Comparison of the Transcriptome between Two Cotton Lines of Different Fiber Color and Quality
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{"title"=>"Comparison of the transcriptome between two cotton lines of different fiber color and quality", "type"=>"journal", "authors"=>[{"first_name"=>"Wenfang", "last_name"=>"Gong", "scopus_author_id"=>"55567497800"}, {"first_name"=>"Shoupu", "last_name"=>"He", "scopus_author_id"=>"37115603600"}, {"first_name"=>"Jiahuan", "last_name"=>"Tian", "scopus_author_id"=>"56430249000"}, {"first_name"=>"Junling", "last_name"=>"Sun", "scopus_author_id"=>"55762552500"}, {"first_name"=>"Zhaoe", "last_name"=>"Pan", "scopus_author_id"=>"36145500100"}, {"first_name"=>"Yinhua", "last_name"=>"Jia", "scopus_author_id"=>"40361221000"}, {"first_name"=>"Gaofei", "last_name"=>"Sun", "scopus_author_id"=>"37102832000"}, {"first_name"=>"Xiongming", "last_name"=>"Du", "scopus_author_id"=>"14624913200"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"600550376", "isbn"=>"1932-6203", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0112966", "scopus"=>"2-s2.0-84912572053", "sgr"=>"84912572053"}, "id"=>"c03af789-c69e-3fa9-a098-1a1ca787fde9", "abstract"=>"© 2014 Gong et al.To understand the mechanism of fiber development and pigmentation formation, the mRNAs of two cotton lines were sequenced: line Z128 (light brown fiber) was a selected mutant from line Z263 (dark brown fiber). The primary walls of the fiber cell in both Z263 and Z128 contain pigments; more pigments were laid in the lumen of the fiber cell in Z263 compared with that in Z128. However, Z263 contained less cellulose than Z128. A total of 71,895 unigenes were generated: 13,278 (20.26%) unigenes were defined as differentially expressed genes (DEGs) by comparing the library of Z128 with that of Z263; 5,345 (8.16%) unigenes were up-regulated and 7,933 (12.10%) unigenes were down-regulated. qRT-PCR and comparative transcriptional analysis demonstrated that the pigmentation formation in brown cotton fiber was possibly the consequence of an interaction between oxidized tannins and glycosylated anthocyanins. Furthermore, our results showed the pigmentation related genes not only regulated the fiber color but also influenced the fiber quality at the fiber elongation stage (10 DPA). The highly expressed flavonoid gene in the fiber elongation stage could be related to the fiber quality. DEGs analyses also revealed that transcript levels of some fiber development genes (Ca2+/CaM, reactive oxygen, ethylene and sucrose phosphate synthase) varied dramatically between these two cotton lines. Copyright:", "link"=>"http://www.mendeley.com/research/comparison-transcriptome-between-two-cotton-lines-different-fiber-color-quality", "reader_count"=>12, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Librarian"=>1, "Student > Doctoral Student"=>2, "Researcher"=>2, "Student > Ph. D. Student"=>2, "Student > Bachelor"=>2, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Librarian"=>1, "Student > Doctoral Student"=>2, "Researcher"=>2, "Student > Ph. D. Student"=>2, "Student > Bachelor"=>2, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>7, "Arts and Humanities"=>1}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>7}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Saudi Arabia"=>1, "Chile"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1797441"], "description"=>"<p>The DEGs enriched terms in GO analysis (P-value<1).</p>", "links"=>[], "tags"=>["Z 128", "fiber development genes", "deg", "sucrose phosphate synthase", "fiber elongation stage", "Z 263", "Different Fiber Color", "line Z 128", "fiber quality", "pigmentation formation", "line Z 263", "dpa", "fiber cell", "Z 128.", "cotton lines"], "article_id"=>1244224, "categories"=>["Uncategorised"], "users"=>["Wenfang Gong", "Shoupu He", "Jiahuan Tian", "Junling Sun", "Zhaoe Pan", "Yinhua Jia", "Gaofei Sun", "Xiongming Du"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112966.t002", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_DEGs_enriched_terms_in_GO_analysis_P_value_lt_1_/1244224", "title"=>"The DEGs enriched terms in GO analysis (P-value<1).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-11-17 03:20:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1797439"], "description"=>"<p>The red and green arrows indicated the up- and down-regulated status detected by comparing gene expression in Z128 with that in Z263. chalcone synthase (CHS); chalcone isomerase (CHI); flavanone 3-hydroxylase (F3H); flavonol synthase (FLS); dihydroflavonol 4-reductase (DFR); leucoanthocyanidin reductase (LAR); anthocyanidin synthase (ANS); UDP-favonoid glucosyl transferase (UFGT); anthocyanidin reductase (ANR); anthocyanin 5-O-glucosyltransferase (5GT).