Next-generation sequencing of flow-sorted wheat chromosome 5D reveals lineage-specific translocations and widespread gene duplications

Abstract

BackgroundThe ~17 Gb hexaploid bread wheat genome is a high priority and a major technical challenge for genomic studies. In particular, the D sub-genome is relatively lacking in genetic diversity, making it both difficult to map genetically, and a target for introgression of agriculturally useful traits. Elucidating its sequence and structure will therefore facilitate wheat breeding and crop improvement.ResultsWe generated shotgun sequences from each arm of flow-sorted Triticum aestivum chromosome 5D using 454 FLX Titanium technology, giving 1.34× and 1.61× coverage of the short (5DS) and long (5DL) arms of the chromosome respectively. By a combination of sequence similarity and assembly-based methods, ~74% of the sequence reads were classified as repetitive elements, and coding sequence models of 1314 (5DS) and 2975 (5DL) genes were generated. The order of conserved genes in syntenic regions of previously sequenced grass genomes were integrated with physical and genetic map positions of 518 wheat markers to establish a virtual gene order for chromosome 5D.ConclusionsThe virtual gene order revealed a large-scale chromosomal rearrangement in the peri-centromeric region of 5DL, and a concentration of non-syntenic genes in the telomeric region of 5DS. Although our data support the large-scale conservation of Triticeae chromosome structure, they also suggest that some regions are evolving rapidly through frequent gene duplications and translocations.Sequence accessionsEBI European Nucleotide Archive, Study no. ERP002330Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1080) contains supplementary material, which is available to authorized users.

Molecular organization and comparative analysis of chromosome 5B of the wild wheat ancestor Triticum dicoccoides

“…3a). This marked abundance was also reported for the unmasked low coverage sequences from T. aestivum 6B29 and 5D19 chromosomes, as well as Ae. tauschii 5D chromosome20, and, is generally attributed to a Transposable Element (TE)-driven capture and subsequent co-proliferation.…”

“…This approach merged non-overlapping sequences of the LCN assembly that matched the same query protein, and resulted in the construction of 4,818 ‘conserved gene models’ for the Tdic5B (Supplementary File 1). Assuming an average coding sequence length of 2000 bases13 and a chromosome length of 840 Mbp17, the genic fraction (~9.63 Mb estimated coding length) of Tdic5B equals to 1.15%, similar to that of Triticum aestivum 5A (~1.23%)13 and 5D (~1.15%)19 chromosomes, but considerably lower than Aegilops tauschii 5D chromosome (2.1-2.9%)20. At a size of approximately 12 Gbp, this genic fraction corresponds to a total estimate of over 68,800 genes for the entire genome of T. dicoccoides .…”

“…The blast parameters were essentially adopted from previous studies to ensure consistency131920 and similarity/identity cutoffs were increased for the close relatives, barley and wheat species. To increase stringency, ‘Best Reciprocal Hit’ approach was applied for protein queries, where BLAST searches were performed as blastx and tblastn, and only reciprocal best hits were retained.…”

The physical map of wheat chromosome 5DS revealed gene duplications and small rearrangements

“…So far, survey sequences for wheat chromosomes 4A, 5A, 5D, 6B, 7BS and 7DS have been published [20–25]. In particular, comparative analyses of the 5D chromosome with its counterpart in the wild progenitor, Ae.…”

What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

“…For enormous genomes like those of lungfishes, aquatic salamanders, pine and lilies, it may be necessary to sort chromosomes for individual sequencing, as has been done for some smaller genomes (e.g. [63]) or to use haploid DNA and invoke novel assembly approaches (e.g. [64]).…”