The Brassica rapa genome is being sequenced as part of the Multinational Brassica Genome Sequencing Project. This B. rapa Ensembl site is delivered by Rothamsted Research (RRes) incorporating gene annotation generated by The John Innes Center (JIC) to allow people to access the Brassica genome through the Ensembl user interface.

Assembly

The genomic sequence within this version of Ensembl includes 974 B. rapa phase two assembled BACs present within GenBank on 03-Jun-09. Within this release no BACs have been assembled into contigs nor assigned to chromosomes, however, the individual BACs and subsequent annotation can be browsed.

Preliminary Annotation

B. rapa BAC annotation has been provided by JIC through an annotation pipeline to identify genes and genomic features.Gene models have been derived using PASA and SNAP gene prediction software. Functional annotation for the gene models is provided through similarity to Arabidopsis thaliana coding sequence and associated Gene Ontology terms. This annotation can also be viewed through the Brassica Genome Gateway.

Additional features

Further annotation generated by RRes is displayed as additional tracks within this version of BrassEnsembl including:

• Arabidopsis coding sequences aligned using BLAT:
  • Alignment parameters: minmatch(2), minscore(30),min identity(80), maxGap(2)
  • Dataset: 32 825 Arabidopsis TAIR v8 coding sequences
  • External links: AtEnsembl transcripts
• A 95k Brassica unigene set generated by JCVI aligned using BLAT:
  • Alignment parameters: default blat (minmatch(2), minscore(30),min identity(90), maxGap(2))
  • Dataset: 94 558 Brassica unigenes
• B. rapa BAC end sequences aligned using Decypher tera-blastn:
  • Alignment parameters: match_score(1), mismatch_score(-3), open_penalty(-5), extend_penalty(-2), gapped_alignment(banded), query_filtered, max_score(10), max alignment number(10), evalue threshold(1e-05), word_size (9), query_increment(3), extension_threshold(20)
  • Dataset: 198 490 B. rapa BAC end sequences obtained from GenBank 23-Jun-09
  • External links: GenBank
• B. rapa ESTs aligned using Decypher tera-blastn:
  • Alignment parameters: match_score(1), mismatch_score(-1), open_penalty(-1), extend_penalty(-2), gapped_alignment(banded), query_filtered, max_score(10), max alignment number(10), evalue threshold(1e-20), word_size(9), query_increment(3), extension_threshold(20)
  • Dataset: 841 790 Brassica ESTs obtained from GenBank 23-Jun-09
  • External links: GenBank

Acknowledgements

RRes would like to thank:

• Nick James and Sean May (NASC) for their assistance in establishing BrassEnsembl
• JIC for providing the gene annotation
• EBI for use of their code