Identification of MicroRNAs and Target Genes in the Fruit and Shoot Tip of Lycium chinense: A Traditional Chinese Medicinal Plant
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{"title"=>"Identification of MicroRNAs and target genes in the fruit and shoot tip of Lycium chinense: A traditional chinese medicinal plant", "type"=>"journal", "authors"=>[{"first_name"=>"A. B.M.", "last_name"=>"Khaldun", "scopus_author_id"=>"56481574200"}, {"first_name"=>"Wenjun", "last_name"=>"Huang", "scopus_author_id"=>"55553558300"}, {"first_name"=>"Sihong", "last_name"=>"Liao", "scopus_author_id"=>"56481027800"}, {"first_name"=>"Haiyan", "last_name"=>"Lv", "scopus_author_id"=>"14822144600"}, {"first_name"=>"Ying", "last_name"=>"Wang", "scopus_author_id"=>"56433728600"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84920964554", "sgr"=>"84920964554", "pui"=>"601290937", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"25587984", "doi"=>"10.1371/journal.pone.0116334"}, "id"=>"7a93d09f-344a-3c43-be3d-e6a751191ec0", "abstract"=>"Although Lycium chinense (goji berry) is an important traditional Chinese medicinal plant, little genome information is available for this plant, particularly at the small-RNA level. Recent findings indicate that the evolutionary role of miRNAs is very important for a better understanding of gene regulation in different plant species. To elucidate small RNAs and their potential target genes in fruit and shoot tissues, high-throughput RNA sequencing technology was used followed by qRT-PCR and RLM 5'-RACE experiments. A total of 60 conserved miRNAs belonging to 31 families and 30 putative novel miRNAs were identified. A total of 62 significantly differentially expressed miRNAs were identified, of which 15 (14 known and 1 novel) were shoot-specific, and 12 (7 known and 5 novel) were fruit-specific. Additionally, 28 differentially expressed miRNAs were recorded as up-regulated in fruit tissues. The predicted potential targets were involved in a wide range of metabolic and regulatory pathways. GO (Gene Ontology) enrichment analysis and the KEGG (Kyoto Encyclopedia of Genes and Genomes) database revealed that \"metabolic pathways\" is the most significant pathway with respect to the rich factor and gene numbers. Moreover, five miRNAs were related to fruit maturation, lycopene biosynthesis and signaling pathways, which might be important for the further study of fruit molecular biology. This study is the first, to detect known and novel miRNAs, and their potential targets, of L. chinense. The data and findings that are presented here might be a good source for the functional genomic study of medicinal plants and for understanding the links among diversified biological pathways.", "link"=>"http://www.mendeley.com/research/identification-micrornas-target-genes-fruit-shoot-tip-lycium-chinense-traditional-chinese-medicinal", "reader_count"=>14, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>4, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>6, "Student > Master"=>1, "Other"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>4, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>6, "Student > Master"=>1, "Other"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>9, "Medicine and Dentistry"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>9}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "group_count"=>0}

Scopus | Further Information

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/1866478"], "description"=>"<p>X-axis, name of the miRNAs family; Y-axis, representing miRNA numbers.</p>", "links"=>[], "tags"=>["Lycium chinense", "novel miRNAs", "gene", "race", "kegg", "rlm", "pathway"], "article_id"=>1289576, "categories"=>["Biological Sciences"], "users"=>["A. B. M. Khaldun", "Wenjun Huang", "Sihong Liao", "Haiyan Lv", "Ying Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0116334.g002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_distribution_of_the_member_numbers_A_and_read_counts_of_each_known_miRNA_families_B_in_L_chinense_/1289576", "title"=>"The distribution of the member numbers (A) and read counts of each known miRNA families (B) in <i>L. chinense</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-01-14 02:51:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1866479"], "description"=>"<p>The number on top of the bars indicates the number of sequences corresponding to the miRNA length; “0” indicates the absence of sequences of that corresponding length. X-axis, length of miRNAs; Y-axis, representing percent of each nucleotide.</p>", "links"=>[], "tags"=>["Lycium chinense", "novel miRNAs", "gene", "race", "kegg", "rlm", "pathway"], "article_id"=>1289577, "categories"=>["Biological Sciences"], "users"=>["A. B. M. Khaldun", "Wenjun Huang", "Sihong Liao", "Haiyan Lv", "Ying Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0116334.g003", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_First_nucleotide_bias_of_novel_miRNA_candidates_in_the_L_chinense_shoot_A_and_fruit_B_libraries_/1289577", "title"=>"First nucleotide bias of novel miRNA candidates in the <i>L. chinense</i> shoot (A) and fruit (B) libraries.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-01-14 02:51:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1866481"], "description"=>"<p>BP, Biological Process; CC, Cellular Component; MF, Molecular Function. Right-hand-side scale, targeted gene numbers corresponding to the GO terms; left-hand-side scale, percent of targeted gene numbers corresponding to the GO terms.