NHCCDB

NHCCDB provides access to and analysis of the Brassica campestris ssp. chinensis NHCC001 genome to support genomics, functional genomics, comparative genomics, and breeding research.

Key Features:

• Genomic Data Access: Comprehensive access to the NHCC001 draft genome with annotation of 105,360 genes categorized into 63 transcription factor families.
• Simple Sequence Repeat (SSR) Resources: Catalog of 127,347 SSRs with 382,041 primer pairs designed for these SSR loci.
• Analytical Tools: A suite of eight analysis tools including sequence alignment, functional genomics, comparative genomics, motif analysis, and a genome browser.
• Data Visualization: Support for eight graphical representations: box plot, Venn diagram, correlation plot (corrplot), quantile-quantile plot (Q-Q plot), Manhattan plot, sequence logo (seqLogo), volcano plot, and heatmap.
• Search and Data Submission: Search capabilities for mining transcription factors and genes and a data submission function for contributing datasets.

Scientific Applications:

• Genomic Research: Exploration of genetic diversity, gene content, and gene function in Brassica campestris ssp. chinensis.
• Breeding Programs: Support for marker-assisted selection and genetic improvement using SSR markers and primer designs.
• Functional Genomics Studies: Identification and characterization of genes and transcription factors for functional analysis.
• Comparative Genomics: Comparative analyses between B. campestris ssp. chinensis and other Brassicaceae species.

Methodology:

Based on the high-quality draft genome sequence of cultivar NHCC001; identification of 127,347 SSRs and design of 382,041 primer pairs; annotation of 105,360 genes and classification into 63 transcription factor families; and provision of sequence alignment, motif analysis, functional and comparative genomics analyses, and a genome browser.