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dc.contributor.authorNelson, Andrew D. L.
dc.contributor.authorDevisetty, Upendra K.
dc.contributor.authorPalos, Kyle
dc.contributor.authorHaug-Baltzell, Asher K.
dc.contributor.authorLyons, Eric
dc.contributor.authorBeilstein, Mark A.
dc.date.accessioned2017-07-06T23:33:00Z
dc.date.available2017-07-06T23:33:00Z
dc.date.issued2017-05-09
dc.identifier.citationEvolinc: A Tool for the Identification and Evolutionary Comparison of Long Intergenic Non-coding RNAs 2017, 8 Frontiers in Geneticsen
dc.identifier.issn1664-8021
dc.identifier.pmid28536600
dc.identifier.doi10.3389/fgene.2017.00052
dc.identifier.urihttp://hdl.handle.net/10150/624658
dc.description.abstractLong intergenic non-coding RNAs (lincRNAs) are an abundant and functionally diverse class of eukaryotic transcripts. Reported lincRNA repertoires in mammals vary, but are commonly in the thousands to tens of thousands of transcripts, covering similar to 90% of the genome. In addition to elucidating function, there is particular interest in understanding the origin and evolution of lincRNAs. Aside from mammals, lincRNA populations have been sparsely sampled, precluding evolutionary analyses focused on their emergence and persistence. Here we present Evolinc, a two-module pipeline designed to facilitate lincRNA discovery and characterize aspects of lincRNA evolution. The first module (Evolinc-I) is a lincRNA identification workflow that also facilitates downstream differential expression analysis and genome browser visualization of identified lincRNAs. The second module (Evolinc-II) is a genomic and transcriptomic comparative analysis workflow that determines the phylogenetic depth to which a lincRNA locus is conserved within a user-defined group of related species. Here we validate lincRNA catalogs generated with Evolinc-I against previously annotated Arabidopsis and human lincRNA data. Evolinc-I recapitulated earlier findings and uncovered an additional 70 Arabidopsis and 43 human lincRNAs. We demonstrate the usefulness of Evolinc-II by examining the evolutionary histories of a public dataset of 5,361 Arabidopsis lincRNAs. We used Evolinc-II to winnow this dataset to 40 lincRNAs conserved across species in Brassicaceae. Finally, we show how Evolinc-II can be used to recover the evolutionary history of a known lincRNA, the human telomerase RNA (TERC). These latter analyses revealed unexpected duplication events as well as the loss and subsequent acquisition of a novel TERC locus in the lineage leading to mice and rats. The Evolinc pipeline is currently integrated in CyVerse's Discovery Environment and is free for use by researchers.
dc.description.sponsorshipNational Science Foundation [IOS-1444490]; NSF-MCB [1409251]en
dc.language.isoenen
dc.publisherFRONTIERS MEDIA SAen
dc.relation.urlhttp://journal.frontiersin.org/article/10.3389/fgene.2017.00052/fullen
dc.rights© 2017 Nelson, Devisetty, Palos, Haug-Baltzell, Lyons and Beilstein. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).en
dc.subjectlincRNAsen
dc.subjectcomparative genomicsen
dc.subjectpipelineen
dc.subjectevolutionen
dc.subjectmolecularen
dc.subjectcomparative transcriptomicsen
dc.titleEvolinc: A Tool for the Identification and Evolutionary Comparison of Long Intergenic Non-coding RNAsen
dc.typeArticleen
dc.contributor.departmentUniv Arizona, Sch Plant Sci, Beilstein Laben
dc.contributor.departmentUniv Arizona, Bio5, CyVerseen
dc.contributor.departmentUniv Arizona, Genet Grad Interdisciplinary Grp, Lyons Laben
dc.identifier.journalFrontiers in Geneticsen
dc.description.noteOpen access journalen
dc.description.collectioninformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
refterms.dateFOA2018-09-11T21:09:14Z
html.description.abstractLong intergenic non-coding RNAs (lincRNAs) are an abundant and functionally diverse class of eukaryotic transcripts. Reported lincRNA repertoires in mammals vary, but are commonly in the thousands to tens of thousands of transcripts, covering similar to 90% of the genome. In addition to elucidating function, there is particular interest in understanding the origin and evolution of lincRNAs. Aside from mammals, lincRNA populations have been sparsely sampled, precluding evolutionary analyses focused on their emergence and persistence. Here we present Evolinc, a two-module pipeline designed to facilitate lincRNA discovery and characterize aspects of lincRNA evolution. The first module (Evolinc-I) is a lincRNA identification workflow that also facilitates downstream differential expression analysis and genome browser visualization of identified lincRNAs. The second module (Evolinc-II) is a genomic and transcriptomic comparative analysis workflow that determines the phylogenetic depth to which a lincRNA locus is conserved within a user-defined group of related species. Here we validate lincRNA catalogs generated with Evolinc-I against previously annotated Arabidopsis and human lincRNA data. Evolinc-I recapitulated earlier findings and uncovered an additional 70 Arabidopsis and 43 human lincRNAs. We demonstrate the usefulness of Evolinc-II by examining the evolutionary histories of a public dataset of 5,361 Arabidopsis lincRNAs. We used Evolinc-II to winnow this dataset to 40 lincRNAs conserved across species in Brassicaceae. Finally, we show how Evolinc-II can be used to recover the evolutionary history of a known lincRNA, the human telomerase RNA (TERC). These latter analyses revealed unexpected duplication events as well as the loss and subsequent acquisition of a novel TERC locus in the lineage leading to mice and rats. The Evolinc pipeline is currently integrated in CyVerse's Discovery Environment and is free for use by researchers.


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