Characterization and Evolution of Conserved MicroRNA through Duplication Events in Date Palm (Phoenix dactylifera)
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{"title"=>"Characterization and Evolution of Conserved MicroRNA through Duplication Events in Date Palm (Phoenix dactylifera)", "type"=>"journal", "authors"=>[{"first_name"=>"Yong", "last_name"=>"Xiao", "scopus_author_id"=>"52164705900"}, {"first_name"=>"Wei", "last_name"=>"Xia", "scopus_author_id"=>"8227791000"}, {"first_name"=>"Yaodong", "last_name"=>"Yang", "scopus_author_id"=>"55543406900"}, {"first_name"=>"Annaliese S.", "last_name"=>"Mason", "scopus_author_id"=>"26536303800"}, {"first_name"=>"Xintao", "last_name"=>"Lei", "scopus_author_id"=>"49661676500"}, {"first_name"=>"Zilong", "last_name"=>"Ma", "scopus_author_id"=>"55479135100"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84881325372", "pui"=>"369535563", "doi"=>"10.1371/journal.pone.0071435", "pmid"=>"23951162", "scopus"=>"2-s2.0-84881325372", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"3909dc35-37cf-3853-a226-c1a37ae6945e", "abstract"=>"MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (Phoenix dactylifera). We conducted a systematic miRNA analysis in date palm, computationally identifying and characterizing the distribution and duplication of conserved miRNAs in this species compared to other published plant genomes. A total of 81 miRNAs belonging to 18 miRNA families were identified in date palm. The majority of miRNAs in date palm and seven other well-studied plant species were located in intergenic regions and located 4 to 5 kb away from the nearest protein-coding genes. Sequence comparison showed that 67% of date palm miRNA members were present in duplicated segments, and that 135 pairs of miRNA-containing segments were duplicated in Arabidopsis, tomato, orange, rice, apple, poplar and soybean with a high similarity of non coding sequences between duplicated segments, indicating genomic duplication was a major force for expansion of conserved miRNAs. Duplicated miRNA pairs in date palm showed divergence in pre-miRNA sequence and in number of promoters, implying that these duplicated pairs may have undergone divergent evolution. Comparisons between date palm and the seven other plant species for the gain/loss of miR167 loci in an ancient segment shared between monocots and dicots suggested that these conserved miRNAs were highly influenced by and diverged as a result of genomic duplication events.", "link"=>"http://www.mendeley.com/research/characterization-evolution-conserved-microrna-through-duplication-events-date-palm-phoenix-dactylife", "reader_count"=>27, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>13, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Other"=>3, "Student > Master"=>3, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>13, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Other"=>3, "Student > Master"=>3, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>20}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>20}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "Norway"=>1, "Brazil"=>1, "United Kingdom"=>1, "Malaysia"=>1, "Switzerland"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1147309", "https://ndownloader.figshare.com/files/1147310", "https://ndownloader.figshare.com/files/1147313", "https://ndownloader.figshare.com/files/1147316", "https://ndownloader.figshare.com/files/1147317", "https://ndownloader.figshare.com/files/1147318", "https://ndownloader.figshare.com/files/1147319"], "description"=>"<div><p>MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (<i>Phoenix dactylifera</i>). We conducted a systematic miRNA analysis in date palm, computationally identifying and characterizing the distribution and duplication of conserved miRNAs in this species compared to other published plant genomes. A total of 81 miRNAs belonging to 18 miRNA families were identified in date palm. The majority of miRNAs in date palm and seven other well-studied plant species were located in intergenic regions and located 4 to 5 kb away from the nearest protein-coding genes. Sequence comparison showed that 67% of date palm miRNA members were present in duplicated segments, and that 135 pairs of miRNA-containing segments were duplicated in <i>Arabidopsis</i>, tomato, orange, rice, apple, poplar and soybean with a high similarity of non coding sequences between duplicated segments, indicating genomic duplication was a major force for expansion of conserved miRNAs. Duplicated miRNA pairs in date palm showed divergence in pre-miRNA sequence and in number of promoters, implying that these duplicated pairs may have undergone divergent evolution. Comparisons between date palm and the seven other plant species for the gain/loss of miR167 loci in an ancient segment shared between monocots and dicots suggested that these conserved miRNAs were highly influenced by and diverged as a result of genomic duplication events.</p></div>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome databases", "Sequence analysis", "genetics", "gene expression", "Sequence databases", "Genome evolution", "Genome sequencing", "algorithms", "Information technology", "databases", "characterization", "conserved", "microrna", "duplication"], "article_id"=>767744, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Yong Xiao", "Wei Xia", "Yaodong Yang", "Annaliese S. Mason", "Xintao Lei", "Zilong Ma"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0071435.s001", "https://dx.doi.org/10.1371/journal.pone.0071435.s002", "https://dx.doi.org/10.1371/journal.pone.0071435.s003", "https://dx.doi.org/10.1371/journal.pone.0071435.s004", "https://dx.doi.org/10.1371/journal.pone.0071435.s005", "https://dx.doi.org/10.1371/journal.pone.0071435.s006", "https://dx.doi.org/10.1371/journal.pone.0071435.s007"], "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Characterization_and_Evolution_of_Conserved_MicroRNA_through_Duplication_Events_in_Date_Palm_Phoenix_dactylifera_/767744", "title"=>"Characterization and Evolution of Conserved MicroRNA through Duplication Events in Date Palm (<i>Phoenix dactylifera</i>)", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-08-08 02:48:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1147307"], "description"=>"*<p>miRNA in brackets represent tandem miRNAs.