A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod <i>Darwinula stevensoni</i>
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 <i>Darwinula stevensoni</i>. We examined long contiguous stretches of DN...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-03-01
|
| Series: | Genes |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2073-4425/12/3/401 |
| _version_ | 1797541742371667968 |
|---|---|
| author | Isa Schön Fernando Rodriguez Matthew Dunn Koen Martens Michael Shribak Irina R. Arkhipova |
| author_facet | Isa Schön Fernando Rodriguez Matthew Dunn Koen Martens Michael Shribak Irina R. Arkhipova |
| author_sort | Isa Schön |
| collection | DOAJ |
| description | 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 <i>Darwinula stevensoni</i>. 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. |
| first_indexed | 2024-03-10T13:20:04Z |
| format | Article |
| id | doaj.art-2979879d3119412982e6029d1267f255 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T13:20:04Z |
| publishDate | 2021-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-2979879d3119412982e6029d1267f2552023-11-21T10:04:46ZengMDPI AGGenes2073-44252021-03-0112340110.3390/genes12030401A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod <i>Darwinula stevensoni</i>Isa Schön0Fernando Rodriguez1Matthew Dunn2Koen Martens3Michael Shribak4Irina R. Arkhipova5Freshwater Biology, OD Nature, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000 Brussels, BelgiumMarine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USAMarine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USAFreshwater Biology, OD Nature, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000 Brussels, BelgiumMarine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USAMarine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USAHow 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 <i>Darwinula stevensoni</i>. 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.https://www.mdpi.com/2073-4425/12/3/401transposable elementsretrotransposonsDNA transposonscrustaceansasexuality |
| spellingShingle | Isa Schön Fernando Rodriguez Matthew Dunn Koen Martens Michael Shribak Irina R. Arkhipova A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod <i>Darwinula stevensoni</i> Genes transposable elements retrotransposons DNA transposons crustaceans asexuality |
| title | A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod <i>Darwinula stevensoni</i> |
| title_full | A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod <i>Darwinula stevensoni</i> |
| title_fullStr | A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod <i>Darwinula stevensoni</i> |
| title_full_unstemmed | A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod <i>Darwinula stevensoni</i> |
| title_short | A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod <i>Darwinula stevensoni</i> |
| title_sort | survey of transposon landscapes in the putative ancient asexual ostracod i darwinula stevensoni i |
| topic | transposable elements retrotransposons DNA transposons crustaceans asexuality |
| url | https://www.mdpi.com/2073-4425/12/3/401 |
| work_keys_str_mv | AT isaschon asurveyoftransposonlandscapesintheputativeancientasexualostracodidarwinulastevensonii AT fernandorodriguez asurveyoftransposonlandscapesintheputativeancientasexualostracodidarwinulastevensonii AT matthewdunn asurveyoftransposonlandscapesintheputativeancientasexualostracodidarwinulastevensonii AT koenmartens asurveyoftransposonlandscapesintheputativeancientasexualostracodidarwinulastevensonii AT michaelshribak asurveyoftransposonlandscapesintheputativeancientasexualostracodidarwinulastevensonii AT irinararkhipova asurveyoftransposonlandscapesintheputativeancientasexualostracodidarwinulastevensonii AT isaschon surveyoftransposonlandscapesintheputativeancientasexualostracodidarwinulastevensonii AT fernandorodriguez surveyoftransposonlandscapesintheputativeancientasexualostracodidarwinulastevensonii AT matthewdunn surveyoftransposonlandscapesintheputativeancientasexualostracodidarwinulastevensonii AT koenmartens surveyoftransposonlandscapesintheputativeancientasexualostracodidarwinulastevensonii AT michaelshribak surveyoftransposonlandscapesintheputativeancientasexualostracodidarwinulastevensonii AT irinararkhipova surveyoftransposonlandscapesintheputativeancientasexualostracodidarwinulastevensonii |