with related viral derived genes also present on the genomes of oomycetes, suggesting a complex history of viral coevolution and integration across the Pseudofungi. H. catenoides has a complex life cycle involving diverse filamentous structures and a flagellated zoospore with a single anterior tinselate flagellum. We use genome comparisons, drug sensitivity analysis and high-throughput culture arrays to investigate the ancestry of oomycete/pseudofungal characteristics, demonstrating that many of the genetic features associated with parasitic traits evolved specifically within the oomycete radiation. Comparative genomics also identified differences in the repertoire of genes associated with filamentous growth between the Fungi and the Pseudofungi, including differences in vesicle trafficking systems, cell-wall synthesis pathways and motor protein repertoire, demonstrating that unique cellular systems underpinned the convergent evolution of filamentous osmotrophic growth in these two eukaryotic groups.
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Affiliation(s)
- Guy Leonard
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Aurélie Labarre
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - David S Milner
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Adam Monier
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Darren Soanes
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Jeremy G Wideman
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Finlay Maguire
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Sam Stevens
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Divya Sain
- Department of Plant Pathology and Microbiology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92506, USA
| | - Xavier Grau-Bové
- Institute of Evolutionary Biology, CSIC-UPF, Barcelona, Catalonia, Spain
| | | | - Jason E Stajich
- Department of Plant Pathology and Microbiology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92506, USA
| | - Konrad Paszkiewicz
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Neil Hall
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Bill Wickstead
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Thomas A Richards
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
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227
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Li Y, Li Y, Jin W, Sharpton TJ, Mackie RI, Cann I, Cheng Y, Zhu W. Combined Genomic, Transcriptomic, Proteomic, and Physiological Characterization of the Growth of Pecoramyces sp. F1 in Monoculture and Co-culture With a Syntrophic Methanogen. Front Microbiol 2019; 10:435. [PMID: 30894845 PMCID: PMC6414434 DOI: 10.3389/fmicb.2019.00435] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/19/2019] [Indexed: 11/13/2022] Open
Abstract
In this study, the effects of a syntrophic methanogen on the growth of Pecoramyces sp. F1 was investigated by characterizing fermentation profiles, as well as functional genomic, transcriptomic, and proteomic analysis. The estimated genome size, GC content, and protein coding regions of strain F1 are 106.83 Mb, 16.07%, and 23.54%, respectively. Comparison of the fungal monoculture with the methanogen co-culture demonstrated that during the fermentation of glucose, the co-culture initially expressed and then down-regulated a large number of genes encoding both enzymes involved in intermediate metabolism and plant cell wall degradation. However, the number of up-regulated proteins doubled at the late-growth stage in the co-culture. In addition, we provide a mechanistic understanding of the metabolism of this fungus in co-culture with a syntrophic methanogen. Further experiments are needed to explore this interaction during degradation of more complex plant cell wall substrates.
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Affiliation(s)
- Yuanfei Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Wei Jin
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.,Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, China
| | - Thomas J Sharpton
- Department of Microbiology - Department of Statistics, Oregon State University, Corvallis, OR, United States
| | - Roderick I Mackie
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Isaac Cann
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States.,Department of Microbiology, University of Illinois at Urbana-Champaign, Champaign, IL, United States.,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.,Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.,Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, China
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228
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Abstract
Rapidly improving sequencing technology coupled with computational developments in sequence assembly are making reference-quality genome assembly economical. Hundreds of vertebrate genome assemblies are now publicly available, and projects are being proposed to sequence thousands of additional species in the next few years. Such dense sampling of the tree of life should give an unprecedented new understanding of evolution and allow a detailed determination of the events that led to the wealth of biodiversity around us. To gain this knowledge, these new genomes must be compared through genome alignment (at the sequence level) and comparative annotation (at the gene level). However, different alignment and annotation methods have different characteristics; before starting a comparative genomics analysis, it is important to understand the nature of, and biases and limitations inherent in, the chosen methods. This review is intended to act as a technical but high-level overview of the field that should provide this understanding. We briefly survey the state of the genome alignment and comparative annotation fields and potential future directions for these fields in a new, large-scale era of comparative genomics.
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Affiliation(s)
- Joel Armstrong
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California 95064, USA;
| | - Ian T Fiddes
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California 95064, USA;
- 10x Genomics, Pleasanton, California 94566, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California 95064, USA;
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California 95064, USA;
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229
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Ibarra Caballero JR, Jeon J, Lee YH, Fraedrich S, Klopfenstein NB, Kim MS, Stewart JE. Genomic comparisons of the laurel wilt pathogen, Raffaelea lauricola, and related tree pathogens highlight an arsenal of pathogenicity related genes. Fungal Genet Biol 2019; 125:84-92. [PMID: 30716558 DOI: 10.1016/j.fgb.2019.01.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 01/09/2019] [Accepted: 01/31/2019] [Indexed: 12/15/2022]
Abstract
Raffaelea lauricola is an invasive fungal pathogen and symbiont of the redbay ambrosia beetle (Xyleborus glabratus) that has caused widespread mortality to redbay (Persea borbonia) and other Lauraceae species in the southeastern USA. We compare two genomes of R. lauricola (C2646 and RL570) to seven other related Ophiostomatales species including R. aguacate (nonpathogenic close relative of R. lauricola), R. quercus-mongolicae (associated with mortality of oaks in Korea), R. quercivora (associated with mortality of oaks in Japan), Grosmannia clavigera (cause of blue stain in conifers), Ophiostoma novo-ulmi (extremely virulent causal agent of Dutch elm disease), O. ulmi (moderately virulent pathogen that cause of Dutch elm disease), and O. piceae (blue-stain saprophyte of conifer logs and lumber). Structural and functional annotations were performed to determine genes that are potentially associated with disease development. Raffaelea lauricola and R. aguacate had the largest genomes, along with the largest number of protein-coding genes, genes encoding secreted proteins, small-secreted proteins, ABC transporters, cytochrome P450 enzymes, CAZYmes, and proteases. Our results indicate that this large genome size was not related to pathogenicity but was likely lineage specific, as the other pathogens in Raffaelea (R. quercus-mongolicae and R. quercivora) had similar genome characteristics to the Ophiostoma species. A diverse repertoire of wood-decaying enzymes were identified in each of the genomes, likely used for toxin neutralization rather than wood degradation. Lastly, a larger number of species-specific, secondary metabolite, synthesis clusters were identified in R. lauricola suggesting that it is well equipped as a pathogen, which could explain its success as a pathogen of a wide range of lauraceous hosts.