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome databases", "Sequence analysis", "genetics", "gene expression", "Sequence databases", "Genome evolution", "Genome sequencing", "algorithms", "Information technology", "databases", "mirna", "pairs", "paralogous", "contigs"], "article_id"=>767742, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Yong Xiao", "Wei Xia", "Yaodong Yang", "Annaliese S. Mason", "Xintao Lei", "Zilong Ma"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0071435.t002", "stats"=>{"downloads"=>5, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Duplicated_miRNA_pairs_detected_in_paralogous_contigs_of_date_palm_/767742", "title"=>"Duplicated miRNA pairs detected in paralogous contigs of date palm.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-08 02:48:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1147301"], "description"=>"<p>A) Alignment of twelve pre-miRNA sequences of miR156. The box to the right indicates the mature miRNA region. The box to the left indicates the star miRNA region. B) Phylogenic tree (formed by Neighbor Joining) for miRNA in the miR156 family. C) Blast2 results for two pairs of paralogous date palm contigs containing pre-miR156. Squares highlight the location of the pre-miRNAs.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome databases", "Sequence analysis", "genetics", "gene expression", "Sequence databases", "Genome evolution", "Genome sequencing", "algorithms", "Information technology", "databases", "sequences", "phylogenic", "microrna156", "pre-mirnas"], "article_id"=>767739, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Yong Xiao", "Wei Xia", "Yaodong Yang", "Annaliese S. Mason", "Xintao Lei", "Zilong Ma"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0071435.g003", "stats"=>{"downloads"=>1, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alignment_of_multiple_sequences_and_phylogenic_analysis_of_microRNA156_pre_miRNAs_in_date_palm_/767739", "title"=>"Alignment of multiple sequences and phylogenic analysis of microRNA156 pre-miRNAs in date palm.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-08 02:48:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1147299"], "description"=>"<p>For distances ranging from 0 to 1 kb, miRNAs were included to be inside genic regions. The protein coding gene densities were calculated from the following data: <i>Arabidopsis thalian</i>a (27228 genes/115.4 Mb), <i>Oryza sativa</i> (40577 genes/398 Mb), <i>Solanum lycopersicum</i> (34721 genes/760 Mb), <i>Populus trichocarpa</i> (45654 genes/410 Mb), <i>Malus domestica</i> (57386 genes/603.9 Mb), <i>Glycine max</i> (46430 genes/950 Mb), <i>Citrus sinensis</i> (29445 genes/320.5 Mb).</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome databases", "Sequence analysis", "genetics", "gene expression", "Sequence databases", "Genome evolution", "Genome sequencing", "algorithms", "Information technology", "databases", "mirnas", "nearest", "coding", "genes"], "article_id"=>767738, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Yong Xiao", "Wei Xia", "Yaodong Yang", "Annaliese S. Mason", "Xintao Lei", "Zilong Ma"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0071435.g002", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distance_of_miRNAs_from_nearest_protein_coding_genes_in_seven_model_plants_/767738", "title"=>"Distance of miRNAs from nearest protein coding genes in seven model plants.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-08 02:48:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1147306"], "description"=>"a<p>“–” Date palm contig (≥6.5kb) has no protein-coding genes;</p>b<p>“+” Presents of protein-coding genes in the contig;</p>c<p>Length of miRNAs flanking region without protein-coding genes;</p>d<p>Distance between miRNA and the nearest protein-coding gene/s.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome databases", "Sequence analysis", "genetics", "gene expression", "Sequence databases", "Genome evolution", "Genome sequencing", "algorithms", "Information technology", "databases", "mirnas"], "article_id"=>767741, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Yong Xiao", "Wei Xia", "Yaodong Yang", "Annaliese S. Mason", "Xintao Lei", "Zilong Ma"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0071435.t001", "stats"=>{"downloads"=>0, "page_views"=>30, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Predicted_miRNAs_in_date_palm_Phoenix_dactylifera_/767741", "title"=>"Predicted miRNAs in date palm (<i>Phoenix dactylifera</i>).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-08 02:48:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1147304"], "description"=>"<p>Each panel shows conserved genes aligned by red lines. Red arrows represent the miR167 loci. The grey horizontal lines represent the homologous regions from different chromosomes. The dots above the grey horizontal lines indicate conserved genes that could be aligned between species, while dots below the grey horizontal lines indicate genes that could not be aligned between species. Ath3 is short for chromosome 3 of <i>Arabidopsis thaliana</i>. Pda, osa, csi, ptc, gma, sly and mdm are short for <i>Phoenix dactylifera</i>, <i>Oryza sativa</i>, <i>Citrus sinensis</i>, <i>Populus trichocarpa</i>, <i>Glycine max</i>, <i>Solanum lycopersicum</i>, and <i>Malus domestica</i>, respectively.