Organellar genome, nuclear ribosomal DNA repeat unit, and microsatellites isolated from a small-scale of 454 GS FLX sequencing on two mosses
[Display omitted] ► 454 shot gun sequencing is a fast and easy method to generate large, multiple copy genomic regions for mosses. ► We assembled nearly complete organellar genomes and the whole nrDNA repeat unit for two Funariaceae. ► The NGS data pool is a rich source for identifying microsatellit...
Gespeichert in:
Veröffentlicht in: | Molecular phylogenetics and evolution 2013-03, Vol.66 (3), p.1089-1094 |
---|---|
Hauptverfasser: | , , , , |
Format: | Artikel |
Sprache: | eng |
Schlagworte: | |
Online-Zugang: | Volltext |
Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
container_end_page | 1094 |
---|---|
container_issue | 3 |
container_start_page | 1089 |
container_title | Molecular phylogenetics and evolution |
container_volume | 66 |
creator | Liu, Yang Forrest, Laura L. Bainard, Jillian D. Budke, Jessica M. Goffinet, Bernard |
description | [Display omitted]
► 454 shot gun sequencing is a fast and easy method to generate large, multiple copy genomic regions for mosses. ► We assembled nearly complete organellar genomes and the whole nrDNA repeat unit for two Funariaceae. ► The NGS data pool is a rich source for identifying microsatellites.
Recent innovations in high-throughput DNA sequencing methodology (next generation sequencing technologies [NGS]) allow for the generation of large amounts of high quality data that may be particularly critical for resolving ambiguous relationships such as those resulting from rapid radiations. Application of NGS technology to bryology is limited to assembling entire nuclear or organellar genomes of selected exemplars of major lineages (e.g., classes). Here we outline how organellar genomes and the entire nuclear ribosomal DNA repeat can be obtained from minimal amounts of moss tissue via small-scale 454 GS FLX sequencing. We sampled two Funariaceae species, Funaria hygrometrica and Entosthodon obtusus, and assembled nearly complete organellar genomes and the whole nuclear ribosomal DNA repeat unit (18S-ITS1-5.8S-ITS2-26S-IGS1-5S-IGS2) for both taxa. Sequence data from these species were compared to sequences from another Funariaceae species, Physcomitrella patens, revealing low overall degrees of divergence of the organellar genomes and nrDNA genes with substitutions spread rather evenly across their length, and high divergence within the external spacers of the nrDNA repeat. Furthermore, we detected numerous microsatellites among the 454 assemblies. This study demonstrates that NGS methodology can be applied to mosses to target large genomic regions and identify microsatellites. |
doi_str_mv | 10.1016/j.ympev.2012.12.006 |
format | Article |
fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_1284289785</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><els_id>S1055790312004848</els_id><sourcerecordid>1284289785</sourcerecordid><originalsourceid>FETCH-LOGICAL-c383t-691fa1da433876e22f4511043b9d72a20cd5511edd0865999d7adc66e77b077b3</originalsourceid><addsrcrecordid>eNp9UU1v1DAQjRCIlpZfgARz5NBs_REn8YFDVWiptKKHUomb5bUnK6-SePEkRf0P_GgctnCs5JE9o_fGM-8VxTvOVpzx-ny3ehz2-LASjItVPozVL4pjzrQqteLy5fJWqmw0k0fFG6IdY5wrrV4XR0KKmjdcHBe_b9PWjtj3NsEWxzjgGYyz6zHnKWwixcH28PnbBSTco51gHsN0Bnb0MASXItkpk8OEBIFinzMPXYoDWKDM7EtytkeIHVSqgus7uFr_AMKfM44ujFuII0y_IgyRCOm0eNXZnvDt031S3F99-X75tVzfXt9cXqxLJ1s5lbXmneXeVlK2TY1CdJXinFVyo30jrGDOq1xA71lbK61z1XpX19g0G5ZDnhQfD333KeZJaDJDILeIMGKcyXDRVqLVTasyVB6gy66UsDP7FAabHg1nZrHB7MxfG8xiQ2aabENmvX_6YN4M6P9z_umeAR8OgM5GY7cpkLm_yx0UY6wSWi2ITwcEZiEeAiZDLmTR0IeEbjI-hmdH-AOdGqNE</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1284289785</pqid></control><display><type>article</type><title>Organellar genome, nuclear ribosomal DNA repeat unit, and microsatellites isolated from a small-scale of 454 GS FLX sequencing on two mosses</title><source>MEDLINE</source><source>ScienceDirect Freedom Collection (Elsevier)</source><creator>Liu, Yang ; Forrest, Laura L. ; Bainard, Jillian D. ; Budke, Jessica M. ; Goffinet, Bernard</creator><creatorcontrib>Liu, Yang ; Forrest, Laura L. ; Bainard, Jillian D. ; Budke, Jessica M. ; Goffinet, Bernard</creatorcontrib><description>[Display omitted]
► 454 shot gun sequencing is a fast and easy method to generate large, multiple copy genomic regions for mosses. ► We assembled nearly complete organellar genomes and the whole nrDNA repeat unit for two Funariaceae. ► The NGS data pool is a rich source for identifying microsatellites.
