BrGSP: the Brassica 'A' genome sequencing project

for update on all ongoing sequencing, including BrGSP, please see here

Overview

The Steering Committee for the MBGP selected Brassica rapa as the first species to be sequenced, as it has the smallest genome (ca. 550 Mb), the lowest frequencies of repetitive sequences and communal BAC libraries and mapping populations are available. Consequently, the Brassica rapa Genome Sequencing Project (BrGSP) was launched, based on the Chinese cabbage line Chiifu-401, and associated BAC libary resources developed in Korea. The 'A' genome of B. rapa is also present in major oil crops of B. napus and B. juncea.

For information: Fort Lauderdale report on data sharing from large-scale biological research projects link

  282 seed BAC in GenBank (Korea)
  >300 BAC sequences in GenBank (chromosome projects)
  >800 BAC sequences completed, but not yet available in GenBank

mbrsp


Original investigations indicated that 40% of the B. rapa genome may be composed of arrays of repetitive sequences (Yang et al. 2005), leaving ca. 330Mb of gene space. This proportion is similar to that for the genome of Medicago, which consists of ca. 50% gene space. A BAC-by-BAC approach to sequencing the gene space was agreed, with all sequenced clones being anchored to the B. rapa linkage map. This was to ensure that all sequences could be related to the genetic linkage map (an attribute not available from shotgun sequencing approaches).

Sequencing within the international project was to be conducted to Phase 2, whereby BACs were to be sequenced to a single ordered and oriented contig, but with some gaps and ambiguous bases allowed). All sequence reads and trace files, as well as the BAC libraries, were to be made publicly available to permit users of the sequence to readily “finish” clones of particular interest if necessary.

See original Concept note.
The international consortium demonstrated their ability to work together by end-sequencing BAC libraries, consisting of ca. 130,000 clones, by groups in Korea, Australia, Germany, Canada, France, USA and UK, in support of the strategy using BAC end sequences to identify overlapping clones. A Korean-funded project already sequenced over 500 seed BAC clones (representing ca. 15% of the B. rapa gene space) that are distributed genome-wide.

Progress and specific projects

Chromosomes-specific projects were in place 2006-2009, but were then superceded by high throughput sequencing strategies.



This Page Was Last Edited: 04-May-2010