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

By

Hinsinger, Damien
Strijk, Joeri

Type

Article

Date of Publication

2019

Original Publication

PhytoKeys

Volume

132

Pages

75--89

Subjects

diversification , Fagaceae , Genomic Diversity , Genomic Resources , phylogenomics , Plastid genome , Quercus , Sections , SNPs , taxonomy

Contributed by

Pensoft Publishers

Language

English

Published by

Sofia, Bulgaria Pensoft Publishers [2010]-

Identifiers

DOI: https://doi.org/10.3897/phytokeys.132.36365

 

Abstract

The genusQuercusL. 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 ofQuercus xanthocladaand compared its sequence with those available from other main taxonomic groups inQuercus. 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.