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Giant tortoise genomes provide insights into longevity and age-related disease. Nat Ecol Evol 2018; 3:87-95. [PMID: 30510174 PMCID: PMC6314442 DOI: 10.1038/s41559-018-0733-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 10/25/2018] [Indexed: 12/21/2022]
Abstract
Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on giant tortoises is scarce. Here, we describe a global analysis of the genomes of Lonesome George-the iconic last member of Chelonoidis abingdonii-and the Aldabra giant tortoise (Aldabrachelys gigantea). Comparison of these genomes with those of related species, using both unsupervised and supervised analyses, led us to detect lineage-specific variants affecting DNA repair genes, inflammatory mediators and genes related to cancer development. Our study also hints at specific evolutionary strategies linked to increased lifespan, and expands our understanding of the genomic determinants of ageing. These new genome sequences also provide important resources to help the efforts for restoration of giant tortoise populations.
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352
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Sarropoulou E, Sundaram AYM, Kaitetzidou E, Kotoulas G, Gilfillan GD, Papandroulakis N, Mylonas CC, Magoulas A. Full genome survey and dynamics of gene expression in the greater amberjack Seriola dumerili. Gigascience 2018; 6:1-13. [PMID: 29126158 PMCID: PMC5751066 DOI: 10.1093/gigascience/gix108] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 11/02/2017] [Indexed: 02/05/2023] Open
Abstract
Background Teleosts of the genus Seriola, commonly known as amberjacks, are of high commercial value in international markets due to their flesh quality and worldwide distribution. The Seriola species of interest to Mediterranean aquaculture is the greater amberjack (Seriola dumerili). This species holds great potential for the aquaculture industry, but in captivity, reproduction has proved to be challenging, and observed growth dysfunction hinders their domestication. Insights into molecular mechanisms may contribute to a better understanding of traits like growth and sex, but investigations to unravel the molecular background of amberjacks have begun only recently. Findings Illumina HiSeq sequencing generated a high-coverage greater amberjack genome sequence comprising 45 909 scaffolds. Comparative mapping to the Japanese yellowtail (Seriola quinqueriadiata) and to the model species medaka (Oryzias latipes) allowed the generation of in silico groups. Additional gonad transcriptome sequencing identified sex-biased transcripts, including known sex-determining and differentiation genes. Investigation of the muscle transcriptome of slow-growing individuals showed that transcripts involved in oxygen and gas transport were differentially expressed compared with fast/normal-growing individuals. On the other hand, transcripts involved in muscle functions were found to be enriched in fast/normal-growing individuals. Conclusion The present study provides the first insights into the molecular background of male and female amberjacks and of fast- and slow-growing fish. Therefore, valuable molecular resources have been generated in the form of a first draft genome and a reference transcriptome. Sex-biased genes, which may also have roles in sex determination or differentiation, and genes that may be responsible for slow growth are suggested.
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Affiliation(s)
- Elena Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture Hellenic Centre for Marine Research Crete, Thalassocosmos, Gournes Pediados, P.O.Box 2214, 71003 Heraklion Crete, Greece
| | - Arvind Y M Sundaram
- Norwegian High Throughput Sequencing Centre, Department of Medical Genetics, Oslo University Hospital (Ullevål), Kirkeveien 166 0450, Oslo, Norway
| | - Elisavet Kaitetzidou
- Institute of Marine Biology, Biotechnology and Aquaculture Hellenic Centre for Marine Research Crete, Thalassocosmos, Gournes Pediados, P.O.Box 2214, 71003 Heraklion Crete, Greece
| | - Georgios Kotoulas
- Institute of Marine Biology, Biotechnology and Aquaculture Hellenic Centre for Marine Research Crete, Thalassocosmos, Gournes Pediados, P.O.Box 2214, 71003 Heraklion Crete, Greece
| | - Gregor D Gilfillan
- Norwegian High Throughput Sequencing Centre, Department of Medical Genetics, Oslo University Hospital (Ullevål), Kirkeveien 166 0450, Oslo, Norway
| | - Nikos Papandroulakis
- Institute of Marine Biology, Biotechnology and Aquaculture Hellenic Centre for Marine Research Crete, Thalassocosmos, Gournes Pediados, P.O.Box 2214, 71003 Heraklion Crete, Greece
| | - Constantinos C Mylonas
- Institute of Marine Biology, Biotechnology and Aquaculture Hellenic Centre for Marine Research Crete, Thalassocosmos, Gournes Pediados, P.O.Box 2214, 71003 Heraklion Crete, Greece
| | - Antonios Magoulas
- Institute of Marine Biology, Biotechnology and Aquaculture Hellenic Centre for Marine Research Crete, Thalassocosmos, Gournes Pediados, P.O.Box 2214, 71003 Heraklion Crete, Greece
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353
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Complete chloroplast genome sequence of Dryopteris fragrans (L.) Schott and the repeat structures against the thermal environment. Sci Rep 2018; 8:16635. [PMID: 30413776 PMCID: PMC6226466 DOI: 10.1038/s41598-018-35061-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 10/15/2018] [Indexed: 01/07/2023] Open
Abstract
Dryopteris fragrans (L.) Schott is a fern growing on the surface of hot rocks and lava. It is exposed to sunlight directly and bears local hot environment. We sequenced the complete nucleotide sequence of its chloroplast (cp) genome. The cp genome was 151,978 bp in length, consisting of a large single-copy region (85,332 bp), a small single-copy region (31,947 bp) and a pair of inverted repeats (17,314 bp). The cp genome contained 112 genes and 345 RNA editing sites in protein-coding genes. Simple sequence repeats (SSRs) and long repeat structure pairs (30–55 bp) were identified. The number and percent of repeat structures are extremely high in ferns. Thermal denaturation experiments showed its cp genome to have numerous, dispersed and high GC percent repeat structures, which conferred the strongest thermal stability. This repeat-heavy genome may provide the molecular basis of how D. fragrans cp survives its hot environment.
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354
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Gong G, Dan C, Xiao S, Guo W, Huang P, Xiong Y, Wu J, He Y, Zhang J, Li X, Chen N, Gui JF, Mei J. Chromosomal-level assembly of yellow catfish genome using third-generation DNA sequencing and Hi-C analysis. Gigascience 2018; 7:5106933. [PMID: 30256939 PMCID: PMC6228179 DOI: 10.1093/gigascience/giy120] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/25/2018] [Accepted: 09/18/2018] [Indexed: 01/12/2023] Open
Abstract
Background The yellow catfish, Pelteobagrus fulvidraco, belonging to the Siluriformes order, is an economically important freshwater aquaculture fish species in Asia, especially in Southern China. The aquaculture industry has recently been facing tremendous challenges in germplasm degeneration and poor disease resistance. As the yellow catfish exhibits notable sex dimorphism in growth, with adult males about two- to three-fold bigger than females, the way in which the aquaculture industry takes advantage of such sex dimorphism is another challenge. To address these issues, a high-quality reference genome of the yellow catfish would be a very useful resource. Findings To construct a high-quality reference genome for the yellow catfish, we generated 51.2 Gb short reads and 38.9 Gb long reads using Illumina and Pacific Biosciences (PacBio) sequencing platforms, respectively. The sequencing data were assembled into a 732.8 Mb genome assembly with a contig N50 length of 1.1 Mb. Additionally, we applied Hi-C technology to identify contacts among contigs, which were then used to assemble contigs into scaffolds, resulting in a genome assembly with 26 chromosomes and a scaffold N50 length of 25.8 Mb. Using 24,552 protein-coding genes annotated in the yellow catfish genome, the phylogenetic relationships of the yellow catfish with other teleosts showed that yellow catfish separated from the common ancestor of channel catfish ∼81.9 million years ago. We identified 1,717 gene families to be expanded in the yellow catfish, and those gene families are mainly enriched in the immune system, signal transduction, glycosphingolipid biosynthesis, and fatty acid biosynthesis. Conclusions Taking advantage of Illumina, PacBio, and Hi-C technologies, we constructed the first high-quality chromosome-level genome assembly for the yellow catfish P. fulvidraco. The genomic resources generated in this work not only offer a valuable reference genome for functional genomics studies of yellow catfish to decipher the economic traits and sex determination but also provide important chromosome information for genome comparisons in the wider evolutionary research community.
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Affiliation(s)
- Gaorui Gong
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Cheng Dan
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Shijun Xiao
- Wuhan Frasergen Bioinformatics, East Lake High-Tech Zone, Wuhan, Hubei, 430075, China
| | - Wenjie Guo
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Peipei Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academyof Sciences, University of the Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Yang Xiong
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Junjie Wu
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yan He
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jicheng Zhang
- Wuhan Frasergen Bioinformatics, East Lake High-Tech Zone, Wuhan, Hubei, 430075, China
| | - Xiaohui Li
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Nansheng Chen
- Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, 266071, China
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Jian-Fang Gui
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jie Mei
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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355
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Cunning R, Bay RA, Gillette P, Baker AC, Traylor-Knowles N. Comparative analysis of the Pocillopora damicornis genome highlights role of immune system in coral evolution. Sci Rep 2018; 8:16134. [PMID: 30382153 PMCID: PMC6208414 DOI: 10.1038/s41598-018-34459-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/19/2018] [Indexed: 12/22/2022] Open
Abstract
Comparative analysis of the expanding genomic resources for scleractinian corals may provide insights into the evolution of these organisms, with implications for their continued persistence under global climate change. Here, we sequenced and annotated the genome of Pocillopora damicornis, one of the most abundant and widespread corals in the world. We compared this genome, based on protein-coding gene orthology, with other publicly available coral genomes (Cnidaria, Anthozoa, Scleractinia), as well as genomes from other anthozoan groups (Actiniaria, Corallimorpharia), and two basal metazoan outgroup phlya (Porifera, Ctenophora). We found that 46.6% of P. damicornis genes had orthologs in all other scleractinians, defining a coral ‘core’ genome enriched in basic housekeeping functions. Of these core genes, 3.7% were unique to scleractinians and were enriched in immune functionality, suggesting an important role of the immune system in coral evolution. Genes occurring only in P. damicornis were enriched in cellular signaling and stress response pathways, and we found similar immune-related gene family expansions in each coral species, indicating that immune system diversification may be a prominent feature of scleractinian coral evolution at multiple taxonomic levels. Diversification of the immune gene repertoire may underlie scleractinian adaptations to symbiosis, pathogen interactions, and environmental stress.
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Affiliation(s)
- R Cunning
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA. .,Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, 1200 South Lake Shore Drive, Chicago, IL, 60605, USA.
| | - R A Bay
- Department of Evolution and Ecology, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - P Gillette
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
| | - A C Baker
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
| | - N Traylor-Knowles
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA.
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356
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Machado AM, Tørresen OK, Kabeya N, Couto A, Petersen B, Felício M, Campos PF, Fonseca E, Bandarra N, Lopes-Marques M, Ferraz R, Ruivo R, Fonseca MM, Jentoft S, Monroig Ó, da Fonseca RR, C Castro LF. " Out of the Can": A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus. Genes (Basel) 2018; 9:E485. [PMID: 30304855 PMCID: PMC6210256 DOI: 10.3390/genes9100485] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/01/2018] [Accepted: 10/02/2018] [Indexed: 12/30/2022] Open
Abstract
Clupeiformes, such as sardines and herrings, represent an important share of worldwide fisheries. Among those, the European sardine (Sardina pilchardus, Walbaum 1792) exhibits significant commercial relevance. While the last decade showed a steady and sharp decline in capture levels, recent advances in culture husbandry represent promising research avenues. Yet, the complete absence of genomic resources from sardine imposes a severe bottleneck to understand its physiological and ecological requirements. We generated 69 Gbp of paired-end reads using Illumina HiSeq X Ten and assembled a draft genome assembly with an N50 scaffold length of 25,579 bp and BUSCO completeness of 82.1% (Actinopterygii). The estimated size of the genome ranges between 655 and 850 Mb. Additionally, we generated a relatively high-level liver transcriptome. To deliver a proof of principle of the value of this dataset, we established the presence and function of enzymes (Elovl2, Elovl5, and Fads2) that have pivotal roles in the biosynthesis of long chain polyunsaturated fatty acids, essential nutrients particularly abundant in oily fish such as sardines. Our study provides the first omics dataset from a valuable economic marine teleost species, the European sardine, representing an essential resource for their effective conservation, management, and sustainable exploitation.
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Affiliation(s)
- André M Machado
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
| | - Ole K Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway.
| | - Naoki Kabeya
- Department of Aquatic Bioscience, The University of Tokyo, Tokyo 113-8654, Japan.
| | - Alvarina Couto
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Bent Petersen
- Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
- Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology, Kedah 08000, Malaysia.
| | - Mónica Felício
- Portuguese Institute for the Sea and Atmosphere, (IPMA), 1749-077 Lisbon, Portugal.
| | - Paula F Campos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Elza Fonseca
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, 4099-022 Porto, Portugal.
| | - Narcisa Bandarra
- Portuguese Institute for the Sea and Atmosphere, (IPMA), 1749-077 Lisbon, Portugal.
| | - Mónica Lopes-Marques
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
| | - Renato Ferraz
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4099-022 Porto, Portugal.
| | - Raquel Ruivo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
| | - Miguel M Fonseca
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway.
- Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630 Kristiansand, Norway.
| | - Óscar Monroig
- Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas (IATS-CSIC), 12595 Ribera de Cabanes, Spain.
| | - Rute R da Fonseca
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
- Center for Macroecology, Evolution, and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark.
| | - L Filipe C Castro
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, 4099-022 Porto, Portugal.