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Affiliation(s)
- Jorge R Ibarra Caballero
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | - Jongbum Jeon
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Stephen Fraedrich
- USDA Forest Service, Southern Research Station, Athens, GA 30602, USA
| | - Ned B Klopfenstein
- USDA Forest Service, Rocky Mountain Research Station, Moscow, ID 83843, USA
| | - Mee-Sook Kim
- USDA Forest Service, Pacific Northwest Research Station, Corvallis, OR 97331, USA
| | - Jane E Stewart
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA.
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230
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Xu CQ, Liu H, Zhou SS, Zhang DX, Zhao W, Wang S, Chen F, Sun YQ, Nie S, Jia KH, Jiao SQ, Zhang RG, Yun QZ, Guan W, Wang X, Gao Q, Bennetzen JL, Maghuly F, Porth I, Van de Peer Y, Wang XR, Ma Y, Mao JF. Genome sequence of Malania oleifera, a tree with great value for nervonic acid production. Gigascience 2019; 8:giy164. [PMID: 30689848 PMCID: PMC6377399 DOI: 10.1093/gigascience/giy164] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 11/12/2018] [Accepted: 12/17/2018] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic makeup and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools. FINDINGS We generated 51 Gb and 135 Gb of raw DNA sequences, using Pacific Biosciences (PacBio) single-molecule real-time and 10× Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Mb and a total length of 1.51 Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10× Genomics reads. Identified repeats constituted ∼82% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long-chain fatty acid were identified and studied in detail. CONCLUSIONS Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology and for the functional genomics of nervonic acid biosynthesis.
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Affiliation(s)
- Chao-Qun Xu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hui Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shan-Shan Zhou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Dong-Xu Zhang
- College of Life Science, Datong University, Datong, Shanxi, 037009, China
| | - Wei Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Sihai Wang
- Yunnan Key Laboratory of Forest Plant Cultivation and Utilization, State Forestry Administration Key Laboratory of Yunnan Rare and Endangered Species Conservation and Propagation, Yunnan Academy of Forestry, Kunming, Yunnan, 650201, China
| | - Fu Chen
- The Camellia Institute, Yunnan Academy of Forestry, Guangnan, Yunnan, 663300, China
| | - Yan-Qiang Sun
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shuai Nie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Kai-Hua Jia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Si-Qian Jiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ren-Gang Zhang
- Beijing Ori-Gene Science and Technology Co. Ltd, Beijing, 102206, China
| | - Quan-Zheng Yun
- Beijing Ori-Gene Science and Technology Co. Ltd, Beijing, 102206, China
| | - Wenbin Guan
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xuewen Wang
- The Camellia Institute, Yunnan Academy of Forestry, Guangnan, Yunnan, 663300, China
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Qiong Gao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jeffrey L Bennetzen
- The Camellia Institute, Yunnan Academy of Forestry, Guangnan, Yunnan, 663300, China
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Fatemeh Maghuly
- Plant Biotechnology Unit (PBU), Dept. Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna 1190, Austria
| | - Ilga Porth
- Département des sciences du bois et de la forêt, 1030, Avenue de la Médecine, Université Laval, Québec (Québec) G1V 0A6, Canada
- Institute for System and Integrated Biology, Pavillon Charles-Eugène-Marchand, 1030, Avenue de la Médecine, Université Laval, Québec (Québec) G1V 0A6, Canada
- Centre d'Étude de la Forêt, 1030, Avenue de la Médecine, Université Laval, Québec (Québec) G1V 0A6, Canada
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology Genetics, University of Pretoria, Private bag X20, Pretoria 0028, South Africa
| | - Xiao-Ru Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Department of Ecology and Environmental Science, UPSC, Umeå University, Umeå SE-901 87, Sweden
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
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231
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Zhang F, Ding Y, Zhu C, Zhou X, Orr MC, Scheu S, Luan Y. Phylogenomics from low‐coverage whole‐genome sequencing. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13145] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Feng Zhang
- Department of EntomologyCollege of Plant ProtectionNanjing Agricultural University Nanjing P. R. China
- Key Laboratory of the Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of Sciences Beijing P. R. China
- J. F. Blumenbach Institute of Zoology and AnthropologyUniversity of Göttingen Göttingen Germany
| | - Yinhuan Ding
- Department of EntomologyCollege of Plant ProtectionNanjing Agricultural University Nanjing P. R. China
| | - Chao‐Dong Zhu
- Key Laboratory of the Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of Sciences Beijing P. R. China
- College of Life SciencesUniversity of Chinese Academy of Sciences Beijing P. R. China
| | - Xin Zhou
- Department of EntomologyChina Agricultural University Beijing P. R. China
| | - Michael C. Orr
- Key Laboratory of the Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of Sciences Beijing P. R. China
| | - Stefan Scheu
- J. F. Blumenbach Institute of Zoology and AnthropologyUniversity of Göttingen Göttingen Germany
| | - Yun‐Xia Luan
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied TechnologyInstitute of Insect Science and TechnologySchool of Life SciencesSouth China Normal University Guangzhou P. R. China
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232
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Davis WJ, Amses KR, Benny GL, Carter-House D, Chang Y, Grigoriev I, Smith ME, Spatafora JW, Stajich JE, James TY. Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi). Mol Phylogenet Evol 2019; 133:152-163. [PMID: 30639767 DOI: 10.1016/j.ympev.2019.01.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/25/2018] [Accepted: 01/04/2019] [Indexed: 11/26/2022]
Abstract
Previous genome-scale phylogenetic analyses of Fungi have under sampled taxa from Zoopagales; this order contains many predacious or parasitic genera, and most have never been grown in pure culture. We sequenced the genomes of 4 zoopagalean taxa that are predators of amoebae, nematodes, or rotifers and the genome of one taxon that is a parasite of amoebae using single cell sequencing methods with whole genome amplification. Each genome was a metagenome, which was assembled and binned using multiple techniques to identify the target genomes. We inferred phylogenies with both super matrix and coalescent approaches using 192 conserved proteins mined from the target genomes and performed ancestral state reconstructions to determine the ancestral trophic lifestyle of the clade. Our results indicate that Zoopagales is monophyletic. Ancestral state reconstructions provide moderate support for mycoparasitism being the ancestral state of the clade.
