Open AccessAssembly and analysis of a qingke reference genome demonstrate its close genetic relation to modern cultivated barley
Author(s) -
Dai Fei,
Wang Xiaolei,
Zhang XiaoQi,
Chen Zhonghua,
Nevo Eviatar,
Jin Gulei,
Wu Dezhi,
Li Chengdao,
Zhang Guoping
Publication year - 2018
Publication title -
plant biotechnology journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.525
H-Index - 115
eISSN - 1467-7652
pISSN - 1467-7644
DOI - 10.1111/pbi.12826
Subject(s) - biology , genome , reference genome , genetics , genetic diversity , gene , whole genome sequencing , hordeum vulgare , sequence assembly , genome size , computational biology , botany , poaceae , population , gene expression , demography , transcriptome , sociology
Summary Qingke , the local name of hulless barley in the Tibetan Plateau, is a staple food for Tibetans. The availability of its reference genome sequences could be useful for studies on breeding and molecular evolution. Taking advantage of the third‐generation sequencer (PacBio), we de novo assembled a 4.84‐Gb genome sequence of qingke, cv . Zangqing320 and anchored a 4.59‐Gb sequence to seven chromosomes. Of the 46,787 annotated ‘high‐confidence’ genes, 31 564 were validated by RNA ‐sequencing data of 39 wild and cultivated barley genotypes with wide genetic diversity, and the results were also confirmed by nonredundant protein database from NCBI . As some gaps in the reference genome of Morex were covered in the reference genome of Zangqing320 by PacBio reads, we believe that the Zangqing320 genome provides the useful supplements for the Morex genome. Using the qingke genome as a reference, we conducted a genome comparison, revealing a close genetic relationship between a hulled barley ( cv . Morex) and a hulless barley ( cv . Zangqing320), which is strongly supported by the low‐diversity regions in the two genomes. Considering the origin of Morex from its breeding pedigree, we then demonstrated a close genomic relationship between modern cultivated barley and qingke . Given this genomic relationship and the large genetic diversity between qingke and modern cultivated barley, we propose that qingke could provide elite genes for barley improvement.