The pig X and Y Chromosomes: structure, sequence, and evolution
We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated ge...
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| Veröffentlicht in: | Genome research 2016-01, Vol.26 (1), p.130-139 |
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| creator | Skinner, Benjamin M Sargent, Carole A Churcher, Carol Hunt, Toby Herrero, Javier Loveland, Jane E Dunn, Matt Louzada, Sandra Fu, Beiyuan Chow, William Gilbert, James Austin-Guest, Siobhan Beal, Kathryn Carvalho-Silva, Denise Cheng, William Gordon, Daria Grafham, Darren Hardy, Matt Harley, Jo Hauser, Heidi Howden, Philip Howe, Kerstin Lachani, Kim Ellis, Peter J I Kelly, Daniel Kerry, Giselle Kerwin, James Ng, Bee Ling Threadgold, Glen Wileman, Thomas Wood, Jonathan M D Yang, Fengtang Harrow, Jen Affara, Nabeel A Tyler-Smith, Chris |
| description | We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes--both single copy and amplified--on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution. |
| doi_str_mv | 10.1101/gr.188839.114 |
| format | Article |
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The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes--both single copy and amplified--on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution.</description><identifier>ISSN: 1088-9051</identifier><identifier>EISSN: 1549-5469</identifier><identifier>DOI: 10.1101/gr.188839.114</identifier><identifier>PMID: 26560630</identifier><language>eng</language><publisher>United States: Cold Spring Harbor Laboratory Press</publisher><subject>Animals ; Base Sequence ; Cats - genetics ; Chromosomes, Mammalian - genetics ; Dogs - genetics ; Evolution, Molecular ; Female ; Gene Conversion ; Gene Expression ; Gene Library ; Gene Order ; Humans ; Male ; Molecular Sequence Data ; Resource ; Sequence Alignment ; Sequence Analysis, DNA ; Swine - genetics ; X Chromosome - genetics ; Y Chromosome - genetics</subject><ispartof>Genome research, 2016-01, Vol.26 (1), p.130-139</ispartof><rights>2016 Skinner et al.; Published by Cold Spring Harbor Laboratory Press.</rights><rights>2016</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c486t-4f709eb9bdf0e3865b4a0e8883431307940ec23d0235c49273ce02a4bf24c7a03</citedby><cites>FETCH-LOGICAL-c486t-4f709eb9bdf0e3865b4a0e8883431307940ec23d0235c49273ce02a4bf24c7a03</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691746/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691746/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26560630$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Skinner, Benjamin M</creatorcontrib><creatorcontrib>Sargent, Carole A</creatorcontrib><creatorcontrib>Churcher, Carol</creatorcontrib><creatorcontrib>Hunt, Toby</creatorcontrib><creatorcontrib>Herrero, Javier</creatorcontrib><creatorcontrib>Loveland, Jane E</creatorcontrib><creatorcontrib>Dunn, Matt</creatorcontrib><creatorcontrib>Louzada, Sandra</creatorcontrib><creatorcontrib>Fu, Beiyuan</creatorcontrib><creatorcontrib>Chow, William</creatorcontrib><creatorcontrib>Gilbert, James</creatorcontrib><creatorcontrib>Austin-Guest, Siobhan</creatorcontrib><creatorcontrib>Beal, Kathryn</creatorcontrib><creatorcontrib>Carvalho-Silva, Denise</creatorcontrib><creatorcontrib>Cheng, William</creatorcontrib><creatorcontrib>Gordon, Daria</creatorcontrib><creatorcontrib>Grafham, Darren</creatorcontrib><creatorcontrib>Hardy, Matt</creatorcontrib><creatorcontrib>Harley, Jo</creatorcontrib><creatorcontrib>Hauser, Heidi</creatorcontrib><creatorcontrib>Howden, Philip</creatorcontrib><creatorcontrib>Howe, Kerstin</creatorcontrib><creatorcontrib>Lachani, Kim</creatorcontrib><creatorcontrib>Ellis, Peter