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Affiliation(s)
- William J Davis
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
| | - Kevin R Amses
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
| | - Gerald L Benny
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Derreck Carter-House
- Department of Microbiology and Plant Pathology, University of California-Riverside, United States
| | - Ying Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Igor Grigoriev
- United States of America Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California-Riverside, United States
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States.
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233
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Abstract
The increasing affordability of sequencing technologies offers many new and exciting opportunities to address a diverse array of biological questions. This is evidenced in entomological research by numerous genomics and transcriptomics studies that attempt to decipher the often complex relationships among different species or orders and to build "omics" resources to drive advancement of the molecular understanding of insect biology. Being able to gauge the quality of the sequencing data is of critical importance to understanding the potential limitations on the types of questions that these data can be reliably used to address. This chapter details the use of the Benchmarking Universal Single-Copy Orthologue (BUSCO) assessment tool to estimate the completeness of transcriptomes, genome assemblies, and annotated gene sets in terms of their expected gene content.
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234
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Abstract
Comparing multiple related genomes can help to improve their structural annotation. The accuracy and consistency of the predicted exon-intron structures of the protein coding genes can be higher when considering all genomes at once rather than annotating one genome at a time.The comparative gene prediction algorithm of AUGUSTUS performs such a multi-genome annotation. A multiple alignment of genomes is used to exploit evolutionary clues to conservation and negative selection. Further, AUGUSTUS exploits the fact that orthologous genes typically have congruent exon-intron structures. Comparative AUGUSTUS simultaneously predicts the genes in all input genomes. In this chapter we walk the reader through a small example from eight vertebrate species, including the construction of an alignment of the input genomes and how to integrate RNA-Seq evidence from multiple species for gene finding.
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Affiliation(s)
- Stefanie Nachtweide
- Institute of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Straße 47, 17487, Greifswald, Germany
| | - Mario Stanke
- Institute of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Straße 47, 17487, Greifswald, Germany.
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235
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Abstract
Genomics drives the current progress in molecular biology, generating unprecedented volumes of data. The scientific value of these sequences depends on the ability to evaluate their completeness using a biologically meaningful approach. Here, we describe the use of the BUSCO tool suite to assess the completeness of genomes, gene sets, and transcriptomes, using their gene content as a complementary method to common technical metrics. The chapter introduces the concept of universal single-copy genes, which underlies the BUSCO methodology, covers the basic requirements to set up the tool, and provides guidelines to properly design the analyses, run the assessments, and interpret and utilize the results.
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Affiliation(s)
- Mathieu Seppey
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Geneva, Switzerland
| | - Mosè Manni
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Geneva, Switzerland
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Geneva, Switzerland.
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236
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Shelenkov AA, Slavokhotova AA, Odintsova TI. Cysmotif Searcher Pipeline for Antimicrobial Peptide Identification in Plant Transcriptomes. BIOCHEMISTRY (MOSCOW) 2018; 83:1424-1432. [PMID: 30482154 DOI: 10.1134/s0006297918110135] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this paper, we present the new Cysmotif searcher pipeline for identification of various antimicrobial peptides (AMPs), the most important components of innate immunity, in plant transcriptomes. Cysmotif searcher reveals and classifies short cysteine-rich amino acid sequences containing an open reading frame and a signal peptide cleavage site. Due to the combination of various search methods, Cysmotif searcher allows to obtain the most complete repertoire of AMPs for one or more transcriptomes in a short amount of time. The pipeline performance is estimated on the model plant Arabidopsis thaliana and nine other plants, including cultivated and wild species. The obtained results are compared to the existing annotation (A. thaliana) and results of conventional homology search (other plants). The comparison is carried out for known families of plant AMPs and newly discovered peptides that could not be assigned to existing families. The applicability of Cysmotif searcher in detecting new AMPs is discussed, and some practical recommendations on the pipeline usage for end users are given. The Cysmotif searcher pipeline is free for academic use and can be downloaded from Github (http://github.com/fallandar/cysmotifsearcher).
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Affiliation(s)
- A A Shelenkov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia. .,Central Research Institute of Epidemiology, Rospotrebnadzor, Moscow, 111123, Russia
| | - A A Slavokhotova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
| | - T I Odintsova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
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237
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Reis M, Vieira CP, Lata R, Posnien N, Vieira J. Origin and Consequences of Chromosomal Inversions in the virilis Group of Drosophila. Genome Biol Evol 2018; 10:3152-3166. [PMID: 30376068 PMCID: PMC6278893 DOI: 10.1093/gbe/evy239] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2018] [Indexed: 02/05/2023] Open
Abstract
In Drosophila, large variations in rearrangement rate have been reported among different lineages and among Muller’s elements. Nevertheless, the mechanisms that are involved in the generation of inversions, their increase in frequency, as well as their impact on the genome are not completely understood. This is in part due to the lack of comparative studies on species distantly related to Drosophila melanogaster. Therefore, we sequenced and assembled the genomes of two species of the virilis phylad (Drosophila novamexicana [15010-1031.00] and Drosophila americana [SF12]), which are diverging from D. melanogaster for more than 40 Myr. Based on these data, we identified the precise location of six novel inversion breakpoints. A molecular characterization provided clear evidence that DAIBAM (a miniature inverted–repeat transposable element) was involved in the generation of eight out of the nine inversions identified. In contrast to what has been previously reported for D. melanogaster and close relatives, ectopic recombination is thus the prevalent mechanism of generating inversions in species of the virilis phylad. Using pool-sequencing data for three populations of D. americana, we also show that common polymorphic inversions create a high degree of genetic differentiation between populations for chromosomes X, 4, and 5 over large physical distances. We did not find statistically significant differences in expression levels between D. americana (SF12) and D. novamexicana (15010-1031.00) strains for the three genes surveyed (CG9588, Fig 4, and fab1) flanking three inversion breakpoints.
