Mikan_GB

Mikan_GB provides a consolidated genomic database to support molecular breeding of mandarin species by hosting hybrid de novo assemblies (Illumina and PacBio), genome annotations, genetic diversity data, and CAPS marker information for Citrus unshiu and Poncirus trifoliata.

Key Features:

• Genome assembly and annotation: Provides assembled genomes of Citrus unshiu (346 Mb) and Poncirus trifoliata (292 Mb) with predicted counts of 41,489 and 34,333 protein-coding genes, respectively, and reports 9,642 and 8,377 genes unique relative to Citrus clementina.
• Integrated database: Consolidates genome annotations, genetic diversity data, and Cleaved Amplified Polymorphic Sequence (CAPS) marker information linked by gene-specific connections.
• Genomic diversity and CAPS markers: Includes detailed polymorphism and CAPS marker data for identifying polymorphisms and facilitating construction and navigation of linkage maps using CAPS markers.
• Polymorphism visualization: Exposes comprehensive polymorphism information through the multiple genome browser TASUKE.

Scientific Applications:

• Mandarin molecular breeding: Supports advancement of mandarin molecular breeding efforts in Japan by providing assembled genomes and marker resources for trait-associated research.
• Gene and marker discovery: Enables identification of candidate genes and CAPS markers associated with agronomic traits using assembled genomes and annotations.
• Linkage map integration: Allows researchers to relate genome sequences to previously reported linkage maps via CAPS markers for mapping and marker-assisted selection.

Methodology:

Hybrid de novo assembly using Illumina and PacBio sequencing data and integration of genome assemblies, annotations, genetic diversity data, and CAPS marker data into a unified database.