Brassica A genome (Brassica rapa)

The Brassica rapa genome was sequenced as a contribution to the Multinational Brassica Genome Sequencing Project and was published in August 2011 (see link). This B. rapa Ensembl site is delivered by Rothamsted Research (RRes) incorporating gene annotation to allow people to access the Brassica genome through the Ensembl user interface.

Assembly

The genomic sequence within this version of Ensembl includes 193 large scaffolds assembled by CAAS-IVF, which have been orientated and assigned to pseudochromosomes using publicly available genetic markers. Scaffolds and KBr BAC sequence not utilised in the pseudochromosomes is also available within within this release.

Preliminary Annotation

Gene prediction of the assembled genomic scaffolds has been conducted by CAAS-IVF using GLEAN and BLAT. BAC annotation has been conducted by an annotation pipeline developed by JIC/JCVI and implemented by RRes using PASA and SNAP gene prediction software. Functional annotation for the gene models is provided through similarity to Arabidopsis thaliana genes (E=1E-5) and Gene Ontology terms are provided through significant similarity to UniprotKB proteins (E=1E-5).

Additional features

Further annotation generated by RRes is displayed as additional tracks within this version of BrassEnsembl. These alignments include links to AlignStore, a database containing more detailed alignment information including alignments, parameters and datasets used in the analysis.

• Arabidopsis coding sequences aligned using BLAT:
  • Alignment parameters: minmatch(2), minscore(30),min identity(80), maxGap(2),evalue threshold(1e-5)
  • Dataset: 33 410 Arabidopsis TAIR v9 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),evalue threshold(1e-20))
  • Dataset: 94 558 Brassica unigenes
• A 135k Brassica unigene set generated by RRes aligned using BLAT:
  • Alignment parameters: default blat (minmatch(2), minscore(30),min identity(90), maxGap(2),evalue threshold(1e-20))
  • Dataset: 135 201 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-50), word_size (9), query_increment(3), extension_threshold(20), percent identity(95)
  • Dataset: 196 837 B. rapa BAC end sequences obtained from GenBank 5-Aug-2010
  • 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), percent identity(90)
  • Dataset: 902 700 Brassica ESTs obtained from GenBank 13-Aug-2010
  • 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