000060688 001__ 60688
000060688 005__ 20190709135441.0
000060688 0247_ $$2doi$$a10.3389/fpls.2017.00184
000060688 0248_ $$2sideral$$a98110
000060688 037__ $$aART-2017-98110
000060688 041__ $$aeng
000060688 100__ $$0(orcid)0000-0002-5462-907X$$aContreras-Moreira, B.$$uUniversidad de Zaragoza
000060688 245__ $$aAnalysis of plant pan-genomes and transcriptomes with GET_HOMOLOGUES-EST, a clustering solution for sequences of the same species
000060688 260__ $$c2017
000060688 5060_ $$aAccess copy available to the general public$$fUnrestricted
000060688 5203_ $$aThe 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.
000060688 536__ $$9info:eu-repo/grantAgreement/ES/MINECO/AGL2010-21929$$9info:eu-repo/grantAgreement/ES/MINECO/AGL2013-487569$$9info:eu-repo/grantAgreement/ES/MINECO/BES-2011-045905
000060688 540__ $$9info:eu-repo/semantics/openAccess$$aby-nc$$uhttp://creativecommons.org/licenses/by-nc/3.0/es/
000060688 590__ $$a3.678$$b2017
000060688 591__ $$aPLANT SCIENCES$$b24 / 222 = 0.108$$c2017$$dQ1$$eT1
000060688 592__ $$a1.731$$b2017
000060688 593__ $$aPlant Science$$c2017$$dQ1
000060688 655_4 $$ainfo:eu-repo/semantics/article$$vinfo:eu-repo/semantics/publishedVersion
000060688 700__ $$aCantalapiedra, C.P.
000060688 700__ $$aGarcía-Pereira, M.J.
000060688 700__ $$aGordon, S.P.
000060688 700__ $$aVogel, J.P.
000060688 700__ $$aIgartua, E.
000060688 700__ $$aCasas, A.M.
000060688 700__ $$aVinuesa, P.
000060688 7102_ $$11002$$2060$$aUniversidad de Zaragoza$$bDpto. Bioq.Biolog.Mol. Celular$$cÁrea Bioquímica y Biolog.Mole.
000060688 773__ $$g8 (2017), 184 [16 pp]$$pFront. plant sci.$$tFRONTIERS IN PLANT SCIENCE$$x1664-462X
000060688 8564_ $$s2829226$$uhttps://zaguan.unizar.es/record/60688/files/texto_completo.pdf$$yVersión publicada
000060688 8564_ $$s23449$$uhttps://zaguan.unizar.es/record/60688/files/texto_completo.jpg?subformat=icon$$xicon$$yVersión publicada
000060688 909CO $$ooai:zaguan.unizar.es:60688$$particulos$$pdriver
000060688 951__ $$a2019-07-09-11:36:16
000060688 980__ $$aARTICLE