Genomic patterns of species diversity and divergence in Eucalyptus
We examined genome‐wide patterns of DNA sequence diversity and divergence among six species of the important tree genus Eucalyptus and investigated their relationship with genomic architecture. Using c. 90 range‐wide individuals of each Eucalyptus species (E. grandis, E. urophylla, E. globulus, E. n...
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| Veröffentlicht in: | The New phytologist 2015-06, Vol.206 (4), p.1378-1390 |
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| creator | Hudson, Corey J Freeman, Jules S Myburg, Alexander A Potts, Brad M Vaillancourt, René E |
| description | We examined genome‐wide patterns of DNA sequence diversity and divergence among six species of the important tree genus Eucalyptus and investigated their relationship with genomic architecture. Using c. 90 range‐wide individuals of each Eucalyptus species (E. grandis, E. urophylla, E. globulus, E. nitens, E. dunnii and E. camaldulensis), genetic diversity and divergence were estimated from 2840 polymorphic diversity arrays technology markers covering the 11 chromosomes. Species differentiating markers (SDMs) identified in each of 15 pairwise species comparisons, along with species diversity (HHW) and divergence (FST), were projected onto the E. grandis reference genome. Across all species comparisons, SDMs totalled 1.1–5.3% of markers and were widely distributed throughout the genome. Marker divergence (FSTand SDMs) and diversity differed among and within chromosomes. Patterns of diversity and divergence were broadly conserved across species and significantly associated with genomic features, including the proximity of markers to genes, the relative number of clusters of tandem duplications, and gene density within or among chromosomes. These results suggest that genomic architecture influences patterns of species diversity and divergence in the genus. This influence is evident across the six species, encompassing diverse phylogenetic lineages, geography and ecology. |
| doi_str_mv | 10.1111/nph.13316 |
| format | Article |
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Using c. 90 range‐wide individuals of each Eucalyptus species (E. grandis, E. urophylla, E. globulus, E. nitens, E. dunnii and E. camaldulensis), genetic diversity and divergence were estimated from 2840 polymorphic diversity arrays technology markers covering the 11 chromosomes. Species differentiating markers (SDMs) identified in each of 15 pairwise species comparisons, along with species diversity (HHW) and divergence (FST), were projected onto the E. grandis reference genome. Across all species comparisons, SDMs totalled 1.1–5.3% of markers and were widely distributed throughout the genome. Marker divergence (FSTand SDMs) and diversity differed among and within chromosomes. Patterns of diversity and divergence were broadly conserved across species and significantly associated with genomic features, including the proximity of markers to genes, the relative number of clusters of tandem duplications, and gene density within or among chromosomes. These results suggest that genomic architecture influences patterns of species diversity and divergence in the genus. This influence is evident across the six species, encompassing diverse phylogenetic lineages, geography and ecology.</description><identifier>ISSN: 0028-646X</identifier><identifier>EISSN: 1469-8137</identifier><identifier>DOI: 10.1111/nph.13316</identifier><identifier>PMID: 25678438</identifier><language>eng</language><publisher>England: Academic Press</publisher><subject>Bayes Theorem ; Biodiversity ; Biomarkers ; Chromosomes ; Chromosomes, Plant - genetics ; Deoxyribonucleic acid ; Divergence ; DNA ; Eucalyptus ; Eucalyptus - genetics ; gene density ; Gene Duplication ; Genes ; Genes, Plant ; Genetic diversity ; Genetic Markers ; Genetic Variation ; Genome, Plant ; Genomes ; genome‐scan ; genomic architecture ; Genomics ; Geography ; Nucleotide sequence ; nucleotide sequences ; outlier ; Phylogeny ; population genomics ; Principal Component Analysis ; speciation ; Species comparisons ; Species diversity ; Species Specificity ; Statistics, Nonparametric ; tandem gene duplication ; trees</subject><ispartof>The New phytologist, 2015-06, Vol.206 (4), p.1378-1390</ispartof><rights>2015 New Phytologist Trust</rights><rights>2015 University of Tasmania New Phytologist © 2015 New Phytologist Trust</rights><rights>2015 University of Tasmania New Phytologist © 2015 New Phytologist Trust.