Recent innovations in high-throughput DNA sequencing methodology (next generation sequencing technologies [NGS]) allow for the generation of large amounts of high quality data that may be particularly critical for resolving ambiguous relationships such as those resulting from rapid radiations. Application of NGS technology to bryology is limited to assembling entire nuclear or organellar genomes of selected exemplars of major lineages (e.g., classes). Here we outline how organellar genomes and the entire nuclear ribosomal DNA repeat can be obtained from minimal amounts of moss tissue via small-scale 454 GS FLX sequencing. We sampled two Funariaceae species, Funaria hygrometrica and Entosthodon obtusus, and assembled nearly complete organellar genomes and the whole nuclear ribosomal DNA repeat unit (18S-ITS1-5.8S-ITS2-26S-IGS1-5S-IGS2) for both taxa. Sequence data from these species were compared to sequences from another Funariaceae species, Physcomitrella patens, revealing low overall degrees of divergence of the organellar genomes and nrDNA genes with substitutions spread rather evenly across their length, and high divergence within the external spacers of the nrDNA repeat. Furthermore, we detected numerous microsatellites among the 454 assemblies. This study demonstrates that NGS methodology can be applied to mosses to target large genomic regions and identify microsatellites.</description><identifier>ISSN: 1055-7903</identifier><identifier>EISSN: 1095-9513</identifier><identifier>DOI: 10.1016/j.ympev.2012.12.006</identifier><identifier>PMID: 23261712</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>Base Sequence ; bryology ; Bryophyta - genetics ; DNA, Ribosomal - genetics ; Entosthodon obtusus ; Funaria hygrometrica ; genes ; Genome, Mitochondrial - genetics ; Genome, Plastid - genetics ; high-throughput nucleotide sequencing ; High-Throughput Nucleotide Sequencing - methods ; High-throughput sequencing ; Microsatellite ; microsatellite repeats ; Microsatellite Repeats - genetics ; Molecular Sequence Data ; mosses and liverworts ; new technology ; nrDNA repeat unit ; Organellar genomes ; Physcomitrella patens ; ribosomal DNA ; Sequence Alignment ; Species Specificity</subject><ispartof>Molecular phylogenetics and evolution, 2013-03, Vol.66 (3), p.1089-1094</ispartof><rights>2012 Elsevier Inc.</rights><rights>Copyright © 2012 Elsevier Inc. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c383t-691fa1da433876e22f4511043b9d72a20cd5511edd0865999d7adc66e77b077b3</citedby><cites>FETCH-LOGICAL-c383t-691fa1da433876e22f4511043b9d72a20cd5511edd0865999d7adc66e77b077b3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.ympev.2012.12.006$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23261712$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Liu, Yang</creatorcontrib><creatorcontrib>Forrest, Laura L.</creatorcontrib><creatorcontrib>Bainard, Jillian D.</creatorcontrib><creatorcontrib>Budke, Jessica M.</creatorcontrib><creatorcontrib>Goffinet, Bernard</creatorcontrib><title>Organellar genome, nuclear ribosomal DNA repeat unit, and microsatellites isolated from a small-scale of 454 GS FLX sequencing on two mosses</title><title>Molecular phylogenetics and evolution</title><addtitle>Mol Phylogenet Evol</addtitle><description>[Display omitted]
► 454 shot gun sequencing is a fast and easy method to generate large, multiple copy genomic regions for mosses. ► We assembled nearly complete organellar genomes and the whole nrDNA repeat unit for two Funariaceae. ► The NGS data pool is a rich source for identifying microsatellites.
