The DNA sequence of medaka chromosome LG22
We report the genomic DNA sequence of a single chromosome (linkage group 22; LG22) of the small teleost fish medaka ( Oryzias latipes) as a first whole chromosome sequence from a non-mammalian vertebrate. The order and orientation of 633 protein-coding genes were deduced from 18,803,338 bp of DNA se...
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| Veröffentlicht in: | Genomics (San Diego, Calif.) Calif.), 2007, Vol.89 (1), p.124-133 |
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| creator | Sasaki, Takashi Shimizu, Atsushi Ishikawa, Sabine K. Imai, Shuichiro Asakawa, Shuichi Murayama, Yuji Khorasani, Maryam Zadeh Mitani, Hiroshi Furutani-Seiki, Makoto Kondoh, Hisato Nanda, Indrajit Schmid, Michael Schartl, Manfred Nonaka, Masaru Takeda, Hiroyuki Hori, Hiroshi Himmelbauer, Heinz Shima, Akihiro Shimizu, Nobuyoshi |
| description | We report the genomic DNA sequence of a single chromosome (linkage group 22; LG22) of the small teleost fish medaka (
Oryzias latipes) as a first whole chromosome sequence from a non-mammalian vertebrate. The order and orientation of 633 protein-coding genes were deduced from 18,803,338 bp of DNA sequence, providing the opportunity to analyze chromosome evolution of vertebrate genomes by direct comparison with the human genome. The average number of genes in the “conserved gene cluster” (CGC), a strict definition of “synteny” at the sequence basis, between medaka and human was 1.6. These and other data suggest that approximately 38.8% of pair-wise gene relationships would have been broken from their common ancestor in the human and medaka lineages and further imply that approx 20,000 (15,520–23,280) breaks would have occurred from the entire genome of the common ancestor. These breaks were generated mainly by intra-chromosomal shufflings at a specific era in the vertebrate lineage. These precise comparative genomics allowed us to identify the pieces of ancient chromosomes of the common vertebrate ancestor and estimate chromosomal evolution in the vertebrate lineage. |
| doi_str_mv | 10.1016/j.ygeno.2006.09.003 |
| format | Article |
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Oryzias latipes) as a first whole chromosome sequence from a non-mammalian vertebrate. The order and orientation of 633 protein-coding genes were deduced from 18,803,338 bp of DNA sequence, providing the opportunity to analyze chromosome evolution of vertebrate genomes by direct comparison with the human genome. The average number of genes in the “conserved gene cluster” (CGC), a strict definition of “synteny” at the sequence basis, between medaka and human was 1.6. These and other data suggest that approximately 38.8% of pair-wise gene relationships would have been broken from their common ancestor in the human and medaka lineages and further imply that approx 20,000 (15,520–23,280) breaks would have occurred from the entire genome of the common ancestor. These breaks were generated mainly by intra-chromosomal shufflings at a specific era in the vertebrate lineage. These precise comparative genomics allowed us to identify the pieces of ancient chromosomes of the common vertebrate ancestor and estimate chromosomal evolution in the vertebrate lineage.