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

Patrick Tran Van,Kamil S Jaron,Paul Simion,Zoé Dumas,Nicolas Galtier,Marc Robinson-Rechavi,Isa Schön,Darren J Parker,Jens Bast,Koen Martens,Yoann Anselmetti,Tanja Schwander

doi:10.1093/g3journal/jkab043

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.

Highlights

Relevance of ostracodsOstracoda are small, bivalved crustaceans, widely occurring in almost all aquatic habitats as part of the meiobenthos and periphyton
Their calcified valves are preserved as microfossils, making them the extant arthropod group with the most extensive fossil record
The group has an estimated (Cambrian) age of c. 500 myr according to a molecular clock (Oakley et al 2013), and c. 450 myr (Ordovician; Maddocks 1982) to 509 myr (Wolfe et al 2016) according to the fossil record. This makes them one of the oldest extant pancrustacean groups (Figure 1). Because of their excellent fossil data, evolutionary events can be dated with real-time estimates making ostracods ideal models for evolutionary research (Butlin and Menozzi 2000; Oakley and Cunningham 2002; Oakley et al 2013; Schon and Martens 2016)

Summary

Introduction

Ostracoda are small, bivalved crustaceans, widely occurring in almost all aquatic habitats as part of the meiobenthos and periphyton. Darwinula stevensoni is the best investigated darwinulid ostracod so far and has been the subject of ecological (Van Doninck et al 2002, 2003a, 2003b; Van den Broecke et al 2013) and molecular research using DNA sequence data from single genes (Schon et al 1998; 2003; Martens et al 2005; Schon et al 2012) These studies revealed that D. stevensoni is most likely apomictic or functionally mitotic (following the definition of apomixis in animals as in Schon et al 2009a). Our aim here is to provide the first reference genome data of nonmarine ostracods from three different species with varying reproductive modes: the putative ancient asexual D. stevensoni and the two obligate sexuals, C. torosa and N. monacha. We generate transcriptomes of these species to facilitate genome annotations

Materials and methods

Results and discussion

Conclusions

Findings

Literature cited