Recent innovations in high-throughput DNA sequencing methodology (next generation sequencing technologies [NGS]) allow for the generation of large amounts of high quality data that may be particularly critical for resolving ambiguous relationships such as those resulting from rapid radiations. Application of NGS technology to bryology is limited to assembling entire nuclear or organellar genomes of selected exemplars of major lineages (e.g., classes). Here we outline how organellar genomes and the entire nuclear ribosomal DNA repeat can be obtained from minimal amounts of moss tissue via small-scale 454 GS FLX sequencing. We sampled two Funariaceae species, Funaria hygrometrica and Entosthodon obtusus, and assembled nearly complete organellar genomes and the whole nuclear ribosomal DNA repeat unit (18S-ITS1-5.8S-ITS2-26S-IGS1-5S-IGS2) for both taxa. Sequence data from these species were compared to sequences from another Funariaceae species, Physcomitrella patens, revealing low overall degrees of divergence of the organellar genomes and nrDNA genes with substitutions spread rather evenly across their length, and high divergence within the external spacers of the nrDNA repeat. Furthermore, we detected numerous microsatellites among the 454 assemblies. This study demonstrates that NGS methodology can be applied to mosses to target large genomic regions and identify microsatellites.</description><subject>Base Sequence</subject><subject>bryology</subject><subject>Bryophyta - genetics</subject><subject>DNA, Ribosomal - genetics</subject><subject>Entosthodon obtusus</subject><subject>Funaria hygrometrica</subject><subject>genes</subject><subject>Genome, Mitochondrial - genetics</subject><subject>Genome, Plastid - genetics</subject><subject>high-throughput nucleotide sequencing</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>High-throughput sequencing</subject><subject>Microsatellite</subject><subject>microsatellite repeats</subject><subject>Microsatellite Repeats - genetics</subject><subject>Molecular Sequence Data</subject><subject>mosses and liverworts</subject><subject>new technology</subject><subject>nrDNA repeat unit</subject><subject>Organellar genomes</subject><subject>Physcomitrella patens</subject><subject>ribosomal DNA</subject><subject>Sequence Alignment</subject><subject>Species Specificity</subject><issn>1055-7903</issn><issn>1095-9513</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9UU1v1DAQjRCIlpZfgARz5NBs_REn8YFDVWiptKKHUomb5bUnK6-SePEkRf0P_GgctnCs5JE9o_fGM-8VxTvOVpzx-ny3ehz2-LASjItVPozVL4pjzrQqteLy5fJWqmw0k0fFG6IdY5wrrV4XR0KKmjdcHBe_b9PWjtj3NsEWxzjgGYyz6zHnKWwixcH28PnbBSTco51gHsN0Bnb0MASXItkpk8OEBIFinzMPXYoDWKDM7EtytkeIHVSqgus7uFr_AMKfM44ujFuII0y_IgyRCOm0eNXZnvDt031S3F99-X75tVzfXt9cXqxLJ1s5lbXmneXeVlK2TY1CdJXinFVyo30jrGDOq1xA71lbK61z1XpX19g0G5ZDnhQfD333KeZJaDJDILeIMGKcyXDRVqLVTasyVB6gy66UsDP7FAabHg1nZrHB7MxfG8xiQ2aabENmvX_6YN4M6P9z_umeAR8OgM5GY7cpkLm_yx0UY6wSWi2ITwcEZiEeAiZDLmTR0IeEbjI-hmdH-AOdGqNE</recordid><startdate>20130301</startdate><enddate>20130301</enddate><creator>Liu, Yang</creator><creator>Forrest, Laura L.</creator><creator>Bainard, Jillian D.</creator><creator>Budke, Jessica M.</creator><creator>Goffinet, Bernard</creator><general>Elsevier Inc</general><scope>FBQ</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>7X8</scope></search><sort><creationdate>20130301</creationdate><title>Organellar genome, nuclear ribosomal DNA repeat unit, and microsatellites isolated from a small-scale of 454 GS FLX sequencing on two mosses</title><author>Liu, Yang ; Forrest, Laura L. ; Bainard, Jillian D. ; Budke, Jessica M. ; Goffinet, Bernard</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c383t-691fa1da433876e22f4511043b9d72a20cd5511edd0865999d7adc66e77b077b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Base Sequence</topic><topic>bryology</topic><topic>Bryophyta - genetics</topic><topic>DNA, Ribosomal - genetics</topic><topic>Entosthodon obtusus</topic><topic>Funaria hygrometrica</topic><topic>genes</topic><topic>Genome, Mitochondrial - genetics</topic><topic>Genome, Plastid - genetics</topic><topic>high-throughput nucleotide sequencing</topic><topic>High-Throughput Nucleotide Sequencing - methods</topic><topic>High-throughput sequencing</topic><topic>Microsatellite</topic><topic>microsatellite repeats</topic><topic>Microsatellite Repeats - genetics</topic><topic>Molecular Sequence Data</topic><topic>mosses and liverworts</topic><topic>new technology</topic><topic>nrDNA repeat unit</topic><topic>Organellar genomes</topic><topic>Physcomitrella patens</topic><topic>ribosomal DNA</topic><topic>Sequence Alignment</topic><topic>Species Specificity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Liu, Yang</creatorcontrib><creatorcontrib>Forrest, Laura L.</creatorcontrib><creatorcontrib>Bainard, Jillian D.</creatorcontrib><creatorcontrib>Budke, Jessica M.</creatorcontrib><creatorcontrib>Goffinet, Bernard</creatorcontrib><collection>AGRIS</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Molecular phylogenetics and evolution</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Liu, Yang</au><au>Forrest, Laura L.</au><au>Bainard, Jillian D.</au><au>Budke, Jessica M.</au><au>Goffinet, Bernard</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Organellar genome, nuclear ribosomal DNA repeat unit, and microsatellites isolated from a small-scale of 454 GS FLX sequencing on two mosses</atitle><jtitle>Molecular phylogenetics and evolution</jtitle><addtitle>Mol Phylogenet Evol</addtitle><date>2013-03-01</date><risdate>2013</risdate><volume>66</volume><issue>3</issue><spage>1089</spage><epage>1094</epage><pages>1089-1094</pages><issn>1055-7903</issn><eissn>1095-9513</eissn><abstract>[Display omitted]
► 454 shot gun sequencing is a fast and easy method to generate large, multiple copy genomic regions for mosses. ► We assembled nearly complete organellar genomes and the whole nrDNA repeat unit for two Funariaceae. ► The NGS data pool is a rich source for identifying microsatellites.