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357
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Rao S, Sharda S, Oddi V, Nandineni MR. The Landscape of Repetitive Elements in the Refined Genome of Chilli Anthracnose Fungus Colletotrichum truncatum. Front Microbiol 2018; 9:2367. [PMID: 30337918 PMCID: PMC6180176 DOI: 10.3389/fmicb.2018.02367] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/14/2018] [Indexed: 12/15/2022] Open
Abstract
The ascomycete fungus Colletotrichum truncatum is a major phytopathogen with a broad host range which causes anthracnose disease of chilli. The genome sequencing of this fungus led to the discovery of functional categories of genes that may play important roles in fungal pathogenicity. However, the presence of gaps in C. truncatum draft assembly prevented the accurate prediction of repetitive elements, which are the key players to determine the genome architecture and drive evolution and host adaptation. We re-sequenced its genome using single-molecule real-time (SMRT) sequencing technology to obtain a refined assembly with lesser and smaller gaps and ambiguities. This enabled us to study its genome architecture by characterising the repetitive sequences like transposable elements (TEs) and simple sequence repeats (SSRs), which constituted 4.9 and 0.38% of the assembled genome, respectively. The comparative analysis among different Colletotrichum species revealed the extensive repeat rich regions, dominated by Gypsy superfamily of long terminal repeats (LTRs), and the differential composition of SSRs in their genomes. Our study revealed a recent burst of LTR amplification in C. truncatum, C. higginsianum, and C. scovillei. TEs in C. truncatum were significantly associated with secretome, effectors and genes in secondary metabolism clusters. Some of the TE families in C. truncatum showed cytosine to thymine transitions indicative of repeat-induced point mutation (RIP). C. orbiculare and C. graminicola showed strong signatures of RIP across their genomes and "two-speed" genomes with extensive AT-rich and gene-sparse regions. Comparative genomic analyses of Colletotrichum species provided an insight into the species-specific SSR profiles. The SSRs in the coding and non-coding regions of the genome revealed the composition of trinucleotide repeat motifs in exons with potential to alter the translated protein structure through amino acid repeats. This is the first genome-wide study of TEs and SSRs in C. truncatum and their comparative analysis with six other Colletotrichum species, which would serve as a useful resource for future research to get insights into the potential role of TEs in genome expansion and evolution of Colletotrichum fungi and for development of SSR-based molecular markers for population genomic studies.
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Affiliation(s)
- Soumya Rao
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | - Saphy Sharda
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Vineesha Oddi
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Madhusudan R. Nandineni
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Laboratory of DNA Fingerprinting Services, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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358
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Bulacio Gil NM, Pajot HF, Rosales Soro MDM, de Figueroa LIC, Kurth D. Genome-wide overview of Trichosporon akiyoshidainum HP-2023, new insights into its mechanism of dye discoloration. 3 Biotech 2018; 8:440. [PMID: 30306009 DOI: 10.1007/s13205-018-1465-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/26/2018] [Indexed: 01/08/2023] Open
Abstract
Trichosporon akiyoshidainum HP-2023 completely discolorised Reactive Black 5 (200 mg/l) in 24 h. Manganese peroxidase and phenoloxidase, but no laccase activities were detected throughout the incubation. Total aromatic amines in media with Reactive Black 5 decreased 83% after 24 h, supporting an oxidative mechanism of azo dye discoloration. To unravel the genetic basis of these activities, the genome of Trichosporon akiyoshidainum HP-2023 was sequenced, assembled and annotated de novo. T. akiyoshidainum HP-2023 genome comprises 30 MB with a G+C content of 60.75% and 9019 gene models. Thirty-three putative carbohydrate-active enzymes with auxiliary activities, probably involved in lignin degradation and dye discoloration, were identified in the annotated genome, including two laccases, four extracellular fungal heme-peroxidases, nineteen hydrogen peroxide-producing enzymes, and four benzoquinone oxidoreductases. This report will facilitate further studies of textile-dye discoloration with this and closely related strains and poses questions about the ligninolytic potential of Trichosporon akiyoshidainum HP-2023 and related species.
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Affiliation(s)
- Natalia María Bulacio Gil
- 1PROIMI-CONICET (Planta Piloto de Procesos Industriales Microbiológicos), Av. Belgrano y Caseros (T4001MVB), Tucuman, Argentina
| | - Hipólito Fernando Pajot
- 1PROIMI-CONICET (Planta Piloto de Procesos Industriales Microbiológicos), Av. Belgrano y Caseros (T4001MVB), Tucuman, Argentina
| | - María Del Milagro Rosales Soro
- 1PROIMI-CONICET (Planta Piloto de Procesos Industriales Microbiológicos), Av. Belgrano y Caseros (T4001MVB), Tucuman, Argentina
| | - Lucía Inés Castellanos de Figueroa
- 1PROIMI-CONICET (Planta Piloto de Procesos Industriales Microbiológicos), Av. Belgrano y Caseros (T4001MVB), Tucuman, Argentina
- 2Microbiología Superior, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - Daniel Kurth
- 1PROIMI-CONICET (Planta Piloto de Procesos Industriales Microbiológicos), Av. Belgrano y Caseros (T4001MVB), Tucuman, Argentina
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359
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Lehmann R, Lightfoot DJ, Schunter C, Michell CT, Ohyanagi H, Mineta K, Foret S, Berumen ML, Miller DJ, Aranda M, Gojobori T, Munday PL, Ravasi T. Finding Nemo's Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula. Mol Ecol Resour 2018; 19:570-585. [PMID: 30203521 PMCID: PMC7379943 DOI: 10.1111/1755-0998.12939] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 07/31/2018] [Accepted: 08/08/2018] [Indexed: 11/29/2022]
Abstract
The iconic orange clownfish, Amphiprion percula, is a model organism for studying the ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, habitat selection and adaptation to climate change. Notably, the orange clownfish is the only reef fish for which a complete larval dispersal kernel has been established and was the first fish species for which it was demonstrated that antipredator responses of reef fishes could be impaired by ocean acidification. Despite its importance, molecular resources for this species remain scarce and until now it lacked a reference genome assembly. Here, we present a de novo chromosome-scale assembly of the genome of the orange clownfish Amphiprion percula. We utilized single-molecule real-time sequencing technology from Pacific Biosciences to produce an initial polished assembly comprised of 1,414 contigs, with a contig N50 length of 1.86 Mb. Using Hi-C-based chromatin contact maps, 98% of the genome assembly were placed into 24 chromosomes, resulting in a final assembly of 908.8 Mb in length with contig and scaffold N50s of 3.12 and 38.4 Mb, respectively. This makes it one of the most contiguous and complete fish genome assemblies currently available. The genome was annotated with 26,597 protein-coding genes and contains 96% of the core set of conserved actinopterygian orthologs. The availability of this reference genome assembly as a community resource will further strengthen the role of the orange clownfish as a model species for research on the ecology and evolution of reef fishes.
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Affiliation(s)
- Robert Lehmann
- KAUST Environmental Epigenetic Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Damien J Lightfoot
- KAUST Environmental Epigenetic Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Celia Schunter
- KAUST Environmental Epigenetic Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Craig T Michell
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Hajime Ohyanagi
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Katsuhiko Mineta
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Sylvain Foret
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.,Evolution, Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Michael L Berumen
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Manuel Aranda
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Philip L Munday
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Timothy Ravasi
- KAUST Environmental Epigenetic Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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360
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Xu S, Xiao S, Zhu S, Zeng X, Luo J, Liu J, Gao T, Chen N. A draft genome assembly of the Chinese sillago (Sillago sinica), the first reference genome for Sillaginidae fishes. Gigascience 2018; 7:5094561. [PMID: 30202912 PMCID: PMC6143730 DOI: 10.1093/gigascience/giy108] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/21/2018] [Accepted: 08/21/2018] [Indexed: 11/15/2022] Open
Abstract
Background Sillaginidae, also known as smelt-whitings, is a family of benthic coastal marine fishes in the Indo-West Pacific that have high ecological and economic importance. Many Sillaginidae species, including the Chinese sillago (Sillago sinica), have been recently described in China, providing valuable material to analyze genetic diversification of the family Sillaginidae. Here, we constructed a reference genome for the Chinese sillago, with the aim to set up a platform for comparative analysis of all species in this family. Findings Using the single-molecule real-time DNA sequencing platform Pacific Biosciences (PacBio) Sequel, we generated ∼27.3 Gb genomic DNA sequences for the Chinese sillago. We reconstructed a genome assembly of 534 Mb using a strategy that takes advantage of complementary strengths of two genome assembly programs, Canu and FALCON. The genome size was consistent with the estimated genome size based on k-mer analysis. The assembled genome consisted of 802 contigs with a contig N50 length of 2.6 Mb. We annotated 22,122 protein-coding genes in the Chinese sillago genomes using a de novo method as well as RNA sequencing data and homologies to other teleosts. According to the phylogenetic analysis using protein-coding genes, the Chinese sillago is closely related to Larimichthys crocea and Dicentrarchus labrax and diverged from their ancestor around 69.5-82.6 million years ago. Conclusions Using long reads generated with PacBio sequencing technology, we have built a draft genome assembly for the Chinese sillago, which is the first reference genome for Sillaginidae species. This genome assembly sets a stage for comparative analysis of the diversification and adaptation of fishes in Sillaginidae.
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Affiliation(s)
- Shengyong Xu
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang316022, China
| | - Shijun Xiao
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, Hubei 430075, China
| | - Shilin Zhu
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, Hubei 430075, China
| | - Xiaofei Zeng
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, Hubei 430075, China
| | - Jing Luo
- School of Life Sciences, Yunnan University, Kunming, Yunnan 650500, China
| | - Jiaqi Liu
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, Hubei 430075, China
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang316022, China
| | - Nansheng Chen
- CAS Key laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, China
- Laboratoryfor Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
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361
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Guo L, Winzer T, Yang X, Li Y, Ning Z, He Z, Teodor R, Lu Y, Bowser TA, Graham IA, Ye K. The opium poppy genome and morphinan production. Science 2018; 362:343-347. [PMID: 30166436 DOI: 10.1126/science.aat4096] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 05/26/2018] [Accepted: 08/21/2018] [Indexed: 12/14/2022]
Abstract
Morphinan-based painkillers are derived from opium poppy (Papaver somniferum L.). We report a draft of the opium poppy genome, with 2.72 gigabases assembled into 11 chromosomes with contig N50 and scaffold N50 of 1.77 and 204 megabases, respectively. Synteny analysis suggests a whole-genome duplication at ~7.8 million years ago and ancient segmental or whole-genome duplication(s) that occurred before the Papaveraceae-Ranunculaceae divergence 110 million years ago. Syntenic blocks representative of phthalideisoquinoline and morphinan components of a benzylisoquinoline alkaloid cluster of 15 genes provide insight into how this cluster evolved. Paralog analysis identified P450 and oxidoreductase genes that combined to form the STORR gene fusion essential for morphinan biosynthesis in opium poppy. Thus, gene duplication, rearrangement, and fusion events have led to evolution of specialized metabolic products in opium poppy.
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Affiliation(s)
- Li Guo
- MOE Key Lab for Intelligent Networks and Networks Security, School of Electronics and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049 China.,The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061 China.,The School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049 China
| | - Thilo Winzer
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Xiaofei Yang
- MOE Key Lab for Intelligent Networks and Networks Security, School of Electronics and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049 China.,Computer Science Department, School of Electronics and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049 China
| | - Yi Li
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Zemin Ning
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Zhesi He
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Roxana Teodor
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Ying Lu
- Shanghai Ocean University, Shanghai, 201306 China
| | - Tim A Bowser
- Sun Pharmaceutical Industries Australia, Princes Highway, Port Fairy, VIC 3284, Australia
| | - Ian A Graham
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK.
| | - Kai Ye
- MOE Key Lab for Intelligent Networks and Networks Security, School of Electronics and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049 China. .,The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061 China.,The School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049 China.,Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
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362
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Discovery of a novel species, Theileria haneyi n. sp., infective to equids, highlights exceptional genomic diversity within the genus Theileria: implications for apicomplexan parasite surveillance. Int J Parasitol 2018; 48:679-690. [DOI: 10.1016/j.ijpara.2018.03.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 03/12/2018] [Accepted: 03/22/2018] [Indexed: 01/29/2023]
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363
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De novo assembly of a young Drosophila Y chromosome using single-molecule sequencing and chromatin conformation capture. PLoS Biol 2018; 16:e2006348. [PMID: 30059545 PMCID: PMC6117089 DOI: 10.1371/journal.pbio.2006348] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 08/30/2018] [Accepted: 07/04/2018] [Indexed: 01/27/2023] Open
Abstract
While short-read sequencing technology has resulted in a sharp increase in the number of species with genome assemblies, these assemblies are typically highly fragmented. Repeats pose the largest challenge for reference genome assembly, and pericentromeric regions and the repeat-rich Y chromosome are typically ignored from sequencing projects. Here, we assemble the genome of Drosophila miranda using long reads for contig formation, chromatin interaction maps for scaffolding and short reads, and optical mapping and bacterial artificial chromosome (BAC) clone sequencing for consensus validation. Our assembly recovers entire chromosomes and contains large fractions of repetitive DNA, including about 41.5 Mb of pericentromeric and telomeric regions, and >100 Mb of the recently formed highly repetitive neo-Y chromosome. While Y chromosome evolution is typically characterized by global sequence loss and shrinkage, the neo-Y increased in size by almost 3-fold because of the accumulation of repetitive sequences. Our high-quality assembly allows us to reconstruct the chromosomal events that have led to the unusual sex chromosome karyotype in D. miranda, including the independent de novo formation of a pair of sex chromosomes at two distinct time points, or the reversion of a former Y chromosome to an autosome.
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364
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Kamm K, Osigus HJ, Stadler PF, DeSalle R, Schierwater B. Trichoplax genomes reveal profound admixture and suggest stable wild populations without bisexual reproduction. Sci Rep 2018; 8:11168. [PMID: 30042472 PMCID: PMC6057997 DOI: 10.1038/s41598-018-29400-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/09/2018] [Indexed: 12/24/2022] Open
Abstract
The phylum Placozoa officially consists of only a single described species, Trichoplax adhaerens, although several lineages can be separated by molecular markers, geographical distributions and environmental demands. The placozoan 16S haplotype H2 (Trichoplax sp. H2) is the most robust and cosmopolitan lineage of placozoans found to date. In this study, its genome was found to be distinct but highly related to the Trichoplax adhaerens reference genome, for remarkably unique reasons. The pattern of variation and allele distribution between the two lineages suggests that both originate from a single interbreeding event in the wild, dating back at least several decades ago, and both seem not to have engaged in sexual reproduction since. We conclude that populations of certain placozoan haplotypes remain stable for long periods without bisexual reproduction. Furthermore, allelic variation within and between the two Trichoplax lineages indicates that successful bisexual reproduction between related placozoan lineages might serve to either counter accumulated negative somatic mutations or to cope with changing environmental conditions. On the other hand, enrichment of neutral or beneficial somatic mutations by vegetative reproduction, combined with rare sexual reproduction, could instantaneously boost genetic variation, generating novel ecotypes and eventually species.
