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UTGB/medaka: genomic resource database for medaka biology.

Ahsan B, Kobayashi D, Yamada T, Kasahara M, Sasaki S, Saito TL, Nagayasu Y, Doi K, Nakatani Y, Qu W, Jindo T, Shimada A, Naruse K, Toyoda A, Kuroki Y, Fujiyama A, Sasaki T, Shimizu A, Asakawa S, Shimizu N, Hashimoto S, Yang J, Lee Y, Matsushima K, Sugano S, Sakaizumi M, Narita T, Ohishi K, Haga S, Ohta F, Nomoto H, Nogata K, Morishita T, Endo T, Shin-I T, Takeda H, Kohara Y, Morishita S - Nucleic Acids Res. (2007)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-0882, Japan.

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/.

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Genetic markers. (A) To display genetic markers on the chromosome of interest, start with the top-level ‘Keyword Search’ view by selecting species as ‘medaka-chr.’ (B) Specify the chromosome number by inputting “CH” followed by the number, e.g. ‘CH01’ or ‘CH16’. (C) Clicking the ‘Search’ button presents all genetic markers horizontally along the chromosome. The distance of a genetic marker from the head of the chromosome is shown in terms of centimorgan (cM). Ultracontigs (series of scaffolds) are categorized into three groups, mapped, unoriented and unordered. Mapped ultracontigs are anchored on the chromosome by multiple genetic markers among which at least one recombination is observed. Unoriented ultracontigs are associated to the specific position on the genetic map, but their directions are unknown because no recombination is observed in the ultracontigs. A cluster of ultracontigs is unordered if it is located on the genetic map but neither the order in the cluster nor the orientation is known because no recombination is observed in the cluster. (D) An enlarged view of the window bounded by two vertical, red lines in Figure 2C. The ultracontig illustrated in the figure has four scaffolds linked by horizontal black lines that represent BAC end pairs. The four blue lines connected to one of the scaffolds from the node labeled with 0.07 cM indicate genetic markers among which no recombination is observed. (E) Clicking the leftmost, blue genetic marker name presents the list of markers surrounding the selected marker. (F) Selecting the scaffold enclosed in the red box displays the view with a variety of precise information associated with the scaffold, which is similar to Figure 1.
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Figure 2: Genetic markers. (A) To display genetic markers on the chromosome of interest, start with the top-level ‘Keyword Search’ view by selecting species as ‘medaka-chr.’ (B) Specify the chromosome number by inputting “CH” followed by the number, e.g. ‘CH01’ or ‘CH16’. (C) Clicking the ‘Search’ button presents all genetic markers horizontally along the chromosome. The distance of a genetic marker from the head of the chromosome is shown in terms of centimorgan (cM). Ultracontigs (series of scaffolds) are categorized into three groups, mapped, unoriented and unordered. Mapped ultracontigs are anchored on the chromosome by multiple genetic markers among which at least one recombination is observed. Unoriented ultracontigs are associated to the specific position on the genetic map, but their directions are unknown because no recombination is observed in the ultracontigs. A cluster of ultracontigs is unordered if it is located on the genetic map but neither the order in the cluster nor the orientation is known because no recombination is observed in the cluster. (D) An enlarged view of the window bounded by two vertical, red lines in Figure 2C. The ultracontig illustrated in the figure has four scaffolds linked by horizontal black lines that represent BAC end pairs. The four blue lines connected to one of the scaffolds from the node labeled with 0.07 cM indicate genetic markers among which no recombination is observed. (E) Clicking the leftmost, blue genetic marker name presents the list of markers surrounding the selected marker. (F) Selecting the scaffold enclosed in the red box displays the view with a variety of precise information associated with the scaffold, which is similar to Figure 1.

Mentions: In UTGB/medaka, biological data are organized along the medaka genome sequence. One can approach a genomic region of interest in three different ways. The first is the typical method that searches for proper keywords, such as scaffold names, gene names and EST accession numbers. The second is to input a sequence of interest, such as a cloned and sequenced gene, into the online mapping window, and subsequently the system returns the list of location candidates of the given sequence with their alignments to the genome and displays the selected location in the main window. The last is to display an overview of all genetic markers on individual chromosomes that are useful in boosting the positional cloning of genes responsible for a specific phenotype. Our database provides a high-resolution mapping of confirmed genetic markers as well as genomic sequences on which individual genetic markers are located. As shown in Figure 1, genomic sequences are associated with a variety of information, e.g. predicted genes, 5′SAGE tags, and ESTs. In the meanwhile, Figure 2 illustrates how to browse the list of genetic markers along the chromosome of interest. The maps of genetic markers shown in Figure 2C and D facilitate chromosome walking towards the locus that is likely to contain responsible genes, and clicking the scaffold on the locus presents precise information, e.g. candidate genes, as shown in Figure 2F.Figure 2.