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Affiliation(s)
- Micael Reis
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung für Entwicklungsbiologie, GZMB Ernst-Caspari-Haus, Universität Göttingen, Germany
| | - Cristina P Vieira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal
| | - Rodrigo Lata
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal
| | - Nico Posnien
- Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung für Entwicklungsbiologie, GZMB Ernst-Caspari-Haus, Universität Göttingen, Germany
| | - Jorge Vieira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal
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238
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Wu YM, Li J, Chen XS. Draft genomes of two blister beetles Hycleus cichorii and Hycleus phaleratus. Gigascience 2018; 7:1-7. [PMID: 29444297 PMCID: PMC5905561 DOI: 10.1093/gigascience/giy006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 01/28/2018] [Indexed: 11/13/2022] Open
Abstract
Background Commonly known as blister beetles or Spanish fly, there are more than 1500 species in the Meloidae family (Hexapoda: Coleoptera: Tenebrionoidea) that produce the potent defensive blistering agent cantharidin. Cantharidin and its derivatives have been used to treat cancers such as liver, stomach, lung, and esophageal cancers. Hycleus cichorii and Hycleus phaleratus are the most commercially important blister beetles in China due to their ability to biosynthesize this potent vesicant. However, there is a lack of genome reference, which has hindered development of studies on the biosynthesis of cantharidin and a better understanding of its biology and pharmacology. Results We report 2 draft genomes and quantified gene sets for the blister beetles H. cichorii and H. phaleratus, 2 complex genomes with >72% repeats and approximately 1% heterozygosity, using Illumina sequencing data. An integrated assembly pipeline was performed for assembly, and most of the coding regions were obtained. Benchmarking universal single-copy orthologs (BUSCO) assessment showed that our assembly obtained more than 98% of the Endopterygota universal single-copy orthologs. Comparison analysis showed that the completeness of coding genes in our assembly was comparable to other beetle genomes such as Dendroctonus ponderosae and Agrilus planipennis. Gene annotation yielded 13 813 and 13 725 protein-coding genes in H. cichorii and H. phaleratus, of which approximately 89% were functionally annotated. BUSCO assessment showed that approximately 86% and 84% of the Endopterygota universal single-copy orthologs were annotated completely in these 2 gene sets, whose completeness is comparable to that of D. ponderosae and A. planipennis. Conclusions Assembly of both blister beetle genomes provides a valuable resource for future biosynthesis of cantharidin and comparative genomic studies of blister beetles and other beetles.
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Affiliation(s)
- Yuan-Ming Wu
- Institute of Entomology/Special Key Laboratory for Development and Utilization of Insect Resources, Guizhou University, Guiyang, Guizhou, P.R. China, 550025.,Department of Parasitology/Laboratory of Pathogenic Biology, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou, P.R. China, 550025
| | - Jiang Li
- Genomics-center, InGene Biotech (Shenzhen) Co., Ltd, Shenzhen, China, 518081
| | - Xiang-Sheng Chen
- Institute of Entomology/Special Key Laboratory for Development and Utilization of Insect Resources, Guizhou University, Guiyang, Guizhou, P.R. China, 550025.,College of Animal Sciences, Guizhou University, Guiyang, Guizhou, P.R. China, 550025
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239
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Pollier J, Vancaester E, Kuzhiumparambil U, Vickers CE, Vandepoele K, Goossens A, Fabris M. A widespread alternative squalene epoxidase participates in eukaryote steroid biosynthesis. Nat Microbiol 2018; 4:226-233. [DOI: 10.1038/s41564-018-0305-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/24/2018] [Indexed: 11/09/2022]
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240
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Abstract
Newly sequenced genomes are being added to the tree of life at an unprecedented fast pace. Increasingly, such new genomes are phylogenetically close to previously sequenced and annotated genomes. In other cases, whole clades of closely related species or strains ought to be annotated simultaneously. Often, in subsequent studies differences between the closely related species or strains are in the focus of research when the shared gene structures prevail. We here review methods for comparative structural genome annotation. The reviewed methods include classical approaches such as the alignment of protein sequences or protein profiles against the genome and comparative gene prediction methods that exploit a genome alignment to annotate a target genome. Newer approaches such as the simultaneous annotation of multiple genomes are also reviewed. We discuss how the methods depend on the phylogenetic placement of genomes, give advice on the choice of methods, and examine the consistency between gene structure annotations in an example. Further, we provide practical advice on genome annotation in general.
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Affiliation(s)
- Stefanie König
- Institut für Mathematik und Informatik, Ernst Moritz Arndt Universität Greifswald, Greifswald, Germany
| | - Lars Romoth
- Institut für Mathematik und Informatik, Ernst Moritz Arndt Universität Greifswald, Greifswald, Germany
| | - Mario Stanke
- Institut für Mathematik und Informatik, Ernst Moritz Arndt Universität Greifswald, Greifswald, Germany.
