Transcriptome sequencing of the blind subterranean mole rat, Spalax galili: utility and potential for the discovery of novel evolutionary patterns
The blind subterranean mole rat (Spalax ehrenbergi superspecies) is a model animal for survival under extreme environments due to its ability to live in underground habitats under severe hypoxic stress and darkness. Here we report the transcriptome sequencing of Spalax galili, a chromosomal type of...
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| Veröffentlicht in: | PloS one 2011-08, Vol.6 (8), p.e21227 |
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| creator | Malik, Assaf Korol, Abraham Hübner, Sariel Hernandez, Alvaro G Thimmapuram, Jyothi Ali, Shahjahan Glaser, Fabian Paz, Arnon Avivi, Aaron Band, Mark |
| description | The blind subterranean mole rat (Spalax ehrenbergi superspecies) is a model animal for survival under extreme environments due to its ability to live in underground habitats under severe hypoxic stress and darkness. Here we report the transcriptome sequencing of Spalax galili, a chromosomal type of S. ehrenbergi. cDNA pools from muscle and brain tissues isolated from animals exposed to hypoxic and normoxic conditions were sequenced using Sanger, GS FLX, and GS FLX Titanium technologies. Assembly of the sequences yielded over 51,000 isotigs with homology to ∼12,000 mouse, rat or human genes. Based on these results, it was possible to detect large numbers of splice variants, SNPs, and novel transcribed regions. In addition, multiple differential expression patterns were detected between tissues and treatments. The results presented here will serve as a valuable resource for future studies aimed at identifying genes and gene regions evolved during the adaptive radiation associated with underground life of the blind mole rat. |
| doi_str_mv | 10.1371/journal.pone.0021227 |
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Here we report the transcriptome sequencing of Spalax galili, a chromosomal type of S. ehrenbergi. cDNA pools from muscle and brain tissues isolated from animals exposed to hypoxic and normoxic conditions were sequenced using Sanger, GS FLX, and GS FLX Titanium technologies. Assembly of the sequences yielded over 51,000 isotigs with homology to ∼12,000 mouse, rat or human genes. Based on these results, it was possible to detect large numbers of splice variants, SNPs, and novel transcribed regions. In addition, multiple differential expression patterns were detected between tissues and treatments. The results presented here will serve as a valuable resource for future studies aimed at identifying genes and gene regions evolved during the adaptive radiation associated with underground life of the blind mole rat.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0021227</identifier><identifier>PMID: 21857902</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Adaptive radiation ; Alternative splicing ; Animals ; Bands ; Base Sequence ; Biological evolution ; Biology ; Brain ; Brain - metabolism ; Brain research ; Cell cycle ; Darkness ; DNA, Complementary - chemistry ; DNA, Complementary - genetics ; Evolution ; Evolution, Molecular ; Extreme environments ; Gene expression ; Gene Expression Profiling - methods ; Gene Library ; Genes ; Genomes ; Genomics ; Homology ; Humans ; Hypoxia ; Medical research ; Mice ; Molecular Sequence Data ; Morphology ; Muscles ; Muscles - metabolism ; Musculoskeletal system ; Mutation ; Open Reading Frames - genetics ; Pan troglodytes ; Polymorphism, Single Nucleotide ; Proteins ; Radiation ; Rats ; Rattus ; Rodents ; Sensors ; Sequence Analysis, DNA - methods ; Single-nucleotide polymorphism ; Spalax ; Spalax - genetics ; Tissues ; Transcriptome ; Trends ; Underground utilities</subject><ispartof>PloS one, 2011-08, Vol.6 (8), p.e21227</ispartof><rights>COPYRIGHT 2011 Public Library of Science</rights><rights>2011 