Survey Sequence

Survey Sequence

With partners in 15 countries, the IWGSC has produced a survey sequence for the genome of the bread wheat cultivar Chinese Spring based on Illumina short read sequence assemblies of each of the 21 chromosomes. Sponsored primarily by Graminor, Biogemma, INRA, and TGAC, this initiative led by Jane Rogers was published in Science in July 2014.

Project Description

The chromosome survey sequence comprises 10.2 Gb sequence assembled with ABySS from Illumina paired end sequence reads covering each chromosome arm (or whole chromosome in the case of 3B) to a depth of between 30x and 241x, after filtering to exclude small, repetitive sequence assemblies (contigs) < 200bp. Around 77% of the assembled sequences contained repeats and after repeat masking, the contig N50 ranged from 1.7kb (3DS) to 8.9kb (6DS). 133,090 gene loci were annotated using homology to related grass genes and 124,201 were assigned to chromosome arms. 44% of these genes spanned at least 70% of the homologous gene length, the remainder being fragmented and therefore not fully structurally defined in the assembly. More than 96% of public wheat ESTs (HarvEST) mapped to the CSS gene sets, indicating that the CSS assemblies contain a high representation of the current gene inventory of the bread wheat genome. Over 75,000 genes were virtually positioned using two complimentary approaches: (1) the GenomeZipper (grass gene synteny + wheat genetic maps); and (2) POPSEQ (genetic map derived from synthetic W7984 x Opata M85 population analysis). Over 3.6 million SNVs were also assigned to individual chromosome arms.

Sequences and assemblies for bread wheat chromosomes and diploid and tetraploid wheat relatives have been deposited in public repositories and can be accessed via the IWGSC Survey sequence repository at the Unité de Recherches en Génomique Information ( URGI ), INRA-Versailles. The GenomeZipper and POPSEQ gene orders are also available, together with the gene models annotated in the survey sequences from the URGI web site.

Project Team Leader

Jane Rogers, IWGSC


See also

Modification date: 16 August 2023 | Publication date: 11 December 2020 | By: ic