</description><identifier>ISSN: 0888-7543</identifier><identifier>EISSN: 1089-8646</identifier><identifier>DOI: 10.1016/j.ygeno.2006.09.003</identifier><identifier>PMID: 17067776</identifier><language>eng</language><publisher>San Diego, CA: Elsevier Inc</publisher><subject>Animals ; Biological and medical sciences ; Chromosomes - genetics ; Chromosomes, Artificial, Bacterial - genetics ; DNA - genetics ; Evolution ; Evolution, Molecular ; Fundamental and applied biological sciences. Psychology ; Genes. Genome ; Genetics of eukaryotes. Biological and molecular evolution ; Genome sequence ; Humans ; Medaka ; Molecular and cellular biology ; Molecular genetics ; Multigene Family ; Oryzias - genetics ; Oryzias latipes ; Species Specificity ; Teleostei ; Tetraodontiformes - genetics</subject><ispartof>Genomics (San Diego, Calif.), 2007, Vol.89 (1), p.124-133</ispartof><rights>2006 Elsevier Inc.</rights><rights>2007 INIST-CNRS</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c418t-9904b6df2f95ac03a945a1723f4d41173d9f503c12e377cdc5b5eaad2c9cadf83</citedby><cites>FETCH-LOGICAL-c418t-9904b6df2f95ac03a945a1723f4d41173d9f503c12e377cdc5b5eaad2c9cadf83</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0888754306002692$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>314,776,780,3537,4010,27900,27901,27902,65306</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=18430039$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17067776$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Sasaki, Takashi</creatorcontrib><creatorcontrib>Shimizu, Atsushi</creatorcontrib><creatorcontrib>Ishikawa, Sabine K.</creatorcontrib><creatorcontrib>Imai, Shuichiro</creatorcontrib><creatorcontrib>Asakawa, Shuichi</creatorcontrib><creatorcontrib>Murayama, Yuji</creatorcontrib><creatorcontrib>Khorasani, Maryam Zadeh</creatorcontrib><creatorcontrib>Mitani, Hiroshi</creatorcontrib><creatorcontrib>Furutani-Seiki, Makoto</creatorcontrib><creatorcontrib>Kondoh, Hisato</creatorcontrib><creatorcontrib>Nanda, Indrajit</creatorcontrib><creatorcontrib>Schmid, Michael</creatorcontrib><creatorcontrib>Schartl, Manfred</creatorcontrib><creatorcontrib>Nonaka, Masaru</creatorcontrib><creatorcontrib>Takeda, Hiroyuki</creatorcontrib><creatorcontrib>Hori, Hiroshi</creatorcontrib><creatorcontrib>Himmelbauer, Heinz</creatorcontrib><creatorcontrib>Shima, Akihiro</creatorcontrib><creatorcontrib>Shimizu, Nobuyoshi</creatorcontrib><title>The DNA sequence of medaka chromosome LG22</title><title>Genomics (San Diego, Calif.)</title><addtitle>Genomics</addtitle><description>We report the genomic DNA sequence of a single chromosome (linkage group 22; LG22) of the small teleost fish medaka (
Oryzias latipes) as a first whole chromosome sequence from a non-mammalian vertebrate. The order and orientation of 633 protein-coding genes were deduced from 18,803,338 bp of DNA sequence, providing the opportunity to analyze chromosome evolution of vertebrate genomes by direct comparison with the human genome. The average number of genes in the “conserved gene cluster” (CGC), a strict definition of “synteny” at the sequence basis, between medaka and human was 1.6. These and other data suggest that approximately 38.8% of pair-wise gene relationships would have been broken from their common ancestor in the human and medaka lineages and further imply that approx 20,000 (15,520–23,280) breaks would have occurred from the entire genome of the common ancestor. These breaks were generated mainly by intra-chromosomal shufflings at a specific era in the vertebrate lineage. These precise comparative genomics allowed us to identify the pieces of ancient chromosomes of the common vertebrate ancestor and estimate chromosomal evolution in the vertebrate lineage.