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Affiliation(s)
- Kai Kamm
- University of Veterinary Medicine Hannover, Foundation, ITZ Ecology and Evolution, Bünteweg 17d, D-30559, Hannover, Germany.
| | - Hans-Jürgen Osigus
- University of Veterinary Medicine Hannover, Foundation, ITZ Ecology and Evolution, Bünteweg 17d, D-30559, Hannover, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Bernd Schierwater
- University of Veterinary Medicine Hannover, Foundation, ITZ Ecology and Evolution, Bünteweg 17d, D-30559, Hannover, Germany. .,Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, USA. .,Yale University, Molecular, Cellular and Developmental Biology, New Haven, CT, 06520, USA.
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365
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Xu Z, Xin T, Bartels D, Li Y, Gu W, Yao H, Liu S, Yu H, Pu X, Zhou J, Xu J, Xi C, Lei H, Song J, Chen S. Genome Analysis of the Ancient Tracheophyte Selaginella tamariscina Reveals Evolutionary Features Relevant to the Acquisition of Desiccation Tolerance. MOLECULAR PLANT 2018; 11:983-994. [PMID: 29777775 DOI: 10.1016/j.molp.2018.05.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 04/30/2018] [Accepted: 05/07/2018] [Indexed: 05/18/2023]
Abstract
Resurrection plants, which are the "gifts" of natural evolution, are ideal models for studying the genetic basis of plant desiccation tolerance. Here, we report a high-quality genome assembly of 301 Mb for the diploid spike moss Selaginella tamariscina, a primitive vascular resurrection plant. We predicated 27 761 protein-coding genes from the assembled S. tamariscina genome, 11.38% (2363) of which showed significant expression changes in response to desiccation. Approximately 60.58% of the S. tamariscina genome was annotated as repetitive DNA, which is an almost 2-fold increase of that in the genome of desiccation-sensitive Selaginella moellendorffii. Genomic and transcriptomic analyses highlight the unique evolution and complex regulations of the desiccation response in S. tamariscina, including species-specific expansion of the oleosin and pentatricopeptide repeat gene families, unique genes and pathways for reactive oxygen species generation and scavenging, and enhanced abscisic acid (ABA) biosynthesis and potentially distinct regulation of ABA signaling and response. Comparative analysis of chloroplast genomes of several Selaginella species revealed a unique structural rearrangement and the complete loss of chloroplast NAD(P)H dehydrogenase (NDH) genes in S. tamariscina, suggesting a link between the absence of the NDH complex and desiccation tolerance. Taken together, our comparative genomic and transcriptomic analyses reveal common and species-specific desiccation tolerance strategies in S. tamariscina, providing significant insights into the desiccation tolerance mechanism and the evolution of resurrection plants.
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Affiliation(s)
- Zhichao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Tianyi Xin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Dorothea Bartels
- Institute of Molecular Plant Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Ying Li
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Wei Gu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Hui Yao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Sai Liu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Haoying Yu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Xiangdong Pu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Jianguo Zhou
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Caicai Xi
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Hetian Lei
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China.
| | - Shilin Chen
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China; Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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366
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Hoffberg SL, Troendle NJ, Glenn TC, Mahmud O, Louha S, Chalopin D, Bennetzen JL, Mauricio R. A High-Quality Reference Genome for the Invasive Mosquitofish Gambusia affinis Using a Chicago Library. G3 (BETHESDA, MD.) 2018; 8:1855-1861. [PMID: 29703783 PMCID: PMC5982815 DOI: 10.1534/g3.118.200101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/19/2018] [Indexed: 11/18/2022]
Abstract
The western mosquitofish, Gambusia affinis, is a freshwater poecilid fish native to the southeastern United States but with a global distribution due to widespread human introduction. Gambusia affinis has been used as a model species for a broad range of evolutionary and ecological studies. We sequenced the genome of a male G. affinis to facilitate genetic studies in diverse fields including invasion biology and comparative genetics. We generated Illumina short read data from paired-end libraries and in vitro proximity-ligation libraries. We obtained 54.9× coverage, N50 contig length of 17.6 kb, and N50 scaffold length of 6.65 Mb. Compared to two other species in the Poeciliidae family, G. affinis has slightly fewer genes that have shorter total, exon, and intron length on average. Using a set of universal single-copy orthologs in fish genomes, we found 95.5% of these genes were complete in the G. affinis assembly. The number of transposable elements in the G. affinis assembly is similar to those of closely related species. The high-quality genome sequence and annotations we report will be valuable resources for scientists to map the genetic architecture of traits of interest in this species.
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Affiliation(s)
| | | | - Travis C Glenn
- Department of Genetics
- Department of Environmental Health Science
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602
| | - Ousman Mahmud
- Department of Genetics
- Department of Computational Biology
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105
| | - Swarnali Louha
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602
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367
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Yin C, Li M, Hu J, Lang K, Chen Q, Liu J, Guo D, He K, Dong Y, Luo J, Song Z, Walters JR, Zhang W, Li F, Chen X. The genomic features of parasitism, Polyembryony and immune evasion in the endoparasitic wasp Macrocentrus cingulum. BMC Genomics 2018; 19:420. [PMID: 29848290 PMCID: PMC5977540 DOI: 10.1186/s12864-018-4783-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 05/11/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Parasitoid wasps are well-known natural enemies of major agricultural pests and arthropod borne diseases. The parasitoid wasp Macrocentrus cingulum (Hymenoptera: Braconidae) has been widely used to control the notorious insect pests Ostrinia furnacalis (Asian Corn Borer) and O. nubilalis (European corn borer). One striking phenomenon exhibited by M. cingulum is polyembryony, the formation of multiple genetically identical offspring from a single zygote. Moreover, M. cingulum employs a passive parasitic strategy by preventing the host's immune system from recognizing the embryo as a foreign body. Thus, the embryos evade the host's immune system and are not encapsulated by host hemocytes. Unfortunately, the mechanism of both polyembryony and immune evasion remains largely unknown. RESULTS We report the genome of the parasitoid wasp M. cingulum. Comparative genomics analysis of M. cingulum and other 11 insects were conducted, finding some gene families with apparent expansion or contraction which might be linked to the parasitic behaviors or polyembryony of M. cingulum. Moreover, we present the evidence that the microRNA miR-14b regulates the polyembryonic development of M. cingulum by targeting the c-Myc Promoter-binding Protein 1 (MBP-1), histone-lysine N-methyltransferase 2E (KMT2E) and segmentation protein Runt. In addition, Hemomucin, an O-glycosylated transmembrane protein, protects the endoparasitoid wasp larvae from being encapsulated by host hemocytes. Motif and domain analysis showed that only the hemomucin in two endoparasitoids, M. cingulum and Venturia canescens, possessing the ability of passive immune evasion has intact mucin domain and similar O-glycosylation patterns, indicating that the hemomucin is a key factor modulating the immune evasion. CONCLUSIONS The microRNA miR-14b participates in the regulation of polyembryonic development, and the O-glycosylation of the mucin domain in the hemomucin confers the passive immune evasion in this wasp. These key findings provide new insights into the polyembryony and immune evasion.
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Affiliation(s)
- Chuanlin Yin
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Meizhen Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Jian Hu
- State Key Laboratory of Biocontrol, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275 China
| | - Kun Lang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Qiming Chen
- State Key Laboratory of Biocontrol, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275 China
| | - Jinding Liu
- College of Information Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 China
| | - Dianhao Guo
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 China
| | - Kang He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Yipei Dong
- State Key Laboratory of Biocontrol, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275 China
| | - Jiapeng Luo
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Zhenkun Song
- State Key Laboratory of Biocontrol, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275 China
| | - James R. Walters
- Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66046 USA
| | - Wenqing Zhang
- State Key Laboratory of Biocontrol, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275 China
| | - Fei Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Xuexin Chen
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
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368
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Rupp O, MacDonald ML, Li S, Dhiman H, Polson S, Griep S, Heffner K, Hernandez I, Brinkrolf K, Jadhav V, Samoudi M, Hao H, Kingham B, Goesmann A, Betenbaugh MJ, Lewis NE, Borth N, Lee KH. A reference genome of the Chinese hamster based on a hybrid assembly strategy. Biotechnol Bioeng 2018; 115:2087-2100. [PMID: 29704459 PMCID: PMC6045439 DOI: 10.1002/bit.26722] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/13/2018] [Accepted: 04/25/2018] [Indexed: 12/20/2022]
Abstract
Accurate and complete genome sequences are essential in biotechnology to facilitate genome‐based cell engineering efforts. The current genome assemblies for Cricetulus griseus, the Chinese hamster, are fragmented and replete with gap sequences and misassemblies, consistent with most short‐read‐based assemblies. Here, we completely resequenced C. griseus using single molecule real time sequencing and merged this with Illumina‐based assemblies. This generated a more contiguous and complete genome assembly than either technology alone, reducing the number of scaffolds by >28‐fold, with 90% of the sequence in the 122 longest scaffolds. Most genes are now found in single scaffolds, including up‐ and downstream regulatory elements, enabling improved study of noncoding regions. With >95% of the gap sequence filled, important Chinese hamster ovary cell mutations have been detected in draft assembly gaps. This new assembly will be an invaluable resource for continued basic and pharmaceutical research.
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Affiliation(s)
- Oliver Rupp
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Madolyn L MacDonald
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware.,Delaware Biotechnology Institute, Newark, Delaware
| | - Shangzhong Li
- Department of Bioengineering, University of California, San Diego, California.,Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, California
| | - Heena Dhiman
- Austrian Center of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Shawn Polson
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware.,Delaware Biotechnology Institute, Newark, Delaware
| | - Sven Griep
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Kelley Heffner
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Inmaculada Hernandez
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Karina Brinkrolf
- Department of Biorescources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Vaibhav Jadhav
- Austrian Center of Industrial Biotechnology, Vienna, Austria
| | - Mojtaba Samoudi
- Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, California.,Department of Pediatrics, University of California, San Diego, California
| | - Haiping Hao
- Johns Hopkins University Deep Sequencing and Microarray Core, Johns Hopkins University, Baltimore, Maryland
| | | | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Michael J Betenbaugh
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Nathan E Lewis
- Department of Bioengineering, University of California, San Diego, California.,Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, California.,Department of Pediatrics, University of California, San Diego, California
| | - Nicole Borth
- Austrian Center of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Kelvin H Lee
- Delaware Biotechnology Institute, Newark, Delaware.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware
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369
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An improved assembly and annotation of the melon (Cucumis melo L.) reference genome. Sci Rep 2018; 8:8088. [PMID: 29795526 PMCID: PMC5967340 DOI: 10.1038/s41598-018-26416-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/09/2018] [Indexed: 12/20/2022] Open
Abstract
We report an improved assembly (v3.6.1) of the melon (Cucumis melo L.) genome and a new genome annotation (v4.0). The optical mapping approach allowed correcting the order and the orientation of 21 previous scaffolds and permitted to correctly define the gap-size extension along the 12 pseudomolecules. A new comprehensive annotation was also built in order to update the previous annotation v3.5.1, released more than six years ago. Using an integrative annotation pipeline, based on exhaustive RNA-Seq collections and ad-hoc transposable element annotation, we identified 29,980 protein-coding loci. Compared to the previous version, the v4.0 annotation improved gene models in terms of completeness of gene structure, UTR regions definition, intron-exon junctions and reduction of fragmented genes. More than 8,000 new genes were identified, one third of them being well supported by RNA-Seq data. To make all the new resources easily exploitable and completely available for the scientific community, a redesigned Melonomics genomic platform was released at http://melonomics.net. The resources produced in this work considerably increase the reliability of the melon genome assembly and resolution of the gene models paving the way for further studies in melon and related species.
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370
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Frantzeskakis L, Kracher B, Kusch S, Yoshikawa-Maekawa M, Bauer S, Pedersen C, Spanu PD, Maekawa T, Schulze-Lefert P, Panstruga R. Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen. BMC Genomics 2018; 19:381. [PMID: 29788921 PMCID: PMC5964911 DOI: 10.1186/s12864-018-4750-6] [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: 01/16/2018] [Accepted: 05/02/2018] [Indexed: 12/30/2022] Open
Abstract
Background Powdery mildews are biotrophic pathogenic fungi infecting a number of economically important plants. The grass powdery mildew, Blumeria graminis, has become a model organism to study host specialization of obligate biotrophic fungal pathogens. We resolved the large-scale genomic architecture of B. graminis forma specialis hordei (Bgh) to explore the potential influence of its genome organization on the co-evolutionary process with its host plant, barley (Hordeum vulgare). Results The near-chromosome level assemblies of the Bgh reference isolate DH14 and one of the most diversified isolates, RACE1, enabled a comparative analysis of these haploid genomes, which are highly enriched with transposable elements (TEs). We found largely retained genome synteny and gene repertoires, yet detected copy number variation (CNV) of secretion signal peptide-containing protein-coding genes (SPs) and locally disrupted synteny blocks. Genes coding for sequence-related SPs are often locally clustered, but neither the SPs nor the TEs reside preferentially in genomic regions with unique features. Extended comparative analysis with different host-specific B. graminis formae speciales revealed the existence of a core suite of SPs, but also isolate-specific SP sets as well as congruence of SP CNV and phylogenetic relationship. We further detected evidence for a recent, lineage-specific expansion of TEs in the Bgh genome. Conclusions The characteristics of the Bgh genome (largely retained synteny, CNV of SP genes, recently proliferated TEs and a lack of significant compartmentalization) are consistent with a “one-speed” genome that differs in its architecture and (co-)evolutionary pattern from the “two-speed” genomes reported for several other filamentous phytopathogens. Electronic supplementary material The online version of this article (10.1186/s12864-018-4750-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lamprinos Frantzeskakis
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Barbara Kracher
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Stefan Kusch
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Makoto Yoshikawa-Maekawa
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Saskia Bauer
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Carsten Pedersen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Pietro D Spanu
- Imperial College, Department of Life Sciences, Sir Alexander Fleming Building, London, SW7 2AZ, UK
| | - Takaki Maekawa
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
| | - Paul Schulze-Lefert
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
| | - Ralph Panstruga
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany.
