Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing

BMC Genomics

Research Article

Noé Fernández-Pozo¹  Josefa Gómez-Maldonado²  Concepción Ávila²  Francisco M. Cánovas²  Pedro Seoane-Zonjic²  M. Gonzalo Claros²  Rafael A. Cañas²  Rocío Bautista²  Isabel Arrillaga³ 

[1] Boyce Thompson Institute for Plant Research, Cornell University, 14853, Ithaca, NY, USA;Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, E-29071, Málaga, Spain;Departamento de Biología Vegetal, Facultad de Farmacia, ERI Biotecmed, Universidad de Valencia, Avda. Vicent Andrés Estellés s/n, 46100, Burjassot, Valencia, Spain;

关键词: BAC;    Bioinformatic pipeline;    Gene capture;    Gene model construct;    Gene structure;    Maritime pine;    Promoter studies;   

DOI  :  10.1186/s12864-016-2490-z

 received in 2015-10-28, accepted in 2016-02-17,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundIn the era of DNA throughput sequencing, assembling and understanding gymnosperm mega-genomes remains a challenge. Although drafts of three conifer genomes have recently been published, this number is too low to understand the full complexity of conifer genomes. Using techniques focused on specific genes, gene models can be established that can aid in the assembly of gene-rich regions, and this information can be used to compare genomes and understand functional evolution.ResultsIn this study, gene capture technology combined with BAC isolation and sequencing was used as an experimental approach to establish de novo gene structures without a reference genome. Probes were designed for 866 maritime pine transcripts to sequence genes captured from genomic DNA. The gene models were constructed using GeneAssembler, a new bioinformatic pipeline, which reconstructed over 82 % of the gene structures, and a high proportion (85 %) of the captured gene models contained sequences from the promoter regulatory region. In a parallel experiment, the P. pinaster BAC library was screened to isolate clones containing genes whose cDNA sequence were already available. BAC clones containing the asparagine synthetase, sucrose synthase and xyloglucan endotransglycosylase gene sequences were isolated and used in this study. The gene models derived from the gene capture approach were compared with the genomic sequences derived from the BAC clones. This combined approach is a particularly efficient way to capture the genomic structures of gene families with a small number of members.ConclusionsThe experimental approach used in this study is a valuable combined technique to study genomic gene structures in species for which a reference genome is unavailable. It can be used to establish exon/intron boundaries in unknown gene structures, to reconstruct incomplete genes and to obtain promoter sequences that can be used for transcriptional studies. A bioinformatics algorithm (GeneAssembler) is also provided as a Ruby gem for this class of analyses.

【 授权许可】

CC BY   
© Seoane-Zonjic et al. 2016