</p>", "links"=>[], "tags"=>["Lycium chinense", "novel miRNAs", "gene", "race", "kegg", "rlm", "pathway"], "article_id"=>1289579, "categories"=>["Biological Sciences"], "users"=>["A. B. M. Khaldun", "Wenjun Huang", "Sihong Liao", "Haiyan Lv", "Ying Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0116334.g004", "stats"=>{"downloads"=>2, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_ontology_terms_and_numbers_of_the_predicted_target_genes_for_differentially_expressed_miRNAs_/1289579", "title"=>"Gene ontology terms and numbers of the predicted target genes for differentially expressed miRNAs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-01-14 02:51:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1866482"], "description"=>"<p>The coloring of the q-values indicates the significance of the rich factor; the circle indicates the target genes that are involved, and the size is proportional to the gene number.</p>", "links"=>[], "tags"=>["Lycium chinense", "novel miRNAs", "gene", "race", "kegg", "rlm", "pathway"], "article_id"=>1289580, "categories"=>["Biological Sciences"], "users"=>["A. B. M. Khaldun", "Wenjun Huang", "Sihong Liao", "Haiyan Lv", "Ying Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0116334.g005", "stats"=>{"downloads"=>2, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_KEGG_analysis_with_the_20_most_enriched_pathways_/1289580", "title"=>"KEGG analysis with the 20 most enriched pathways.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-01-14 02:51:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1866483"], "description"=>"<p>X-axis, name of the miRNAs that were selected for qRT-PCR; column above the X-axis, miRNAs that were up-regulated in the fruit; column below the X-axis, miRNAs that were up-regulated in the shoot.</p>", "links"=>[], "tags"=>["Lycium chinense", "novel miRNAs", "gene", "race", "kegg", "rlm", "pathway"], "article_id"=>1289581, "categories"=>["Biological Sciences"], "users"=>["A. B. M. Khaldun", "Wenjun Huang", "Sihong Liao", "Haiyan Lv", "Ying Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0116334.g006", "stats"=>{"downloads"=>3, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_ratios_Fruit_Shoot_of_miRNAs_in_L_chinense_based_on_the_qRT_PCR_A_and_deep_sequencing_B_results_/1289581", "title"=>"Expression ratios (Fruit/Shoot) of miRNAs in <i>L. chinense</i> based on the qRT-PCR (A) and deep sequencing (B) results.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-01-14 02:51:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1866484"], "description"=>"<p>Arrows showing the 5’-ends of cleavage products.</p>", "links"=>[], "tags"=>["Lycium chinense", "novel miRNAs", "gene", "race", "kegg", "rlm", "pathway"], "article_id"=>1289582, "categories"=>["Biological Sciences"], "users"=>["A. B. M. Khaldun", "Wenjun Huang", "Sihong Liao", "Haiyan Lv", "Ying Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0116334.g007", "stats"=>{"downloads"=>3, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Target_validation_of_known_L_chinense_miRNAs_/1289582", "title"=>"Target validation of known <i>L. chinense</i> miRNAs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-01-14 02:51:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1866485"], "description"=>"<p>N%, undetectable gaps at base calling.</p><p>Statistical summary of the data that were generated by high-throughput small-RNA sequencing in goji.</p>", "links"=>[], "tags"=>["Lycium chinense", "novel miRNAs", "gene", "race", "kegg", "rlm", "pathway"], "article_id"=>1289583, "categories"=>["Biological Sciences"], "users"=>["A. B. M. Khaldun", "Wenjun Huang", "Sihong Liao", "Haiyan Lv", "Ying Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0116334.t001", "stats"=>{"downloads"=>5, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Statistical_summary_of_the_data_that_were_generated_by_high_throughput_small_RNA_sequencing_in_goji_/1289583", "title"=>"Statistical summary of the data that were generated by high-throughput small-RNA sequencing in goji.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-01-14 02:51:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1866486"], "description"=>"<p>Known miRNAs, perfect matching mature miRNA sequences in the miRBase miRNA repository; Novel miRNAs, new mature miRNA sequences that were detected by characteristic stem-loop hairpins and minimum free energy (MFE); rRNAs, tRNAs, snRNAs, and snoRNAs are non-coding sRNAs; TAS, transacting small interfering RNAs; Unannotated, reads that had no known information.</p><p>Number of reads for each small RNA classification as identified in <i>goji</i>.</p>", "links"=>[], "tags"=>["Lycium chinense", "novel miRNAs", "gene", "race", "kegg", "rlm", "pathway"], "article_id"=>1289584, "categories"=>["Biological Sciences"], "users"=>["A. B. M. Khaldun", "Wenjun Huang", "Sihong Liao", "Haiyan Lv", "Ying Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0116334.t002", "stats"=>{"downloads"=>5, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_reads_for_each_small_RNA_classification_as_identified_in_goji_/1289584", "title"=>"Number of reads for each small RNA classification as identified in <i>goji</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-01-14 02:51:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1866487"], "description"=>"<p>ML, mature sequence length; PL, Precursor length; miRNA*, the sequences that can form miRNA::miRNA* with miRNA variants.