MBrSP: the Brassica 'A' genome sequencing project

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.

mbrsp
Recent investigations have 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 ensures that all sequences can be related to the genetic linkage map (an attribute not available from shotgun sequencing approaches).

Sequencing within the international project is to be conducted to Phase 2, whereby BACs are 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, are to be made publicly available to permit users of the sequence to readily “finish” clones of particular interest if necessary.

The international consortium has already 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 has 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 are now underway, and more expected to commence during the next two years.