</p>", "links"=>[], "tags"=>["Z 128", "fiber development genes", "deg", "sucrose phosphate synthase", "fiber elongation stage", "Z 263", "Different Fiber Color", "line Z 128", "fiber quality", "pigmentation formation", "line Z 263", "dpa", "fiber cell", "Z 128.", "cotton lines"], "article_id"=>1244222, "categories"=>["Uncategorised"], "users"=>["Wenfang Gong", "Shoupu He", "Jiahuan Tian", "Junling Sun", "Zhaoe Pan", "Yinhua Jia", "Gaofei Sun", "Xiongming Du"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112966.g005", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_schematic_of_pigment_formation_in_cotton_fiber_/1244222", "title"=>"The schematic of pigment formation in cotton fiber.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-17 03:20:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1797435"], "description"=>"<p>This figure was created by comparing gene expression levels of Z128 to Z263. FDR≤0.001, |log<sub>2</sub>Ratio| ≥1 was used as threshold, red dots represented up-regulated genes, green dots represented the down-regulated genes, and blue dots represented gene expression with no significant difference.</p>", "links"=>[], "tags"=>["Z 128", "fiber development genes", "deg", "sucrose phosphate synthase", "fiber elongation stage", "Z 263", "Different Fiber Color", "line Z 128", "fiber quality", "pigmentation formation", "line Z 263", "dpa", "fiber cell", "Z 128.", "cotton lines"], "article_id"=>1244218, "categories"=>["Uncategorised"], "users"=>["Wenfang Gong", "Shoupu He", "Jiahuan Tian", "Junling Sun", "Zhaoe Pan", "Yinhua Jia", "Gaofei Sun", "Xiongming Du"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112966.g004", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mapping_of_all_expressed_unigenes_/1244218", "title"=>"Mapping of all expressed unigenes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-17 03:20:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1797444"], "description"=>"<p>1: ratio indicated log2(z128_RPKM/Z263_RPKM);</p><p>2: “U” indicated that this unigene was up-regulated; “D” indicated down-regulated.</p><p>Fiber development related DEGs of brown and white fibers.</p>", "links"=>[], "tags"=>["Z 128", "fiber development genes", "deg", "sucrose phosphate synthase", "fiber elongation stage", "Z 263", "Different Fiber Color", "line Z 128", "fiber quality", "pigmentation formation", "line Z 263", "dpa", "fiber cell", "Z 128.", "cotton lines"], "article_id"=>1244227, "categories"=>["Uncategorised"], "users"=>["Wenfang Gong", "Shoupu He", "Jiahuan Tian", "Junling Sun", "Zhaoe Pan", "Yinhua Jia", "Gaofei Sun", "Xiongming Du"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112966.t005", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fiber_development_related_DEGs_of_brown_and_white_fibers_/1244227", "title"=>"Fiber development related DEGs of brown and white fibers.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-11-17 03:20:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1797429"], "description"=>"<p>All-unigenes classified by GO analysis.</p>", "links"=>[], "tags"=>["Z 128", "fiber development genes", "deg", "sucrose phosphate synthase", "fiber elongation stage", "Z 263", "Different Fiber Color", "line Z 128", "fiber quality", "pigmentation formation", "line Z 263", "dpa", "fiber cell", "Z 128.", "cotton lines"], "article_id"=>1244212, "categories"=>["Uncategorised"], "users"=>["Wenfang Gong", "Shoupu He", "Jiahuan Tian", "Junling Sun", "Zhaoe Pan", "Yinhua Jia", "Gaofei Sun", "Xiongming Du"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112966.g002", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_All_unigenes_classified_by_GO_analysis_/1244212", "title"=>"All-unigenes classified by GO analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-17 03:20:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1797443"], "description"=>"<p>1: ratio indicated log2(z128_RPKM/Z263_RPKM).</p><p>2: “U” indicated that this unigene was up-regulated; “D” indicated down-regulated.</p><p>The involved unigenes in Flavone and flavonol biosynthesis and Anthocyanin biosynthesis pathways.</p>", "links"=>[], "tags"=>["Z 128", "fiber development genes", "deg", "sucrose phosphate synthase", "fiber elongation stage", "Z 263", "Different Fiber Color", "line Z 128", "fiber quality", "pigmentation formation", "line Z 263", "dpa", "fiber cell", "Z 128.", "cotton lines"], "article_id"=>1244226, "categories"=>["Uncategorised"], "users"=>["Wenfang Gong", "Shoupu He", "Jiahuan Tian", "Junling Sun", "Zhaoe Pan", "Yinhua Jia", "Gaofei Sun", "Xiongming Du"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112966.t004", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_involved_unigenes_in_Flavone_and_flavonol_biosynthesis_and_Anthocyanin_biosynthesis_pathways_/1244226", "title"=>"The involved unigenes in Flavone and flavonol biosynthesis and Anthocyanin biosynthesis pathways.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-11-17 03:20:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1797431"], "description"=>"<p>A–Z represented different functions classified by GO analysis, respectively.