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Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming

Abstract. The genus Quercus L. contains several of the most economically important species for timber production in the Northern Hemisphere. It was one of the first genera described, but genetic diversity at a global scale within and amongst oak species remains unclear, despite numerous regional or...

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Autores principales: Hinsinger, Damien Daniel, Strijk, Joeri Sergej
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Pensoft Publishers 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6783484/
https://www.ncbi.nlm.nih.gov/pubmed/31607787
http://dx.doi.org/10.3897/phytokeys.132.36365
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author Hinsinger, Damien Daniel
Strijk, Joeri Sergej
author_facet Hinsinger, Damien Daniel
Strijk, Joeri Sergej
author_sort Hinsinger, Damien Daniel
collection PubMed
description Abstract. The genus Quercus L. contains several of the most economically important species for timber production in the Northern Hemisphere. It was one of the first genera described, but genetic diversity at a global scale within and amongst oak species remains unclear, despite numerous regional or species-specific assessments. To evaluate global plastid diversity in oaks, we sequenced the complete chloroplast of Quercus xanthoclada and compared its sequence with those available from other main taxonomic groups in Quercus. We quantify genomic divergence amongst oaks and performed a sliding window analysis to detect the most variable regions amongst members of the various clades, as well as divergent regions occurring in specific pairs of species. We identified private and shared SNPs amongst oaks species and sections and stress the need for a large global assessment of genetic diversity in this economically and ecologically important genus.
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spelling pubmed-67834842019-10-11 Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming Hinsinger, Damien Daniel Strijk, Joeri Sergej PhytoKeys Research Article Abstract. The genus Quercus L. contains several of the most economically important species for timber production in the Northern Hemisphere. It was one of the first genera described, but genetic diversity at a global scale within and amongst oak species remains unclear, despite numerous regional or species-specific assessments. To evaluate global plastid diversity in oaks, we sequenced the complete chloroplast of Quercus xanthoclada and compared its sequence with those available from other main taxonomic groups in Quercus. We quantify genomic divergence amongst oaks and performed a sliding window analysis to detect the most variable regions amongst members of the various clades, as well as divergent regions occurring in specific pairs of species. We identified private and shared SNPs amongst oaks species and sections and stress the need for a large global assessment of genetic diversity in this economically and ecologically important genus. Pensoft Publishers 2019-10-01 /pmc/articles/PMC6783484/ /pubmed/31607787 http://dx.doi.org/10.3897/phytokeys.132.36365 Text en Damien Daniel Hinsinger, Joeri Sergej Strijk http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Hinsinger, Damien Daniel
Strijk, Joeri Sergej
Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming
title Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming
title_full Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming
title_fullStr Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming
title_full_unstemmed Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming
title_short Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming
title_sort plastome of quercus xanthoclada and comparison of genomic diversity amongst selected quercus species using genome skimming
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6783484/
https://www.ncbi.nlm.nih.gov/pubmed/31607787
http://dx.doi.org/10.3897/phytokeys.132.36365
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