Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta)
The goal of this research was to investigate whether there has been a whole-genome duplication (WGD) in the ancestry of Sphagnum (peatmoss) or the class Sphagnopsida, and to determine if the timing of any such duplication(s) and patterns of paralog retention could help explain the rapid radiation an...
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Veröffentlicht in: | The New phytologist 2016-07, Vol.211 (1), p.300-318 |
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creator | Devos, Nicolas Szövényi, Péter Weston, David J Rothfels, Carl J Johnson, Matthew G Shaw, A Jonathan |
description | The goal of this research was to investigate whether there has been a whole-genome duplication (WGD) in the ancestry of Sphagnum (peatmoss) or the class Sphagnopsida, and to determine if the timing of any such duplication(s) and patterns of paralog retention could help explain the rapid radiation and current ecological dominance of peatmosses.
RNA sequencing (RNA-seq) data were generated for nine taxa in Sphagnopsida (Bryophyta). Analyses of frequency plots for synonymous substitutions per synonymous site (K
s) between paralogous gene pairs and reconciliation of 578 gene trees were conducted to assess evidence of large-scale or genome-wide duplication events in each transcriptome.
Both K
s frequency plots and gene tree-based analyses indicate multiple duplication events in the history of the Sphagnopsida. The most recent WGD event predates divergence of Sphagnum from the two other genera of Sphagnopsida. Duplicate retention is highly variable across species, which might be best explained by local adaptation.
Our analyses indicate that the last WGD could have been an important factor underlying the diversification of peatmosses and facilitated their rise to ecological dominance in peatlands. The timing of the duplication events and their significance in the evolutionary history of peat mosses are discussed. |
doi_str_mv | 10.1111/nph.13887 |
format | Article |
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RNA sequencing (RNA-seq) data were generated for nine taxa in Sphagnopsida (Bryophyta). Analyses of frequency plots for synonymous substitutions per synonymous site (K
s) between paralogous gene pairs and reconciliation of 578 gene trees were conducted to assess evidence of large-scale or genome-wide duplication events in each transcriptome.
Both K
s frequency plots and gene tree-based analyses indicate multiple duplication events in the history of the Sphagnopsida. The most recent WGD event predates divergence of Sphagnum from the two other genera of Sphagnopsida. Duplicate retention is highly variable across species, which might be best explained by local adaptation.
Our analyses indicate that the last WGD could have been an important factor underlying the diversification of peatmosses and facilitated their rise to ecological dominance in peatlands. The timing of the duplication events and their significance in the evolutionary history of peat mosses are discussed.</description><identifier>ISSN: 0028-646X</identifier><identifier>EISSN: 1469-8137</identifier><identifier>DOI: 10.1111/nph.13887</identifier><identifier>PMID: 26900928</identifier><language>eng</language><publisher>England: New Phytologist Trust</publisher><subject>BASIC BIOLOGICAL SCIENCES ; Biological Evolution ; Gene Duplication ; Genome, Plant ; High-Throughput Nucleotide Sequencing ; molecular dating ; paleopolyploidy ; peatmoss ; Phylogeny ; Plant Proteins - genetics ; Plant Proteins - metabolism ; reconciliation ; Sphagnopsida - genetics ; Sphagnum ; synonymous substitutions per synonymous site (Ks) plot ; Transcriptome ; whole‐genome duplication (WGD)</subject><ispartof>The New phytologist, 2016-07, Vol.211 (1), p.300-318</ispartof><rights>2016 New Phytologist Trust</rights><rights>2016 The Authors. New Phytologist © 2016 New Phytologist Trust</rights><rights>2016 The Authors. New Phytologist © 2016 New Phytologist Trust.</rights><rights>Copyright © 2016 New Phytologist Trust</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4537-b269ec4dc0ec44834eda8c53b0a9287d51a8bbdb9aff94a46a0088ffbccbd77b3</citedby><cites>FETCH-LOGICAL-c4537-b269ec4dc0ec44834eda8c53b0a9287d51a8bbdb9aff94a46a0088ffbccbd77b3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/newphytologist.211.1.300$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/newphytologist.211.1.300$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>230,314,780,784,803,885,1417,1433,27924,27925,45574,45575,46409,46833,58017,58250</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26900928$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/servlets/purl/1326556$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Devos, Nicolas</creatorcontrib><creatorcontrib>Szövényi, Péter</creatorcontrib><creatorcontrib>Weston, David J</creatorcontrib><creatorcontrib>Rothfels, Carl J</creatorcontrib><creatorcontrib>Johnson, Matthew G</creatorcontrib><creatorcontrib>Shaw, A Jonathan</creatorcontrib><creatorcontrib>Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)</creatorcontrib><title>Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta)</title><title>The New phytologist</title><addtitle>New Phytol</addtitle><description>The goal of this research was to investigate whether there has been a whole-genome duplication (WGD) in the ancestry of Sphagnum (peatmoss) or the class Sphagnopsida, and to determine if the timing of any such duplication(s) and patterns of paralog retention could help explain the rapid radiation and current ecological dominance of peatmosses.
