Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine.

<h4>Background</h4>Numerous endemic mammals, including dwarf elephants, goats, hippos and deers, evolved in isolation in the Mediterranean islands during the Pliocene and Pleistocene. Most of them subsequently became extinct during the Holocene. Recently developed high-throughput sequenc...

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Autores principales:	Oscar Ramírez, Elena Gigli, Pere Bover, Josep Antoni Alcover, Jaume Bertranpetit, Jose Castresana, Carles Lalueza-Fox
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2009
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5ab6c14d9a6543398ae70653707846fe
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spelling	oai:doaj.org-article:5ab6c14d9a6543398ae70653707846fe2021-11-25T06:22:31ZPaleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine.1932-620310.1371/journal.pone.0005670https://doaj.org/article/5ab6c14d9a6543398ae70653707846fe2009-05-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19461892/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Numerous endemic mammals, including dwarf elephants, goats, hippos and deers, evolved in isolation in the Mediterranean islands during the Pliocene and Pleistocene. Most of them subsequently became extinct during the Holocene. Recently developed high-throughput sequencing technologies could provide a unique tool for retrieving genomic data from these extinct species, making it possible to study their evolutionary history and the genetic bases underlying their particular, sometimes unique, adaptations. METHODOLOGY/PRINCIPALS FINDINGS: A DNA extraction of a approximately 6,000 year-old bone sample from an extinct caprine (Myotragus balearicus) from the Balearic Islands in the Western Mediterranean, has been subjected to shotgun sequencing with the GS FLX 454 platform. Only 0.27% of the resulting sequences, identified from alignments with the cow genome and comprising 15,832 nucleotides, with an average length of 60 nucleotides, proved to be endogenous.<h4>Conclusions</h4>A phylogenetic tree generated with Myotragus sequences and those from other artiodactyls displays an identical topology to that generated from mitochondrial DNA data. Despite being in an unfavourable thermal environment, which explains the low yield of endogenous sequences, our study demonstrates that it is possible to obtain genomic data from extinct species from temperate regions.Oscar RamírezElena GigliPere BoverJosep Antoni AlcoverJaume BertranpetitJose CastresanaCarles Lalueza-FoxPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 4, Iss 5, p e5670 (2009)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Oscar Ramírez Elena Gigli Pere Bover Josep Antoni Alcover Jaume Bertranpetit Jose Castresana Carles Lalueza-Fox Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine.
description	<h4>Background</h4>Numerous endemic mammals, including dwarf elephants, goats, hippos and deers, evolved in isolation in the Mediterranean islands during the Pliocene and Pleistocene. Most of them subsequently became extinct during the Holocene. Recently developed high-throughput sequencing technologies could provide a unique tool for retrieving genomic data from these extinct species, making it possible to study their evolutionary history and the genetic bases underlying their particular, sometimes unique, adaptations. METHODOLOGY/PRINCIPALS FINDINGS: A DNA extraction of a approximately 6,000 year-old bone sample from an extinct caprine (Myotragus balearicus) from the Balearic Islands in the Western Mediterranean, has been subjected to shotgun sequencing with the GS FLX 454 platform. Only 0.27% of the resulting sequences, identified from alignments with the cow genome and comprising 15,832 nucleotides, with an average length of 60 nucleotides, proved to be endogenous.<h4>Conclusions</h4>A phylogenetic tree generated with Myotragus sequences and those from other artiodactyls displays an identical topology to that generated from mitochondrial DNA data. Despite being in an unfavourable thermal environment, which explains the low yield of endogenous sequences, our study demonstrates that it is possible to obtain genomic data from extinct species from temperate regions.
format	article
author	Oscar Ramírez Elena Gigli Pere Bover Josep Antoni Alcover Jaume Bertranpetit Jose Castresana Carles Lalueza-Fox
author_facet	Oscar Ramírez Elena Gigli Pere Bover Josep Antoni Alcover Jaume Bertranpetit Jose Castresana Carles Lalueza-Fox
author_sort	Oscar Ramírez
title	Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine.
title_short	Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine.
title_full	Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine.
title_fullStr	Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine.
title_full_unstemmed	Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine.
title_sort	paleogenomics in a temperate environment: shotgun sequencing from an extinct mediterranean caprine.
publisher	Public Library of Science (PLoS)
publishDate	2009
url	https://doaj.org/article/5ab6c14d9a6543398ae70653707846fe
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Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine.

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