Evolution of Two Short Interspersed Elements in Callorhinchus milii (Chondrichthyes, Holocephali) and Related Elements in Sharks and the Coelacanth

Genome Biology and Evolution
Andrea LuchettiBarbara Mantovani

Abstract

Short interspersed elements (SINEs) are non-autonomous retrotransposons. Although they usually show fast evolutionary rates, in some instances highly conserved domains (HCDs) have been observed in elements with otherwise divergent sequences and from distantly related species. Here, we document the life history of two HCD-SINE families in the elephant shark Callorhinchus milii, one specific to the holocephalan lineage (CmiSINEs) and another one (SacSINE1-CM) with homologous elements in sharks and the coelacanth (SacSINE1s, LmeSINE1s). The analyses of their relationships indicated that these elements share the same 3'-tail, which would have allowed both elements to rise to high copy number by exploiting the C. milii L2-2_CM long interspersed element (LINE) enzymes. Molecular clock analysis on SINE activity in C. milii genome evidenced two replication bursts occurring right after two major events in the holocephalan evolution: the end-Permian mass extinction and the radiation of modern Holocephali. Accordingly, the same analysis on the coelacanth homologous elements, LmeSINE1, identified a replication wave close to the split age of the two extant Latimeria species. The genomic distribution of the studied SINEs pointed out contrast...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Mar 17, 1999·Proceedings of the National Academy of Sciences of the United States of America·N Gilbert, D Labuda
Jul 16, 1999·Molecular Biology and Evolution·M LabradorA Fontdevila
Apr 25, 2000·Journal of Molecular Biology·N Gilbert, D Labuda
Nov 9, 2001·Annual Review of Genetics·M Negroni, H Buc
Jul 27, 2002·Science·Samuel AparicioSydney Brenner
Apr 8, 2003·Molecular Biology and Evolution·Vladimir V Kapitonov, Jerzy Jurka
Aug 12, 2005·Cytogenetic and Genome Research·M-A GrandbastienC Mhiri
Aug 12, 2005·Cytogenetic and Genome Research·K Ohshima, N Okada
May 24, 2006·Genome Research·Hidenori NishiharaNorihiro Okada
Nov 7, 2007·Nature Reviews. Genetics·Thomas WickerAlan H Schulman
Mar 13, 2008·Proceedings of the National Academy of Sciences of the United States of America·Takeshi SasakiNorihiro Okada
Mar 15, 2008·Genome Research·David A RayNancy L Craig
May 9, 2008·Genome Research·Jürgen SchmitzJürgen Brosius
May 28, 2009·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·David W ZehYoichi Ishida
Jan 28, 2010·Gene·Rita RebolloCristina Vieira
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Dec 4, 2010·BMC Evolutionary Biology·Gennady ChurakovJürgen Schmitz
Apr 23, 2011·Molecular Biology and Evolution·Oliver Piskurek, Daniel J Jackson
Jun 2, 2011·Mobile DNA·Keith R Oliver, Wayne K Greene
Jun 16, 2011·Heredity·D A Kramerov, N S Vassetzky
Sep 21, 2011·Biology Direct·Jerzy JurkaKenji K Kojima
Dec 17, 2011·Science·Benjamin L KingRandall D Dahn
Jul 5, 2012·Genome Dynamics·J Schmitz
Dec 4, 2012·Nucleic Acids Research·Nikita S Vassetzky, Dmitri A Kramerov
Apr 20, 2013·Nature·Chris T AmemiyaKerstin Lindblad-Toh
Aug 29, 2013·Genomics·Andrea Luchetti, Barbara Mantovani
Jan 10, 2014·Nature·Byrappa VenkateshWesley C Warren
Aug 5, 2014·Nature Structural & Molecular Biology·Biswajoy Roy-ChaudhuriMark A Kay
Oct 8, 2014·Journal of Evolutionary Biology·A Belyayev

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Citations

Oct 6, 2018·Molecular Ecology Resources·Castrense SavojardoBarbara Mantovani
Jun 2, 2020·Current Genomics·Luis M Vaschetto, Natalia Ortiz

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Methods Mentioned

BETA
environmental stresses

Software Mentioned

intersectBed
RepeatMasker
TinT
BEDTools
BLAST Search
BLAST

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