‘Mikan’ memeans citrus fruits in Japanese. Mikan Genome Database 2 (MiGD2) is a citrus poymorphism resource for breeding, physiology, genomics and genetics of citrus. MiGD provides the following contents: (1) TASUKE+: comparative genome browser which shows genome-wide variants and depth of coverage of re-sequencing data among citrus species, (2) JBrowse: the annotation for satsuma mandarin (Citrus unshiu) genomes which newly assembled by MiGD team and Kazusa DNA Research Institure, (3) CAPS Marker: CAPS maker database including 2,696 primer sets and restriction enzyme with electrophoresis photos, (4) BLAST: BLAST service against gene and genome sequences of three citrus species, thale-cress, and tomato, (5) BLAT: BLAT service against gene and genome sequences of three citrus species, thale-cress, and tomato, (6) Genome Cuter: Genome Cutter service against gene and genome sequences of three citrus species, thale-cress, and tomato, (7) MinimalMarker: service of minimal DNA marker set detection for cultivar discrimination, (8) MARCO: service of parentage estimation using DNA markers, and (9) Genoem & Annotaiton: genome sequence and annotation data of C. unshiu.
Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO)
Institute of Fruit Tree and Tea Science, NARO
Faculty of Agriculture, Shizuoka University
International College, National Taiwan University
Kawahara Y, Endo T, Omura M, Teramoto Y, Itoh T, Fujii H, Shimada T (2020) Mikan Genome Database (MiGD): integrated database of the genome annotation, genomic diversity, and CAPS marker information for mandarin molecular breeding. Breeding Science. [doi: 10.1270/jsbbs.19097]
Isobe S, Fujii H, Shirasawa K, Kawahara Y, Endo T, Shimada T (2023) Haploid-resolved and chromosome-scale genome assembly in Citrus unshiu and its parental species, C. nobilis and C. kinokuni. biorxiv. [doi: 10.1101/2023.06.02.543356]
Kumagai M, Kim J, Itoh R and Itoh T (2013) TASUKE: a web-based visualization program for large-scale resequencing data. Bioinformatics. 29 (14): 1806-1808. [doi: 10.1093/bioinformatics/btt295] [PMID: 23749962]
Numa H and Itoh T (2014) MEGANTE: A Web-based System for Integrated Plant Genome Annotation. Plant and Cell Physiology, 55(1): e2. [doi: 10.1093/pcp/pct157] [PMID: 24253915]
Ninomiya T, Shimada T, Endo T, Nonaka K, Omura M and Fujii H (2015) Development of citrus cultivar identification by CAPS markers and parentage analysis. Hort Res (Japan), 14: 127-133. (In Japanese with English abstract) [doi: 10.2503/hrj.14.127]
Nonaka K, Fujii H, Kita M, Shimada T, Endo T, Yoshioka T and Omura M (2017) Identification and parentage analysis of citrus cultivars developed in Japan by CAPS markers. Hort J, 88: 208-221. [doi: 10.2503/hortj.OKD-026]
Fujii, H., T. Narita, H. Oshino, T. Kawakami, H. Goto, T. Yoshioka, M. Omura and T. Shimada (2019) CAPS markers with stability and reproductivity for discriminating major citrus cultivars in Japan. DNA polyporphism. 27: 71-79.
Ohta S, Endo T, Shimada T, Fujii H, Omura M et al. (2015) Construction of genetic linkage map and graphical genotyping of pseudo-backcrossed F2 (BC’2) progeny to introduce a CTV resistance from Poncirus trifoliata (L.) Raf. into Citrus by introgression breeding. Tree Genet Genom. 11: 797. [doi: 10.1007/s11295-014-0797-y]
Shimada T, Fujii H, Endo T, Omura M. et al. (2014) Construction of a citrus framework genetic map anchored by 708 gene-based markers. Tree Genet Genom. 10: 1001-1013. [doi: 10.1007/s11295-014-0738-9]
Fujii H, Ogata T, Shimada T, Endo T, Iketani H, Shimizu T, Yamamoto T, Omura M (2013) Minimal Marker: an algorithm and computer program for the identificaiton of minimal sets of discriminating DNA markeras for efficient variety identification. J. Bioinform. Comput. Biol. 11(02) 1250022.
Fujii H, Hosaka F, Endo T, Shimada T, Terakami S, Yamamoto T. MARCO: a computer software for parentage inference using molecular markers. Acta Horticultae in press.