</description><subject>Animals</subject><subject>Biological and medical sciences</subject><subject>Chromosomes - genetics</subject><subject>Chromosomes, Artificial, Bacterial - genetics</subject><subject>DNA - genetics</subject><subject>Evolution</subject><subject>Evolution, Molecular</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genes. Genome</subject><subject>Genetics of eukaryotes. Biological and molecular evolution</subject><subject>Genome sequence</subject><subject>Humans</subject><subject>Medaka</subject><subject>Molecular and cellular biology</subject><subject>Molecular genetics</subject><subject>Multigene Family</subject><subject>Oryzias - genetics</subject><subject>Oryzias latipes</subject><subject>Species Specificity</subject><subject>Teleostei</subject><subject>Tetraodontiformes - genetics</subject><issn>0888-7543</issn><issn>1089-8646</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkEtPAjEURhujEUR_gYmZjS5MZryddvpYuCCoaEJ0g-um9CGDDMUWTPj3DkLCTld3c-7Jl4PQJYYCA2Z3s2Lz4RahKAFYAbIAIEeoi0HIXDDKjlEXhBA5ryjpoLOUZgAgiShPUQdzYJxz1kW346nLHl77WXJfa7cwLgs-a5zVnzoz0xiakELjstGwLM_Ridfz5C72t4fenx7Hg-d89DZ8GfRHuaFYrHIpgU6Y9aWXlTZAtKSVxrwknlqKMSdW-gqIwaUjnBtrqknltLalkUZbL0gP3ey8yxjaTWmlmjoZN5_rhQvrpJggTADG_4JYcsoZbI1kB5oYUorOq2WsGx03CoPatlQz9dtSbVsqkKpt2X5d7fXrSVvk8LOP1wLXe0Ano-c-6oWp04ETlLQe2XL3O8611b5rF1Uy9ba1raMzK2VD_eeQHypJkMY</recordid><startdate>2007</startdate><enddate>2007</enddate><creator>Sasaki, Takashi</creator><creator>Shimizu, Atsushi</creator><creator>Ishikawa, Sabine K.</creator><creator>Imai, Shuichiro</creator><creator>Asakawa, Shuichi</creator><creator>Murayama, Yuji</creator><creator>Khorasani, Maryam Zadeh</creator><creator>Mitani, Hiroshi</creator><creator>Furutani-Seiki, Makoto</creator><creator>Kondoh, Hisato</creator><creator>Nanda, Indrajit</creator><creator>Schmid, Michael</creator><creator>Schartl, Manfred</creator><creator>Nonaka, Masaru</creator><creator>Takeda, Hiroyuki</creator><creator>Hori, Hiroshi</creator><creator>Himmelbauer, Heinz</creator><creator>Shima, Akihiro</creator><creator>Shimizu, Nobuyoshi</creator><general>Elsevier Inc</general><general>Elsevier</general><scope>6I.</scope><scope>AAFTH</scope><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>2007</creationdate><title>The DNA sequence of medaka chromosome LG22</title><author>Sasaki, Takashi ; Shimizu, Atsushi ; Ishikawa, Sabine K. ; Imai, Shuichiro ; Asakawa, Shuichi ; Murayama, Yuji ; Khorasani, Maryam Zadeh ; Mitani, Hiroshi ; Furutani-Seiki, Makoto ; Kondoh, Hisato ; Nanda, Indrajit ; Schmid, Michael ; Schartl, Manfred ; Nonaka, Masaru ; Takeda, Hiroyuki ; Hori, Hiroshi ; Himmelbauer, Heinz ; Shima, Akihiro ; Shimizu, Nobuyoshi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c418t-9904b6df2f95ac03a945a1723f4d41173d9f503c12e377cdc5b5eaad2c9cadf83</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>Animals</topic><topic>Biological and medical sciences</topic><topic>Chromosomes - genetics</topic><topic>Chromosomes, Artificial, Bacterial - genetics</topic><topic>DNA - genetics</topic><topic>Evolution</topic><topic>Evolution, Molecular</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genes. Genome</topic><topic>Genetics of eukaryotes. Biological and molecular evolution</topic><topic>Genome sequence</topic><topic>Humans</topic><topic>Medaka</topic><topic>Molecular and cellular biology</topic><topic>Molecular genetics</topic><topic>Multigene Family</topic><topic>Oryzias - genetics</topic><topic>Oryzias latipes</topic><topic>Species Specificity</topic><topic>Teleostei</topic><topic>Tetraodontiformes - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Sasaki, Takashi</creatorcontrib><creatorcontrib>Shimizu, Atsushi</creatorcontrib><creatorcontrib>Ishikawa, Sabine K.