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241
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Esfeld K, Berardi AE, Moser M, Bossolini E, Freitas L, Kuhlemeier C. Pseudogenization and Resurrection of a Speciation Gene. Curr Biol 2018; 28:3776-3786.e7. [PMID: 30472000 DOI: 10.1016/j.cub.2018.10.019] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/05/2018] [Accepted: 10/05/2018] [Indexed: 12/13/2022]
Abstract
A persistent question in evolutionary biology is how complex phenotypes evolve and whether phenotypic transitions are reversible. Multiple losses of floral pigmentation have been documented in the angiosperms, but color re-gain has not yet been described, supporting that re-gain is unlikely. Pollinator-mediated selection in Petunia has resulted in several color shifts comprised of both losses and gains of color. The R2R3-MYB transcription factor AN2 has been identified as a major locus responsible for shifts in pollinator preference. Whereas the loss of visible color has previously been attributed to repeated pseudogenization of AN2, here, we describe the mechanism of an independent re-gain of floral color via AN2 evolution. In P. secreta, purple color is restored through the improbable resurrection of AN2 gene function from a non-functional AN2-ancestor by a single reading-frame-restoring mutation. Thus, floral color evolution in Petunia is mechanistically dependent on AN2 functionality, highlighting its role as a hotspot in color transitions and a speciation gene for the genus.
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Affiliation(s)
- Korinna Esfeld
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Andrea E Berardi
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Michel Moser
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Eligio Bossolini
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Loreta Freitas
- Department of Genetics, University Fed Rio Grande do Sul, POB 15053, Porto Alegre, 91501970 Rio Grande do Sul, Brazil
| | - Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland.
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242
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Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature 2018; 564:64-70. [PMID: 30464347 PMCID: PMC6292497 DOI: 10.1038/s41586-018-0734-6] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 10/18/2018] [Indexed: 12/19/2022]
Abstract
Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. Here we sequence the genome of the Mediterranean amphioxus (Branchiostoma lanceolatum) and characterize DNA methylation, chromatin accessibility, histone modifications and transcriptomes across multiple developmental stages and adult tissues to investigate the evolution of the regulation of the chordate genome. Comparisons with vertebrates identify an intermediate stage in the evolution of differentially methylated enhancers, and a high conservation of gene expression and its cis-regulatory logic between amphioxus and vertebrates that occurs maximally at an earlier mid-embryonic phylotypic period. We analyse regulatory evolution after whole-genome duplications, and find that—in vertebrates—over 80% of broadly expressed gene families with multiple paralogues derived from whole-genome duplications have members that restricted their ancestral expression, and underwent specialization rather than subfunctionalization. Counter-intuitively, paralogues that restricted their expression increased the complexity of their regulatory landscapes. These data pave the way for a better understanding of the regulatory principles that underlie key vertebrate innovations. Genomic, epigenomic and transcriptomic data derived from the Mediterranean amphioxus (Branchiostoma lanceolatum) provide insights into the evolution of the genomic regulatory landscape of chordates.
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243
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Zhu J, Jiang F, Wang X, Yang P, Bao Y, Zhao W, Wang W, Lu H, Wang Q, Cui N, Li J, Chen X, Luo L, Yu J, Kang L, Cui F. Genome sequence of the small brown planthopper, Laodelphax striatellus. Gigascience 2018; 6:1-12. [PMID: 29136191 PMCID: PMC5740986 DOI: 10.1093/gigascience/gix109] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/03/2017] [Indexed: 12/17/2022] Open
Abstract
Background Laodelphax striatellus Fallén (Hemiptera: Delphacidae) is one of the most destructive rice pests. L. striatellus is different from 2 other rice planthoppers with a released genome sequence, Sogatella furcifera and Nilaparvata lugens, in many biological characteristics, such as host range, dispersal capacity, and vectoring plant viruses. Deciphering the genome of L. striatellus will further the understanding of the genetic basis of the biological differences among the 3 rice planthoppers. Findings A total of 190 Gb of Illumina data and 32.4 Gb of Pacbio data were generated and used to assemble a high-quality L. striatellus genome sequence, which is 541 Mb in length and has a contig N50 of 118 Kb and a scaffold N50 of 1.08 Mb. Annotated repetitive elements account for 25.7% of the genome. A total of 17 736 protein-coding genes were annotated, capturing 97.6% and 98% of the BUSCO eukaryote and arthropoda genes, respectively. Compared with N. lugens and S. furcifera, L. striatellus has the smallest genome and the lowest gene number. Gene family expansion and transcriptomic analyses provided hints to the genomic basis of the differences in important traits such as host range, migratory habit, and plant virus transmission between L. striatellus and the other 2 planthoppers. Conclusions We report a high-quality genome assembly of L. striatellus, which is an important genomic resource not only for the study of the biology of L. striatellus and its interactions with plant hosts and plant viruses, but also for comparison with other planthoppers.
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Affiliation(s)
- Junjie Zhu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Jiang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianhui Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Pengcheng Yang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanyuan Bao
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wan Zhao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hong Lu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qianshuo Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Na Cui
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofang Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lan Luo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinting Yu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng Cui
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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244
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Olson PD, Zarowiecki M, James K, Baillie A, Bartl G, Burchell P, Chellappoo A, Jarero F, Tan LY, Holroyd N, Berriman M. Genome-wide transcriptome profiling and spatial expression analyses identify signals and switches of development in tapeworms. EvoDevo 2018; 9:21. [PMID: 30455861 PMCID: PMC6225667 DOI: 10.1186/s13227-018-0110-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 10/05/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Tapeworms are agents of neglected tropical diseases responsible for significant health problems and economic loss. They also exhibit adaptations to a parasitic lifestyle that confound comparisons of their development with other animals. Identifying the genetic factors regulating their complex ontogeny is essential to understanding unique aspects of their biology and for advancing novel therapeutics. Here we use RNA sequencing to identify up-regulated signalling components, transcription factors and post-transcriptional/translational regulators (genes of interest, GOI) in the transcriptomes of Larvae and different regions of segmented worms in the tapeworm Hymenolepis microstoma and combine this with spatial gene expression analyses of a selection of genes. RESULTS RNA-seq reads collectively mapped to 90% of the > 12,000 gene models in the H. microstoma v.2 genome assembly, demonstrating that the transcriptome profiles captured a high percentage of predicted genes. Contrasts made between the transcriptomes of Larvae and whole, adult worms, and between the Scolex-Neck, mature strobila and gravid strobila, resulted in 4.5-30% of the genes determined to be differentially expressed. Among these, we identified 190 unique GOI up-regulated in one or more contrasts, including a large range of zinc finger, homeobox and other transcription factors, components of Wnt, Notch, Hedgehog and TGF-β/BMP signalling, and post-transcriptional regulators (e.g. Boule, Pumilio). Heatmap clusterings based on overall expression and on select groups of genes representing 'signals' and 'switches' showed that expression in the Scolex-Neck region is more similar to that of Larvae than to the mature or gravid regions of the adult worm, which was further reflected in large overlap of up-regulated GOI. CONCLUSIONS Spatial expression analyses in Larvae and adult worms corroborated inferences made from quantitative RNA-seq data and in most cases indicated consistency with canonical roles of the genes in other animals, including free-living flatworms. Recapitulation of developmental factors up-regulated during larval metamorphosis suggests that strobilar growth involves many of the same underlying gene regulatory networks despite the significant disparity in developmental outcomes. The majority of genes identified were investigated in tapeworms for the first time, setting the stage for advancing our understanding of developmental genetics in an important group of flatworm parasites.