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371
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Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast. BMC Genomics 2018; 19:364. [PMID: 29764372 PMCID: PMC5952469 DOI: 10.1186/s12864-018-4751-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/02/2018] [Indexed: 12/31/2022] Open
Abstract
Background The black yeast Hortaea werneckii (Dothideomycetes, Ascomycota) is one of the most extremely halotolerant fungi, capable of growth at NaCl concentrations close to saturation. Although dothideomycetous fungi are typically haploid, the reference H. werneckii strain has a diploid genome consisting of two subgenomes with a high level of heterozygosity. Results In order to explain the origin of the H. werneckii diploid genome we here report the genome sequencing of eleven strains isolated from different habitats and geographic locations. Comparison of nine diploid and two haploid strains showed that the reference genome was likely formed by hybridization between two haploids and not by endoreduplication as suggested previously. Results also support additional hybridization events in the evolutionary history of investigated strains, however exchange of genetic material in the species otherwise appears to be rare. Possible links between such unusual reproduction and the extremotolerance of H. werneckii remain to be investigated. Conclusions H. werneckii appears to be able to form persistent haploid as well as diploid strains, is capable of occasional hybridization between relatively heterozygous haploids, but is otherwise limited to clonal reproduction. The reported data and the first identification of haploid H. werneckii strains establish this species as a good model for studying the effects of ploidy and hybridization in an extremotolerant system unperturbed by frequent genetic recombination. Electronic supplementary material The online version of this article (10.1186/s12864-018-4751-5) contains supplementary material, which is available to authorized users.
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372
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Tørresen OK, Brieuc MSO, Solbakken MH, Sørhus E, Nederbragt AJ, Jakobsen KS, Meier S, Edvardsen RB, Jentoft S. Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats. BMC Genomics 2018; 19:240. [PMID: 29636006 PMCID: PMC5894186 DOI: 10.1186/s12864-018-4616-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 03/22/2018] [Indexed: 02/06/2023] Open
Abstract
Background Increased availability of genome assemblies for non-model organisms has resulted in invaluable biological and genomic insight into numerous vertebrates, including teleosts. Sequencing of the Atlantic cod (Gadus morhua) genome and the genomes of many of its relatives (Gadiformes) demonstrated a shared loss of the major histocompatibility complex (MHC) II genes 100 million years ago. An improved version of the Atlantic cod genome assembly shows an extreme density of tandem repeats compared to other vertebrate genome assemblies. Highly contiguous assemblies are therefore needed to further investigate the unusual immune system of the Gadiformes, and whether the high density of tandem repeats found in Atlantic cod is a shared trait in this group. Results Here, we have sequenced and assembled the genome of haddock (Melanogrammus aeglefinus) – a relative of Atlantic cod – using a combination of PacBio and Illumina reads. Comparative analyses reveal that the haddock genome contains an even higher density of tandem repeats outside and within protein coding sequences than Atlantic cod. Further, both species show an elevated number of tandem repeats in genes mainly involved in signal transduction compared to other teleosts. A characterization of the immune gene repertoire demonstrates a substantial expansion of MCHI in Atlantic cod compared to haddock. In contrast, the Toll-like receptors show a similar pattern of gene losses and expansions. For the NOD-like receptors (NLRs), another gene family associated with the innate immune system, we find a large expansion common to all teleosts, with possible lineage-specific expansions in zebrafish, stickleback and the codfishes. Conclusions The generation of a highly contiguous genome assembly of haddock revealed that the high density of short tandem repeats as well as expanded immune gene families is not unique to Atlantic cod – but possibly a feature common to all, or most, codfishes. A shared expansion of NLR genes in teleosts suggests that the NLRs have a more substantial role in the innate immunity of teleosts than other vertebrates. Moreover, we find that high copy number genes combined with variable genome assembly qualities may impede complete characterization of these genes, i.e. the number of NLRs in different teleost species might be underestimates. Electronic supplementary material The online version of this article (10.1186/s12864-018-4616-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ole K Tørresen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway.
| | - Marine S O Brieuc
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Monica H Solbakken
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Elin Sørhus
- Institute of Marine Research, Bergen, Norway
| | - Alexander J Nederbragt
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway.,Biomedical Informatics Research Group, Department of Informatics, University of Oslo, Oslo, Norway
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | | | | | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway.
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373
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Guarnieri MT, Levering J, Henard CA, Boore JL, Betenbaugh MJ, Zengler K, Knoshaug EP. Genome Sequence of the Oleaginous Green Alga, Chlorella vulgaris UTEX 395. Front Bioeng Biotechnol 2018; 6:37. [PMID: 29675409 PMCID: PMC5895722 DOI: 10.3389/fbioe.2018.00037] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 03/19/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Michael T Guarnieri
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Jennifer Levering
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
| | - Calvin A Henard
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
| | | | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Karsten Zengler
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
| | - Eric P Knoshaug
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
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374
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Lie KK, Tørresen OK, Solbakken MH, Rønnestad I, Tooming-Klunderud A, Nederbragt AJ, Jentoft S, Sæle Ø. Loss of stomach, loss of appetite? Sequencing of the ballan wrasse (Labrus bergylta) genome and intestinal transcriptomic profiling illuminate the evolution of loss of stomach function in fish. BMC Genomics 2018; 19:186. [PMID: 29510660 PMCID: PMC5840709 DOI: 10.1186/s12864-018-4570-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 02/28/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The ballan wrasse (Labrus bergylta) belongs to a large teleost family containing more than 600 species showing several unique evolutionary traits such as lack of stomach and hermaphroditism. Agastric fish are found throughout the teleost phylogeny, in quite diverse and unrelated lineages, indicating stomach loss has occurred independently multiple times in the course of evolution. By assembling the ballan wrasse genome and transcriptome we aimed to determine the genetic basis for its digestive system function and appetite regulation. Among other, this knowledge will aid the formulation of aquaculture diets that meet the nutritional needs of agastric species. RESULTS Long and short read sequencing technologies were combined to generate a ballan wrasse genome of 805 Mbp. Analysis of the genome and transcriptome assemblies confirmed the absence of genes that code for proteins involved in gastric function. The gene coding for the appetite stimulating protein ghrelin was also absent in wrasse. Gene synteny mapping identified several appetite-controlling genes and their paralogs previously undescribed in fish. Transcriptome profiling along the length of the intestine found a declining expression gradient from the anterior to the posterior, and a distinct expression profile in the hind gut. CONCLUSIONS We showed gene loss has occurred for all known genes related to stomach function in the ballan wrasse, while the remaining functions of the digestive tract appear intact. The results also show appetite control in ballan wrasse has undergone substantial changes. The loss of ghrelin suggests that other genes, such as motilin, may play a ghrelin like role. The wrasse genome offers novel insight in to the evolutionary traits of this large family. As the stomach plays a major role in protein digestion, the lack of genes related to stomach digestion in wrasse suggests it requires formulated diets with higher levels of readily digestible protein than those for gastric species.
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Affiliation(s)
- Kai K. Lie
- Institute of Marine Research, P.O. Box. 1870, Nordnes, 5817 Bergen, NO Norway
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, 0316 Oslo, NO Norway
| | - Monica Hongrø Solbakken
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, 0316 Oslo, NO Norway
| | - Ivar Rønnestad
- Department of Biology, University of Bergen, P.O. Box 7803, 5020 Bergen, NO Norway
| | - Ave Tooming-Klunderud
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, 0316 Oslo, NO Norway
| | - Alexander J. Nederbragt
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, 0316 Oslo, NO Norway
- Biomedical Informatics Research Group, Department of Informatics, University of Oslo, P.O. Box 1066, Blindern, 0316 Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, 0316 Oslo, NO Norway
| | - Øystein Sæle
- Institute of Marine Research, P.O. Box. 1870, Nordnes, 5817 Bergen, NO Norway
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375
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Clonal genome evolution and rapid invasive spread of the marbled crayfish. Nat Ecol Evol 2018; 2:567-573. [DOI: 10.1038/s41559-018-0467-9] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 01/04/2018] [Indexed: 12/22/2022]
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376
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Fu Y, Yang Y, Zhang H, Farley G, Wang J, Quarles KA, Weng Z, Zamore PD. The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology. eLife 2018; 7:31628. [PMID: 29376823 PMCID: PMC5844692 DOI: 10.7554/elife.31628] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 01/26/2018] [Indexed: 12/30/2022] Open
Abstract
We report a draft assembly of the genome of Hi5 cells from the lepidopteran insect pest, Trichoplusia ni, assigning 90.6% of bases to one of 28 chromosomes and predicting 14,037 protein-coding genes. Chemoreception and detoxification gene families reveal T. ni-specific gene expansions that may explain its widespread distribution and rapid adaptation to insecticides. Transcriptome and small RNA data from thorax, ovary, testis, and the germline-derived Hi5 cell line show distinct expression profiles for 295 microRNA- and >393 piRNA-producing loci, as well as 39 genes encoding small RNA pathway proteins. Nearly all of the W chromosome is devoted to piRNA production, and T. ni siRNAs are not 2´-O-methylated. To enable use of Hi5 cells as a model system, we have established genome editing and single-cell cloning protocols. The T. ni genome provides insights into pest control and allows Hi5 cells to become a new tool for studying small RNAs ex vivo. A common moth called the cabbage looper is becoming increasingly relevant to the scientific community. Its caterpillars are a serious threat to cabbage, broccoli and cauliflower crops, and they have started to resist the pesticides normally used to control them. Moreover, the insect’s germline cells – the ones that will produce sperm and eggs – are used in laboratories as ‘factories’ to artificially produce proteins of interest. The germline cells also host a group of genetic mechanisms called RNA silencing. One of these processes is known as piRNA, and it protects the genome against ‘jumping genes’. These genetic elements can cause mutations by moving from place to place in the DNA: in germline cells, piRNA suppresses them before the genetic information is transmitted to the next generation. Not all germline cells grow equally well under experimental conditions, or are easy to use to examine piRNA mechanisms in a laboratory. The germline cells from the cabbage looper, on the other hand, have certain characteristics that would make them ideal to study piRNA in insects. However, the genome of the moth had not yet been fully resolved. This hinders research on new ways of controlling the pest, on how to use the germline cells to produce more useful proteins, or on piRNA. Decoding a genome requires several steps. First, the entire genetic information is broken in short sections that can then be deciphered. Next, these segments need to be ‘assembled’ – put together, and in the right order, to reconstitute the entire genome. Certain portions of the genome, which are formed of repeats of the same sections, can be difficult to assemble. Finally, the genome must be annotated: the different regions – such as the genes – need to be identified and labeled. Here, Fu et al. assembled and annotated the genome of the cabbage looper, and in the process developed strategies that could be used for other species with a lot of repeated sequences in their genomes. Having access to the looper’s full genetic information makes it possible to use their germline cells to produce new types of proteins, for example for pharmaceutical purposes. Fu et al. went on to make working with these cells even easier by refining protocols so that modern research techniques, such as the gene-editing technology CRISPR-Cas9, can be used on the looper germline cells. The mapping of the genome also revealed that the genes involved in removing toxins from the insects’ bodies are rapidly evolving, which may explain why the moths readily become resistant to insecticides. This knowledge could help finding new ways of controlling the pest. Finally, the genes involved in RNA silencing were labeled: results show that an entire chromosome is the source of piRNAs. Combined with the new protocols developed by Fu et al., this could make cabbage looper germline cells the default option for any research into the piRNA mechanism. How piRNA works in the moth could inform work on human piRNA, as these processes are highly similar across the animal kingdom.
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Affiliation(s)
- Yu Fu
- Bioinformatics Program, Boston University, Boston, United States.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States
| | - Yujing Yang
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
| | - Han Zhang
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
| | - Gwen Farley
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
| | - Junling Wang
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
| | - Kaycee A Quarles
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States
| | - Phillip D Zamore
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
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377
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Tkavc R, Matrosova VY, Grichenko OE, Gostinčar C, Volpe RP, Klimenkova P, Gaidamakova EK, Zhou CE, Stewart BJ, Lyman MG, Malfatti SA, Rubinfeld B, Courtot M, Singh J, Dalgard CL, Hamilton T, Frey KG, Gunde-Cimerman N, Dugan L, Daly MJ. Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149. Front Microbiol 2018; 8:2528. [PMID: 29375494 PMCID: PMC5766836 DOI: 10.3389/fmicb.2017.02528] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/05/2017] [Indexed: 02/03/2023] Open
Abstract
Highly concentrated radionuclide waste produced during the Cold War era is stored at US Department of Energy (DOE) production sites. This radioactive waste was often highly acidic and mixed with heavy metals, and has been leaking into the environment since the 1950s. Because of the danger and expense of cleanup of such radioactive sites by physicochemical processes, in situ bioremediation methods are being developed for cleanup of contaminated ground and groundwater. To date, the most developed microbial treatment proposed for high-level radioactive sites employs the radiation-resistant bacterium Deinococcus radiodurans. However, the use of Deinococcus spp. and other bacteria is limited by their sensitivity to low pH. We report the characterization of 27 diverse environmental yeasts for their resistance to ionizing radiation (chronic and acute), heavy metals, pH minima, temperature maxima and optima, and their ability to form biofilms. Remarkably, many yeasts are extremely resistant to ionizing radiation and heavy metals. They also excrete carboxylic acids and are exceptionally tolerant to low pH. A special focus is placed on Rhodotorula taiwanensis MD1149, which was the most resistant to acid and gamma radiation. MD1149 is capable of growing under 66 Gy/h at pH 2.3 and in the presence of high concentrations of mercury and chromium compounds, and forming biofilms under high-level chronic radiation and low pH. We present the whole genome sequence and annotation of R. taiwanensis strain MD1149, with a comparison to other Rhodotorula species. This survey elevates yeasts to the frontier of biology's most radiation-resistant representatives, presenting a strong rationale for a role of fungi in bioremediation of acidic radioactive waste sites.