</creatorcontrib><creatorcontrib>Imai, Shuichiro</creatorcontrib><creatorcontrib>Asakawa, Shuichi</creatorcontrib><creatorcontrib>Murayama, Yuji</creatorcontrib><creatorcontrib>Khorasani, Maryam Zadeh</creatorcontrib><creatorcontrib>Mitani, Hiroshi</creatorcontrib><creatorcontrib>Furutani-Seiki, Makoto</creatorcontrib><creatorcontrib>Kondoh, Hisato</creatorcontrib><creatorcontrib>Nanda, Indrajit</creatorcontrib><creatorcontrib>Schmid, Michael</creatorcontrib><creatorcontrib>Schartl, Manfred</creatorcontrib><creatorcontrib>Nonaka, Masaru</creatorcontrib><creatorcontrib>Takeda, Hiroyuki</creatorcontrib><creatorcontrib>Hori, Hiroshi</creatorcontrib><creatorcontrib>Himmelbauer, Heinz</creatorcontrib><creatorcontrib>Shima, Akihiro</creatorcontrib><creatorcontrib>Shimizu, Nobuyoshi</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Genomics (San Diego, Calif.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sasaki, Takashi</au><au>Shimizu, Atsushi</au><au>Ishikawa, Sabine K.</au><au>Imai, Shuichiro</au><au>Asakawa, Shuichi</au><au>Murayama, Yuji</au><au>Khorasani, Maryam Zadeh</au><au>Mitani, Hiroshi</au><au>Furutani-Seiki, Makoto</au><au>Kondoh, Hisato</au><au>Nanda, Indrajit</au><au>Schmid, Michael</au><au>Schartl, Manfred</au><au>Nonaka, Masaru</au><au>Takeda, Hiroyuki</au><au>Hori, Hiroshi</au><au>Himmelbauer, Heinz</au><au>Shima, Akihiro</au><au>Shimizu, Nobuyoshi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The DNA sequence of medaka chromosome LG22</atitle><jtitle>Genomics (San Diego, Calif.)</jtitle><addtitle>Genomics</addtitle><date>2007</date><risdate>2007</risdate><volume>89</volume><issue>1</issue><spage>124</spage><epage>133</epage><pages>124-133</pages><issn>0888-7543</issn><eissn>1089-8646</eissn><abstract>We report the genomic DNA sequence of a single chromosome (linkage group 22; LG22) of the small teleost fish medaka (
Oryzias latipes) as a first whole chromosome sequence from a non-mammalian vertebrate. The order and orientation of 633 protein-coding genes were deduced from 18,803,338 bp of DNA sequence, providing the opportunity to analyze chromosome evolution of vertebrate genomes by direct comparison with the human genome. The average number of genes in the “conserved gene cluster” (CGC), a strict definition of “synteny” at the sequence basis, between medaka and human was 1.6. These and other data suggest that approximately 38.8% of pair-wise gene relationships would have been broken from their common ancestor in the human and medaka lineages and further imply that approx 20,000 (15,520–23,280) breaks would have occurred from the entire genome of the common ancestor. These breaks were generated mainly by intra-chromosomal shufflings at a specific era in the vertebrate lineage. These precise comparative genomics allowed us to identify the pieces of ancient chromosomes of the common vertebrate ancestor and estimate chromosomal evolution in the vertebrate lineage.</abstract><cop>San Diego, CA</cop><pub>Elsevier Inc</pub><pmid>17067776</pmid><doi>10.1016/j.ygeno.2006.09.003</doi><tpages>10</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Animals Biological and medical sciences Chromosomes - genetics Chromosomes, Artificial, Bacterial - genetics DNA - genetics Evolution Evolution, Molecular Fundamental and applied biological sciences. Psychology Genes. Genome Genetics of eukaryotes. Biological and molecular evolution Genome sequence Humans Medaka Molecular and cellular biology Molecular genetics Multigene Family Oryzias - genetics Oryzias latipes Species Specificity Teleostei Tetraodontiformes - genetics |
| title | The DNA sequence of medaka chromosome LG22 |
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