Phylogenomic Analyses of Nuclear Genes Reveal the Evolutionary Relationships within the BEP Clade and the Evidence of Positive Selection in Poaceae
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{"title"=>"Phylogenomic Analyses of Nuclear Genes Reveal the Evolutionary Relationships within the BEP Clade and the Evidence of Positive Selection in Poaceae", "type"=>"journal", "authors"=>[{"first_name"=>"Lei", "last_name"=>"Zhao", "scopus_author_id"=>"8548331900"}, {"first_name"=>"Ning", "last_name"=>"Zhang", "scopus_author_id"=>"56608513000"}, {"first_name"=>"Peng Fei", "last_name"=>"Ma", "scopus_author_id"=>"9747483400"}, {"first_name"=>"Qi", "last_name"=>"Liu", "scopus_author_id"=>"24168891800"}, {"first_name"=>"De Zhu", "last_name"=>"Li", "scopus_author_id"=>"7405325347"}, {"first_name"=>"Zhen Hua", "last_name"=>"Guo", "scopus_author_id"=>"7404657380"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"doi"=>"10.1371/journal.pone.0064642", "sgr"=>"84878443264", "issn"=>"19326203", "pui"=>"369030971", "pmid"=>"23734211", "scopus"=>"2-s2.0-84878443264"}, "id"=>"b5061f39-64ab-3f40-bf29-3b59b65f56b7", "abstract"=>"BEP clade of the grass family (Poaceae) is composed of three subfamilies, i.e. Bambusoideae, Ehrhartoideae, and Pooideae. Controversies on the phylogenetic relationships among three subfamilies still persist in spite of great efforts. However, previous evidence was mainly provided from plastid genes with only a few nuclear genes utilized. Given different evolutionary histories recorded by plastid and nuclear genes, it is indispensable to uncover their relationships based on nuclear genes. Here, eleven species with whole-sequenced genome and six species with transcriptomic data were included in this study. A total of 121 one-to-one orthologous groups (OGs) were identified and phylogenetic trees were reconstructed by different tree-building methods. Genes which might have undergone positive selection and played important roles in adaptive evolution were also investigated from 314 and 173 one-to-one OGs in two bamboo species and 14 grass species, respectively. Our results support the ((B, P) E) topology with high supporting values. Besides, our findings also indicate that 24 and nine orthologs with statistically significant evidence of positive selection are mainly involved in abiotic and biotic stress response, reproduction and development, plant metabolism and enzyme etc. from two bamboo species and 14 grass species, respectively. In summary, this study demonstrates the power of phylogenomic approach to shed lights on the evolutionary relationships within the BEP clade, and offers valuable insights into adaptive evolution of the grass family.", "link"=>"http://www.mendeley.com/research/phylogenomic-analyses-nuclear-genes-reveal-evolutionary-relationships-within-bep-clade-evidence-posi", "reader_count"=>50, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Student > Doctoral Student"=>2, "Researcher"=>13, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>1, "Other"=>5, "Student > Master"=>5, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Student > Doctoral Student"=>2, "Researcher"=>13, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>1, "Other"=>5, "Student > Master"=>5, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>37, "Chemical Engineering"=>1, "Chemistry"=>1, "Computer Science"=>1, "Economics, Econometrics and Finance"=>1, "Energy"=>1}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>1}, "Energy"=>{"Energy"=>1}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>37}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>1}, "Chemical Engineering"=>{"Chemical Engineering"=>1}}, "reader_count_by_country"=>{"Norway"=>1, "Mexico"=>1}, "group_count"=>3}

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/1069969"], "description"=>"<p>GO classification for 173 orthologs of Poaceae.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary processes", "Evolutionary selection", "Evolutionary systematics", "phylogenetics", "Organismal evolution", "Plant evolution", "genetics", "Plant genetics", "Plant science", "Plant genomics", "Plant phylogenetics", "classification", "173", "orthologs"], "article_id"=>708607, "categories"=>["Biological Sciences"], "users"=>["Lei Zhao", "Ning Zhang", "Peng-Fei Ma", "Qi Liu", "De-Zhu Li", "Zhen-Hua Guo"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0064642.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GO_classification_for_173_orthologs_of_Poaceae_/708607", "title"=>"GO classification for 173 orthologs of Poaceae.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-05-29 02:23:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1069970"], "description"=>"<p>Statistical confidence (<i>P</i> values) for alternative phylogenomic hypothesis of the BEP Clade from the concatenation analyses.