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Affiliation(s)
- Rok Tkavc
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Vera Y Matrosova
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Olga E Grichenko
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Robert P Volpe
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Polina Klimenkova
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Elena K Gaidamakova
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Carol E Zhou
- Lawrence Livermore National Laboratory, Computing Applications and Research Department, Livermore, CA, United States
| | - Benjamin J Stewart
- Biosciences and Biotechnology Division, Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Mathew G Lyman
- Biosciences and Biotechnology Division, Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Stephanie A Malfatti
- Biosciences and Biotechnology Division, Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Bonnee Rubinfeld
- Biosciences and Biotechnology Division, Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Melanie Courtot
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - Jatinder Singh
- Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Clifton L Dalgard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,The American Genome Center, Bethesda, MD, United States
| | - Theron Hamilton
- Biological Defense Research Directorate, Naval Medical Research Center, Fredrick, MD, United States
| | - Kenneth G Frey
- Biological Defense Research Directorate, Naval Medical Research Center, Fredrick, MD, United States
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Lawrence Dugan
- Biosciences and Biotechnology Division, Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Michael J Daly
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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378
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Bana NÁ, Nyiri A, Nagy J, Frank K, Nagy T, Stéger V, Schiller M, Lakatos P, Sugár L, Horn P, Barta E, Orosz L. The red deer Cervus elaphus genome CerEla1.0: sequencing, annotating, genes, and chromosomes. Mol Genet Genomics 2018; 293:665-684. [PMID: 29294181 DOI: 10.1007/s00438-017-1412-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 12/19/2017] [Indexed: 12/22/2022]
Abstract
We present here the de novo genome assembly CerEla1.0 for the red deer, Cervus elaphus, an emblematic member of the natural megafauna of the Northern Hemisphere. Humans spread the species in the South. Today, the red deer is also a farm-bred animal and is becoming a model animal in biomedical and population studies. Stag DNA was sequenced at 74× coverage by Illumina technology. The ALLPATHS-LG assembly of the reads resulted in 34.7 × 103 scaffolds, 26.1 × 103 of which were utilized in Cer.Ela1.0. The assembly spans 3.4 Gbp. For building the red deer pseudochromosomes, a pre-established genetic map was used for main anchor points. A nearly complete co-linearity was found between the mapmarker sequences of the deer genetic map and the order and orientation of the orthologous sequences in the syntenic bovine regions. Syntenies were also conserved at the in-scaffold level. The cM distances corresponded to 1.34 Mbp uniformly along the deer genome. Chromosomal rearrangements between deer and cattle were demonstrated. 2.8 × 106 SNPs, 365 × 103 indels and 19368 protein-coding genes were identified in CerEla1.0, along with positions for centromerons. CerEla1.0 demonstrates the utilization of dual references, i.e., when a target genome (here C. elaphus) already has a pre-established genetic map, and is combined with the well-established whole genome sequence of a closely related species (here Bos taurus). Genome-wide association studies (GWAS) that CerEla1.0 (NCBI, MKHE00000000) could serve for are discussed.
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Affiliation(s)
- Nóra Á Bana
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Szent-Györgyi Albert str. 4, Gödöllő, 2100, Hungary.,Department of Animal Breeding Technology and Management Faculty of Agricultural and Environmental Sciences, Kaposvár University, Guba Sándor str. 40, Kaposvár, 7400, Hungary
| | - Anna Nyiri
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Szent-Györgyi Albert str. 4, Gödöllő, 2100, Hungary
| | - János Nagy
- Department of Animal Breeding Technology and Management Faculty of Agricultural and Environmental Sciences, Kaposvár University, Guba Sándor str. 40, Kaposvár, 7400, Hungary
| | - Krisztián Frank
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Szent-Györgyi Albert str. 4, Gödöllő, 2100, Hungary.,Department of Animal Breeding Technology and Management Faculty of Agricultural and Environmental Sciences, Kaposvár University, Guba Sándor str. 40, Kaposvár, 7400, Hungary
| | - Tibor Nagy
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Szent-Györgyi Albert str. 4, Gödöllő, 2100, Hungary
| | - Viktor Stéger
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Szent-Györgyi Albert str. 4, Gödöllő, 2100, Hungary
| | - Mátyás Schiller
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Szent-Györgyi Albert str. 4, Gödöllő, 2100, Hungary
| | - Péter Lakatos
- 1st Department of Internal Medicine, Semmelweis University, Korányi Sándor str. 2/a, Budapest, 1083, Hungary
| | - László Sugár
- Department of Animal Breeding Technology and Management Faculty of Agricultural and Environmental Sciences, Kaposvár University, Guba Sándor str. 40, Kaposvár, 7400, Hungary
| | - Péter Horn
- Department of Animal Breeding Technology and Management Faculty of Agricultural and Environmental Sciences, Kaposvár University, Guba Sándor str. 40, Kaposvár, 7400, Hungary
| | - Endre Barta
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Szent-Györgyi Albert str. 4, Gödöllő, 2100, Hungary.,Department of Biochemistry and Molecular Biology, University of Debrecen, Nagyerdei ave 98, Debrecen, 4032, Hungary
| | - László Orosz
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Szent-Györgyi Albert str. 4, Gödöllő, 2100, Hungary. .,Department of Genetics, Faculty of Sciences, Eötvös Loránd University, Pázmány Péter ave. 1/c, Budapest, 1117, Hungary.
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379
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Aziz RK, Ackermann HW, Petty NK, Kropinski AM. Essential Steps in Characterizing Bacteriophages: Biology, Taxonomy, and Genome Analysis. Methods Mol Biol 2018; 1681:197-215. [PMID: 29134597 DOI: 10.1007/978-1-4939-7343-9_15] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Because of the rise in antimicrobial resistance there has been a significant increase in interest in phages for therapeutic use. Furthermore, the cost of sequencing phage genomes has decreased to the point where it is being used as a teaching tool for genomics. Unfortunately, the quality of the descriptions of the phage and its annotation frequently are substandard. The following chapter is designed to help people working on phages, particularly those new to the field, to accurately describe their newly isolated viruses.
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Affiliation(s)
- Ramy Karam Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Qasr El-Ainy, 11562, Cairo, Egypt.
| | - Hans-Wolfgang Ackermann
- Department of Microbiology, Immunology, and Infectiology, Faculty of Medicine, Université Laval, Quebec, QC, Canada, G1X 4C6
| | - Nicola K Petty
- The ithree Institute, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Andrew M Kropinski
- Departments of Food Science, Molecular and Cellular Biology, and Pathobiology, University of Guelph, Guelph, ON, Canada, N1G 2W1
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380
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Abstract
A high-quality, annotated genome assembly is the foundation for many downstream studies. However, obtaining such an assembly is a complex, reiterative process that requires the assimilation of high-quality data and combines different approaches and data types. While some software packages incorporating multiple steps of genome assembly are commercially available, they may not be flexible enough to be routinely applied to all organisms, particularly to nonmodel species such as pathogenic oomycetes and fungi. If researchers understand and apply the most appropriate, currently available tools for each step, it is possible to customize parameters and optimize results for their organism of study. Based on our experience of de novo assembly and annotation of several oomycete species, this chapter provides a modular workflow from processing of raw reads, to initial assembly generation, through optimization, chromosome-scale scaffolding and annotation, outlining input and output data as well as examples and alternative software used for each step. The accompanying Notes provide background information for each step as well as alternative options. The final result of this workflow could be an annotated, high-quality, validated, chromosome-scale assembly or a draft assembly of sufficient quality to meet specific needs of a project.
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Affiliation(s)
- Kyle Fletcher
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, Davis, CA, USA
| | - Richard Michelmore
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, Davis, CA, USA.
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381
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Landolfo S, Ianiri G, Camiolo S, Porceddu A, Mulas G, Chessa R, Zara G, Mannazzu I. CAR gene cluster and transcript levels of carotenogenic genes in Rhodotorula mucilaginosa. Microbiology (Reading) 2018; 164:78-87. [DOI: 10.1099/mic.0.000588] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sara Landolfo
- Department of Agricultural Sciences, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Giuseppe Ianiri
- Department of Agricultural, Environmental and Food Sciences, Università degli Studi del Molise, Via Francesco de Sanctis, 86100 Campobasso, Italy
- Present address: Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Salvatore Camiolo
- Department of Agricultural Sciences, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Andrea Porceddu
- Department of Agricultural Sciences, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Giuliana Mulas
- Department of Agricultural Sciences, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Rossella Chessa
- Department of Agricultural Sciences, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Giacomo Zara
- Department of Agricultural Sciences, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Ilaria Mannazzu
- Department of Agricultural Sciences, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy
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382
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Jones SJM, Taylor GA, Chan S, Warren RL, Hammond SA, Bilobram S, Mordecai G, Suttle CA, Miller KM, Schulze A, Chan AM, Jones SJ, Tse K, Li I, Cheung D, Mungall KL, Choo C, Ally A, Dhalla N, Tam AKY, Troussard A, Kirk H, Pandoh P, Paulino D, Coope RJN, Mungall AJ, Moore R, Zhao Y, Birol I, Ma Y, Marra M, Haulena M. The Genome of the Beluga Whale (Delphinapterus leucas). Genes (Basel) 2017; 8:genes8120378. [PMID: 29232881 PMCID: PMC5748696 DOI: 10.3390/genes8120378] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/28/2017] [Accepted: 12/01/2017] [Indexed: 12/17/2022] Open
Abstract
The beluga whale is a cetacean that inhabits arctic and subarctic regions, and is the only living member of the genus Delphinapterus. The genome of the beluga whale was determined using DNA sequencing approaches that employed both microfluidic partitioning library and non-partitioned library construction. The former allowed for the construction of a highly contiguous assembly with a scaffold N50 length of over 19 Mbp and total reconstruction of 2.32 Gbp. To aid our understanding of the functional elements, transcriptome data was also derived from brain, duodenum, heart, lung, spleen, and liver tissue. Assembled sequence and all of the underlying sequence data are available at the National Center for Biotechnology Information (NCBI) under the Bioproject accession number PRJNA360851A.
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Affiliation(s)
- Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Gregory A Taylor
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Simon Chan
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - René L Warren
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - S Austin Hammond
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Steven Bilobram
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Gideon Mordecai
- Department of Earth, Ocean & Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
- Institute for the Oceans & Fisheries, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Curtis A Suttle
- Department of Earth, Ocean & Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
- Institute for the Oceans & Fisheries, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Kristina M Miller
- Fisheries and Oceans Canada, Molecular Genetics Section, Pacific Biological Station, Nanaimo, BC V9R 5K6, Canada.
| | - Angela Schulze
- Fisheries and Oceans Canada, Molecular Genetics Section, Pacific Biological Station, Nanaimo, BC V9R 5K6, Canada.
| | - Amy M Chan
- Department of Earth, Ocean & Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
- Institute for the Oceans & Fisheries, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Samantha J Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Kane Tse
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Irene Li
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Dorothy Cheung
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Caleb Choo
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Adrian Ally
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Noreen Dhalla
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Angela K Y Tam
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Armelle Troussard
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Heather Kirk
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Pawan Pandoh
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Daniel Paulino
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Robin J N Coope
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Marco Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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383
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Jones SJ, Haulena M, Taylor GA, Chan S, Bilobram S, Warren RL, Hammond SA, Mungall KL, Choo C, Kirk H, Pandoh P, Ally A, Dhalla N, Tam AKY, Troussard A, Paulino D, Coope RJN, Mungall AJ, Moore R, Zhao Y, Birol I, Ma Y, Marra M, Jones SJM. The Genome of the Northern Sea Otter (Enhydra lutris kenyoni). Genes (Basel) 2017; 8:genes8120379. [PMID: 29232880 PMCID: PMC5748697 DOI: 10.3390/genes8120379] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/28/2017] [Accepted: 12/01/2017] [Indexed: 11/21/2022] Open
Abstract
The northern sea otter inhabits coastal waters of the northern Pacific Ocean and is the largest member of the Mustelidae family. DNA sequencing methods that utilize microfluidic partitioned and non-partitioned library construction were used to establish the sea otter genome. The final assembly provided 2.426 Gbp of highly contiguous assembled genomic sequences with a scaffold N50 length of over 38 Mbp. We generated transcriptome data derived from a lymphoma to aid in the determination of functional elements. The assembled genome sequence and underlying sequence data are available at the National Center for Biotechnology Information (NCBI) under the BioProject accession number PRJNA388419.
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Affiliation(s)
- Samantha J Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | | | - Gregory A Taylor
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Simon Chan
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Steven Bilobram
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - René L Warren
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - S Austin Hammond
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Caleb Choo
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Heather Kirk
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Pawan Pandoh
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Adrian Ally
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Noreen Dhalla
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Angela K Y Tam
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Armelle Troussard
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Daniel Paulino
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Robin J N Coope
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
| | - Marco Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
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384
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Chen C, Bock CH, Wood BW. Draft genome sequence of Venturia carpophila, the causal agent of peach scab. Stand Genomic Sci 2017; 12:68. [PMID: 29213355 PMCID: PMC5712196 DOI: 10.1186/s40793-017-0280-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 11/20/2017] [Indexed: 11/10/2022] Open
Abstract
Venturia carpophila causes peach scab, a disease that renders peach (Prunus persica) fruit unmarketable. We report a high-quality draft genome sequence (36.9 Mb) of V. carpophila from an isolate collected from a peach tree in central Georgia in the United States. The genome annotation is described and a phylogenetic analysis of the pathogen is presented. The genome sequence will be a useful resource for various studies on the pathogen, including the biology and ecology, taxonomy and phylogeny, host interaction and coevolution, isolation and characterization of genes of interest, and development of molecular markers for genotyping and mapping.
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Affiliation(s)
- Chunxian Chen
- USDA, Agricultural Research Service, Southeastern Fruit and Tree Nut Research Lab, 21 Dunbar Road, Byron, GA 31008 USA
| | - Clive H. Bock
- USDA, Agricultural Research Service, Southeastern Fruit and Tree Nut Research Lab, 21 Dunbar Road, Byron, GA 31008 USA
| | - Bruce W. Wood
- USDA, Agricultural Research Service, Southeastern Fruit and Tree Nut Research Lab, 21 Dunbar Road, Byron, GA 31008 USA
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385
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Gallant JR, Losilla M, Tomlinson C, Warren WC. The Genome and Adult Somatic Transcriptome of the Mormyrid Electric Fish Paramormyrops kingsleyae. Genome Biol Evol 2017; 9:3525-3530. [PMID: 29240929 PMCID: PMC5751062 DOI: 10.1093/gbe/evx265] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2017] [Indexed: 12/23/2022] Open
Abstract
Several studies have begun to elucidate the genetic and developmental processes underlying major vertebrate traits. Few of these traits have evolved repeatedly in vertebrates, preventing the analysis of molecular mechanisms underlying these traits comparatively. Electric organs have evolved multiple times among vertebrates, presenting a unique opportunity to understand the degree of constraint and repeatability of the evolutionary processes underlying novel vertebrate traits. As there is now a completed genome sequence representing South American electric eels, we were motivated to obtain genomic sequence from a linage that independently evolved electric organs to facilitate future comparative analyses of the evolution and development of electric organs. We report here the sequencing and de novo assembly of the genome of the mormyrid Paramormyrops kingsleyae using short-read sequencing. In addition, we have completed a somatic transcriptome from 11 tissues to construct a gene expression atlas of predicted genes from this assembly, enabling us to identify candidate housekeeping genes as well as genes differentially expressed in the major somatic tissues of the mormyrid electric fish. We anticipate that this resource will greatly facilitate comparative studies on the evolution and development of electric organs and electroreceptors.