</rights><rights>Copyright © 2015 New Phytologist Trust</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5826-d01da4b3f57c42daec6d2cd99107c87817cb3bea2aca9b90ebccb4c8e771be573</citedby><cites>FETCH-LOGICAL-c5826-d01da4b3f57c42daec6d2cd99107c87817cb3bea2aca9b90ebccb4c8e771be573</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/newphytologist.206.4.1378$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/newphytologist.206.4.1378$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>314,776,780,799,1411,1427,27901,27902,45550,45551,46384,46808,57992,58225</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25678438$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Hudson, Corey J</creatorcontrib><creatorcontrib>Freeman, Jules S</creatorcontrib><creatorcontrib>Myburg, Alexander A</creatorcontrib><creatorcontrib>Potts, Brad M</creatorcontrib><creatorcontrib>Vaillancourt, René E</creatorcontrib><title>Genomic patterns of species diversity and divergence in Eucalyptus</title><title>The New phytologist</title><addtitle>New Phytol</addtitle><description>We examined genome‐wide patterns of DNA sequence diversity and divergence among six species of the important tree genus Eucalyptus and investigated their relationship with genomic architecture. Using c. 90 range‐wide individuals of each Eucalyptus species (E. grandis, E. urophylla, E. globulus, E. nitens, E. dunnii and E. camaldulensis), genetic diversity and divergence were estimated from 2840 polymorphic diversity arrays technology markers covering the 11 chromosomes. Species differentiating markers (SDMs) identified in each of 15 pairwise species comparisons, along with species diversity (HHW) and divergence (FST), were projected onto the E. grandis reference genome. Across all species comparisons, SDMs totalled 1.1–5.3% of markers and were widely distributed throughout the genome. Marker divergence (FSTand SDMs) and diversity differed among and within chromosomes. Patterns of diversity and divergence were broadly conserved across species and significantly associated with genomic features, including the proximity of markers to genes, the relative number of clusters of tandem duplications, and gene density within or among chromosomes. These results suggest that genomic architecture influences patterns of species diversity and divergence in the genus. This influence is evident across the six species, encompassing diverse phylogenetic lineages, geography and ecology.</description><subject>Bayes Theorem</subject><subject>Biodiversity</subject><subject>Biomarkers</subject><subject>Chromosomes</subject><subject>Chromosomes, Plant - genetics</subject><subject>Deoxyribonucleic acid</subject><subject>Divergence</subject><subject>DNA</subject><subject>Eucalyptus</subject><subject>Eucalyptus - genetics</subject><subject>gene density</subject><subject>Gene Duplication</subject><subject>Genes</subject><subject>Genes, Plant</subject><subject>Genetic diversity</subject><subject>Genetic Markers</subject><subject>Genetic Variation</subject><subject>Genome, Plant</subject><subject>Genomes</subject><subject>genome‐scan</subject><subject>genomic architecture</subject><subject>Genomics</subject><subject>Geography</subject><subject>Nucleotide sequence</subject><subject>nucleotide sequences</subject><subject>outlier</subject><subject>Phylogeny</subject><subject>population genomics</subject><subject>Principal Component Analysis</subject><subject>speciation</subject><subject>Species comparisons</subject><subject>Species diversity</subject><subject>Species Specificity</subject><subject>Statistics, Nonparametric</subject><subject>tandem gene duplication</subject><subject>trees</subject><issn>0028-646X</issn><issn>1469-8137</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkUFv1DAQhS1ERZfCgT8AkbjQQ7ZjO7GdI1SlrVQBElTiZjnOZOtVNk7thCr_Hm_T9oAE-DKy9L039nuEvKGwpumc9MPNmnJOxTOyooWockW5fE5WAEzlohA_D8nLGLcAUJWCvSCHrBRSFVytyKdz7P3O2Www44ihj5lvszigdRizxv3CEN04Z6ZvltsGe4uZ67OzyZpuHsYpviIHrekivn6YR-T689mP04v86uv55enHq9yWiom8AdqYouZtKW3BGoNWNMw2VUVBWiUVlbbmNRpmrKnqCrC2ti6sQilpjaXkR-TD4jsEfzthHPXORYtdZ3r0U9RUAi2BgRT_R4UCWgEv9-j7P9Ctn0KfPqJZSTlUKoX5L4oKWXFRgFKJOl4oG3yMAVs9BLczYdYU9L4pnZrS900l9u2D41TvsHkiH6tJwMkC3LkO57876S_fLh4t14tiG0cfnhQ93g038-g7v3Hp4QyELpJU7le8WwSt8dpsgov6-jvbpwhUSZHS-Q0gc7Wr</recordid><startdate>201506</startdate><enddate>201506</enddate><creator>Hudson, Corey J</creator><creator>Freeman, Jules S</creator><creator>Myburg, Alexander A</creator><creator>Potts, Brad M</creator><creator>Vaillancourt, René E</creator><general>Academic Press</general><general>New Phytologist Trust</general><general>Wiley Subscription Services, 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>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></search><sort><creationdate>201506</creationdate><title>Genomic patterns of species diversity and divergence in