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary processes", "Evolutionary selection", "Evolutionary systematics", "phylogenetics", "Organismal evolution", "Plant evolution", "genetics", "Plant genetics", "Plant science", "Plant genomics", "Plant phylogenetics", "phylogenomic", "bep", "clade", "concatenation"], "article_id"=>708608, "categories"=>["Biological Sciences"], "users"=>["Lei Zhao", "Ning Zhang", "Peng-Fei Ma", "Qi Liu", "De-Zhu Li", "Zhen-Hua Guo"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0064642.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Statistical_confidence_P_values_for_alternative_phylogenomic_hypothesis_of_the_BEP_Clade_from_the_concatenation_analyses_/708608", "title"=>"Statistical confidence (<i>P</i> values) for alternative phylogenomic hypothesis of the BEP Clade from the concatenation analyses.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-05-29 02:23:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/1069971"], "description"=>"<p>24 OGs with evidence for strong and weak positive selection in two bamboos.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary processes", "Evolutionary selection", "Evolutionary systematics", "phylogenetics", "Organismal evolution", "Plant evolution", "genetics", "Plant genetics", "Plant science", "Plant genomics", "Plant phylogenetics", "ogs"], "article_id"=>708609, "categories"=>["Biological Sciences"], "users"=>["Lei Zhao", "Ning Zhang", "Peng-Fei Ma", "Qi Liu", "De-Zhu Li", "Zhen-Hua Guo"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0064642.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_24_OGs_with_evidence_for_strong_and_weak_positive_selection_in_two_bamboos_/708609", "title"=>"24 OGs with evidence for strong and weak positive selection in two bamboos.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-05-29 02:23:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/1069972"], "description"=>"a<p>N50 and N90 are defined as the length of the smallest contig N in the sorted list of all contigs where the cumulative length from the largest contig to contig N is at least 50% and 90% of the total length, respectively.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary processes", "Evolutionary selection", "Evolutionary systematics", "phylogenetics", "Organismal evolution", "Plant evolution", "genetics", "Plant genetics", "Plant science", "Plant genomics", "Plant phylogenetics", "contigs", "transcripts", "assembled", "trinity"], "article_id"=>708610, "categories"=>["Biological Sciences"], "users"=>["Lei Zhao", "Ning Zhang", "Peng-Fei Ma", "Qi Liu", "De-Zhu Li", "Zhen-Hua Guo"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0064642.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Statistical_summary_of_contigs_and_final_transcripts_assembled_by_Trinity_and_TGICL_/708610", "title"=>"Statistical summary of contigs and final transcripts assembled by Trinity and TGICL.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-05-29 02:23:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/1069973"], "description"=>"a<p><i>P value</i> of LRT between models M1a vs M2a or M7 vs M8.</p>b<p>When <i>P value</i> of LRT is lower 0.05, positively selected sites (PSS) estimated by BEB (BEB Value >85%), and sites in bold have BEB Value >95%.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary processes", "Evolutionary selection", "Evolutionary systematics", "phylogenetics", "Organismal evolution", "Plant evolution", "genetics", "Plant genetics", "Plant science", "Plant genomics", "Plant phylogenetics", "detecting", "positively"], "article_id"=>708611, "categories"=>["Biological Sciences"], "users"=>["Lei Zhao", "Ning Zhang", "Peng-Fei Ma", "Qi Liu", "De-Zhu Li", "Zhen-Hua Guo"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0064642.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Site_Models_used_for_detecting_positively_selected_sites_/708611", "title"=>"Site Models used for detecting positively selected sites.