Tanaka, T., Kobayashi, F., Joshi, G.P., Onuki, R., Sakai, H., Kanamori, H., Wu, J., Šimková, H., Nasuda, S., Endo, T.R., Hayakawa, K., Doležel, J., Ogihara, Y., Itoh, T., Matsumoto, T., Handa, H.
Advances in wheat genetics: From genome to field : 111-116, 2015

Keywords: Annotation, Chromosome 6B, Genome sequencing, Marker construction, RNA gene, Synteny
Abstract: International Wheat Genome Sequencing Consortium (IWGSC) decided to adopt the strategy of chromosome sorting and short read assembly to overcome diffi culties of wheat genome sequencing derived from the hexaploid status, the large genome size (about 17 Gb) and high repeat contents (more than 80 %). Our Japanese group was responsible for the sequencing of wheat chromosome 6B. Using DNAs from the fl ow-sorted chromosome arms, we conducted whole-chromosome shotgun sequencing of chromosome 6B. We sequenced more than 12 million reads obtained from the short and long arms by GS-FLX Titanium, and assembled contigs of 235 Mb for 6BS and 273 Mb for 6BL were generated by GS assembler 2.7 (Roche). These assemblies cover 56.6 % and 54.9 % of estimated sizes of 6BS (415 Mb) and 6BL (498 Mb), respectively. We annotated repetitive regions covering more than 80 % of contigs, 4,798 possible expressed loci, and various kinds of RNA genes using our annotation pipeline. We also found the evolutionary conserved regions among syntenic chromosomes from four grass genomes. For application of the 6B sequences to wheat genomics, various kinds of markers, such as simple sequence repeat (SSR) and insertion site-based polymorphism (ISBP) markers were constructed. Combination of the marker data with the comparative genome analysis will lay a strong foundation of functional genomics of the group-6 chromosomes in wheat.
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IEB authors: Jaroslav Doležel, Hana Šimková