期刊
FRONTIERS IN PLANT SCIENCE
卷 8, 期 -, 页码 -出版社
FRONTIERS MEDIA SA
DOI: 10.3389/fpls.2017.00184
关键词
comparative genomics; pan-genome; RNA-seq; core-genome; accessory genome; Arabidopsis thaliana; barley
资金
- DGA - Obra Social La Caixa [GA-LC-059-2011]
- Spanish MINECO [AGL2013-48756-R, CSIC13-4E-2490, BES-2011-045905, AGL2010-21929]
- CONACyT-Mexico [179133]
- DGAPA-PAPIIT/UNAM [IN211814]
- Fundacion ARAID
- U. S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility [DE-AC02-05CH11231]
The pan-genome of a species is defined as the union of all the genes and noncoding sequences found in all its individuals. However, constructing a pan-genome for plants with large genomes is daunting both in sequencing cost and the scale of the required computational analysis. A more affordable alternative is to focus on the genic repertoire by using transcriptomic data. Here, the software GET_HOMOLOGUES-EST was benchmarked with genomic and RNA-seq data of 19 Arabidopsis thaliana ecotypes and then applied to the analysis of transcripts from 16 Hordeum vulgare genotypes. The goal was to sample their pan-genomes and classify sequences as core, if detected in all accessions, or accessory, when absent in some of them. The resulting sequence clusters were used to simulate pan-genome growth, and to compile Average Nucleotide Identity matrices that summarize intra-species variation. Although transcripts were found to under-estimate pan-genome size by at least 10%, we concluded that clusters of expressed sequences can recapitulate phylogeny and reproduce two properties observed in A. thaliana gene models: accessory loci show lower expression and higher non-synonymous substitution rates than core genes. Finally, accessory sequences were observed to preferentially encode transposon components in both species, plus disease resistance genes in cultivated barleys, and a variety of protein domains from other families that appear frequently associated with presence/absence variation in the literature. These results demonstrate that pan-genome analyses are useful to explore germplasm diversity.
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