A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication

It has become clear in recent years that many genes in a given species may not be found in a single genotype thus using sequences from a single genotype as reference may not be adequate for various applications. In this study we constructed a pan-transcriptome for barley by de novo assembling 288 se...

Full description

Saved in:
Bibliographic Details
Published in:BMC genomics 2019-01, Vol.20 (1), p.12-12, Article 12
Main Authors: Ma, Yanling, Liu, Miao, Stiller, Jiri, Liu, Chunji
Format: Article
Language:English
Subjects:
Archives & records
Barley
Bioinformatics
Corn
Crop diseases
Cultivated
Cultivation
Disease resistance
Domestication
Evolution
Gene expression
Genes
Genetic aspects
Genomes
Genomics
Genotype & phenotype
Genotypes
Grain cultivation
Kinases
Novel transcripts
Novels
Pan-transcriptome
Physiological aspects
Plant diseases
Plant genetics
Resistance
Ribonucleic acid
Rice
RNA
Sorghum
Wild
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:It has become clear in recent years that many genes in a given species may not be found in a single genotype thus using sequences from a single genotype as reference may not be adequate for various applications. In this study we constructed a pan-transcriptome for barley by de novo assembling 288 sets of RNA-seq data from 32 cultivated barley genotypes and 31 wild barley genotypes. The pan-transcriptome consists of 756,632 transcripts with an average N50 length of 1240 bp. Of these, 289,697 (38.2%) were not found in the genome of the international reference genotype Morex. The novel transcripts are enriched with genes associated with responses to different stresses and stimuli. At the pan-transcriptome level, genotypes of wild barley have a higher proportion of disease resistance genes than cultivated ones. We demonstrate that the use of the pan-transcriptome dramatically improved the efficiency in detecting variation in barley. Analysing the pan-transcriptome also found that, compared with those in other categories, disease resistance genes have gone through stronger selective pressures during domestication.
ISSN:1471-2164
1471-2164
DOI:10.1186/s12864-018-5357-7