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Affiliation(s)
- Jason R Gallant
- Department of Integrative Biology, Michigan State University
| | | | - Chad Tomlinson
- McDonnell Genome Institute, Washington University, St Louis
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386
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Kramer GJ, Nodwell JR. Chromosome level assembly and secondary metabolite potential of the parasitic fungus Cordyceps militaris. BMC Genomics 2017; 18:912. [PMID: 29178836 PMCID: PMC5702197 DOI: 10.1186/s12864-017-4307-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/15/2017] [Indexed: 01/30/2023] Open
Abstract
Background Cordyceps militaris is an insect pathogenic fungus that is prized for its use in traditional medicine. This and other entomopathogenic fungi are understudied sources for the discovery of new bioactive molecules. In this study, PacBio SMRT long read sequencing technology was used to sequence the genome of C. militaris with a focus on the genetic potential for secondary metabolite production in the genome assembly of this fungus. Results This is first chromosome level assembly of a species in the Cordyceps genera. In this seven chromosome assembly of 33.6 Mba there were 9371 genes identified. Cordyceps militaris was determined to have the MAT 1-1-1 and MAT 1-1-2 mating type genes. Secondary metabolite analysis revealed the potential for at least 36 distinct metabolites from a variety of classes. Three of these gene clusters had homology with clusters producing desmethylbassianin, equisetin and emericellamide that had been studied in other fungi. Conclusion Our assembly and analysis has revealed that C. militaris has a wealth of gene clusters for secondary metabolite production distributed among seven chromosomes. The identification of these gene clusters will facilitate the future study and identification of the secondary metabolites produced by this entomopathogenic fungus. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4307-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Glenna J Kramer
- Department of Biochemistry, University of Toronto, MaRS Centre, West Tower, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Justin R Nodwell
- Department of Biochemistry, University of Toronto, MaRS Centre, West Tower, 661 University Avenue, Toronto, ON, M5G 1M1, Canada.
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387
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Bowman MJ, Pulman JA, Liu TL, Childs KL. A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa. BMC Bioinformatics 2017; 18:522. [PMID: 29178822 PMCID: PMC5702205 DOI: 10.1186/s12859-017-1942-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 11/15/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Accurate structural annotation depends on well-trained gene prediction programs. Training data for gene prediction programs are often chosen randomly from a subset of high-quality genes that ideally represent the variation found within a genome. One aspect of gene variation is GC content, which differs across species and is bimodal in grass genomes. When gene prediction programs are trained on a subset of grass genes with random GC content, they are effectively being trained on two classes of genes at once, and this can be expected to result in poor results when genes are predicted in new genome sequences. RESULTS We find that gene prediction programs trained on grass genes with random GC content do not completely predict all grass genes with extreme GC content. We show that gene prediction programs that are trained with grass genes with high or low GC content can make both better and unique gene predictions compared to gene prediction programs that are trained on genes with random GC content. By separately training gene prediction programs with genes from multiple GC ranges and using the programs within the MAKER genome annotation pipeline, we were able to improve the annotation of the Oryza sativa genome compared to using the standard MAKER annotation protocol. Gene structure was improved in over 13% of genes, and 651 novel genes were predicted by the GC-specific MAKER protocol. CONCLUSIONS We present a new GC-specific MAKER annotation protocol to predict new and improved gene models and assess the biological significance of this method in Oryza sativa. We expect that this protocol will also be beneficial for gene prediction in any organism with bimodal or other unusual gene GC content.
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Affiliation(s)
- Megan J Bowman
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, Room 166, East Lansing, MI, 48824, USA.,Van Andel Research Institute, Grand Rapids, MI, 49506, USA
| | - Jane A Pulman
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, Room 166, East Lansing, MI, 48824, USA.,Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, MI, 48824, USA.,Centre for Genomics Research, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Tiffany L Liu
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, Room 166, East Lansing, MI, 48824, USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, Room 166, East Lansing, MI, 48824, USA. .,Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, MI, 48824, USA.
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388
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First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (Formerly Scedosporium prolificans). G3-GENES GENOMES GENETICS 2017; 7:3831-3836. [PMID: 28963165 PMCID: PMC5677167 DOI: 10.1534/g3.117.300107] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Here we describe the sequencing and assembly of the pathogenic fungus Lomentospora prolificans using a combination of short, highly accurate Illumina reads and additional coverage in very long Oxford Nanopore reads. The resulting assembly is highly contiguous, containing a total of 37,627,092 bp with over 98% of the sequence in just 26 scaffolds. Annotation identified 8896 protein-coding genes. Pulsed-field gel analysis suggests that this organism contains at least 7 and possibly 11 chromosomes, the two longest of which have sizes corresponding closely to the sizes of the longest scaffolds, at 6.6 and 5.7 Mb.
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389
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Meiser A, Otte J, Schmitt I, Grande FD. Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungi. Sci Rep 2017; 7:14881. [PMID: 29097759 PMCID: PMC5668418 DOI: 10.1038/s41598-017-14576-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 10/12/2017] [Indexed: 01/07/2023] Open
Abstract
The metagenome skimming approach, i.e. low coverage shotgun sequencing of multi-species assemblages and subsequent reconstruction of individual genomes, is increasingly used for in-depth genomic characterization of ecological communities. This approach is a promising tool for reconstructing genomes of facultative symbionts, such as lichen-forming fungi, from metagenomic reads. However, no study has so far tested accuracy and completeness of assemblies based on metagenomic sequences compared to assemblies based on pure culture strains of lichenized fungi. Here we assembled the genomes of Evernia prunastri and Pseudevernia furfuracea based on metagenomic sequences derived from whole lichen thalli. We extracted fungal contigs using two different taxonomic binning methods, and performed gene prediction on the fungal contig subsets. We then assessed quality and completeness of the metagenome-based assemblies using genome assemblies as reference which are based on pure culture strains of the two fungal species. Our comparison showed that we were able to reconstruct fungal genomes from uncultured lichen thalli, and also cover most of the gene space (86-90%). Metagenome skimming will facilitate genome mining, comparative (phylo)genomics, and population genetics of lichen-forming fungi by circumventing the time-consuming, sometimes unfeasible, step of aposymbiotic cultivation.
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Affiliation(s)
- Anjuli Meiser
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, D-60486, Frankfurt, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, D-60486, Frankfurt, Germany
| | - Imke Schmitt
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany.
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, D-60486, Frankfurt, Germany.
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, D-60486, Frankfurt, Germany.
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390
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Ioannidis P, Simao FA, Waterhouse RM, Manni M, Seppey M, Robertson HM, Misof B, Niehuis O, Zdobnov EM. Genomic Features of the Damselfly Calopteryx splendens Representing a Sister Clade to Most Insect Orders. Genome Biol Evol 2017; 9:415-430. [PMID: 28137743 PMCID: PMC5381652 DOI: 10.1093/gbe/evx006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2017] [Indexed: 12/14/2022] Open
Abstract
Insects comprise the most diverse and successful animal group with over one million described species that are found in almost every terrestrial and limnic habitat, with many being used as important models in genetics, ecology, and evolutionary research. Genome sequencing projects have greatly expanded the sampling of species from many insect orders, but genomic resources for species of certain insect lineages have remained relatively limited to date. To address this paucity, we sequenced the genome of the banded demoiselle, Calopteryx splendens, a damselfly (Odonata: Zygoptera) belonging to Palaeoptera, the clade containing the first winged insects. The 1.6 Gbp C. splendens draft genome assembly is one of the largest insect genomes sequenced to date and encodes a predicted set of 22,523 protein-coding genes. Comparative genomic analyses with other sequenced insects identified a relatively small repertoire of C. splendens detoxification genes, which could explain its previously noted sensitivity to habitat pollution. Intriguingly, this repertoire includes a cytochrome P450 gene not previously described in any insect genome. The C. splendens immune gene repertoire appears relatively complete and features several genes encoding novel multi-domain peptidoglycan recognition proteins. Analysis of chemosensory genes revealed the presence of both gustatory and ionotropic receptors, as well as the insect odorant receptor coreceptor gene (OrCo) and at least four partner odorant receptors (ORs). This represents the oldest known instance of a complete OrCo/OR system in insects, and provides the molecular underpinning for odonate olfaction. The C. splendens genome improves the sampling of insect lineages that diverged before the radiation of Holometabola and offers new opportunities for molecular-level evolutionary, ecological, and behavioral studies.
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Affiliation(s)
- Panagiotis Ioannidis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Felipe A Simao
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Robert M Waterhouse
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Mosè Manni
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Mathieu Seppey
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Oliver Niehuis
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
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391
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Zhang L, Xu P, Cai Y, Ma L, Li S, Li S, Xie W, Song J, Peng L, Yan H, Zou L, Ma Y, Zhang C, Gao Q, Wang J. The draft genome assembly of Rhododendron delavayi Franch. var. delavayi. Gigascience 2017; 6:1-11. [PMID: 29020749 PMCID: PMC5632301 DOI: 10.1093/gigascience/gix076] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 05/28/2017] [Accepted: 08/04/2017] [Indexed: 01/16/2023] Open
Abstract
Rhododendron delavayi Franch. is globally famous as an ornamental plant. Its distribution in southwest China covers several different habitats and environments. However, not much research had been conducted on Rhododendron spp. at the molecular level, which hinders understanding of its evolution, speciation, and synthesis of secondary metabolites, as well as its wide adaptability to different environments. Here, we report the genome assembly and gene annotation of R. delavayi var. delavayi (the second genome sequenced in the Ericaceae), which will facilitate the study of the family. The genome assembly will have further applications in genome-assisted cultivar breeding. The final size of the assembled R. delavayi var. delavayi genome (695.09 Mb) was close to the 697.94 Mb, estimated by k-mer analysis. A total of 336.83 gigabases (Gb) of raw Illumina HiSeq 2000 reads were generated from 9 libraries (with insert sizes ranging from 170 bp to 40 kb), achieving a raw sequencing depth of ×482.6. After quality filtering, 246.06 Gb of clean reads were obtained, giving ×352.55 coverage depth. Assembly using Platanus gave a total scaffold length of 695.09 Mb, with a contig N50 of 61.8 kb and a scaffold N50 of 637.83 kb. Gene prediction resulted in the annotation of 32 938 protein-coding genes. The genome completeness was evaluated by CEGMA and BUSCO and reached 95.97% and 92.8%, respectively. The gene annotation completeness was also evaluated by CEGMA and BUSCO and reached 97.01% and 87.4%, respectively. Genome annotation revealed that 51.77% of the R. delavayi genome is composed of transposable elements, and 37.48% of long terminal repeat elements (LTRs). The de novo assembled genome of R. delavayi var. delavayi (hereinafter referred to as R. delavayi) is the second genomic resource of the family Ericaceae and will provide a valuable resource for research on future comparative genomic studies in Rhododendron species. The availability of the R. delavayi genome sequence will hopefully provide a tool for scientists to tackle open questions regarding molecular mechanisms underlying environmental interactions in the genus Rhododendron, more accurately understand the evolutionary processes and systematics of the genus, facilitate the identification of genes encoding pharmaceutically important compounds, and accelerate molecular breeding to release elite varieties.
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Affiliation(s)
- Lu Zhang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
- Key Lab of Yunnan Flower Breeding, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
| | - Pengwei Xu
- BGI-Shenzhen, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Yanfei Cai
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
- Key Lab of Yunnan Flower Breeding, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
| | - Lulin Ma
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
- Key Lab of Yunnan Flower Breeding, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
| | - Shifeng Li
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
- Key Lab of Yunnan Flower Breeding, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
| | - Shufa Li
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
- Key Lab of Yunnan Flower Breeding, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
| | - Weijia Xie
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
- Key Lab of Yunnan Flower Breeding, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
| | - Jie Song
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
- Key Lab of Yunnan Flower Breeding, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
| | - Lvchun Peng
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
- Key Lab of Yunnan Flower Breeding, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
| | - Huijun Yan
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
- Key Lab of Yunnan Flower Breeding, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
| | - Ling Zou
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
- Key Lab of Yunnan Flower Breeding, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
| | - Yongpeng Ma
- Kunming Botanical Garden, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei Road, Panlong District, Kunming, Yunnan 650201, China
| | - Chengjun Zhang
- Germplasm Bank of Wild species, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei Road, Panlong District, Kunming, Yunnan 650201, China
| | - Qiang Gao
- BGI-Shenzhen, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Jihua Wang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
- Key Lab of Yunnan Flower Breeding, No. 2238 Beijing Road, Panlong District, Kunming 650205, China
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392
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Gouin A, Bretaudeau A, Nam K, Gimenez S, Aury JM, Duvic B, Hilliou F, Durand N, Montagné N, Darboux I, Kuwar S, Chertemps T, Siaussat D, Bretschneider A, Moné Y, Ahn SJ, Hänniger S, Grenet ASG, Neunemann D, Maumus F, Luyten I, Labadie K, Xu W, Koutroumpa F, Escoubas JM, Llopis A, Maïbèche-Coisne M, Salasc F, Tomar A, Anderson AR, Khan SA, Dumas P, Orsucci M, Guy J, Belser C, Alberti A, Noel B, Couloux A, Mercier J, Nidelet S, Dubois E, Liu NY, Boulogne I, Mirabeau O, Le Goff G, Gordon K, Oakeshott J, Consoli FL, Volkoff AN, Fescemyer HW, Marden JH, Luthe DS, Herrero S, Heckel DG, Wincker P, Kergoat GJ, Amselem J, Quesneville H, Groot AT, Jacquin-Joly E, Nègre N, Lemaitre C, Legeai F, d'Alençon E, Fournier P. Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges. Sci Rep 2017; 7:11816. [PMID: 28947760 PMCID: PMC5613006 DOI: 10.1038/s41598-017-10461-4] [Citation(s) in RCA: 182] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/19/2017] [Indexed: 12/30/2022] Open
Abstract
Emergence of polyphagous herbivorous insects entails significant adaptation to recognize, detoxify and digest a variety of host-plants. Despite of its biological and practical importance - since insects eat 20% of crops - no exhaustive analysis of gene repertoires required for adaptations in generalist insect herbivores has previously been performed. The noctuid moth Spodoptera frugiperda ranks as one of the world’s worst agricultural pests. This insect is polyphagous while the majority of other lepidopteran herbivores are specialist. It consists of two morphologically indistinguishable strains (“C” and “R”) that have different host plant ranges. To describe the evolutionary mechanisms that both enable the emergence of polyphagous herbivory and lead to the shift in the host preference, we analyzed whole genome sequences from laboratory and natural populations of both strains. We observed huge expansions of genes associated with chemosensation and detoxification compared with specialist Lepidoptera. These expansions are largely due to tandem duplication, a possible adaptation mechanism enabling polyphagy. Individuals from natural C and R populations show significant genomic differentiation. We found signatures of positive selection in genes involved in chemoreception, detoxification and digestion, and copy number variation in the two latter gene families, suggesting an adaptive role for structural variation.