RNA sequencing (RNA-seq) data were generated for nine taxa in Sphagnopsida (Bryophyta). Analyses of frequency plots for synonymous substitutions per synonymous site (K
s) between paralogous gene pairs and reconciliation of 578 gene trees were conducted to assess evidence of large-scale or genome-wide duplication events in each transcriptome.
Both K
s frequency plots and gene tree-based analyses indicate multiple duplication events in the history of the Sphagnopsida. The most recent WGD event predates divergence of Sphagnum from the two other genera of Sphagnopsida. Duplicate retention is highly variable across species, which might be best explained by local adaptation.
Our analyses indicate that the last WGD could have been an important factor underlying the diversification of peatmosses and facilitated their rise to ecological dominance in peatlands. The timing of the duplication events and their significance in the evolutionary history of peat mosses are discussed.</description><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>Biological Evolution</subject><subject>Gene Duplication</subject><subject>Genome, Plant</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>molecular dating</subject><subject>paleopolyploidy</subject><subject>peatmoss</subject><subject>Phylogeny</subject><subject>Plant Proteins - genetics</subject><subject>Plant Proteins - metabolism</subject><subject>reconciliation</subject><subject>Sphagnopsida - genetics</subject><subject>Sphagnum</subject><subject>synonymous substitutions per synonymous site (Ks) plot</subject><subject>Transcriptome</subject><subject>whole‐genome duplication (WGD)</subject><issn>0028-646X</issn><issn>1469-8137</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kc9uFSEUxonR2OvVhS9giG7axbQwzB9mWRu1Jo2aqIk7wjBn7nDDwBQYm3kBn1vunbYLE1kAgd_3cTgfQq8pOadpXNhpOKeM8_oJ2tCiajJOWf0UbQjJeVYV1a8T9CKEPSGkKav8OTrJqybtc75Bfy6tNEuAgF2Po5c2KK-n6EbAAW5nsCpdefgN0uBxNlFPBrC0SoON2Ei_gywomc66eTJayaidxQm3MWBtcRyONITo_OGF79Mgd9ZNQXcSn773i5uGJcqzl-hZL02AV_frFv38-OHH1XV28_XT56vLm0wVJauzNhUOqugUSXPBWQGd5KpkLZHpN3VXUsnbtmsb2fdNIYtKEsJ537dKtV1dt2yL3q6-LkQtgtIR1KCctaCioCyvyrJK0OkKTd6lFoQoRh0UGCMtuDkIWjcspxVpWELf_YPu3exTS49UXjQlT_AWna2U8i4ED72YvB6lXwQl4pCgSAmKY4KJfXPvOLcjdI_kQ2QJuFiBO21g-b-T-PLt-sEyWxX7QwyPCgt3h-Y743Y6FZ4nMRWMEPYXbrO4vw</recordid><startdate>201607</startdate><enddate>201607</enddate><creator>Devos, Nicolas</creator><creator>Szövényi, Péter</creator><creator>Weston, David J</creator><creator>Rothfels, Carl J</creator><creator>Johnson, Matthew G</creator><creator>Shaw, A Jonathan</creator><general>New Phytologist Trust</general><general>Wiley Subscription Services, Inc</general><general>Wiley</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>7QO</scope><scope>7SN</scope><scope>8FD</scope><scope>C1K</scope><scope>F1W</scope><scope>FR3</scope><scope>H95</scope><scope>L.G</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>OIOZB</scope><scope>OTOTI</scope></search><sort><creationdate>201607</creationdate><title>Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta)</title><author>Devos, Nicolas ; 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RNA sequencing (RNA-seq) data were generated for nine taxa in Sphagnopsida (Bryophyta). Analyses of frequency plots for synonymous substitutions per synonymous site (K
s) between paralogous gene pairs and reconciliation of 578 gene trees were conducted to assess evidence of large-scale or genome-wide duplication events in each transcriptome.
Both K
s frequency plots and gene tree-based analyses indicate multiple duplication events in the history of the Sphagnopsida. The most recent WGD event predates divergence of Sphagnum from the two other genera of Sphagnopsida. Duplicate retention is highly variable across species, which might be best explained by local adaptation.
Our analyses indicate that the last WGD could have been an important factor underlying the diversification of peatmosses and facilitated their rise to ecological dominance in peatlands. The timing of the duplication events and their significance in the evolutionary history of peat mosses are discussed.</abstract><cop>England</cop><pub>New Phytologist Trust</pub><pmid>26900928</pmid><doi>10.1111/nph.13887</doi><tpages>19</tpages><oa>free_for_read</oa></addata></record> |
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subjects | BASIC BIOLOGICAL SCIENCES Biological Evolution Gene Duplication Genome, Plant High-Throughput Nucleotide Sequencing molecular dating paleopolyploidy peatmoss Phylogeny Plant Proteins - genetics Plant Proteins - metabolism reconciliation Sphagnopsida - genetics Sphagnum synonymous substitutions per synonymous site (Ks) plot Transcriptome whole‐genome duplication (WGD) |
title | Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta) |
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