Brassica Genome
Brassica Genome provides integrated genomic browsers and analytical resources for comparative and functional analysis of Brassica rapa and Brassica oleracea genomes.
Key Features:
- B. rapa Genome Browser: Detailed genomic view including comprehensive annotation of the repeat fraction for B. rapa.
- GBrowse2 visualization: Genome visualization implemented with GBrowse2 for browsing annotated genomic features.
- B. rapa gene models: Annotation and modeling of 41,174 protein-coding genes reflecting the species' triplicated genome structure.
- B. oleracea Pan-Genome Browser: Access to single nucleotide polymorphisms (SNPs) and functional gene annotations across the B. oleracea pan-genome.
- Pan-genome comparative features: Comparative display of genetic variation across B. oleracea strains and cultivars within the pan-genome framework.
- BlastGbrowse Portal: BLAST searches against B. rapa and B. oleracea pan-genomes with linking of BLAST hits to corresponding genome browser entries.
- Polyploidy and fractionation analysis: Tools and annotations supporting investigation of genome triplication consequences and gene loss (fractionation) among triplicated segments.
- Gene family size and functional evolution analysis: Data and annotations to assess variation in gene family sizes and structural/functional evolution within Brassica species.
Scientific Applications:
- Genome Annotation and Analysis: Annotation and modeling of protein-coding genes and repeat content in B. rapa to study gene structure and function.
- Polyploid Genome Evolution Studies: Comparative analyses using Arabidopsis thaliana as an outgroup to investigate consequences of genome triplication and fractionation in Brassica.
- Comparative Genomics of B. oleracea: Pan-genome SNP and functional annotation analysis to compare genetic variation across strains and cultivars.
- Genetic Improvement of Crops: Use of annotated genome sequences and comparative insights to inform genetic studies aimed at improving Brassica oil and vegetable crops.
Methodology:
Leveraging high-throughput sequencing data to construct draft genome sequences, followed by genome annotation and comparative genomics using Arabidopsis thaliana as a reference.
Topics
Details
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Added:
- 8/16/2016
- Last Updated:
- 11/25/2024
Operations
Publications
Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun J, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park B, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IAP, Batley J, Kim J, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Wang J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon S, Choi S, Lee T, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z. The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics. 2011;43(10):1035-1039. doi:10.1038/ng.919. PMID:21873998.