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Affiliation(s)
- Anaïs Gouin
- INRIA, IRISA, GenScale, Campus de Beaulieu, Rennes, 35042, France
| | - Anthony Bretaudeau
- INRA, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, 35042, France.,INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Kiwoong Nam
- DGIMI, INRA, Univ. Montpellier, 34095, Montpellier, France
| | - Sylvie Gimenez
- DGIMI, INRA, Univ. Montpellier, 34095, Montpellier, France
| | - Jean-Marc Aury
- CEA, Genoscope, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Bernard Duvic
- DGIMI, INRA, Univ. Montpellier, 34095, Montpellier, France
| | - Frédérique Hilliou
- Université Côte d'Azur, INRA, CNRS, Institut Sophia Agrobiotech, 06903 Sophia-Antipolis, France
| | - Nicolas Durand
- Sorbonne Universités, UPMC University Paris 06, Institute of Ecology and Environmental Sciences of Paris, 75005, Paris, France
| | - Nicolas Montagné
- Sorbonne Universités, UPMC University Paris 06, Institute of Ecology and Environmental Sciences of Paris, 75005, Paris, France
| | | | - Suyog Kuwar
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany
| | - Thomas Chertemps
- Sorbonne Universités, UPMC University Paris 06, Institute of Ecology and Environmental Sciences of Paris, 75005, Paris, France
| | - David Siaussat
- Sorbonne Universités, UPMC University Paris 06, Institute of Ecology and Environmental Sciences of Paris, 75005, Paris, France
| | - Anne Bretschneider
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany
| | - Yves Moné
- DGIMI, INRA, Univ. Montpellier, 34095, Montpellier, France
| | - Seung-Joon Ahn
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany
| | - Sabine Hänniger
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany
| | | | - David Neunemann
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Isabelle Luyten
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Karine Labadie
- CEA, Genoscope, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Wei Xu
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, 6150, Australia
| | - Fotini Koutroumpa
- INRA, Institute of Ecology and Environmental Sciences, 78000, Versailles, France.,Laboratory of Mammalian Genetics, Center for DNA Fingerprinting and Diagnostics (CDFD), Lab block: Tuljaguda (Opp. MJ Market), Nampally, Hyderabad, 500 001, India
| | | | - Angel Llopis
- Department of Genetics, Universitat de València, 46100, Burjassot, Valencia, Spain.,Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI-BIOTECMED), Universitat de València, 46100, Burjassot, Valencia, Spain
| | - Martine Maïbèche-Coisne
- Sorbonne Universités, UPMC University Paris 06, Institute of Ecology and Environmental Sciences of Paris, 75005, Paris, France
| | - Fanny Salasc
- DGIMI, INRA, Univ. Montpellier, 34095, Montpellier, France.,EPHE, PSL Research University, UMR1333 - DGIMI, Pathologie comparée des Invertébrés CC101, F-34095, Montpellier cedex 5, France
| | - Archana Tomar
- Laboratory of Mammalian Genetics, Center for DNA Fingerprinting and Diagnostics (CDFD), Lab block: Tuljaguda (Opp. MJ Market), Nampally, Hyderabad, 500 001, India
| | - Alisha R Anderson
- CSIRO Ecosystem Sciences, Black Mountain, Canberra, ACT 2600, Australia
| | - Sher Afzal Khan
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany
| | - Pascaline Dumas
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Science Park 904, 1090 GE, Amsterdam, The Netherlands
| | - Marion Orsucci
- DGIMI, INRA, Univ. Montpellier, 34095, Montpellier, France
| | - Julie Guy
- CEA, Genoscope, 2 rue Gaston Crémieux, 91000, Evry, France
| | | | | | - Benjamin Noel
- CEA, Genoscope, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Arnaud Couloux
- CEA, Genoscope, 2 rue Gaston Crémieux, 91000, Evry, France
| | | | - Sabine Nidelet
- Plateforme MGX, C/o institut de Génomique Fonctionnelle, 141, rue de la Cardonille, 34094, Montpellier cedex 05, France
| | - Emeric Dubois
- Plateforme MGX, C/o institut de Génomique Fonctionnelle, 141, rue de la Cardonille, 34094, Montpellier cedex 05, France
| | - Nai-Yong Liu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, 650224, China
| | - Isabelle Boulogne
- Sorbonne Universités, UPMC University Paris 06, Institute of Ecology and Environmental Sciences of Paris, 75005, Paris, France
| | - Olivier Mirabeau
- INRA, Institute of Ecology and Environmental Sciences, 78000, Versailles, France
| | - Gaelle Le Goff
- Université Côte d'Azur, INRA, CNRS, Institut Sophia Agrobiotech, 06903 Sophia-Antipolis, France
| | - Karl Gordon
- CSIRO, Clunies Ross St, (GPO Box 1700), Acton, ACT 2601, Australia
| | - John Oakeshott
- CSIRO, Clunies Ross St, (GPO Box 1700), Acton, ACT 2601, Australia
| | - Fernando L Consoli
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias 11, 13418-900, Piracicaba, Brazil
| | | | - Howard W Fescemyer
- Department of Biology, 208 Mueller Laboratory, The Pennsylvania State University, University Park, 16802, Pennsylvania, USA
| | - James H Marden
- Department of Biology, 208 Mueller Laboratory, The Pennsylvania State University, University Park, 16802, Pennsylvania, USA
| | - Dawn S Luthe
- Department of Plant Science, 102 Tyson Building, The Pennsylvania State University, University Park, 16802, Pennsylvania, USA
| | - Salvador Herrero
- Department of Genetics, Universitat de València, 46100, Burjassot, Valencia, Spain
| | - David G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany
| | - Patrick Wincker
- CEA, Genoscope, 2 rue Gaston Crémieux, 91000, Evry, France.,CNRS UMR 8030, 2 rue Gaston Crémieux, 91000, Evry, France.,Université d'Evry Val D'Essonne, 91000, Evry, France
| | - Gael J Kergoat
- INRA, UMR1062 CBGP, IRD, CIRAD, Montpellier SupAgro, 755 Avenue du campus Agropolis, 34988, Montferrier/Lez, France
| | - Joelle Amselem
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | | | - Astrid T Groot
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany.,Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Science Park 904, 1090 GE, Amsterdam, The Netherlands
| | | | - Nicolas Nègre
- DGIMI, INRA, Univ. Montpellier, 34095, Montpellier, France.
| | - Claire Lemaitre
- INRIA, IRISA, GenScale, Campus de Beaulieu, Rennes, 35042, France.
| | - Fabrice Legeai
- INRIA, IRISA, GenScale, Campus de Beaulieu, Rennes, 35042, France
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393
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Annotated Draft Genome Assemblies for the Northern Bobwhite ( Colinus virginianus) and the Scaled Quail ( Callipepla squamata) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size. G3-GENES GENOMES GENETICS 2017; 7:3047-3058. [PMID: 28717047 PMCID: PMC5592930 DOI: 10.1534/g3.117.043083] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Northern bobwhite (Colinus virginianus; hereafter bobwhite) and scaled quail (Callipepla squamata) populations have suffered precipitous declines across most of their US ranges. Illumina-based first- (v1.0) and second- (v2.0) generation draft genome assemblies for the scaled quail and the bobwhite produced N50 scaffold sizes of 1.035 and 2.042 Mb, thereby producing a 45-fold improvement in contiguity over the existing bobwhite assembly, and ≥90% of the assembled genomes were captured within 1313 and 8990 scaffolds, respectively. The scaled quail assembly (v1.0 = 1.045 Gb) was ∼20% smaller than the bobwhite (v2.0 = 1.254 Gb), which was supported by kmer-based estimates of genome size. Nevertheless, estimates of GC content (41.72%; 42.66%), genome-wide repetitive content (10.40%; 10.43%), and MAKER-predicted protein coding genes (17,131; 17,165) were similar for the scaled quail (v1.0) and bobwhite (v2.0) assemblies, respectively. BUSCO analyses utilizing 3023 single-copy orthologs revealed a high level of assembly completeness for the scaled quail (v1.0; 84.8%) and the bobwhite (v2.0; 82.5%), as verified by comparison with well-established avian genomes. We also detected 273 putative segmental duplications in the scaled quail genome (v1.0), and 711 in the bobwhite genome (v2.0), including some that were shared among both species. Autosomal variant prediction revealed ∼2.48 and 4.17 heterozygous variants per kilobase within the scaled quail (v1.0) and bobwhite (v2.0) genomes, respectively, and estimates of historic effective population size were uniformly higher for the bobwhite across all time points in a coalescent model. However, large-scale declines were predicted for both species beginning ∼15-20 KYA.
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394
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Edger PP, Smith R, McKain MR, Cooley AM, Vallejo-Marin M, Yuan Y, Bewick AJ, Ji L, Platts AE, Bowman MJ, Childs KL, Washburn JD, Schmitz RJ, Smith GD, Pires JC, Puzey JR. Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower. THE PLANT CELL 2017; 29:2150-2167. [PMID: 28814644 PMCID: PMC5635986 DOI: 10.1105/tpc.17.00010] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 07/25/2017] [Accepted: 08/13/2017] [Indexed: 05/18/2023]
Abstract
Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally more dominant, having retained more genes and being more highly expressed, a phenomenon termed subgenome dominance. The genomic features that determine how quickly and which subgenome dominates within a newly formed polyploid remain poorly understood. To investigate the rate of emergence of subgenome dominance, we examined gene expression, gene methylation, and transposable element (TE) methylation in a natural, <140-year-old allopolyploid (Mimulus peregrinus), a resynthesized interspecies triploid hybrid (M. robertsii), a resynthesized allopolyploid (M. peregrinus), and progenitor species (M. guttatus and M. luteus). We show that subgenome expression dominance occurs instantly following the hybridization of divergent genomes and significantly increases over generations. Additionally, CHH methylation levels are reduced in regions near genes and within TEs in the first-generation hybrid, intermediate in the resynthesized allopolyploid, and are repatterned differently between the dominant and recessive subgenomes in the natural allopolyploid. Subgenome differences in levels of TE methylation mirror the increase in expression bias observed over the generations following hybridization. These findings provide important insights into genomic and epigenomic shock that occurs following hybridization and polyploid events and may also contribute to uncovering the mechanistic basis of heterosis and subgenome dominance.
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Affiliation(s)
- Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
- Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI 48824
| | - Ronald Smith
- Department of Applied Science, The College of William and Mary, Williamsburg, Virginia 23185
| | | | - Arielle M Cooley
- Biology Department, Whitman College, Walla Walla, Washington 99362
| | - Mario Vallejo-Marin
- Biological and Environmental Sciences, University of Stirling, Stirling FK9 4LA, United Kingdom
| | - Yaowu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
| | - Adam J Bewick
- Department of Genetics, University of Georgia, Athens, Georgia 30602
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602
| | - Adrian E Platts
- McGill Centre for Bioinformatics, McGill University, Montreal, Quebec H3A 0E9, Canada
| | - Megan J Bowman
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan 48824
| | - Jacob D Washburn
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia 30602
| | - Gregory D Smith
- Department of Applied Science, The College of William and Mary, Williamsburg, Virginia 23185
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
| | - Joshua R Puzey
- Department of Biology, The College of William and Mary, Williamsburg, Virginia 23185
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395
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Ibarra-Laclette E, Sánchez-Rangel D, Hernández-Domínguez E, Pérez-Torres CA, Ortiz-Castro R, Villafán E, Alonso-Sánchez A, Rodríguez-Haas B, López-Buenfil A, García-Avila C, Ramírez-Pool JA. Draft Genome Sequence of the Phytopathogenic Fungus Fusarium euwallaceae, the Causal Agent of Fusarium Dieback. GENOME ANNOUNCEMENTS 2017; 5:e00881-17. [PMID: 28860245 PMCID: PMC5578843 DOI: 10.1128/genomea.00881-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 07/26/2017] [Indexed: 01/15/2023]
Abstract
Here, we report the genome of Fusarium euwallaceae strain HFEW-16-IV-019, an isolate obtained from Kuroshio shot hole borer (a Euwallacea sp.). These beetles were collected in Tijuana, Mexico, from elm trees showing typical symptoms of Fusarium dieback. The final assembly consists of 287 scaffolds spanning 48,274,071 bp and 13,777 genes.