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-05-29 02:23:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/1069974", "https://ndownloader.figshare.com/files/1069975", "https://ndownloader.figshare.com/files/1069976", "https://ndownloader.figshare.com/files/1069977", "https://ndownloader.figshare.com/files/1069978", "https://ndownloader.figshare.com/files/1069979", "https://ndownloader.figshare.com/files/1069980", "https://ndownloader.figshare.com/files/1069981", "https://ndownloader.figshare.com/files/1069982", "https://ndownloader.figshare.com/files/1069983", "https://ndownloader.figshare.com/files/1069984", "https://ndownloader.figshare.com/files/1069985", "https://ndownloader.figshare.com/files/1069986", "https://ndownloader.figshare.com/files/1069987", "https://ndownloader.figshare.com/files/1069988", "https://ndownloader.figshare.com/files/1069989", "https://ndownloader.figshare.com/files/1069990", "https://ndownloader.figshare.com/files/1069991", "https://ndownloader.figshare.com/files/1069992", "https://ndownloader.figshare.com/files/1069993", "https://ndownloader.figshare.com/files/1069994", "https://ndownloader.figshare.com/files/1069995", "https://ndownloader.figshare.com/files/1069996", "https://ndownloader.figshare.com/files/1069997", "https://ndownloader.figshare.com/files/1069998"], "description"=>"<div><p>BEP clade of the grass family (Poaceae) is composed of three subfamilies, i.e. Bambusoideae, Ehrhartoideae, and Pooideae. Controversies on the phylogenetic relationships among three subfamilies still persist in spite of great efforts. However, previous evidence was mainly provided from plastid genes with only a few nuclear genes utilized. Given different evolutionary histories recorded by plastid and nuclear genes, it is indispensable to uncover their relationships based on nuclear genes. Here, eleven species with whole-sequenced genome and six species with transcriptomic data were included in this study. A total of 121 one-to-one orthologous groups (OGs) were identified and phylogenetic trees were reconstructed by different tree-building methods. Genes which might have undergone positive selection and played important roles in adaptive evolution were also investigated from 314 and 173 one-to-one OGs in two bamboo species and 14 grass species, respectively. Our results support the ((B, P) E) topology with high supporting values. Besides, our findings also indicate that 24 and nine orthologs with statistically significant evidence of positive selection are mainly involved in abiotic and biotic stress response, reproduction and development, plant metabolism and enzyme etc. from two bamboo species and 14 grass species, respectively. In summary, this study demonstrates the power of phylogenomic approach to shed lights on the evolutionary relationships within the BEP clade, and offers valuable insights into adaptive evolution of the grass family.</p></div>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary processes", "Evolutionary selection", "Evolutionary systematics", "phylogenetics", "Organismal evolution", "Plant evolution", "genetics", "Plant genetics", "Plant science", "Plant genomics", "Plant phylogenetics", "genes", "evolutionary", "relationships", "bep", "clade"], "article_id"=>708612, "categories"=>["Biological Sciences"], "users"=>["Lei Zhao", "Ning Zhang", "Peng-Fei Ma", "Qi Liu", "De-Zhu Li", "Zhen-Hua Guo"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0064642.s001", "https://dx.doi.org/10.1371/journal.pone.0064642.s002", "https://dx.doi.org/10.1371/journal.pone.0064642.s003", "https://dx.doi.org/10.1371/journal.pone.0064642.s004", "https://dx.doi.org/10.1371/journal.pone.0064642.s005", "https://dx.doi.org/10.1371/journal.pone.0064642.s006", "https://dx.doi.org/10.1371/journal.pone.0064642.s007", "https://dx.doi.org/10.1371/journal.pone.0064642.s008", "https://dx.doi.org/10.1371/journal.pone.0064642.s009", "https://dx.doi.org/10.1371/journal.pone.0064642.s010", "https://dx.doi.org/10.1371/journal.pone.0064642.s011", "https://dx.doi.org/10.1371/journal.pone.0064642.s012", "https://dx.doi.org/10.1371/journal.pone.0064642.s013", "https://dx.doi.org/10.1371/journal.pone.0064642.s014", "https://dx.doi.org/10.1371/journal.pone.0064642.s015", "https://dx.doi.org/10.1371/journal.pone.0064642.s016", "https://dx.doi.org/10.1371/journal.pone.0064642.s017", "https://dx.doi.org/10.1371/journal.pone.0064642.s018", "https://dx.doi.org/10.1371/journal.pone.0064642.s019", "https://dx.doi.org/10.1371/journal.pone.0064642.s020", "https://dx.doi.org/10.1371/journal.pone.0064642.s021", "https://dx.doi.org/10.1371/journal.pone.0064642.s022", "https://dx.doi.org/10.1371/journal.pone.0064642.s023", "https://dx.doi.org/10.1371/journal.pone.0064642.s024", "https://dx.doi.org/10.1371/journal.pone.0064642.s025"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenomic_Analyses_of_Nuclear_Genes_Reveal_the_Evolutionary_Relationships_within_the_BEP_Clade_and_the_Evidence_of_Positive_Selection_in_Poaceae_/708612", "title"=>"Phylogenomic Analyses of Nuclear Genes Reveal the Evolutionary Relationships within the BEP Clade and the Evidence of Positive Selection in Poaceae", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-05-29 02:23:32"}

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Relative Metric

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