Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome

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.

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

“…This was similar to previous analyses of Chromosome 3B (Pingault et al 2015), and IR is also predominant in barley (Panahi et al 2015). Alternative splicing coupled to nonsense mediated decay (NMD) regulates gene expression (Lykke-Andersen and Jensen 2015).…”

Ca2+/Cation Antiporters (CaCA): Identification, Characterization and Expression Profiling in Bread Wheat (Triticum aestivum L.)

“…The tissue specific expression was analyzed using the data generated from three developmental stages of each root, leaf, stem, spike and grain in duplicates (Pingault et al, 2015). The data is available for download at https://urgi.versailles.inra.fr/files/RNASeqWheat/.…”

“…The unavailability of genomic information, composite nature of genome and complexity in application of modern functional genomics tools could be the probable reason for the same. In recent years, the genome sequence and numerous development and stress related high throughput RNA sequence data have been available from T. aestivum (IWGSC, 2014; Zhang et al, 2014b, 2016; Liu Z. et al, 2015; Pingault et al, 2015), which enabled the genome wide characterization of various gene families (Shumayla et al, 2016a,b; Zeng et al, 2016). Since the CaCA proteins are involved in several vital functions from development to stress response, there characterization becomes essential in an important food crop like T. aestivum .…”

Virus-Induced Gene Silencing Identifies an Important Role of the TaRSR1 Transcription Factor in Starch Synthesis in Bread Wheat

“…The genetic or epigenetic modifications have brought genomic asymmetry toward a diploid-like mode of expression, because either of mutation, elimination or repression of most genes that, in most cases, confine the activity of sets of genes to only one genome [17]. With the recent release and annotation of the bread wheat genome, it is now possible to expand better characterize its growth, development, and responses to biotic and abiotic stresses [18,19]. …”