Malik et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Malik et al. 2011</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c691t-aea177bc83f00e0fd7852bb005bdc0c5f8f76f6eab967976be1befeca82b90353</citedby><cites>FETCH-LOGICAL-c691t-aea177bc83f00e0fd7852bb005bdc0c5f8f76f6eab967976be1befeca82b90353</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/PMC3155515/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155515/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,725,778,782,862,883,2098,2917,23849,27907,27908,53774,53776,79351,79352</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21857902$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Michalak, Pawel</contributor><creatorcontrib>Malik, Assaf</creatorcontrib><creatorcontrib>Korol, Abraham</creatorcontrib><creatorcontrib>Hübner, Sariel</creatorcontrib><creatorcontrib>Hernandez, Alvaro G</creatorcontrib><creatorcontrib>Thimmapuram, Jyothi</creatorcontrib><creatorcontrib>Ali, Shahjahan</creatorcontrib><creatorcontrib>Glaser, Fabian</creatorcontrib><creatorcontrib>Paz, Arnon</creatorcontrib><creatorcontrib>Avivi, Aaron</creatorcontrib><creatorcontrib>Band, Mark</creatorcontrib><title>Transcriptome sequencing of the blind subterranean mole rat, Spalax galili: utility and potential for the discovery of novel evolutionary patterns</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The blind subterranean mole rat (Spalax ehrenbergi superspecies) is a model animal for survival under extreme environments due to its ability to live in underground habitats under severe hypoxic stress and darkness. Here we report the transcriptome sequencing of Spalax galili, a chromosomal type of S. ehrenbergi. cDNA pools from muscle and brain tissues isolated from animals exposed to hypoxic and normoxic conditions were sequenced using Sanger, GS FLX, and GS FLX Titanium technologies. Assembly of the sequences yielded over 51,000 isotigs with homology to ∼12,000 mouse, rat or human genes. Based on these results, it was possible to detect large numbers of splice variants, SNPs, and novel transcribed regions. In addition, multiple differential expression patterns were detected between tissues and treatments. The results presented here will serve as a valuable resource for future studies aimed at identifying genes and gene regions evolved during the adaptive radiation associated with underground life of the blind mole rat.</description><subject>Adaptive radiation</subject><subject>Alternative splicing</subject><subject>Animals</subject><subject>Bands</subject><subject>Base Sequence</subject><subject>Biological evolution</subject><subject>Biology</subject><subject>Brain</subject><subject>Brain - metabolism</subject><subject>Brain research</subject><subject>Cell cycle</subject><subject>Darkness</subject><subject>DNA, Complementary - chemistry</subject><subject>DNA, Complementary - genetics</subject><subject>Evolution</subject><subject>Evolution, Molecular</subject><subject>Extreme environments</subject><subject>Gene expression</subject><subject>Gene Expression Profiling - methods</subject><subject>Gene Library</subject><subject>Genes</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Homology</subject><subject>Humans</subject><subject>Hypoxia</subject><subject>Medical research</subject><subject>Mice</subject><subject>Molecular Sequence Data</subject><subject>Morphology</subject><subject>Muscles</subject><subject>Muscles - metabolism</subject><subject>Musculoskeletal system</subject><subject>Mutation</subject><subject>Open Reading Frames - genetics</subject><subject>Pan troglodytes</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Proteins</subject><subject>Radiation</subject><subject>Rats</subject><subject>Rattus</subject><subject>Rodents</subject><subject>Sensors</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Single-nucleotide polymorphism</subject><subject>Spalax</subject><subject>Spalax - genetics</subject><subject>Tissues</subject><subject>Transcriptome</subject><subject>Trends</subject><subject>Underground utilities</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNk99qFDEUxgdRbK2-gWhAEAR3TSYzyawXQin-WSgUbPU2JJmT3ZRsMibZpX0Nn9hsd1p2QUHmIuHM7_uSfMmpqpcETwnl5MN1WEcv3XQIHqYY16Su-aPqmMxoPWE1po_35kfVs5SuMW5px9jT6qgmXctnuD6ufl9F6ZOOdshhBSjBrzV4bf0CBYPyEpBy1vcorVWGWFCQHq2CAxRlfo8uB-nkDVpIZ539iNa5DPkWyaIYQgafrXTIhHjn1Nukwwbi7dbal5lDsAmuiIKXpTrIXNbw6Xn1xEiX4MU4nlQ_vny-Ovs2Ob_4Oj87PZ9oNiN5IkESzpXuqMEYsOl519ZKlUOqXmPdms5wZhhINWN8xpkCosCAll2tZpi29KR6vfMdXEhijDMJQjFvKaN8S8x3RB_ktRiiXZV9iiCtuCuEuBAyZqsdCA6Nphh3rOWsqXWjZN8x3PC-q7lqTVO8Po2rrdUKel3CidIdmB7-8XYpFmEjKGnblmw382Y0iKFcUsr_2PJIlTsBYb0JxUyvSvTitOGs6-qm6Qo1_QtVvh5WVpcHZWypHwjeHQgKk-EmL-Q6JTG__P7_7MXPQ_btHrsE6fIyjW8iHYLNDtQxpBTBPCRHsNj2w30aYtsPYuyHInu1n_qD6L4B6B_-Zwmn</recordid><startdate>20110812</startdate><enddate>20110812</enddate><creator>Malik, Assaf</creator><creator>Korol, Abraham</creator><creator>Hübner, Sariel</creator><creator>Hernandez, Alvaro G</creator><creator>Thimmapuram, Jyothi</creator><creator>Ali, Shahjahan</creator><creator>Glaser, Fabian</creator><creator>Paz, Arnon</creator><creator>Avivi, Aaron</creator><creator>Band, Mark</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</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>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20110812</creationdate><title>Transcriptome sequencing of the blind subterranean mole rat, Spalax galili: utility and potential for the discovery of novel evolutionary patterns</title><author>Malik, Assaf ; Korol, Abraham ; Hübner, Sariel ; Hernandez, Alvaro G ; Thimmapuram, Jyothi ; Ali, Shahjahan ; Glaser, Fabian ; Paz, Arnon ; Avivi, Aaron ; Band, Mark</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c691t-aea177bc83f00e0fd7852bb005bdc0c5f8f76f6eab967976be1befeca82b90353</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Adaptive radiation</topic><topic>Alternative splicing</topic><topic>Animals</topic><topic>Bands</topic><topic>Base Sequence</topic><topic>Biological evolution</topic><topic>Biology</topic><topic>Brain</topic><topic>Brain - 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Here we report the transcriptome sequencing of Spalax galili, a chromosomal type of S. ehrenbergi. cDNA pools from muscle and brain tissues isolated from animals exposed to hypoxic and normoxic conditions were sequenced using Sanger, GS FLX, and GS FLX Titanium technologies. Assembly of the sequences yielded over 51,000 isotigs with homology to ∼12,000 mouse, rat or human genes. Based on these results, it was possible to detect large numbers of splice variants, SNPs, and novel transcribed regions. In addition, multiple differential expression patterns were detected between tissues and treatments. 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| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Adaptive radiation Alternative splicing Animals Bands Base Sequence Biological evolution Biology Brain Brain - metabolism Brain research Cell cycle Darkness DNA, Complementary - chemistry DNA, Complementary - genetics Evolution Evolution, Molecular Extreme environments Gene expression Gene Expression Profiling - methods Gene Library Genes Genomes Genomics Homology Humans Hypoxia Medical research Mice Molecular Sequence Data Morphology Muscles Muscles - metabolism Musculoskeletal system Mutation Open Reading Frames - genetics Pan troglodytes Polymorphism, Single Nucleotide Proteins Radiation Rats Rattus Rodents Sensors Sequence Analysis, DNA - methods Single-nucleotide polymorphism Spalax Spalax - genetics Tissues Transcriptome Trends Underground utilities |
| title | Transcriptome sequencing of the blind subterranean mole rat, Spalax galili: utility and potential for the discovery of novel evolutionary patterns |
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