Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

Full name: Mikan Genome Database
Description: A comprehensive atlas of regulomes and their systems, global structural properties, and system-level elements
Year founded: 2019
Last update: 2019-08-06
Real time : Checking...
Country/Region: Japan
Data type:
Data object:
Database category:
Major organism:

Contact information

University/Institution: National Agriculture and Food Research Organization
Address: National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka 424-0292, Japan
City: Shimizu
Province/State: Shizuoka
Country/Region: Japan
Contact name (PI/Team): Takehiko Shimada
Contact email (PI/Helpdesk):


Mikan Genome Database (MiGD): integrated database of genome annotation, genomic diversity, and CAPS marker information for mandarin molecular breeding. [PMID: 32523402]
Yoshihiro Kawahara, Tomoko Endo, Mitsuo Omura, Yumiko Teramoto, Takeshi Itoh, Hiroshi Fujii, Takehiko Shimada

Citrus species are some of the most valuable and widely consumed fruits globally. The genome sequences of representative citrus (e.g., , , ) species have been released but the research base for mandarin molecular breeding is still poor. We assembled the genomes of and , two important species for citrus industry in Japan, using hybrid assembly of Illumina and PacBio sequence data, and developed the Mikan Genome Database (MiGD). The assembled genome sizes of and are 346 and 292 Mb, respectively, similar to those of citrus species in public databases; they are predicted to possess 41,489 and 34,333 protein-coding genes in their draft genome sequences, with 9,642 and 8,377 specific genes when compared to , respectively. MiGD is an integrated database of genome annotation, genetic diversity, and Cleaved Amplified Polymorphic Sequence (CAPS) marker information, with these contents being mutually linked by genes. MiGD facilitates access to genome sequences of interest from previously reported linkage maps through CAPS markers and obtains polymorphism information through the multiple genome browser TASUKE. The genomic resources in MiGD ( could provide valuable information for mandarin molecular breeding in Japan.

Breed. Sci.. 2020:70(2) | 2 Citations (from Europe PMC, 2021-06-19)


All databases:
2774/5061 (45.208%)
Gene genome and annotation:
826/1350 (38.889%)
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Created on: 2020-11-11
Curated by:
lin liu [2021-02-19]
Zhao Li [2020-11-25]
Zhao Li [2020-11-24]
Ming Chen [2020-11-11]