</p><p>Description of 30 potentially mature novel miRNAs.</p>", "links"=>[], "tags"=>["Lycium chinense", "novel miRNAs", "gene", "race", "kegg", "rlm", "pathway"], "article_id"=>1289585, "categories"=>["Biological Sciences"], "users"=>["A. B. M. Khaldun", "Wenjun Huang", "Sihong Liao", "Haiyan Lv", "Ying Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0116334.t003", "stats"=>{"downloads"=>4, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Description_of_30_potentially_mature_novel_miRNAs_/1289585", "title"=>"Description of 30 potentially mature novel miRNAs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-01-14 02:51:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1866488"], "description"=>"<p>TPM, normalized transcripts per million; Signature-TRUE, differentially expressed miRNAs;</p><p>*, significant at <i>P</i> <0.05;</p><p>**, significant at <i>P</i> < 0.01.</p><p>Significantly differentially expressed miRNAs showing 3 or more log2-fold expression changes.</p>", "links"=>[], "tags"=>["Lycium chinense", "novel miRNAs", "gene", "race", "kegg", "rlm", "pathway"], "article_id"=>1289586, "categories"=>["Biological Sciences"], "users"=>["A. B. M. Khaldun", "Wenjun Huang", "Sihong Liao", "Haiyan Lv", "Ying Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0116334.t004", "stats"=>{"downloads"=>3, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Significantly_differentially_expressed_miRNAs_showing_3_or_more_log2_fold_expression_changes_/1289586", "title"=>"Significantly differentially expressed miRNAs showing 3 or more log2-fold expression changes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-01-14 02:51:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1866492", "https://ndownloader.figshare.com/files/1866493", "https://ndownloader.figshare.com/files/1866494", "https://ndownloader.figshare.com/files/1866495", "https://ndownloader.figshare.com/files/1866496", "https://ndownloader.figshare.com/files/1866497", "https://ndownloader.figshare.com/files/1866498", "https://ndownloader.figshare.com/files/1866499", "https://ndownloader.figshare.com/files/1866500"], "description"=>"<div><p>Although <i>Lycium chinense</i> (goji berry) is an important traditional Chinese medicinal plant, little genome information is available for this plant, particularly at the small-RNA level. Recent findings indicate that the evolutionary role of miRNAs is very important for a better understanding of gene regulation in different plant species. To elucidate small RNAs and their potential target genes in fruit and shoot tissues, high-throughput RNA sequencing technology was used followed by qRT-PCR and RLM 5’-RACE experiments. A total of 60 conserved miRNAs belonging to 31 families and 30 putative novel miRNAs were identified. A total of 62 significantly differentially expressed miRNAs were identified, of which 15 (14 known and 1 novel) were shoot-specific, and 12 (7 known and 5 novel) were fruit-specific. Additionally, 28 differentially expressed miRNAs were recorded as up-regulated in fruit tissues. The predicted potential targets were involved in a wide range of metabolic and regulatory pathways. GO (Gene Ontology) enrichment analysis and the KEGG (Kyoto Encyclopedia of Genes and Genomes) database revealed that “metabolic pathways” is the most significant pathway with respect to the rich factor and gene numbers. Moreover, five miRNAs were related to fruit maturation, lycopene biosynthesis and signaling pathways, which might be important for the further study of fruit molecular biology. This study is the first, to detect known and novel miRNAs, and their potential targets, of <i>L. chinense</i>. The data and findings that are presented here might be a good source for the functional genomic study of medicinal plants and for understanding the links among diversified biological pathways.</p></div>", "links"=>[], "tags"=>["Lycium chinense", "novel miRNAs", "gene", "race", "kegg", "rlm", "pathway"], "article_id"=>1289590, "categories"=>["Biological Sciences"], "users"=>["A. B. M. Khaldun", "Wenjun Huang", "Sihong Liao", "Haiyan Lv", "Ying Wang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0116334.s001", "https://dx.doi.org/10.1371/journal.pone.0116334.s002", "https://dx.doi.org/10.1371/journal.pone.0116334.s003", "https://dx.doi.org/10.1371/journal.pone.0116334.s004", "https://dx.doi.org/10.1371/journal.pone.0116334.s005", "https://dx.doi.org/10.1371/journal.pone.0116334.s006", "https://dx.doi.org/10.1371/journal.pone.0116334.s007", "https://dx.doi.org/10.1371/journal.pone.0116334.s008", "https://dx.doi.org/10.1371/journal.pone.0116334.s009"], "stats"=>{"downloads"=>26, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Identification_of_MicroRNAs_and_Target_Genes_in_the_Fruit_and_Shoot_Tip_of_Lycium_chinense_A_Traditional_Chinese_Medicinal_Plant/1289590", "title"=>"Identification of MicroRNAs and Target Genes in the Fruit and Shoot Tip of <i>Lycium chinense</i>: A Traditional Chinese Medicinal Plant", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-01-14 02:51:55"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"7", "full-text"=>"8", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"5"}

Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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