Eucalyptus</title><author>Hudson, Corey J ; Freeman, Jules S ; Myburg, Alexander A ; Potts, Brad M ; Vaillancourt, René E</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5826-d01da4b3f57c42daec6d2cd99107c87817cb3bea2aca9b90ebccb4c8e771be573</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Bayes Theorem</topic><topic>Biodiversity</topic><topic>Biomarkers</topic><topic>Chromosomes</topic><topic>Chromosomes, Plant - genetics</topic><topic>Deoxyribonucleic acid</topic><topic>Divergence</topic><topic>DNA</topic><topic>Eucalyptus</topic><topic>Eucalyptus - genetics</topic><topic>gene density</topic><topic>Gene Duplication</topic><topic>Genes</topic><topic>Genes, Plant</topic><topic>Genetic diversity</topic><topic>Genetic Markers</topic><topic>Genetic Variation</topic><topic>Genome, Plant</topic><topic>Genomes</topic><topic>genome‐scan</topic><topic>genomic architecture</topic><topic>Genomics</topic><topic>Geography</topic><topic>Nucleotide sequence</topic><topic>nucleotide sequences</topic><topic>outlier</topic><topic>Phylogeny</topic><topic>population genomics</topic><topic>Principal Component Analysis</topic><topic>speciation</topic><topic>Species comparisons</topic><topic>Species diversity</topic><topic>Species Specificity</topic><topic>Statistics, Nonparametric</topic><topic>tandem gene duplication</topic><topic>trees</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hudson, Corey J</creatorcontrib><creatorcontrib>Freeman, Jules S</creatorcontrib><creatorcontrib>Myburg, Alexander A</creatorcontrib><creatorcontrib>Potts, Brad M</creatorcontrib><creatorcontrib>Vaillancourt, René E</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>Biotechnology Research Abstracts</collection><collection>Ecology Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>Engineering Research Database</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>The New phytologist</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hudson, Corey J</au><au>Freeman, Jules S</au><au>Myburg, Alexander A</au><au>Potts, Brad M</au><au>Vaillancourt, René E</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genomic patterns of species diversity and divergence in Eucalyptus</atitle><jtitle>The New phytologist</jtitle><addtitle>New Phytol</addtitle><date>2015-06</date><risdate>2015</risdate><volume>206</volume><issue>4</issue><spage>1378</spage><epage>1390</epage><pages>1378-1390</pages><issn>0028-646X</issn><eissn>1469-8137</eissn><abstract>We examined genome‐wide patterns of DNA sequence diversity and divergence among six species of the important tree genus Eucalyptus and investigated their relationship with genomic architecture. Using c. 90 range‐wide individuals of each Eucalyptus species (E. grandis, E. urophylla, E. globulus, E. nitens, E. dunnii and E. camaldulensis), genetic diversity and divergence were estimated from 2840 polymorphic diversity arrays technology markers covering the 11 chromosomes. Species differentiating markers (SDMs) identified in each of 15 pairwise species comparisons, along with species diversity (HHW) and divergence (FST), were projected onto the E. grandis reference genome. Across all species comparisons, SDMs totalled 1.1–5.3% of markers and were widely distributed throughout the genome. Marker divergence (FSTand SDMs) and diversity differed among and within chromosomes. Patterns of diversity and divergence were broadly conserved across species and significantly associated with genomic features, including the proximity of markers to genes, the relative number of clusters of tandem duplications, and gene density within or among chromosomes. These results suggest that genomic architecture influences patterns of species diversity and divergence in the genus. This influence is evident across the six species, encompassing diverse phylogenetic lineages, geography and ecology.</abstract><cop>England</cop><pub>Academic Press</pub><pmid>25678438</pmid><doi>10.1111/nph.13316</doi><tpages>13</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Bayes Theorem Biodiversity Biomarkers Chromosomes Chromosomes, Plant - genetics Deoxyribonucleic acid Divergence DNA Eucalyptus Eucalyptus - genetics gene density Gene Duplication Genes Genes, Plant Genetic diversity Genetic Markers Genetic Variation Genome, Plant Genomes genome‐scan genomic architecture Genomics Geography Nucleotide sequence nucleotide sequences outlier Phylogeny population genomics Principal Component Analysis speciation Species comparisons Species diversity Species Specificity Statistics, Nonparametric tandem gene duplication trees |
| title | Genomic patterns of species diversity and divergence in Eucalyptus |
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