title: Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species.
abstract: The pan-genome of a species is defined as the union of all the genes and non-coding 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 19Arabidopsis thalianaecotypes and then applied to the analysis of transcripts from 16Hordeum vulgaregenotypes. 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 inA. thalianagene 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.
authors.affiliation: Estación Experimental de Aula Dei - Consejo Superior de Investigaciones CientíficasZaragoza, Spain; Fundación ARAIDZaragoza, Spain.
authors.forename: Bruno
authors.initials: B
authors.lastname: Contreras-Moreira
authors.affiliation: Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas Zaragoza, Spain.
authors.forename: Carlos P
authors.initials: CP
authors.lastname: Cantalapiedra
authors.affiliation: Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas Zaragoza, Spain.
authors.forename: María J
authors.initials: MJ
authors.lastname: García-Pereira
authors.affiliation: DOE Joint Genome Institute, Walnut Creek CA, USA.
authors.forename: Sean P
authors.initials: SP
authors.lastname: Gordon
authors.affiliation: DOE Joint Genome Institute, Walnut Creek CA, USA.
authors.forename: John P
authors.initials: JP
authors.lastname: Vogel
authors.affiliation: Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas Zaragoza, Spain.
authors.forename: Ernesto
authors.initials: E
authors.lastname: Igartua
authors.affiliation: Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas Zaragoza, Spain.
authors.forename: Ana M
authors.initials: AM
authors.lastname: Casas
authors.affiliation: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico.
authors.forename: Pablo
authors.initials: P
authors.lastname: Vinuesa
keywords: Arabidopsis thaliana; RNA-seq; accessory genome; barley; comparative genomics; core-genome; pan-genome