UTGB/medaka: genomic resource database for medaka biology.

Ahsan B, Kobayashi D, Yamada T, Kasahara M, Sasaki S, Saito TL, Nagayasu Y, Doi K, Nakatani Y, Qu W, Jindo T, Shimada A, Naruse K, Toyoda A, Kuroki Y, Fujiyama A, Sasaki T, Shimizu A, Asakawa S, Shimizu N, Hashimoto S, Yang J, Lee Y, Matsushima K, Sugano S, Sakaizumi M, Narita T, Ohishi K, Haga S, Ohta F, Nomoto H, Nogata K, Morishita T, Endo T, Shin-I T, Takeda H, Kohara Y, Morishita S - Nucleic Acids Res. (2007)

Genetic markers. (A) To display genetic markers on the chromosome of interest, start with the top-level ‘Keyword Search’ view by selecting species as ‘medaka-chr.’ (B) Specify the chromosome number by inputting “CH” followed by the number, e.g. ‘CH01’ or ‘CH16’. (C) Clicking the ‘Search’ button presents all genetic markers horizontally along the chromosome. The distance of a genetic marker from the head of the chromosome is shown in terms of centimorgan (cM). Ultracontigs (series of scaffolds) are categorized into three groups, mapped, unoriented and unordered. Mapped ultracontigs are anchored on the chromosome by multiple genetic markers among which at least one recombination is observed. Unoriented ultracontigs are associated to the specific position on the genetic map, but their directions are unknown because no recombination is observed in the ultracontigs. A cluster of ultracontigs is unordered if it is located on the genetic map but neither the order in the cluster nor the orientation is known because no recombination is observed in the cluster. (D) An enlarged view of the window bounded by two vertical, red lines in Figure 2C. The ultracontig illustrated in the figure has four scaffolds linked by horizontal black lines that represent BAC end pairs. The four blue lines connected to one of the scaffolds from the node labeled with 0.07 cM indicate genetic markers among which no recombination is observed. (E) Clicking the leftmost, blue genetic marker name presents the list of markers surrounding the selected marker. (F) Selecting the scaffold enclosed in the red box displays the view with a variety of precise information associated with the scaffold, which is similar to Figure 1.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238888&req=5

Figure 2: Genetic markers. (A) To display genetic markers on the chromosome of interest, start with the top-level ‘Keyword Search’ view by selecting species as ‘medaka-chr.’ (B) Specify the chromosome number by inputting “CH” followed by the number, e.g. ‘CH01’ or ‘CH16’. (C) Clicking the ‘Search’ button presents all genetic markers horizontally along the chromosome. The distance of a genetic marker from the head of the chromosome is shown in terms of centimorgan (cM). Ultracontigs (series of scaffolds) are categorized into three groups, mapped, unoriented and unordered. Mapped ultracontigs are anchored on the chromosome by multiple genetic markers among which at least one recombination is observed. Unoriented ultracontigs are associated to the specific position on the genetic map, but their directions are unknown because no recombination is observed in the ultracontigs. A cluster of ultracontigs is unordered if it is located on the genetic map but neither the order in the cluster nor the orientation is known because no recombination is observed in the cluster. (D) An enlarged view of the window bounded by two vertical, red lines in Figure 2C. The ultracontig illustrated in the figure has four scaffolds linked by horizontal black lines that represent BAC end pairs. The four blue lines connected to one of the scaffolds from the node labeled with 0.07 cM indicate genetic markers among which no recombination is observed. (E) Clicking the leftmost, blue genetic marker name presents the list of markers surrounding the selected marker. (F) Selecting the scaffold enclosed in the red box displays the view with a variety of precise information associated with the scaffold, which is similar to Figure 1.
Mentions: In UTGB/medaka, biological data are organized along the medaka genome sequence. One can approach a genomic region of interest in three different ways. The first is the typical method that searches for proper keywords, such as scaffold names, gene names and EST accession numbers. The second is to input a sequence of interest, such as a cloned and sequenced gene, into the online mapping window, and subsequently the system returns the list of location candidates of the given sequence with their alignments to the genome and displays the selected location in the main window. The last is to display an overview of all genetic markers on individual chromosomes that are useful in boosting the positional cloning of genes responsible for a specific phenotype. Our database provides a high-resolution mapping of confirmed genetic markers as well as genomic sequences on which individual genetic markers are located. As shown in Figure 1, genomic sequences are associated with a variety of information, e.g. predicted genes, 5′SAGE tags, and ESTs. In the meanwhile, Figure 2 illustrates how to browse the list of genetic markers along the chromosome of interest. The maps of genetic markers shown in Figure 2C and D facilitate chromosome walking towards the locus that is likely to contain responsible genes, and clicking the scaffold on the locus presents precise information, e.g. candidate genes, as shown in Figure 2F.Figure 2.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-0882, Japan.

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/.

Show MeSH
Related in: MedlinePlus