Dataset Information

UTGB/medaka: genomic resource database for medaka biology.

ABSTRACT: Medaka (Oryzias latipes) is a small egg-laying freshwater teleost native to East Asia that has become an excellent model system for developmental genetics and evolutionary biology. The draft medaka genome sequence (700 Mb) was reported in June 2007, and its substantial genomic resources have been opened to the public through the University of Tokyo Genome Browser Medaka (UTGB/medaka) database. This database provides basic genomic information, such as predicted genes, expressed sequence tags (ESTs), guanine/cytosine (GC) content, repeats and comparative genomics, as well as unique data resources including (i) 2473 genetic markers and experimentally confirmed PCR primers that amplify these markers, (ii) 142,414 bacterial artificial chromosome (BAC) and 217,344 fosmid end sequences that amount to 15.0- and 11.1-fold clone coverage of the entire genome, respectively, and were used for draft genome assembly, (iii) 16,519,460 single nucleotide polymorphisms (SNPs), and 2 859 905 insertions/deletions detected between two medaka inbred strain genomes and (iv) 841 235 5'-end serial analyses of gene-expression (SAGE) tags that identified 344 266 transcription start sites on the genome. UTGB/medaka is available at: http://medaka.utgenome.org/.

SUBMITTER: Ahsan B

PROVIDER: S-EPMC2238888 | biostudies-literature | 2008 Jan

REPOSITORIES: biostudies-literature

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UTGB/medaka: genomic resource database for medaka biology.

Ahsan Budrul B Kobayashi Daisuke D Yamada Tomoyuki T Kasahara Masahiro M Sasaki Shin S Saito Taro L TL Nagayasu Yukinobu Y Doi Koichiro K Nakatani Yoichiro Y Qu Wei W Jindo Tomoko T Shimada Atsuko A Naruse Kiyoshi K Toyoda Atsushi A Kuroki Yoko Y Fujiyama Asao A Sasaki Takashi T Shimizu Atsushi A Asakawa Shuichi S Shimizu Nobuyoshi N Hashimoto Shin-ichi S Yang Jun J Lee Yongjun Y Matsushima Kouji K Sugano Sumio S Sakaizumi Mitsuru M Narita Takanori T Ohishi Kazuko K Haga Shinobu S Ohta Fumiko F Nomoto Hisayo H Nogata Keiko K Morishita Tomomi T Endo Tomoko T Shin-I Tadasu T Takeda Hiroyuki H Kohara Yuji Y Morishita Shinichi S

Nucleic acids research 20071011 Database issue

Medaka (Oryzias latipes) is a small egg-laying freshwater teleost native to East Asia that has become an excellent model system for developmental genetics and evolutionary biology. The draft medaka genome sequence (700 Mb) was reported in June 2007, and its substantial genomic resources have been opened to the public through the University of Tokyo Genome Browser Medaka (UTGB/medaka) database. This database provides basic genomic information, such as predicted genes, expressed sequence tags (EST ...[more]

PMID: 17932069

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Project description:Background: Date palm (Phoenix dactylifera L.) is a cultivated woody plant with agricultural and economic importance in many countries around the world. With the advantages of next generation sequencing technologies, genome sequences for many date palm cultivars have been released recently. Short sequence repeat (SSR) and single nucleotide polymorphism (SNP) can be identified from these genomic data, and have been proven to be very useful biomarkers in plant genome analysis and breeding. Results: Here, we first improved the date palm genome assembly using 130X of HiSeq data generated in our lab. Then 246,445 SSRs (214,901 SSRs and 31,544 compound SSRs) were annotated in this genome assembly; among the SSRs, mononucleotide SSRs (58.92%) were the most abundant, followed by di- (29.92%), tri- (8.14%), tetra- (2.47%), penta- (0.36%), and hexa-nucleotide SSRs (0.19%). The high-quality PCR primer pairs were designed for most (174,497; 70.81% out of total) SSRs. We also annotated 6,375,806 SNPs with raw read depth≥3 in 90% cultivars. To further reduce false positive SNPs, we only kept 5,572,650 (87.40% out of total) SNPs with at least 20% cultivars support for downstream analyses. The high-quality PCR primer pairs were also obtained for 4,177,778 (65.53%) SNPs. We reconstructed the phylogenetic relationships among the 62 cultivars using these variants and found that they can be divided into three clusters, namely North Africa, Egypt - Sudan, and Middle East - South Asian, with Egypt - Sudan being the admixture of North Africa and Middle East - South Asian cultivars; we further confirmed these clusters using principal component analysis. Moreover, 34,346 SSRs and 4,177,778 SNPs with PCR primers were assigned to shared cultivars for cultivar classification and diversity analysis. All these SSRs, SNPs and their classification are available in our database, and can be used for cultivar identification, comparison, and molecular breeding. Conclusion:DRDB is a comprehensive genomic resource database of date palm. It can serve as a bioinformatics platform for date palm genomics, genetics, and molecular breeding. DRDB is freely available at http://drdb.big.ac.cn/home.

Dataset Information

UTGB/medaka: genomic resource database for medaka biology.

Publications

UTGB/medaka: genomic resource database for medaka biology.

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