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First annotated draft genomes of nonmarine ostracods (Ostracoda, Crustacea) with different reproductive modes

Patrick Tran Van, Yoann Anselmetti, Jens Bast, Zoé Dumas, Nicolas Galtier, Kamil S Jaron, Koenraad Martens (UGent) , Darren J Parker, Marc Robinson-Rechavi, Tanja Schwander, et al.
(2021) G3-GENES GENOMES GENETICS. 11(4).
Author
Organization
Abstract
Ostracods are one of the oldest crustacean groups with an excellent fossil record and high importance for phylogenetic analyses but genome resources for this class are still lacking. We have successfully assembled and annotated the first reference genomes for three species of nonmarine ostracods; two with obligate sexual reproduction (Cyprideis torosa and Notodromas monacha) and the putative ancient asexual Darwinula stevensoni. This kind of genomic research has so far been impeded by the small size of most ostracods and the absence of genetic resources such as linkage maps or BAC libraries that were available for other crustaceans. For genome assembly, we used an Illumina-based sequencing technology, resulting in assemblies of similar sizes for the three species (335-382 Mb) and with scaffold numbers and their N50 (19-56 kb) in the same orders of magnitude. Gene annotations were guided by transcriptome data from each species. The three assemblies are relatively complete with BUSCO scores of 92-96. The number of predicted genes (13,771-17,776) is in the same range as Branchiopoda genomes but lower than in most malacostracan genomes. These three reference genomes from nonmarine ostracods provide the urgently needed basis to further develop ostracods as models for evolutionary and ecological research.
Keywords
Genetics (clinical), Genetics, Molecular Biology, ancient asexual, sexual, Darwinula stevensoni, Cyprideis torosa, DARWINULA-STEVENSONI CRUSTACEA, CYPRIDEIS-TOROSA JONES, ASEXUAL REPRODUCTION, LIFE-CYCLE, DNA-REPAIR, ANCIENT, POPULATION, EVOLUTION, SEQUENCE, SEX

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Citation

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MLA
Tran Van, Patrick, et al. “First Annotated Draft Genomes of Nonmarine Ostracods (Ostracoda, Crustacea) with Different Reproductive Modes.” G3-GENES GENOMES GENETICS, edited by B J Andrews, vol. 11, no. 4, 2021, doi:10.1093/g3journal/jkab043.
APA
Tran Van, P., Anselmetti, Y., Bast, J., Dumas, Z., Galtier, N., Jaron, K. S., … Schön, I. (2021). First annotated draft genomes of nonmarine ostracods (Ostracoda, Crustacea) with different reproductive modes. G3-GENES GENOMES GENETICS, 11(4). https://doi.org/10.1093/g3journal/jkab043
Chicago author-date
Tran Van, Patrick, Yoann Anselmetti, Jens Bast, Zoé Dumas, Nicolas Galtier, Kamil S Jaron, Koenraad Martens, et al. 2021. “First Annotated Draft Genomes of Nonmarine Ostracods (Ostracoda, Crustacea) with Different Reproductive Modes.” Edited by B J Andrews. G3-GENES GENOMES GENETICS 11 (4). https://doi.org/10.1093/g3journal/jkab043.
Chicago author-date (all authors)
Tran Van, Patrick, Yoann Anselmetti, Jens Bast, Zoé Dumas, Nicolas Galtier, Kamil S Jaron, Koenraad Martens, Darren J Parker, Marc Robinson-Rechavi, Tanja Schwander, Paul Simion, and Isa Schön. 2021. “First Annotated Draft Genomes of Nonmarine Ostracods (Ostracoda, Crustacea) with Different Reproductive Modes.” Ed by. B J Andrews. G3-GENES GENOMES GENETICS 11 (4). doi:10.1093/g3journal/jkab043.
Vancouver
1.
Tran Van P, Anselmetti Y, Bast J, Dumas Z, Galtier N, Jaron KS, et al. First annotated draft genomes of nonmarine ostracods (Ostracoda, Crustacea) with different reproductive modes. Andrews BJ, editor. G3-GENES GENOMES GENETICS. 2021;11(4).
IEEE
[1]
P. Tran Van et al., “First annotated draft genomes of nonmarine ostracods (Ostracoda, Crustacea) with different reproductive modes,” G3-GENES GENOMES GENETICS, vol. 11, no. 4, 2021.
@article{01GXX3S01V9QE90RHX4R371BS4,
  abstract     = {{Ostracods are one of the oldest crustacean groups with an excellent fossil record and high importance for phylogenetic analyses but genome resources for this class are still lacking. We have successfully assembled and annotated the first reference genomes for three species of nonmarine ostracods; two with obligate sexual reproduction (Cyprideis torosa and Notodromas monacha) and the putative ancient asexual Darwinula stevensoni. This kind of genomic research has so far been impeded by the small size of most ostracods and the absence of genetic resources such as linkage maps or BAC libraries that were available for other crustaceans. For genome assembly, we used an Illumina-based sequencing technology, resulting in assemblies of similar sizes for the three species (335-382 Mb) and with scaffold numbers and their N50 (19-56 kb) in the same orders of magnitude. Gene annotations were guided by transcriptome data from each species. The three assemblies are relatively complete with BUSCO scores of 92-96. The number of predicted genes (13,771-17,776) is in the same range as Branchiopoda genomes but lower than in most malacostracan genomes. These three reference genomes from nonmarine ostracods provide the urgently needed basis to further develop ostracods as models for evolutionary and ecological research.}},
  articleno    = {{jkab043}},
  author       = {{Tran Van, Patrick and Anselmetti, Yoann and Bast, Jens and Dumas, Zoé and Galtier, Nicolas and Jaron, Kamil S and Martens, Koenraad and Parker, Darren J and Robinson-Rechavi, Marc and Schwander, Tanja and Simion, Paul and Schön, Isa}},
  editor       = {{Andrews, B J}},
  issn         = {{2160-1836}},
  journal      = {{G3-GENES GENOMES GENETICS}},
  keywords     = {{Genetics (clinical),Genetics,Molecular Biology,ancient asexual,sexual,Darwinula stevensoni,Cyprideis torosa,DARWINULA-STEVENSONI CRUSTACEA,CYPRIDEIS-TOROSA JONES,ASEXUAL REPRODUCTION,LIFE-CYCLE,DNA-REPAIR,ANCIENT,POPULATION,EVOLUTION,SEQUENCE,SEX}},
  language     = {{eng}},
  number       = {{4}},
  pages        = {{9}},
  title        = {{First annotated draft genomes of nonmarine ostracods (Ostracoda, Crustacea) with different reproductive modes}},
  url          = {{http://doi.org/10.1093/g3journal/jkab043}},
  volume       = {{11}},
  year         = {{2021}},
}
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