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome databases", "Sequence analysis", "genetics", "gene expression", "Sequence databases", "Genome evolution", "Genome sequencing", "algorithms", "Information technology", "databases", "contigpdk_30s943301", "containing", "mir167", "locus", "orthologous", "segments"], "article_id"=>767740, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Yong Xiao", "Wei Xia", "Yaodong Yang", "Annaliese S. Mason", "Xintao Lei", "Zilong Ma"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0071435.g004", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relationship_between_date_palm_contigPDK_30s943301_containing_an_miR167_locus_and_orthologous_segments_from_seven_other_plant_species_/767740", "title"=>"Relationship between date palm contigPDK_30s943301 containing an miR167 locus and orthologous segments from seven other plant species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-08 02:48:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1147297"], "description"=>"<p>The taxonomic tree was constructed in the Interactive Tree Of Life (<a href=\"http://itol.embl.de/\" target=\"_blank\">http://itol.embl.de/</a>) from taxonomy numbers in NCBI (<a href=\"http://www.ncbi.nlm.nih.gov/Taxonomy/\" target=\"_blank\">http://www.ncbi.nlm.nih.gov/Taxonomy/</a>). The history of miRNA genes was reconstructed using the maximum likelihood procedure implanted in COUNT software. The dates of genomic duplication events are from references. The black bars represent the conserved segment, and the triangles indicate the presence of an miR167 locus in the extant plant genomes. Total refers to the total number of miRNA genes in a specific plant, and the number in brackets is the number of miRNA families.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome databases", "Sequence analysis", "genetics", "gene expression", "Sequence databases", "Genome evolution", "Genome sequencing", "algorithms", "Information technology", "databases", "21", "conserved", "mirna"], "article_id"=>767737, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Yong Xiao", "Wei Xia", "Yaodong Yang", "Annaliese S. Mason", "Xintao Lei", "Zilong Ma"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0071435.g001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_gain_and_loss_of_21_conserved_miRNA_families_across_date_palm_and_seven_other_plant_species_/767737", "title"=>"The gain and loss of 21 conserved miRNA families across date palm and seven other plant species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-08 02:48:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1147308"], "description"=>"a<p>MicroRNA located in the contig;</p>b<p>Arabidopsis thaliana (ath), Citrus sinensis (csi), Glycine max (gma), Oryza sativa (osa), Solanum lycopersicum (sly), Populus trichocarpa (ptc), and Malus domestica (mdm).</p>c<p>Numbers in brackets represent numbers of conserved genes in orthologous blocks.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome databases", "Sequence analysis", "genetics", "gene expression", "Sequence databases", "Genome evolution", "Genome sequencing", "algorithms", "Information technology", "databases", "segments"], "article_id"=>767743, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Yong Xiao", "Wei Xia", "Yaodong Yang", "Annaliese S. Mason", "Xintao Lei", "Zilong Ma"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0071435.t003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Orthologous_segments_between_date_palm_Phoenix_dactylifera_and_seven_other_plant_species_/767743", "title"=>"Orthologous segments between date palm (<i>Phoenix dactylifera</i>) and seven other plant species.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-08 02:48:53"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"8", "full-text"=>"10", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"5", "cited-by"=>"0", "year"=>"2018", "month"=>"5"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
  • {"unique-ip"=>"6", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"14", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"8", "full-text"=>"4", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"8", "full-text"=>"9", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"9", "full-text"=>"9", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"4", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"7", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"10", "full-text"=>"11", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"7", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}

Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[269, 466, 588, 697, 800, 896, 988, 1076, 1165, 1254, 1340, 1417]}, {"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[266, 468, 593, 703, 804, 903, 993, 1084, 1171, 1256, 1339, 1422, 1492]}, {"subject_area"=>"/Biology and life sciences/Biotechnology", "average_usage"=>[259, 472, 622, 759, 885, 1009, 1123, 1232, 1335, 1437, 1533, 1627, 1698]}, {"subject_area"=>"/Biology and life sciences/Evolutionary biology", "average_usage"=>[302, 488, 607, 717, 832, 931, 1024, 1117, 1212, 1302, 1389, 1469, 1535]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[284, 491, 620, 738, 843, 945, 1043, 1137, 1225, 1315, 1400, 1479, 1555]}, {"subject_area"=>"/Biology and life sciences/Molecular biology", "average_usage"=>[272, 466, 589, 702, 806, 903, 995, 1086, 1176, 1258, 1347, 1422, 1493]}, {"subject_area"=>"/Biology and life sciences/Organisms", "average_usage"=>[281, 484, 611, 728, 835, 934, 1030, 1123, 1214, 1299, 1383, 1464]}, {"subject_area"=>"/Biology and life sciences/Plant science", "average_usage"=>[269, 451, 577, 699, 812, 922, 1019, 1126, 1225, 1309, 1404, 1493, 1563]}]}
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