Recent innovations in high-throughput DNA sequencing methodology (next generation sequencing technologies [NGS]) allow for the generation of large amounts of high quality data that may be particularly critical for resolving ambiguous relationships such as those resulting from rapid radiations. Application of NGS technology to bryology is limited to assembling entire nuclear or organellar genomes of selected exemplars of major lineages (e.g., classes). Here we outline how organellar genomes and the entire nuclear ribosomal DNA repeat can be obtained from minimal amounts of moss tissue via small-scale 454 GS FLX sequencing. We sampled two Funariaceae species, Funaria hygrometrica and Entosthodon obtusus, and assembled nearly complete organellar genomes and the whole nuclear ribosomal DNA repeat unit (18S-ITS1-5.8S-ITS2-26S-IGS1-5S-IGS2) for both taxa. Sequence data from these species were compared to sequences from another Funariaceae species, Physcomitrella patens, revealing low overall degrees of divergence of the organellar genomes and nrDNA genes with substitutions spread rather evenly across their length, and high divergence within the external spacers of the nrDNA repeat. Furthermore, we detected numerous microsatellites among the 454 assemblies. This study demonstrates that NGS methodology can be applied to mosses to target large genomic regions and identify microsatellites.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>23261712</pmid><doi>10.1016/j.ympev.2012.12.006</doi><tpages>6</tpages></addata></record> |
fulltext | fulltext |
identifier | ISSN: 1055-7903 |
ispartof | Molecular phylogenetics and evolution, 2013-03, Vol.66 (3), p.1089-1094 |
issn | 1055-7903 1095-9513 |
language | eng |
recordid | cdi_proquest_miscellaneous_1284289785 |
source | MEDLINE; ScienceDirect Freedom Collection (Elsevier) |
subjects | Base Sequence bryology Bryophyta - genetics DNA, Ribosomal - genetics Entosthodon obtusus Funaria hygrometrica genes Genome, Mitochondrial - genetics Genome, Plastid - genetics high-throughput nucleotide sequencing High-Throughput Nucleotide Sequencing - methods High-throughput sequencing Microsatellite microsatellite repeats Microsatellite Repeats - genetics Molecular Sequence Data mosses and liverworts new technology nrDNA repeat unit Organellar genomes Physcomitrella patens ribosomal DNA Sequence Alignment Species Specificity |
title | Organellar genome, nuclear ribosomal DNA repeat unit, and microsatellites isolated from a small-scale of 454 GS FLX sequencing on two mosses |
url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-24T06%3A42%3A09IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Organellar%20genome,%20nuclear%20ribosomal%20DNA%20repeat%20unit,%20and%20microsatellites%20isolated%20from%20a%20small-scale%20of%20454%20GS%20FLX%20sequencing%20on%20two%20mosses&rft.jtitle=Molecular%20phylogenetics%20and%20evolution&rft.au=Liu,%20Yang&rft.date=2013-03-01&rft.volume=66&rft.issue=3&rft.spage=1089&rft.epage=1094&rft.pages=1089-1094&rft.issn=1055-7903&rft.eissn=1095-9513&rft_id=info:doi/10.1016/j.ympev.2012.12.006&rft_dat=%3Cproquest_cross%3E1284289785%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1284289785&rft_id=info:pmid/23261712&rft_els_id=S1055790312004848&rfr_iscdi=true |