About: Stepwise evolution of two giant composite LTR-retrotransposon-like elements DA and Xiao

Facets (new session)
Description
Metadata
Settings
- owl:sameAs
- Inference Rule:

About: Stepwise evolution of two giant composite LTR-retrotransposon-like elements DA and Xiao Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Stepwise evolution of two giant composite LTR-retrotransposon-like elements DA and Xiao
Creator	Li, Xuanyang Patel, Neil Slife, Jennifer Zhao, Shaying
Source	Medline; PMC
abstract	BACKGROUND: We recently discovered two composite long terminal repeat (LTR)-retrotransposon-like elements which we named DA (~300 kb) and Xiao (~30 kb), meaning big and small in Chinese respectively. Xiao and DA (three types of DA identified) were found to have been derived from several donor sites and have spread to 30 loci in the human genome, totaling to 5 Mb. Our bioinformatics analyses with the released human, chimp, rhesus macaque, orangutan, and marmoset genomic sequences indicate that DA and Xiao emerged ~25 million years (Myr) ago. RESULTS: To better understand the evolution of these two complex elements, we investigated various internal junctions of DA and Xiao as well as orthologous genomic sites of the 30 DA/Xiao loci in non-human primates including great apes, lesser apes, Old World monkeys, New World monkeys, and a prosimian. We found that Xiao and type I DA first emerged in the genome between 25 and 18 Myr ago, whereas type II and Type III DAs emerged between 14 and 7 Myr ago. Xiao and DA were most active in great apes, with their amplification peaking during 25-14 and 14-7 Myr ago, respectively. Neither DA nor Xiao seem to have been active in the human and chimp genomes during last 6 Myr. CONCLUSION: The study has led to a more accurate age determination of the DA and Xiao elements than our previous bioinformatics analyses, and indicates that the amplification activity of the elements coincided with that of group I HERV-Es during evolution. It has also illustrated an evolutionary path with stepwise structural changes for the elements during past 25 Myr, and in doing so has shed more light on these two intriguing and complex elements that have reshaped our genome.
has issue date	2009-06-05(xsd:dateTime)
bibo:doi	10.1186/1471-2148-9-128
bibo:pmid	19500371
has license	cc-by
sha1sum (hex)	3a2fe662fce281e831bf7706e83d7b399b367167
schema:url	https://doi.org/10.1186/1471-2148-9-128
resource representing a document's title	Stepwise evolution of two giant composite LTR-retrotransposon-like elements DA and Xiao
has PubMed Central identifier	PMC2700803
has PubMed identifier	19500371
schema:publication	BMC Evol Biol
resource representing a document's body	covid:3a2fe662fce281e831bf7706e83d7b399b367167#body_text
is schema:about of	named entity 'sequences' named entity 'Xiao' named entity 'SMALL' named entity 'ELEMENTS' named entity 'GENOMIC' named entity 'OUR' named entity 'SEQUENCES' named entity 'LOCI' named entity 'elements' named entity 'meaning' named entity 'identified' named entity 'orangutan' named entity 'long terminal repeat' named entity 'retrotransposon' named entity 'human genome' named entity 'type II' named entity 'PCR' named entity 'bonobo' named entity 'draft genome' named entity 'LINEs' named entity 'PCR' named entity 'genome' named entity 'HERV' named entity 'loci' named entity 'SINEs' named entity 'type II' named entity 'chromosome' named entity 'E. coli' named entity 'Lagothrix lagotricha' named entity 'human genome' named entity 'transposon' named entity 'primers' named entity 'orangutan' named entity 'genome' named entity 'lesser apes' named entity 'genome' named entity 'loci' named entity 'great apes' named entity 'primate' named entity 'insertion sequences' named entity 'LINEs' named entity 'primers' named entity 'target site duplication' named entity 'rhesus macaque' named entity 'Lemur catta' named entity 'genome' named entity 'chromosome' named entity 'retrotransposon' named entity 'prosimian' named entity 'rhesus macaque' named entity 'primates' named entity 'chr2' named entity 'primers' named entity 'common ancestor' named entity 'Primates' named entity 'genomes' named entity 'bacteria' named entity 'type II' named entity 'genomes' named entity 'primer pairs' named entity 'bonobo' named entity 'orangutan' named entity 'PCR reaction' named entity 'TSD' named entity 'Ateles geoffroyi' named entity 'HERV' named entity 'genomes' named entity 'human lineage' named entity 'loci' named entity 'loci' named entity 'great apes' named entity 'genome' named entity 'retrotransposons' named entity 'orangutan' named entity 'PCR' named entity 'Macaca nemestrina' named entity 'genomic DNA' named entity 'lemur'

Faceted Search & Find service v1.13.91 as of Mar 24 2020

Alternative Linked Data Documents: Sponger | ODE Content Formats:

RDF

ODATA

Microdata

About

OpenLink Virtuoso version 07.20.3229 as of Jul 10 2020, on Linux (x86_64-pc-linux-gnu), Single-Server Edition (94 GB total memory)
Data on this page belongs to its respective rights holders.
Virtuoso Faceted Browser Copyright © 2009-2024 OpenLink Software