J I</creatorcontrib><creatorcontrib>Kelly, Daniel</creatorcontrib><creatorcontrib>Kerry, Giselle</creatorcontrib><creatorcontrib>Kerwin, James</creatorcontrib><creatorcontrib>Ng, Bee Ling</creatorcontrib><creatorcontrib>Threadgold, Glen</creatorcontrib><creatorcontrib>Wileman, Thomas</creatorcontrib><creatorcontrib>Wood, Jonathan M D</creatorcontrib><creatorcontrib>Yang, Fengtang</creatorcontrib><creatorcontrib>Harrow, Jen</creatorcontrib><creatorcontrib>Affara, Nabeel A</creatorcontrib><creatorcontrib>Tyler-Smith, Chris</creatorcontrib><title>The pig X and Y Chromosomes: structure, sequence, and evolution</title><title>Genome research</title><addtitle>Genome Res</addtitle><description>We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes--both single copy and amplified--on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution.</description><subject>Animals</subject><subject>Base Sequence</subject><subject>Cats - genetics</subject><subject>Chromosomes, Mammalian - genetics</subject><subject>Dogs - genetics</subject><subject>Evolution, Molecular</subject><subject>Female</subject><subject>Gene Conversion</subject><subject>Gene Expression</subject><subject>Gene Library</subject><subject>Gene Order</subject><subject>Humans</subject><subject>Male</subject><subject>Molecular Sequence Data</subject><subject>Resource</subject><subject>Sequence Alignment</subject><subject>Sequence Analysis, DNA</subject><subject>Swine - genetics</subject><subject>X Chromosome - genetics</subject><subject>Y Chromosome - genetics</subject><issn>1088-9051</issn><issn>1549-5469</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkc1Lw0AQxRdRbK0evUqOHozOZjfJrgdFil9Q8FJBT8tmM2kjSbbuJgX_exNai948zQzz4zFvHiGnFC4pBXq1cJdUCMFkP_I9MqYxl2HME7nf9yBEKCGmI3Lk_QcAMC7EIRlFSZxAwmBMbudLDFblIngLdJMH78F06Wxtva3RXwe-dZ1pO4cXgcfPDhvTdwOHa1t1bWmbY3JQ6MrjybZOyOvD_Xz6FM5eHp-nd7PQcJG0IS9SkJjJLC8AmUjijGvA4W7OKINUckATsRwiFhsuo5QZhEjzrIi4STWwCbnZ6K66rMbcYNM6XamVK2vtvpTVpfq7acqlWti16j9BU570AudbAWd7J75VdekNVpVu0HZe0TRlgiUyEv9AYw6CCTqohhvUOOu9w2J3EQU15KMWTm3y6Ufe82e_bezon0DYN-jsikc</recordid><startdate>20160101</startdate><enddate>20160101</enddate><creator>Skinner, Benjamin M</creator><creator>Sargent, Carole A</creator><creator>Churcher, Carol</creator><creator>Hunt, Toby</creator><creator>Herrero, Javier</creator><creator>Loveland, Jane E</creator><creator>Dunn, Matt</creator><creator>Louzada, Sandra</creator><creator>Fu, Beiyuan</creator><creator>Chow, William</creator><creator>Gilbert, James</creator><creator>Austin-Guest, Siobhan</creator><creator>Beal, Kathryn</creator><creator>Carvalho-Silva, Denise</creator><creator>Cheng, William</creator><creator>Gordon, Daria</creator><creator>Grafham, Darren</creator><creator>Hardy, Matt</creator><creator>Harley, Jo</creator><creator>Hauser, Heidi</creator><creator>Howden, Philip</creator><creator>Howe, Kerstin</creator><creator>Lachani, Kim</creator><creator>Ellis, Peter J I</creator><creator>Kelly, Daniel</creator><creator>Kerry, Giselle</creator><creator>Kerwin, James</creator><creator>Ng, Bee Ling</creator><creator>Threadgold, Glen</creator><creator>Wileman, Thomas</creator><creator>Wood, Jonathan M D</creator><creator>Yang, Fengtang</creator><creator>Harrow, Jen</creator><creator>Affara, Nabeel A</creator><creator>Tyler-Smith, Chris</creator><general>Cold Spring Harbor Laboratory