National Research Council of Italy

Institute of Biosciences and BioResources

DISBA logo CNR logo
IBBR publication #2537

First insights into the transcriptome and development of new genomic tools of a widespread circum-Mediterranean tree species, Pinus halepensis Mill

Pinosio S, Gonzalez-Martinez SC Bagnoli F, Cattonaro F, Grivet D, Marroni F, Lorenzo Z, Pausas JG, Verdu M, Vendramin GG

Molecular Ecology Resources 14: 846-856. [ISSN: 1755-098X] (2014)
doi: 10.1111/1755-0998.12232

Aleppo pine (Pinus halepensis Mill.) is a relevant conifer species for studying adaptive responses to drought and fire regimes in the Mediterranean region. In this study, we performed Illumina next-generation sequencing of two phenotypically divergent Aleppo pine accessions with the aims of (i) characterizing the transcriptome through Illumina RNA-Seq on trees phenotypically divergent for adaptive traits linked to fire adaptation and drought, (ii) performing a functional annotation of the assembled transcriptome, (iii) identifying genes with accelerated evolutionary rates, (iv) studying the expression levels of the annotated genes and (v) developing gene-based markers for population genomic and association genetic studies. The assembled transcriptome consisted of 48629 contigs and covered about 54.6Mbp. The comparison of Aleppo pine transcripts to Picea sitchensis protein-coding sequences resulted in the detection of 34014 SNPs across species, with a Ka/Ks average value of 0.216, suggesting that the majority of the assembled genes are under negative selection. Several genes were differentially expressed across the two pine accessions with contrasted phenotypes, including a glutathione-s-transferase, a cellulose synthase and a cobra-like protein. A large number of new markers (3334 amplifiable SSRs and 28236 SNPs) have been identified which should facilitate future population genomics and association genetics in this species. A 384-SNP Oligo Pool Assay for genotyping with the Illumina VeraCode technology has been designed which showed an high overall SNP conversion rate (76.6%). Our results showed that Illumina next-generation sequencing is a valuable technology to obtain an extensive overview on whole transcriptomes of nonmodel species with large genomes

Actions
Select by Year
Select by Type
Select by Author
*
*
*
*
Istituto di Bioscienze e Biorisorse (IBBR/CNR)
Via G. Amendola 165/A, I-70126 Bari (Italy)
Copyright © 2012-2024. All Rights Reserved.