Transcriptome sequencing of the blind subterranean mole rat, Spalax galili: Utility and potential for the discovery of novel evolutionary patterns

Handle URI:
http://hdl.handle.net/10754/325288
Title:
Transcriptome sequencing of the blind subterranean mole rat, Spalax galili: Utility and potential for the discovery of novel evolutionary patterns
Authors:
Malik, Assaf; Korol, Abraham; Hübner, Sariel; Hernandez, Alvaro G.; Thimmapuram, Jyothi; Ali, Shahjahan; Glaser, Fabian; Paz, Arnon; Avivi, Aaron; Band, Mark
Abstract:
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. 2011 Malik et al.
Citation:
Malik A, Korol A, Hübner S, Hernandez AG, Thimmapuram J, et al. (2011) Transcriptome Sequencing of the Blind Subterranean Mole Rat, Spalax galili: Utility and Potential for the Discovery of Novel Evolutionary Patterns. PLoS ONE 6: e21227. doi:10.1371/journal.pone.0021227.
Publisher:
Public Library of Science (PLoS)
Journal:
PLoS ONE
Issue Date:
12-Aug-2011
DOI:
10.1371/journal.pone.0021227
PubMed ID:
21857902
PubMed Central ID:
PMC3155515
Type:
Article
ISSN:
19326203
Appears in Collections:
Articles

Full metadata record

DC FieldValue Language
dc.contributor.authorMalik, Assafen
dc.contributor.authorKorol, Abrahamen
dc.contributor.authorHübner, Sarielen
dc.contributor.authorHernandez, Alvaro G.en
dc.contributor.authorThimmapuram, Jyothien
dc.contributor.authorAli, Shahjahanen
dc.contributor.authorGlaser, Fabianen
dc.contributor.authorPaz, Arnonen
dc.contributor.authorAvivi, Aaronen
dc.contributor.authorBand, Marken
dc.date.accessioned2014-08-27T09:45:05Z-
dc.date.available2014-08-27T09:45:05Z-
dc.date.issued2011-08-12en
dc.identifier.citationMalik A, Korol A, Hübner S, Hernandez AG, Thimmapuram J, et al. (2011) Transcriptome Sequencing of the Blind Subterranean Mole Rat, Spalax galili: Utility and Potential for the Discovery of Novel Evolutionary Patterns. PLoS ONE 6: e21227. doi:10.1371/journal.pone.0021227.en
dc.identifier.issn19326203en
dc.identifier.pmid21857902en
dc.identifier.doi10.1371/journal.pone.0021227en
dc.identifier.urihttp://hdl.handle.net/10754/325288en
dc.description.abstractThe 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. 2011 Malik et al.en
dc.language.isoenen
dc.publisherPublic Library of Science (PLoS)en
dc.rightsMalik et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en
dc.rightsArchived with thanks to PLoS ONEen
dc.subjectcomplementary DNAen
dc.subjectcomplementary DNAen
dc.subjecttranscriptomeen
dc.subjectanimal tissueen
dc.subjectbrain tissueen
dc.subjectgene expressionen
dc.subjectgene sequenceen
dc.subjectgenetic transcriptionen
dc.subjectgenetic variabilityen
dc.subjecthypoxiaen
dc.subjectmole raten
dc.subjectmolecular evolutionen
dc.subjectmuscle tissueen
dc.subjectnucleotide sequenceen
dc.subjectraten
dc.subjectsequence homologyen
dc.subjectsingle nucleotide polymorphismen
dc.subjectSpalax galilien
dc.subjecttranscriptomicsen
dc.subjectunindexed sequenceen
dc.subjectanoxiaen
dc.subjectbrainen
dc.subjectchemistryen
dc.subjectDNA sequenceen
dc.subjectgene expression profilingen
dc.subjectgene libraryen
dc.subjectgeneticsen
dc.subjectmetabolismen
dc.subjectmethodologyen
dc.subjectmolecular evolutionen
dc.subjectmolecular geneticsen
dc.subjectmouseen
dc.subjectmuscleen
dc.subjectnucleotide sequenceen
dc.subjectopen reading frameen
dc.subjectAnimaliaen
dc.subjectNannospalax ehrenbergien
dc.subjectRattusen
dc.subjectSpalacinaeen
dc.subjectSpalax galilien
dc.subjectAnoxiaen
dc.subjectBase Sequenceen
dc.subjectBrainen
dc.subjectDNA, Complementaryen
dc.subjectEvolution, Molecularen
dc.subjectGene Expression Profilingen
dc.subjectGene Libraryen
dc.subjectMiceen
dc.subjectMolecular Sequence Dataen
dc.subjectMusclesen
dc.subjectOpen Reading Framesen
dc.subjectPolymorphism, Single Nucleotideen
dc.subjectRatsen
dc.subjectSequence Analysis, DNAen
dc.subjectSpalaxen
dc.subjectTranscriptomeen
dc.titleTranscriptome sequencing of the blind subterranean mole rat, Spalax galili: Utility and potential for the discovery of novel evolutionary patternsen
dc.typeArticleen
dc.identifier.journalPLoS ONEen
dc.identifier.pmcidPMC3155515en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionInstitute of Evolution, University of Haifa, Haifa, Israelen
dc.contributor.institutionW. M. Keck Center for Comparative and Functional Genomics, University of Illinois, Urbana, IL, United Statesen
dc.contributor.institutionBioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion - Israel Institute of Technology, Haifa, Israelen
dc.contributor.institutionDepartment of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israelen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorAli, Shahjahanen

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