Press</general><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>7X8</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>5PM</scope></search><sort><creationdate>20160101</creationdate><title>The pig X and Y Chromosomes: structure, sequence, and evolution</title><author>Skinner, Benjamin M ; Sargent, Carole A ; Churcher, Carol ; Hunt, Toby ; Herrero, Javier ; Loveland, Jane E ; Dunn, Matt ; Louzada, Sandra ; Fu, Beiyuan ; Chow, William ; Gilbert, James ; Austin-Guest, Siobhan ; Beal, Kathryn ; Carvalho-Silva, Denise ; Cheng, William ; Gordon, Daria ; Grafham, Darren ; Hardy, Matt ; Harley, Jo ; Hauser, Heidi ; Howden, Philip ; Howe, Kerstin ; Lachani, Kim ; Ellis, Peter J I ; Kelly, Daniel ; Kerry, Giselle ; Kerwin, James ; Ng, Bee Ling ; Threadgold, Glen ; Wileman, Thomas ; Wood, Jonathan M D ; Yang, Fengtang ; Harrow, Jen ; Affara, Nabeel A ; Tyler-Smith, Chris</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c486t-4f709eb9bdf0e3865b4a0e8883431307940ec23d0235c49273ce02a4bf24c7a03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Animals</topic><topic>Base Sequence</topic><topic>Cats - 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Academic</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>PubMed Central (Full Participant titles)</collection><jtitle>Genome research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Skinner, Benjamin M</au><au>Sargent, Carole A</au><au>Churcher, Carol</au><au>Hunt, Toby</au><au>Herrero, Javier</au><au>Loveland, Jane E</au><au>Dunn, Matt</au><au>Louzada, Sandra</au><au>Fu, Beiyuan</au><au>Chow, William</au><au>Gilbert, James</au><au>Austin-Guest, Siobhan</au><au>Beal, Kathryn</au><au>Carvalho-Silva, Denise</au><au>Cheng, William</au><au>Gordon, Daria</au><au>Grafham, Darren</au><au>Hardy, Matt</au><au>Harley, Jo</au><au>Hauser, Heidi</au><au>Howden, Philip</au><au>Howe, Kerstin</au><au>Lachani, Kim</au><au>Ellis, Peter J I</au><au>Kelly, Daniel</au><au>Kerry, Giselle</au><au>Kerwin, James</au><au>Ng, Bee Ling</au><au>Threadgold, Glen</au><au>Wileman, Thomas</au><au>Wood, Jonathan M D</au><au>Yang, Fengtang</au><au>Harrow, Jen</au><au>Affara, Nabeel A</au><au>Tyler-Smith, Chris</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The pig X and Y Chromosomes: structure, sequence, and evolution</atitle><jtitle>Genome research</jtitle><addtitle>Genome Res</addtitle><date>2016-01-01</date><risdate>2016</risdate><volume>26</volume><issue>1</issue><spage>130</spage><epage>139</epage><pages>130-139</pages><issn>1088-9051</issn><eissn>1549-5469</eissn><abstract>We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes--both single copy and amplified--on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution.</abstract><cop>United States</cop><pub>Cold Spring Harbor Laboratory Press</pub><pmid>26560630</pmid><doi>10.1101/gr.188839.114</doi><tpages>10</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | Genome research, 2016-01, Vol.26 (1), p.130-139 |
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| language | eng |
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| source | MEDLINE; PubMed Central; Alma/SFX Local Collection |
| subjects | Animals Base Sequence Cats - genetics Chromosomes, Mammalian - genetics Dogs - genetics Evolution, Molecular Female Gene Conversion Gene Expression Gene Library Gene Order Humans Male Molecular Sequence Data Resource Sequence Alignment Sequence Analysis, DNA Swine - genetics X Chromosome - genetics Y Chromosome - genetics |
| title | The pig X and Y Chromosomes: structure, sequence, and evolution |
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