Mobile Element Evolution Playing Jigsaw—SINEs in Gastropod and Bivalve Mollusks

SINEs (Short INterspersed Elements) are widely distributed among eukaryotes. Some SINE families are organized in superfamilies characterized by a shared central domain. These central domains are conserved across species, classes, and even phyla. Here we report the identification of two novel such su...

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Main Authors:	Matetovici, Irina, Sajgo, Szilard, Ianc, Bianca, Ochis, Cornelia, Bulzu, Paul, Popescu, Octavian, Damert, Annette
Format:	Online
Language:	English
Published:	Oxford University Press 2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4758252/

id	pubmed-4758252
recordtype	oai_dc
spelling	pubmed-47582522016-03-04 Mobile Element Evolution Playing Jigsaw—SINEs in Gastropod and Bivalve Mollusks Matetovici, Irina Sajgo, Szilard Ianc, Bianca Ochis, Cornelia Bulzu, Paul Popescu, Octavian Damert, Annette Research Article SINEs (Short INterspersed Elements) are widely distributed among eukaryotes. Some SINE families are organized in superfamilies characterized by a shared central domain. These central domains are conserved across species, classes, and even phyla. Here we report the identification of two novel such superfamilies in the genomes of gastropod and bivalve mollusks. The central conserved domain of the first superfamily is present in SINEs in Caenogastropoda and Vetigastropoda as well as in all four subclasses of Bivalvia. We designated the domain MESC (Romanian for MElc—snail and SCoica—mussel) because it appears to be restricted to snails and mussels. The second superfamily is restricted to Caenogastropoda. Its central conserved domain—Snail—is related to the Nin-DC domain. Furthermore, we provide evidence that a 40-bp subdomain of the SINE V-domain is conserved in SINEs in mollusks and arthropods. It is predicted to form a stable stem-loop structure that is preserved in the context of the overall SINE RNA secondary structure in invertebrates. Our analysis also recovered short retrotransposons with a Long INterspersed Element (LINE)-derived 5′ end. These share the body and/or the tail with transfer RNA (tRNA)-derived SINEs within and across species. Finally, we identified CORE SINEs in gastropods and bivalves—extending the distribution range of this superfamily. Oxford University Press 2016-01-06 /pmc/articles/PMC4758252/ /pubmed/26739168 http://dx.doi.org/10.1093/gbe/evv257 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Matetovici, Irina Sajgo, Szilard Ianc, Bianca Ochis, Cornelia Bulzu, Paul Popescu, Octavian Damert, Annette
spellingShingle	Matetovici, Irina Sajgo, Szilard Ianc, Bianca Ochis, Cornelia Bulzu, Paul Popescu, Octavian Damert, Annette Mobile Element Evolution Playing Jigsaw—SINEs in Gastropod and Bivalve Mollusks
author_facet	Matetovici, Irina Sajgo, Szilard Ianc, Bianca Ochis, Cornelia Bulzu, Paul Popescu, Octavian Damert, Annette
author_sort	Matetovici, Irina
title	Mobile Element Evolution Playing Jigsaw—SINEs in Gastropod and Bivalve Mollusks
title_short	Mobile Element Evolution Playing Jigsaw—SINEs in Gastropod and Bivalve Mollusks
title_full	Mobile Element Evolution Playing Jigsaw—SINEs in Gastropod and Bivalve Mollusks
title_fullStr	Mobile Element Evolution Playing Jigsaw—SINEs in Gastropod and Bivalve Mollusks
title_full_unstemmed	Mobile Element Evolution Playing Jigsaw—SINEs in Gastropod and Bivalve Mollusks
title_sort	mobile element evolution playing jigsaw—sines in gastropod and bivalve mollusks
description	SINEs (Short INterspersed Elements) are widely distributed among eukaryotes. Some SINE families are organized in superfamilies characterized by a shared central domain. These central domains are conserved across species, classes, and even phyla. Here we report the identification of two novel such superfamilies in the genomes of gastropod and bivalve mollusks. The central conserved domain of the first superfamily is present in SINEs in Caenogastropoda and Vetigastropoda as well as in all four subclasses of Bivalvia. We designated the domain MESC (Romanian for MElc—snail and SCoica—mussel) because it appears to be restricted to snails and mussels. The second superfamily is restricted to Caenogastropoda. Its central conserved domain—Snail—is related to the Nin-DC domain. Furthermore, we provide evidence that a 40-bp subdomain of the SINE V-domain is conserved in SINEs in mollusks and arthropods. It is predicted to form a stable stem-loop structure that is preserved in the context of the overall SINE RNA secondary structure in invertebrates. Our analysis also recovered short retrotransposons with a Long INterspersed Element (LINE)-derived 5′ end. These share the body and/or the tail with transfer RNA (tRNA)-derived SINEs within and across species. Finally, we identified CORE SINEs in gastropods and bivalves—extending the distribution range of this superfamily.
publisher	Oxford University Press
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4758252/
_version_	1613540310970793984

Mobile Element Evolution Playing Jigsaw—SINEs in Gastropod and Bivalve Mollusks

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