Next-Generation Survey Sequencing and the Molecular Organization of Wheat Chromosome 6B

Abstract

Common wheat (Triticum aestivum L.) is one of the most important cereals in the world. To improve wheat quality and productivity, the genomic sequence of wheat must be determined. The large genome size (∼17 Gb/1 C) and the hexaploid status of wheat have hampered the genome sequencing of wheat. However, flow sorting of individual chromosomes has allowed us to purify and separately shotgun-sequence a pair of telocentric chromosomes. Here, we describe a result from the survey sequencing of wheat chromosome 6B (914 Mb/1 C) using massively parallel 454 pyrosequencing. From the 4.94 and 5.51 Gb shotgun sequence data from the two chromosome arms of 6BS and 6BL, 235 and 273 Mb sequences were assembled to cover ∼55.6 and 54.9% of the total genomic regions, respectively. Repetitive sequences composed 77 and 86% of the assembled sequences on 6BS and 6BL, respectively. Within the assembled sequences, we predicted a total of 4798 non-repetitive gene loci with the evidence of expression from the wheat transcriptome data. The numbers and chromosomal distribution patterns of the genes for tRNAs and microRNAs in wheat 6B were investigated, and the results suggested a significant involvement of DNA transposon diffusion in the evolution of these non-protein-coding RNA genes. A comparative analysis of the genomic sequences of wheat 6B and monocot plants clearly indicated the evolutionary conservation of gene contents.

Harnessing NGS and Big Data Optimally: Comparison of miRNA Prediction from Assembled versus Non-assembled Sequencing Data—The Case of the Grass Aegilops tauschii Complex Genome

“…Consistently, in this research, 45 out of 46 miRNAs, exclusively predicted from the survey sequences, were categorized as 'repeat related' ( Table 2). The repetitive elements found in the hairpins of these 'repeat-related' miRNAs almost exclusively belonged to the DNA transposons, in particular to the Ty1 and En-Spm super families, consistent with previous findings (Table 3) (Kantar et al, 2012;Lucas and Budak, 2012;Mayer et al, 2014;Tanaka et al, 2013). The high number of repeat-related miRNAs predicted only from the non-assembled sequences brings about the possibility that assembly-based miRNA identification may overlook some genuine miRNAs, which may lead to misleading interpretations, particularly with regard to miRNA evolution.…”

“…Using this increasingly available sequence information to elucidate genomics backgrounds, some researchers have used raw reads in their analysis (Hernandez et al, 2012;Kurtoglu et al, 2013Kurtoglu et al, , 2014, while others have constructed assemblies from survey sequences using various programs such as Velvet, gsAssembler, andSOAPdenovo (Berkman et al, 2011, 2012;Brenchley et al, 2012;Jia et al, 2013;Kurtoglu et al, 2014;Tanaka et al, 2013).…”

“…Although in silico methods have initially used partial sequences, such as expressed sequence tags (ESTs) or genome survey sequences (GSSs) for miRNA identification (Budak and Akpinar, 2011;Kantar et al, 2010;Pandey et al, 2013;Schreiber et al, 2011;Yin et al, 2010;Unver and Budak, 2009), the recent increase in sequence availability has also accelerated miRNA identification studies in chromosome, whole genome, and whole transcriptome scales, including individual survey sequences or assemblies constructed from sequence reads ( Jia et al, 2013;Kantar et al, 2012;Kurtoglu et al, 2013Kurtoglu et al, , 2014Lucas and Budak, 2012;Tanaka et al, 2013;Vitulo et al, 2011).…”

Genetic mapping of the Cre8 locus for resistance against cereal cyst nematode (Heterodera avenae Woll.) in wheat

“…Considering the rapidly expanding sequence information that is becoming available for chromosome 6B of wheat (Tanaka et al 2013) and the bioinformatic resources exploiting synteny with closely related species such as barley, an alternate (or complementary) strategy for the identification of the Cre8 resistance gene could involve the use of marker sequence information from this mapping study as the starting point for a candidate-gene approach.…”

Sequencing of Wheat Chromosome 6B: Toward Functional Genomics

“…Under the framework of IWGSC, sequencing project of chromosome 6B was started in Japan in 2011 and the fi rst survey sequences of 6B was released in 2013 (Tanaka et al 2014 ). In this analysis, the DNA libraries of sorted 6B chromosome arms were constructed and sequenced independently using the 454 GS-FLX Titanium (Roche, CT, USA).…”