G C A T T A C G G C A T genes Article A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod Darwinula stevensoni Isa Schön 1,2,*,† , Fernando Rodriguez 3,† , Matthew Dunn 3, Koen Martens 1,4 , Michael Shribak 3 and Irina R. Arkhipova 3 1 Freshwater Biology, OD Nature, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000 Brussels, Belgium; [email protected] 2 Center of Environmental Sciences (CMK), University of Hasselt, 3590 Diepenbeek, Belgium 3 Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA; [email protected] (F.R.); [email protected] (M.D.); [email protected] (M.S.); [email protected] (I.R.A.) 4 Dept Biology, University of Ghent, 9000 Ghent, Belgium * Correspondence: [email protected] † These authors contributed equally to this work. 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, Citation: Schön, I.; Rodriguez, F.; mariner/Tc, hAT, CMC, Sola2, Ginger, Merlin, Harbinger, MITEs and helitrons, with the prevalence Dunn, M.; Martens, K.; Shribak, M.; of DNA transposons. The predominantly low levels of sequence diversity indicate that many TEs Arkhipova, I.R. A Survey of are or have recently been active. In the fosmid data, no correlation was found between telomeric Transposon Landscapes in the repeats and non-LTR retrotransposons, which are present near telomeres in other taxa. Most TEs Putative Ancient Asexual Ostracod in the fosmid data were located outside of introns and almost none were found in exons. We also Darwinula stevensoni. Genes 2021, 12, report an N-terminal Myb/SANT-like DNA-binding domain in site-specific R4/Dong non-LTR 401. https://doi.org/10.3390/ genes12030401 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 Academic Editor: Zoltan Ivics asexual ostracods. Received: 10 February 2021 Keywords: transposable elements; retrotransposons; DNA transposons; crustaceans; asexuality Accepted: 6 March 2021 Published: 11 March 2021 Publisher’s Note: MDPI stays neutral 1. Introduction with regard to jurisdictional claims in The influence of reproductive mode on transposon content and distribution in eukary- published maps and institutional affil- otic genomes remains a subject of debate as it seems to be shaped by several evolutionary iations. forces acting in opposite directions. Sexual reproduction is expected to greatly facilitate the spread of vertically transmitted transposons in populations [1], as has been experimentally shown in yeast (see for example [2] or [3]). All asexuals originate from sexual ancestors. If they inherited transposons, the absence Copyright: © 2021 by the authors. of meiotic recombination should lead to reduced efficacy of selection and accumulation of Licensee MDPI, Basel, Switzerland. deleterious mutations [4] and transposons, at least in finite populations [5,6]. Empirical This article is an open access article evidence for these predictions comes from non-recombining sex chromosomes (e.g., [7]) distributed under the terms and and other non-recombining parts of the genome [8,9]. Such unrestrained transposable conditions of the Creative Commons element (TE) proliferation should eventually drive asexual lineages to extinction unless Attribution (CC BY) license (https:// asexual hosts can keep TE copy numbers under tight control [10–12], with putative ancient creativecommons.org/licenses/by/ asexual bdelloids as the most striking example [10,13,14] of having reduced numbers of 4.0/). Genes 2021, 12, 401. https://doi.org/10.3390/genes12030401 https://www.mdpi.com/journal/genes Genes 2021, 12, x FOR PEER REVIEW 2 of 17 Genes 2021, 12, 401 2 of 16 putative ancient asexual bdelloids as the most striking example [10,13,14] of having re- duced numbers of vertically transmitted retrotransposons while they still harbor some DNA transposons that can be horizontally transmitted. In line with these predictions, vertically transmitted retrotransposons while they still harbor some DNA transposons sexual Daphnia pulex have higher loads of DNA transposons [15], LTR retrotransposons that can be horizontally transmitted. In line with these predictions, sexual Daphnia pulex [16] or more insertion polymorphisms of transposons [17] than their asexual counter- have higher loads of DNA transposons [15], LTR retrotransposons [16] or more insertion parts. Comparative genomic studies on asexual and sexual arthropods [18], nematodes polymorphisms of transposons [17] than their asexual counterparts. Comparative genomic [19], evening primroses [20] and green algae [21], however, did not show any significant studies on asexual and sexual arthropods [18], nematodes [19], evening primroses [20] and effect of the reproductive mode on transposon content and evolution. Other genomic green algae [21], however, did not show any significant effect of the reproductive mode studieson transposon reported content higher and transposon evolution. loads Other in genomicasexuals, studiesas for example reported for higher root-knot transposon nem- atodesloads in [22] asexuals, or parasitic as for wasps example [23]. for root-knot nematodes [22] or parasitic wasps [23]. TheseThese contrasting resultsresults can can be be partly partly explained explained by differentby different lineage lineage ages [ages24]. Purg-[24]. Purginging of transposons of transposons in asexuals in asexuals can takecan atake very a longvery time,long time, and transposons and transposons are expected are ex- pectedto accumulate to accumulate if they if cannot they cannot be removed be removed [25]. Theoretical[25]. Theoretical studies studies [26,27 [26,27]] and anand ever- an ever-increasingincreasing number number of genomic of genomic studies studies from fr differentom different host host organisms organisms [28,29 [28,29]] suggest suggest that thatadditional additional factors factors besides besides the reproductive the reproducti modeve mode will alsowill influencealso influence transposon transposon diversity di- versityand load, and such load, as such initial as transposon initial transposon load in sexualload in ancestors, sexual ancestors, DNA methylation, DNA methylation, popula- populationtion size [30 size], environmental [30], environmental fluctuations fluctuations [27], strengths[27], strengths of selection of selection and driftand drift [19], [19], and andmolecular molecular defense defense mechanisms mechanisms against against transposable transposable elements. elements. DNA DNA transposons transposons are more are morefrequently frequently transmitted transmitted horizontally horizontally (as in (as the in example the example of insects; of insects; [31]) than [31]) retrotrans- than re- trotransposons,posons, and are and expected are expected to be less to affectedbe less affected by the reproductive by the reproductive mode. mode. ToTo better understandunderstand transposontransposon evolution, evolution, their their molecular molecular characteristics characteristics and and biolog- bio- logicalical effects, effects, additional additionalin vivoin vivoand andin vitro in vitrostudies studies are thusare thus required required [28], especially[28], especially from fromnon-model non-model organisms. organisms. The The continuous continuous increase increase of genomic of genomic data data has has also also revealed revealed the theextent extent of lineage-specific of lineage-specific transposon transposon diversities, diversities, which which further further increases increases the methodolog-the method- ologicalical challenges challenges of analyzing of analyzing these these elements elemen [28ts ][28] and and provides provides additional additional motivation motivation for forstudying studying them them in ain wide a wide range range of organisms.of organisms. TheThe ostracod ostracod family family Darwinulidae Darwinulidae is is one one of of the few examples of putative ancient asexualasexual animals [[32–35],32–35], toto which which bdelloid bdelloid rotifers rotifers also also belong belong [36 ].[36]. Fossil Fossil data data indicate indicate that thatsome some darwinulids darwinulids might might have have been asexualbeen asexual for 200 for million 200 million years [years37], and [37], the and type the species type speciesof this familyof this family that is investigatedthat is investigated here, Darwinula here, Darwinula stevensoni stevensoni(Figure (Figure1), might 1), might have beenhave beenasexual asexual for about for 25about million 25 million years [38 years]. There [38]. is onlyThere one is studyonly one on transposable study on transposable elements of elementsdarwinulid of ostracodsdarwinulid describing ostracods novel describi LINE-likeng novel retroelements LINE-like [ 39re],troelements and long, contiguous