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Affiliation(s)
| | - Diana Sánchez-Rangel
- Red de Estudios Moleculares Avanzados, Instituto de Ecología AC, Xalapa, Veracruz, Mexico
- Cátedra CONACYT en el Instituto de Ecología AC, Xalapa, Veracruz, Mexico
| | - Eric Hernández-Domínguez
- Red de Estudios Moleculares Avanzados, Instituto de Ecología AC, Xalapa, Veracruz, Mexico
- Cátedra CONACYT en el Instituto de Ecología AC, Xalapa, Veracruz, Mexico
| | - Claudia-Anahí Pérez-Torres
- Red de Estudios Moleculares Avanzados, Instituto de Ecología AC, Xalapa, Veracruz, Mexico
- Cátedra CONACYT en el Instituto de Ecología AC, Xalapa, Veracruz, Mexico
| | - Randy Ortiz-Castro
- Red de Estudios Moleculares Avanzados, Instituto de Ecología AC, Xalapa, Veracruz, Mexico
- Cátedra CONACYT en el Instituto de Ecología AC, Xalapa, Veracruz, Mexico
| | - Emanuel Villafán
- Red de Estudios Moleculares Avanzados, Instituto de Ecología AC, Xalapa, Veracruz, Mexico
| | | | | | - Abel López-Buenfil
- Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Unidad Integral de Diagnóstico, Servicios y Constatación, Tecámac, Estado de México, Mexico
| | - Clemente García-Avila
- Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Unidad Integral de Diagnóstico, Servicios y Constatación, Tecámac, Estado de México, Mexico
| | - José-Abrahán Ramírez-Pool
- Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Unidad Integral de Diagnóstico, Servicios y Constatación, Tecámac, Estado de México, Mexico
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396
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Rao S, Nandineni MR. Genome sequencing and comparative genomics reveal a repertoire of putative pathogenicity genes in chilli anthracnose fungus Colletotrichum truncatum. PLoS One 2017; 12:e0183567. [PMID: 28846714 PMCID: PMC5573122 DOI: 10.1371/journal.pone.0183567] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 08/07/2017] [Indexed: 12/16/2022] Open
Abstract
Colletotrichum truncatum, a major fungal phytopathogen, causes the anthracnose disease on an economically important spice crop chilli (Capsicum annuum), resulting in huge economic losses in tropical and sub-tropical countries. It follows a subcuticular intramural infection strategy on chilli with a short, asymptomatic, endophytic phase, which contrasts with the intracellular hemibiotrophic lifestyle adopted by most of the Colletotrichum species. However, little is known about the molecular determinants and the mechanism of pathogenicity in this fungus. A high quality whole genome sequence and gene annotation based on transcriptome data of an Indian isolate of C. truncatum from chilli has been obtained. Analysis of the genome sequence revealed a rich repertoire of pathogenicity genes in C. truncatum encoding secreted proteins, effectors, plant cell wall degrading enzymes, secondary metabolism associated proteins, with potential roles in the host-specific infection strategy, placing it next only to the Fusarium species. The size of genome assembly, number of predicted genes and some of the functional categories were similar to other sequenced Colletotrichum species. The comparative genomic analyses with other species and related fungi identified some unique genes and certain highly expanded gene families of CAZymes, proteases and secondary metabolism associated genes in the genome of C. truncatum. The draft genome assembly and functional annotation of potential pathogenicity genes of C. truncatum provide an important genomic resource for understanding the biology and lifestyle of this important phytopathogen and will pave the way for designing efficient disease control regimens.
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Affiliation(s)
- Soumya Rao
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, Telangana, India
- Graduate studies, Manipal University, Manipal, Karnataka, India
| | - Madhusudan R. Nandineni
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, Telangana, India
- Laboratory of DNA Fingerprinting Services, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, Telangana, India
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397
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Moll KM, Zhou P, Ramaraj T, Fajardo D, Devitt NP, Sadowsky MJ, Stupar RM, Tiffin P, Miller JR, Young ND, Silverstein KAT, Mudge J. Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula. BMC Genomics 2017; 18:578. [PMID: 28778149 PMCID: PMC5545040 DOI: 10.1186/s12864-017-3971-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/31/2017] [Indexed: 12/16/2022] Open
Abstract
Background Third generation sequencing technologies, with sequencing reads in the tens- of kilo-bases, facilitate genome assembly by spanning ambiguous regions and improving continuity. This has been critical for plant genomes, which are difficult to assemble due to high repeat content, gene family expansions, segmental and tandem duplications, and polyploidy. Recently, high-throughput mapping and scaffolding strategies have further improved continuity. Together, these long-range technologies enable quality draft assemblies of complex genomes in a cost-effective and timely manner. Results Here, we present high quality genome assemblies of the model legume plant, Medicago truncatula (R108) using PacBio, Dovetail Chicago (hereafter, Dovetail) and BioNano technologies. To test these technologies for plant genome assembly, we generated five assemblies using all possible combinations and ordering of these three technologies in the R108 assembly. While the BioNano and Dovetail joins overlapped, they also showed complementary gains in continuity and join numbers. Both technologies spanned repetitive regions that PacBio alone was unable to bridge. Combining technologies, particularly Dovetail followed by BioNano, resulted in notable improvements compared to Dovetail or BioNano alone. A combination of PacBio, Dovetail, and BioNano was used to generate a high quality draft assembly of R108, a M. truncatula accession widely used in studies of functional genomics. As a test for the usefulness of the resulting genome sequence, the new R108 assembly was used to pinpoint breakpoints and characterize flanking sequence of a previously identified translocation between chromosomes 4 and 8, identifying more than 22.7 Mb of novel sequence not present in the earlier A17 reference assembly. Conclusions Adding Dovetail followed by BioNano data yielded complementary improvements in continuity over the original PacBio assembly. This strategy proved efficient and cost-effective for developing a quality draft assembly compared to traditional reference assemblies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3971-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Karen M Moll
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA.,Montana State University, Center for Biofilm Engineering, Bozeman, MT, 59717, USA
| | - Peng Zhou
- Department of Plant Biology, University of Minnesota, Saint Paul, MN, USA
| | - Thiruvarangan Ramaraj
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA
| | - Diego Fajardo
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA
| | - Nicholas P Devitt
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA
| | - Michael J Sadowsky
- Department of Soil, Water & Climate, Plant and Microbial Biology and BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA
| | | | - Nevin D Young
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA
| | | | - Joann Mudge
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA.
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398
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Schwager EE, Sharma PP, Clarke T, Leite DJ, Wierschin T, Pechmann M, Akiyama-Oda Y, Esposito L, Bechsgaard J, Bilde T, Buffry AD, Chao H, Dinh H, Doddapaneni H, Dugan S, Eibner C, Extavour CG, Funch P, Garb J, Gonzalez LB, Gonzalez VL, Griffiths-Jones S, Han Y, Hayashi C, Hilbrant M, Hughes DST, Janssen R, Lee SL, Maeso I, Murali SC, Muzny DM, Nunes da Fonseca R, Paese CLB, Qu J, Ronshaugen M, Schomburg C, Schönauer A, Stollewerk A, Torres-Oliva M, Turetzek N, Vanthournout B, Werren JH, Wolff C, Worley KC, Bucher G, Gibbs RA, Coddington J, Oda H, Stanke M, Ayoub NA, Prpic NM, Flot JF, Posnien N, Richards S, McGregor AP. The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. BMC Biol 2017. [PMID: 28756775 DOI: 10.1186/s12915-017-0399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. RESULTS We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication. CONCLUSIONS Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes.
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Affiliation(s)
- Evelyn E Schwager
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
- Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Prashant P Sharma
- Department of Zoology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Thomas Clarke
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA
- Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA
- J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD, 20850, USA
| | - Daniel J Leite
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Torsten Wierschin
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany
| | - Matthias Pechmann
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
- Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Yasuko Akiyama-Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan
- Osaka Medical College, Takatsuki, Osaka, Japan
| | - Lauren Esposito
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| | - Jesper Bechsgaard
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Trine Bilde
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Alexandra D Buffry
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - HarshaVardhan Doddapaneni
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cornelius Eibner
- Department of Genetics, Friedrich-Schiller-University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Peter Funch
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Jessica Garb
- Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Luis B Gonzalez
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Vanessa L Gonzalez
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA
| | - Sam Griffiths-Jones
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Yi Han
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cheryl Hayashi
- Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
| | - Maarten Hilbrant
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
- Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, 75236, Uppsala, Sweden
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Rodrigo Nunes da Fonseca
- Nucleo em Ecologia e Desenvolvimento SocioAmbiental de Macaé (NUPEM), Campus Macaé, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, 27941-222, Brazil
| | - Christian L B Paese
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Matthew Ronshaugen
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Christoph Schomburg
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Anna Schönauer
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Angelika Stollewerk
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Montserrat Torres-Oliva
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Natascha Turetzek
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Bram Vanthournout
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
- Evolution and Optics of Nanostructure group (EON), Biology Department, Ghent University, Gent, Belgium
| | - John H Werren
- Biology Department, University of Rochester, Rochester, NY, 14627, USA
| | - Carsten Wolff
- Humboldt-Universität of Berlin, Institut für Biologie, Philippstr.13, 10115, Berlin, Germany
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach-Institute, GZMB, Georg-August-University, Göttingen Campus, Justus von Liebig Weg 11, 37077, Göttingen, Germany.
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Jonathan Coddington
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA.
| | - Hiroki Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan.
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan.
| | - Mario Stanke
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany.
| | - Nadia A Ayoub
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA.
| | - Nikola-Michael Prpic
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Jean-François Flot
- Université libre de Bruxelles (ULB), Evolutionary Biology & Ecology, C.P. 160/12, Avenue F.D. Roosevelt 50, 1050, Brussels, Belgium.
| | - Nico Posnien
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
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399
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Schwager EE, Sharma PP, Clarke T, Leite DJ, Wierschin T, Pechmann M, Akiyama-Oda Y, Esposito L, Bechsgaard J, Bilde T, Buffry AD, Chao H, Dinh H, Doddapaneni H, Dugan S, Eibner C, Extavour CG, Funch P, Garb J, Gonzalez LB, Gonzalez VL, Griffiths-Jones S, Han Y, Hayashi C, Hilbrant M, Hughes DST, Janssen R, Lee SL, Maeso I, Murali SC, Muzny DM, Nunes da Fonseca R, Paese CLB, Qu J, Ronshaugen M, Schomburg C, Schönauer A, Stollewerk A, Torres-Oliva M, Turetzek N, Vanthournout B, Werren JH, Wolff C, Worley KC, Bucher G, Gibbs RA, Coddington J, Oda H, Stanke M, Ayoub NA, Prpic NM, Flot JF, Posnien N, Richards S, McGregor AP. The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. BMC Biol 2017; 15:62. [PMID: 28756775 PMCID: PMC5535294 DOI: 10.1186/s12915-017-0399-x] [Citation(s) in RCA: 197] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/21/2017] [Indexed: 12/15/2022] Open
Abstract
Background The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. Results We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication. Conclusions Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0399-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evelyn E Schwager
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.,Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Prashant P Sharma
- Department of Zoology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Thomas Clarke
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA.,Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA.,J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD, 20850, USA
| | - Daniel J Leite
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Torsten Wierschin
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany
| | - Matthias Pechmann
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.,Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Yasuko Akiyama-Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan.,Osaka Medical College, Takatsuki, Osaka, Japan
| | - Lauren Esposito
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| | - Jesper Bechsgaard
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Trine Bilde
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Alexandra D Buffry
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - HarshaVardhan Doddapaneni
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cornelius Eibner
- Department of Genetics, Friedrich-Schiller-University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Peter Funch
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Jessica Garb
- Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Luis B Gonzalez
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Vanessa L Gonzalez
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA
| | - Sam Griffiths-Jones
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Yi Han
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cheryl Hayashi
- Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
| | - Maarten Hilbrant
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.,Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, 75236, Uppsala, Sweden
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Rodrigo Nunes da Fonseca
- Nucleo em Ecologia e Desenvolvimento SocioAmbiental de Macaé (NUPEM), Campus Macaé, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, 27941-222, Brazil
| | - Christian L B Paese
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Matthew Ronshaugen
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Christoph Schomburg
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Anna Schönauer
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Angelika Stollewerk
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Montserrat Torres-Oliva
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Natascha Turetzek
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Bram Vanthournout
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark.,Evolution and Optics of Nanostructure group (EON), Biology Department, Ghent University, Gent, Belgium
| | - John H Werren
- Biology Department, University of Rochester, Rochester, NY, 14627, USA
| | - Carsten Wolff
- Humboldt-Universität of Berlin, Institut für Biologie, Philippstr.13, 10115, Berlin, Germany
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach-Institute, GZMB, Georg-August-University, Göttingen Campus, Justus von Liebig Weg 11, 37077, Göttingen, Germany.
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Jonathan Coddington
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA.
| | - Hiroki Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan. .,Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan.
| | - Mario Stanke
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany.
| | - Nadia A Ayoub
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA.
| | - Nikola-Michael Prpic
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Jean-François Flot
- Université libre de Bruxelles (ULB), Evolutionary Biology & Ecology, C.P. 160/12, Avenue F.D. Roosevelt 50, 1050, Brussels, Belgium.
| | - Nico Posnien
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
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Edwards KD, Fernandez-Pozo N, Drake-Stowe K, Humphry M, Evans AD, Bombarely A, Allen F, Hurst R, White B, Kernodle SP, Bromley JR, Sanchez-Tamburrino JP, Lewis RS, Mueller LA. A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency. BMC Genomics 2017; 18:448. [PMID: 28625162 PMCID: PMC5474855 DOI: 10.1186/s12864-017-3791-6] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 05/12/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tobacco (Nicotiana tabacum) is an important plant model system that has played a key role in the early development of molecular plant biology. The tobacco genome is large and its characterisation challenging because it is an allotetraploid, likely arising from hybridisation between diploid N. sylvestris and N. tomentosiformis ancestors. A draft assembly was recently published for N. tabacum, but because of the aforementioned genome complexities it was of limited utility due to a high level of fragmentation. RESULTS Here we report an improved tobacco genome assembly, which, aided by the application of optical mapping, achieves an N50 size of 2.17 Mb and enables anchoring of 64% of the genome to pseudomolecules; a significant increase from the previous value of 19%. We use this assembly to identify two homeologous genes that explain the differentiation of the burley tobacco market class, with potential for greater understanding of Nitrogen Utilization Efficiency and Nitrogen Use Efficiency in plants; an important trait for future sustainability of agricultural production. CONCLUSIONS Development of an improved genome assembly for N. tabacum enables what we believe to be the first successful map-based gene discovery for the species, and demonstrates the value of an improved assembly for future research in this model and commercially-important species.
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Affiliation(s)
- K. D. Edwards
- Plant Biotechnology Division, British American Tobacco, Cambridge, UK
| | | | - K. Drake-Stowe
- Crop Science Department, North Carolina State University, Raleigh, NC USA
| | - M. Humphry
- Plant Biotechnology Division, British American Tobacco, Cambridge, UK
| | - A. D. Evans
- Plant Biotechnology Division, British American Tobacco, Cambridge, UK
| | - A. Bombarely
- Boyce Thompson Institute, Ithaca, NY USA
- Present address Department of Horticulture, Virginia Tech, Blacksburg, VA USA
| | - F. Allen
- Plant Biotechnology Division, British American Tobacco, Cambridge, UK
| | - R. Hurst
- Plant Biotechnology Division, British American Tobacco, Cambridge, UK
| | - B. White
- Plant Biotechnology Division, British American Tobacco, Cambridge, UK
| | - S. P. Kernodle
- Crop Science Department, North Carolina State University, Raleigh, NC USA
| | - J. R. Bromley
- Plant Biotechnology Division, British American Tobacco, Cambridge, UK
| | | | - R. S. Lewis
- Crop Science Department, North Carolina State University, Raleigh, NC USA
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