Abstract
BackgroundThe genus Brassica includes the most extensively cultivated vegetable crops worldwide. Investigation of the Brassica genome presents excellent challenges to study plant genome evolution and divergence of gene function associated with polyploidy and genome hybridization. A physical map of the B. rapa genome is a fundamental tool for analysis of Brassica "A" genome structure. Integration of a physical map with an existing genetic map by linking genetic markers and BAC clones in the sequencing pipeline provides a crucial resource for the ongoing genome sequencing effort and assembly of whole genome sequences.ResultsA genome-wide physical map of the B. rapa genome was constructed by the capillary electrophoresis-based fingerprinting of 67,468 Bacterial Artificial Chromosome (BAC) clones using the five restriction enzyme SNaPshot technique. The clones were assembled into contigs by means of FPC v8.5.3. After contig validation and manual editing, the resulting contig assembly consists of 1,428 contigs and is estimated to span 717 Mb in physical length. This map provides 242 anchored contigs on 10 linkage groups to be served as seed points from which to continue bidirectional chromosome extension for genome sequencing.ConclusionThe map reported here is the first physical map for Brassica "A" genome based on the High Information Content Fingerprinting (HICF) technique. This physical map will serve as a fundamental genomic resource for accelerating genome sequencing, assembly of BAC sequences, and comparative genomics between Brassica genomes. The current build of the B. rapa physical map is available at the B. rapa Genome Project website for the user community.
Highlights
The genus Brassica includes the most extensively cultivated vegetable crops worldwide
We have chosen the High Information Content Fingerprinting (HICF) fingerprinting method based on its well-established format with a commercially available SNaPshot labeling kit (ABI) and increased throughput using the ABI 3730 xl sequencer [17,21]
A total of 99,456 Bacterial Artificial Chromosome (BAC) clones (~22.5× coverage) from the three independent libraries were fingerprinted by digestion with five restriction enzyme combinations (EcoRI, BamHI, XbaI, XhoI, and HaeIII) followed by SNaPshot reagent labeling of four colors at the 3' ends of the restriction fragments and sizing on the ABI 3730 xl (Table 1)
Summary
The genus Brassica includes the most extensively cultivated vegetable crops worldwide. Investigation of the Brassica genome presents excellent challenges to study plant genome evolution and divergence of gene function associated with polyploidy and genome hybridization. The complex genome organization of the Brassica species as a result of multiple rounds of polyploidy and genome hybridization makes the identification of orthologous relationships of genes between the genomes highly difficult. A following extensive interspersed gene loss or gain events and large scale chromosomal rearrangements including segmental duplications or deletions in the Brassica lineage complicated the orthologous relationships of the loci between the two genomes [2]. Investigation of the Brassica genome provides substantial opportunities to study the divergence of gene function and genome evolution associated with polyploidy, extensive duplication and hybridization
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