Abstract
BackgroundBecause of its size, allohexaploid nature, and high repeat content, the bread wheat genome is a good model to study the impact of the genome structure on gene organization, function, and regulation. However, because of the lack of a reference genome sequence, such studies have long been hampered and our knowledge of the wheat gene space is still limited. The access to the reference sequence of the wheat chromosome 3B provided us with an opportunity to study the wheat transcriptome and its relationships to genome and gene structure at a level that has never been reached before.ResultsBy combining this sequence with RNA-seq data, we construct a fine transcriptome map of the chromosome 3B. More than 8,800 transcription sites are identified, that are distributed throughout the entire chromosome. Expression level, expression breadth, alternative splicing as well as several structural features of genes, including transcript length, number of exons, and cumulative intron length are investigated. Our analysis reveals a non-monotonic relationship between gene expression and structure and leads to the hypothesis that gene structure is determined by its function, whereas gene expression is subject to energetic cost. Moreover, we observe a recombination-based partitioning at the gene structure and function level.ConclusionsOur analysis provides new insights into the relationships between gene and genome structure and function. It reveals mechanisms conserved with other plant species as well as superimposed evolutionary forces that shaped the wheat gene space, likely participating in wheat adaptation.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0601-9) contains supplementary material, which is available to authorized users.
Highlights
Because of its size, allohexaploid nature, and high repeat content, the bread wheat genome is a good model to study the impact of the genome structure on gene organization, function, and regulation
By combining deep transcriptome sequencing data covering the whole plant development with the reference sequence of the chromosome, we identified transcriptionally active regions distributed throughout the entire chromosome
Ninety-five percent of the reads matched sequences annotated as genic regions whereas the remaining 5% mapped to regions where no protein-coding gene was predicted by the annotation [33]
Summary
Allohexaploid nature, and high repeat content, the bread wheat genome is a good model to study the impact of the genome structure on gene organization, function, and regulation. Because of the lack of a reference genome sequence, such studies have long been hampered and our knowledge of the wheat gene space is still limited. Bread wheat is a good model for studying complex genome species. With its large 17-Gb, allohexaploid (6x = 2n = 42, AABBDD) and highly repetitive (>80% transposable elements) genome, wheat is one of the most complex crop species. Cotton is a polyploid species but has a smaller genome (2.5 Gb) [20] and so far only wild diploid relatives were sequenced [21,22]. The maize and sorghum genomes are highly repetitive but are diploid and smaller in size [7,8]
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