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Affiliation(s)
- Peter D. Olson
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Magdalena Zarowiecki
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Katherine James
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Andrew Baillie
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Georgie Bartl
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Phil Burchell
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Azita Chellappoo
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Francesca Jarero
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Li Ying Tan
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Nancy Holroyd
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Matt Berriman
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
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245
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Dong Y, Sun Q, Zhang Y, Wang X, Liu P, Xiao Y, Fang Z. Complete genome of Gongronella sp. w5 provides insight into its relationship with plant. J Biotechnol 2018; 286:1-4. [DOI: 10.1016/j.jbiotec.2018.08.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 08/30/2018] [Accepted: 08/31/2018] [Indexed: 10/28/2022]
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246
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Roach MJ, Johnson DL, Bohlmann J, van Vuuren HJJ, Jones SJM, Pretorius IS, Schmidt SA, Borneman AR. Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay. PLoS Genet 2018; 14:e1007807. [PMID: 30458008 PMCID: PMC6279053 DOI: 10.1371/journal.pgen.1007807] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/04/2018] [Accepted: 11/02/2018] [Indexed: 01/08/2023] Open
Abstract
Chardonnay is the basis of some of the world's most iconic wines and its success is underpinned by a historic program of clonal selection. There are numerous clones of Chardonnay available that exhibit differences in key viticultural and oenological traits that have arisen from the accumulation of somatic mutations during centuries of asexual propagation. However, the genetic variation that underlies these differences remains largely unknown. To address this knowledge gap, a high-quality, diploid-phased Chardonnay genome assembly was produced from single-molecule real time sequencing, and combined with re-sequencing data from 15 different Chardonnay clones. There were 1620 markers identified that distinguish the 15 clones. These markers were reliably used for clonal identification of independently sourced genomic material, as well as in identifying a potential genetic basis for some clonal phenotypic differences. The predicted parentage of the Chardonnay haplomes was elucidated by mapping sequence data from the predicted parents of Chardonnay (Gouais blanc and Pinot noir) against the Chardonnay reference genome. This enabled the detection of instances of heterosis, with differentially-expanded gene families being inherited from the parents of Chardonnay. Most surprisingly however, the patterns of nucleotide variation present in the Chardonnay genome indicate that Pinot noir and Gouais blanc share an extremely high degree of kinship that has resulted in the Chardonnay genome displaying characteristics that are indicative of inbreeding.
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Affiliation(s)
- Michael J. Roach
- The Australian Wine Research Institute, Glen Osmond, South Australia, Australia
| | - Daniel L. Johnson
- The Australian Wine Research Institute, Glen Osmond, South Australia, Australia
| | - Joerg Bohlmann
- Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hennie J. J. van Vuuren
- Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J. M. Jones
- Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Isak S. Pretorius
- Chancellery, Macquarie University, Sydney, New South Wales, Australia
| | - Simon A. Schmidt
- The Australian Wine Research Institute, Glen Osmond, South Australia, Australia
| | - Anthony R. Borneman
- The Australian Wine Research Institute, Glen Osmond, South Australia, Australia
- Department of Genetics and Evolution, University of Adelaide, South Australia, Australia
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247
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Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M, Durbin R, Earl D, Ferguson-Smith A, Flicek P, Flint J, Frankish A, Fu B, Gerstein M, Gilbert J, Goodstadt L, Harrow J, Howe K, Ibarra-Soria X, Kolmogorov M, Lelliott C, Logan DW, Loveland J, Mathews CE, Mott R, Muir P, Nachtweide S, Navarro FC, Odom DT, Park N, Pelan S, Pham SK, Quail M, Reinholdt L, Romoth L, Shirley L, Sisu C, Sjoberg-Herrera M, Stanke M, Steward C, Thomas M, Threadgold G, Thybert D, Torrance J, Wong K, Wood J, Yalcin B, Yang F, Adams DJ, Paten B, Keane TM. Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci. Nat Genet 2018; 50:1574-1583. [PMID: 30275530 PMCID: PMC6205630 DOI: 10.1038/s41588-018-0223-8] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/02/2018] [Indexed: 12/11/2022]
Abstract
We report full-length draft de novo genome assemblies for 16 widely used inbred mouse strains and find extensive strain-specific haplotype variation. We identify and characterize 2,567 regions on the current mouse reference genome exhibiting the greatest sequence diversity. These regions are enriched for genes involved in pathogen defence and immunity and exhibit enrichment of transposable elements and signatures of recent retrotransposition events. Combinations of alleles and genes unique to an individual strain are commonly observed at these loci, reflecting distinct strain phenotypes. We used these genomes to improve the mouse reference genome, resulting in the completion of 10 new gene structures. Also, 62 new coding loci were added to the reference genome annotation. These genomes identified a large, previously unannotated, gene (Efcab3-like) encoding 5,874 amino acids. Mutant Efcab3-like mice display anomalies in multiple brain regions, suggesting a possible role for this gene in the regulation of brain development.
