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

Abstract

How asexual reproduction shapes transposable element (TE) content and diversity in eukaryotic genomes remains debated. We performed an initial survey of TE load and diversity in the putative ancient asexual ostracod Darwinula stevensoni. We examined long contiguous stretches of DNA in clones from a genomic fosmid library, totaling about 2.5 Mb, and supplemented these data with results on TE abundance and diversity from an Illumina draft genome. In contrast to other TE studies in putatively ancient asexuals, which revealed relatively low TE content, we found that at least 19% of the fosmid dataset and 26% of the genome assembly corresponded to known transposons. We observed a high diversity of transposon families, including LINE, gypsy, PLE, mariner/Tc, hAT, CMC, Sola2, Ginger, Merlin, Harbinger, MITEs and helitrons, with the prevalence of DNA transposons. The predominantly low levels of sequence diversity indicate that many TEs are or have recently been active. In the fosmid data, no correlation was found between telomeric repeats and non-LTR retrotransposons, which are present near telomeres in other taxa. Most TEs in the fosmid data were located outside of introns and almost none were found in exons. We also report an N-terminal Myb/SANT-like DNA-binding domain in site-specific R4/Dong non-LTR retrotransposons. Although initial results on transposable loads need to be verified with high quality draft genomes, this study provides important first insights into TE dynamics in putative ancient asexual ostracods.

An Ancient Clade of Penelope-Like Retroelements with Permuted Domains Is Present in the Green Lineage and Protists, and Dominates Many Invertebrate Genomes

“…While cataloguing PLEs in several recently sequenced genomes, such as an acanthocephalan ( Pomphorhynchus laevis ) and a bdelloid rotifer ( Didymodactylos carnosus ), as well as a darwinulid ostracod ( Darwinula stevensoni ) ( Mauer et al 2020 ; Nowell et al 2021 ; Schön et al 2021) , we noticed the absence of the GIY–YIG domain at the C-terminus of several PLEs, which is typically indicative of EN− PLEs. In these cases, however, extending the 5′-end of the frequently truncated PLE copies revealed a conserved N-terminal GIY–YIG EN domain, typically 220–275 aa in length.…”

An ancient clade ofPenelope-like retroelements with permuted domains is present in the green lineage and protists, and dominates many invertebrate genomes

“…While cataloguing PLEs in several recently sequenced genomes, such as the acanthocephalan (Pomphorhynchus laevis) and a bdelloid rotifer (Didymodactylos carnosus), as well as a darwinulid ostracod (Darwinula stevensoni) (Mauer, et al 2020;Nowell, et al 2021;Schön, et al 2021), we noticed the absence of the GIY-YIG domain at the C-terminus of several PLEs, which is typically indicative of EN-PLEs. In these cases, however, extending the 5'-end of the frequently truncated PLE copies revealed a conserved N-terminal GIY-YIG EN domain, typically 220-275 aa in length.…”

Sexual Signals Persist over Deep Time: Ancient Co-option of Bioluminescence for Courtship Displays in Cypridinid Ostracods

“…We included outgroups from all four noncypridinid families of Myodocopida, sequencing one species each of Rutidermatidae and Sarsiellidae, and two of Philomedidae. We also used published sequence data from a cylindroleberid (SRX2085850) ( Schwentner et al 2018 ) and predicted proteins from the genome of Darwinula stevensoni (ENA PRJEB38362) ( Schön et al 2021 ). For transcriptome sequencing, we combined RNA from whole bodies of up to 10 pooled individuals (collected by signal but with identity corroborated by morphological features).…”