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

Yanling Ma,Chunji Liu,Jiri Stiller,Miao Liu

doi:10.1186/s12864-018-5357-7

Abstract

BackgroundIt 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.ResultsIn 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.ConclusionsWe 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.

Highlights

It has become clear in recent years that many genes in a given species may not be found in a single genotype using sequences from a single genotype as reference may not be adequate for various applications
The data consisted of a total of 6,321,262,514 reads downloaded from the EMBL (European Molecular Biology Lab)/EBI (European Bioinformatics Institute)-European Nucleotide Archive (ENA) database and the National Center for Biotechnology Information (NCBI) Short Sequence Read Archive (SRA) database
Gene ontology (GO) classification for biological processes indicates a large proportion of the novel Coding DNA sequence (CDS) was involved with ‘response to biotic and abiotic stimuli’ and ‘defense response’

Summary

Introduction

It has become clear in recent years that many genes in a given species may not be found in a single genotype using sequences from a single genotype as reference may not be adequate for various applications. The phenomenon that an individual contains only a proportion of the genes in a given species was initially noticed in microbes [1]. This phenomenon led to the concept of pan-genome which consists of core and dispensable genomes [2, 3]. The core component contains genes shared by all individuals of a given species and the remainder belong to the dispensable component [3]. Reports on pan-genome for major crop species appeared only in recent years. Similar to that observed in various microbes, large proportions of genes in different crop species have been found to be dispensable. Dispensable genes account for about 20% of the genomes in soybean (Glycine soja) [4] and Brassica oleracea [5], 36% in bread wheat (Triticum aestivum) [6, 7], 50% in maize (Zea mays) [8, 9] and 43% in rice (Oryza sativa L.) [10]

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Conclusion