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MESH Headings
- Animals
- Animals, Laboratory
- Chromosome Mapping/veterinary
- Genetic Loci
- Genome
- Haplotypes/genetics
- Mice
- Mice, Inbred BALB C/genetics
- Mice, Inbred C3H/genetics
- Mice, Inbred C57BL/genetics
- Mice, Inbred CBA/genetics
- Mice, Inbred DBA/genetics
- Mice, Inbred NOD/genetics
- Mice, Inbred Strains/classification
- Mice, Inbred Strains/genetics
- Molecular Sequence Annotation
- Phylogeny
- Polymorphism, Single Nucleotide
- Species Specificity
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Affiliation(s)
- Jingtao Lilue
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Anthony G. Doran
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Ian T. Fiddes
- Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Monica Abrudan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Joel Armstrong
- Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Ruth Bennett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - William Chow
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Joanna Collins
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Stephan Collins
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique UMR7104, Institut National de la Santé et de la Recherche Médicale U964, Université de Strasbourg, 67404 Illkirch, France
- Centre des Sciences du Goût et de l’Alimentation, University of Bourgogne Franche-Comté, 21000 Dijon, France
| | - Anne Czechanski
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Petr Danecek
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Mark Diekhans
- Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Dirk-Dominik Dolle
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Matt Dunn
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Richard Durbin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Downing Site, Cambridge CB2 3EH, UK
| | - Dent Earl
- Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Anne Ferguson-Smith
- Department of Genetics, University of Cambridge, Downing Site, Cambridge CB2 3EH, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Jonathan Flint
- Brain Research Institute, University of California, 695 Charles E Young Dr S, Los Angeles, CA 90095, USA
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Beiyuan Fu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Mark Gerstein
- Yale Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - James Gilbert
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Leo Goodstadt
- OxFORD Asset Management, OxAM House, 6 George Street, Oxford OX1 2BW
| | - Jennifer Harrow
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Kerstin Howe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | | | - Mikhail Kolmogorov
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Chris Lelliott
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Darren W. Logan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Jane Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Clayton E. Mathews
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Richard Mott
- Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
| | - Paul Muir
- Yale Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Stefanie Nachtweide
- Institute of Mathematics and Computer Science, University of Greifswald, Domstraße 11, 17489 Greifswald, Germany
| | - Fabio C.P. Navarro
- Yale Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Duncan T. Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics, 69120 Heidelberg, Germany
| | - Naomi Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Sarah Pelan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Son K Pham
- BioTuring Inc., San Diego, California, CA92121
| | - Mike Quail
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Laura Reinholdt
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Lars Romoth
- Institute of Mathematics and Computer Science, University of Greifswald, Domstraße 11, 17489 Greifswald, Germany
| | - Lesley Shirley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Cristina Sisu
- Yale Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Bioscience, Brunel University London, Uxbridge UB8 3PH, UK
| | - Marcela Sjoberg-Herrera
- Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Mario Stanke
- Institute of Mathematics and Computer Science, University of Greifswald, Domstraße 11, 17489 Greifswald, Germany
| | - Charles Steward
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Mark Thomas
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Glen Threadgold
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - David Thybert
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - James Torrance
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Kim Wong
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Jonathan Wood
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Binnaz Yalcin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique UMR7104, Institut National de la Santé et de la Recherche Médicale U964, Université de Strasbourg, 67404 Illkirch, France
| | - Fengtang Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - David J. Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Benedict Paten
- Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Thomas M. Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- School of Life Sciences, University of Nottingham, Nottingham, UK
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248
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Richards DJ, Renaud L, Agarwal N, Starr Hazard E, Hyde J, Hardiman G. De Novo Hepatic Transcriptome Assembly and Systems Level Analysis of Three Species of Dietary Fish, Sardinops sagax, Scomber japonicus, and Pleuronichthys verticalis. Genes (Basel) 2018; 9:genes9110521. [PMID: 30366465 PMCID: PMC6266404 DOI: 10.3390/genes9110521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 10/17/2018] [Indexed: 12/31/2022] Open
Abstract
The monitoring of marine species as sentinels for ecosystem health has long been a valuable tool worldwide, providing insight into how both anthropogenic pollution and naturally occurring phenomena (i.e., harmful algal blooms) may lead to human and animal dietary concerns. The marine environments contain many contaminants of anthropogenic origin that have sufficient similarities to steroid and thyroid hormones, to potentially disrupt normal endocrine physiology in humans, fish, and other animals. An appropriate understanding of the effects of these endocrine disrupting chemicals (EDCs) on forage fish (e.g., sardine, anchovy, mackerel) can lead to significant insight into how these contaminants may affect local ecosystems in addition to their potential impacts on human health. With advancements in molecular tools (e.g., high-throughput sequencing, HTS), a genomics approach offers a robust toolkit to discover putative genetic biomarkers in fish exposed to these chemicals. However, the lack of available sequence information for non-model species has limited the development of these genomic toolkits. Using HTS and de novo assembly technology, the present study aimed to establish, for the first time for Sardinops sagax (Pacific sardine), Scomber japonicas (Pacific chub mackerel) and Pleuronichthys verticalis (hornyhead turbot), a de novo global transcriptome database of the liver, the primary organ involved in detoxification. The assembled transcriptomes provide a foundation for further downstream validation, comparative genomic analysis and biomarker development for future applications in ecotoxicogenomic studies, as well as environmental evaluation (e.g., climate change) and public health safety (e.g., dietary screening).
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Affiliation(s)
- Dylan J Richards
- Bioengineering Department, Clemson University, Charleston, SC 29425, USA.
| | - Ludivine Renaud
- Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA.
- Center for Genomic Medicine, Bioinformatics, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Nisha Agarwal
- Biomedical Informatics Research Center, San Diego State University, San Diego, CA 92182, USA.
| | - E Starr Hazard
- Center for Genomic Medicine, Bioinformatics, Medical University of South Carolina, Charleston, SC 29425, USA.
