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

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 non-marine 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 (335-382Mb) 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 non-marine ostracods provide the urgently needed basis to further develop ostracods as models for evolutionary and ecological research.

A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod Darwinula stevensoni

“…Details on potentially overlapping contigs are provided in Table S4. Our analyses revealed a high diversity of TEs in the selected clones from the fosmid library of D. stevensoni and the Illumina draft genome [45], including LINE-like retrotransposons, LTR retrotransposons, various cut-and-paste DNA transposons and Helitrons (Figure 3A,B). DNA transposons were best represented at 8.9% in the fosmids and 11.8% in the Illumina data, and belonged to Tc/mariner (most abundant, showing an excellent agreement at ~8% in both datasets; Figure 3A,B), hAT, Ginger, Merlin, Harbinger, and CMC-like DNA transposons, plus some uncharacterized DNA transposons.…”

“…Besides the fosmid DNA sequence data, we also analyzed a recently published Illumina draft genome (European Nucleotide Archive accession number PRJEB38362) of D. stevensoni [45] for its TE content and diversity. This draft genome was assembled from DNA extractions of a single female, followed by whole genome amplification to provide sufficient material for the preparation of three 2 × 125 bp paired-end libraries (average insert sizes of 250-300, 550 and 700 bp), and two mate-pair libraries (average insert sizes of 3000 and 5000 bp), which were sequenced on an Illumina HiSeq 3000 system.…”

“…This draft genome was assembled from DNA extractions of a single female, followed by whole genome amplification to provide sufficient material for the preparation of three 2 × 125 bp paired-end libraries (average insert sizes of 250-300, 550 and 700 bp), and two mate-pair libraries (average insert sizes of 3000 and 5000 bp), which were sequenced on an Illumina HiSeq 3000 system. The assembly has a size of 382.1 Mb, an N50 of 56.4 kb, an arthropod Benchmarking set of Universal Single-Copy Orthologs (BUSCO) score of 93.7% (complete single-copy genes) and consists of 62,118 scaffolds [45].…”

“…The high diversity of TEs in the fosmid data is also illustrated in 38 selected contigs containing mariner-1 (Figure 5A) and mariner-2 DNA TEs (Figure 5C,D), a mixture of DNA, LINE-like and LTR TEs (Figure 5B), and LINE-like RTE (Figure 5E) and CR1 (Figure 5F) TEs. [45]. The plot was constructed using the REPET library obtained with the Illumina assembly.…”

“…Average TE abundance estimated at the contig level was similar, with 13.7-14.7% (RepeatMasker) and 16.5-16.9% (Censor; Table S3A). [45]. The plot was constructed using the REPET library obtained with the Illumina assembly.…”