- Academic Affairs Faculty & Computational Biology Resource Center, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - John Hyde
- NOAA Fisheries, Southwest Fisheries Science Center, La Jolla, CA 92037, USA.
| | - Gary Hardiman
- Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA.
- Center for Genomic Medicine, Bioinformatics, Medical University of South Carolina, Charleston, SC 29425, USA.
- Biomedical Informatics Research Center, San Diego State University, San Diego, CA 92182, USA.
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA.
- Laboratory for Marine Systems Biology, Hollings Marine Laboratory, Charleston, SC 29412, USA.
- School of Biological Sciences & Institute for Global Food Security, Queens University Belfast, Stranmillis Road, Belfast BT9 5AG, UK.
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249
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Shpirer E, Diamant A, Cartwright P, Huchon D. A genome wide survey reveals multiple nematocyst-specific genes in Myxozoa. BMC Evol Biol 2018; 18:138. [PMID: 30208843 PMCID: PMC6134521 DOI: 10.1186/s12862-018-1253-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 08/22/2018] [Indexed: 12/02/2022] Open
Abstract
Background Myxozoa represents a diverse group of microscopic endoparasites whose life cycle involves two hosts: a vertebrate (usually a fish) and an invertebrate (usually an annelid worm). Despite lacking nearly all distinguishing animal characteristics, given that each life cycle stage consists of no more than a few cells, molecular phylogenetic studies have revealed that myxozoans belong to the phylum Cnidaria, which includes corals, sea anemones, and jellyfish. Myxozoa, however, do possess a polar capsule; an organelle that is homologous to the stinging structure unique to Cnidaria: the nematocyst. Previous studies have identified in Myxozoa a number of protein-coding genes that are specific to nematocytes (the cells producing nematocysts) and thus restricted to Cnidaria. Determining which other genes are also homologous with the myxozoan polar capsule genes could provide insight into both the conservation and changes that occurred during nematocyst evolution in the transition to endoparasitism. Results Previous studies have examined the phylogeny of two cnidarian-restricted gene families: minicollagens and nematogalectins. Here we identify and characterize seven additional cnidarian-restricted genes in myxozoan genomes using a phylogenetic approach. Four of the seven had never previously been identified as cnidarian-specific and none have been studied in a phylogenetic context. A majority of the proteins appear to be involved in the structure of the nematocyst capsule and tubule. No venom proteins were identified among the cnidarian-restricted genes shared by myxozoans. Conclusions Given the highly divergent forms that comprise Cnidaria, obtaining insight into the processes underlying their ancient diversification remains challenging. In their evolutionary transition to microscopic endoparasites, myxozoans lost nearly all traces of their cnidarian ancestry, with the one prominent exception being their nematocysts (or polar capsules). Thus nematocysts, and the genes that code for their structure, serve as rich sources of information to support the cnidarian origin of Myxozoa. Electronic supplementary material The online version of this article (10.1186/s12862-018-1253-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Erez Shpirer
- School of Zoology, Tel Aviv University, Tel Aviv, Israel
| | - Arik Diamant
- National Center for Mariculture, Israel Oceanographic and Limnological Research, Eilat, Israel
| | - Paulyn Cartwright
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, USA.
| | - Dorothée Huchon
- School of Zoology, Tel Aviv University, Tel Aviv, Israel. .,The Steinhardt Museum of Natural History and National Research Center, Tel Aviv University, Tel Aviv, Israel.
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250
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Edwards RJ, Tuipulotu DE, Amos TG, O'Meally D, Richardson MF, Russell TL, Vallinoto M, Carneiro M, Ferrand N, Wilkins MR, Sequeira F, Rollins LA, Holmes EC, Shine R, White PA. Draft genome assembly of the invasive cane toad, Rhinella marina. Gigascience 2018; 7:5096832. [PMID: 30101298 PMCID: PMC6145236 DOI: 10.1093/gigascience/giy095] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/22/2018] [Indexed: 12/28/2022] Open
Abstract
Background The cane toad (Rhinella marina formerly Bufo marinus) is a species native to Central and South America that has spread across many regions of the globe. Cane toads are known for their rapid adaptation and deleterious impacts on native fauna in invaded regions. However, despite an iconic status, there are major gaps in our understanding of cane toad genetics. The availability of a genome would help to close these gaps and accelerate cane toad research. Findings We report a draft genome assembly for R. marina, the first of its kind for the Bufonidae family. We used a combination of long-read Pacific Biosciences RS II and short-read Illumina HiSeq X sequencing to generate 359.5 Gb of raw sequence data. The final hybrid assembly of 31,392 scaffolds was 2.55 Gb in length with a scaffold N50 of 168 kb. BUSCO analysis revealed that the assembly included full length or partial fragments of 90.6% of tetrapod universal single-copy orthologs (n = 3950), illustrating that the gene-containing regions have been well assembled. Annotation predicted 25,846 protein coding genes with similarity to known proteins in Swiss-Prot. Repeat sequences were estimated to account for 63.9% of the assembly. Conclusions The R. marina draft genome assembly will be an invaluable resource that can be used to further probe the biology of this invasive species. Future analysis of the genome will provide insights into cane toad evolution and enrich our understanding of their interplay with the ecosystem at large.
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Affiliation(s)
- Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Daniel Enosi Tuipulotu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Timothy G Amos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Denis O'Meally
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Camperdown, NSW, 2052, Australia
| | - Mark F Richardson
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, VIC, 3216, Australia.,Bioinformatics Core Research Group, Deakin University, Geelong, VIC, 3216, Australia
| | - Tonia L Russell
- Ramaciotti Centre for Genomics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Marcelo Vallinoto
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Laboratório de Evolução, Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Nuno Ferrand
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park, South Africa
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.,Ramaciotti Centre for Genomics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Fernando Sequeira
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Lee A Rollins
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, VIC, 3216, Australia.,Evolution and Ecology Research Centre, School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - Richard Shine
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Peter A White
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
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