</p>", "links"=>[], "tags"=>["Z 128", "fiber development genes", "deg", "sucrose phosphate synthase", "fiber elongation stage", "Z 263", "Different Fiber Color", "line Z 128", "fiber quality", "pigmentation formation", "line Z 263", "dpa", "fiber cell", "Z 128.", "cotton lines"], "article_id"=>1244215, "categories"=>["Uncategorised"], "users"=>["Wenfang Gong", "Shoupu He", "Jiahuan Tian", "Junling Sun", "Zhaoe Pan", "Yinhua Jia", "Gaofei Sun", "Xiongming Du"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112966.g003", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_COG_classification_of_all_unigenes_/1244215", "title"=>"COG classification of all-unigenes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-17 03:20:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1797445"], "description"=>"<div><p>To understand the mechanism of fiber development and pigmentation formation, the mRNAs of two cotton lines were sequenced: line Z128 (light brown fiber) was a selected mutant from line Z263 (dark brown fiber). The primary walls of the fiber cell in both Z263 and Z128 contain pigments; more pigments were laid in the lumen of the fiber cell in Z263 compared with that in Z128. However, Z263 contained less cellulose than Z128. A total of 71,895 unigenes were generated: 13,278 (20.26%) unigenes were defined as differentially expressed genes (DEGs) by comparing the library of Z128 with that of Z263; 5,345 (8.16%) unigenes were up-regulated and 7,933 (12.10%) unigenes were down-regulated. qRT-PCR and comparative transcriptional analysis demonstrated that the pigmentation formation in brown cotton fiber was possibly the consequence of an interaction between oxidized tannins and glycosylated anthocyanins. Furthermore, our results showed the pigmentation related genes not only regulated the fiber color but also influenced the fiber quality at the fiber elongation stage (10 DPA). The highly expressed flavonoid gene in the fiber elongation stage could be related to the fiber quality. DEGs analyses also revealed that transcript levels of some fiber development genes (Ca<sup>2+</sup>/CaM, reactive oxygen, ethylene and sucrose phosphate synthase) varied dramatically between these two cotton lines.</p></div>", "links"=>[], "tags"=>["Z 128", "fiber development genes", "deg", "sucrose phosphate synthase", "fiber elongation stage", "Z 263", "Different Fiber Color", "line Z 128", "fiber quality", "pigmentation formation", "line Z 263", "dpa", "fiber cell", "Z 128.", "cotton lines"], "article_id"=>1244228, "categories"=>["Uncategorised"], "users"=>["Wenfang Gong", "Shoupu He", "Jiahuan Tian", "Junling Sun", "Zhaoe Pan", "Yinhua Jia", "Gaofei Sun", "Xiongming Du"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112966", "stats"=>{"downloads"=>4, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_the_Transcriptome_between_Two_Cotton_Lines_of_Different_Fiber_Color_and_Quality_/1244228", "title"=>"Comparison of the Transcriptome between Two Cotton Lines of Different Fiber Color and Quality", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-11-17 03:20:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1797442"], "description"=>"<p>The top 10 DEGs enriched pathways in KEGG analysis.</p>", "links"=>[], "tags"=>["Z 128", "fiber development genes", "deg", "sucrose phosphate synthase", "fiber elongation stage", "Z 263", "Different Fiber Color", "line Z 128", "fiber quality", "pigmentation formation", "line Z 263", "dpa", "fiber cell", "Z 128.", "cotton lines"], "article_id"=>1244225, "categories"=>["Uncategorised"], "users"=>["Wenfang Gong", "Shoupu He", "Jiahuan Tian", "Junling Sun", "Zhaoe Pan", "Yinhua Jia", "Gaofei Sun", "Xiongming Du"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112966.t003", "stats"=>{"downloads"=>4, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_top_10_DEGs_enriched_pathways_in_KEGG_analysis_/1244225", "title"=>"The top 10 DEGs enriched pathways in KEGG analysis.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-11-17 03:20:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1797427"], "description"=>"<p>Statistical analyses were performed at 95% condence with IBM SPSS Statistics 11.0 (SPSS Inc., Chicago, USA). Values with an asterisk represented a significant differe- nce at P<0.05. The fiber microstructure of Z263 (C I) and Z128 (C II) was observed under a microscope (×3000 and ×2500, respectively).</p>", "links"=>[], "tags"=>["Z 128", "fiber development genes", "deg", "sucrose phosphate synthase", "fiber elongation stage", "Z 263", "Different Fiber Color", "line Z 128", "fiber quality", "pigmentation formation", "line Z 263", "dpa", "fiber cell", "Z 128.", "cotton lines"], "article_id"=>1244210, "categories"=>["Uncategorised"], "users"=>["Wenfang Gong", "Shoupu He", "Jiahuan Tian", "Junling Sun", "Zhaoe Pan", "Yinhua Jia", "Gaofei Sun", "Xiongming Du"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112966.g001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_fiber_color_yield_quality_and_microstructure_of_Z128_and_Z263_/1244210", "title"=>"The fiber color, yield, quality and microstructure of Z128 and Z263.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-17 03:20:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1797440"], "description"=>"<p>The primers used in this study.</p>", "links"=>[], "tags"=>["Z 128", "fiber development genes", "deg", "sucrose phosphate synthase", "fiber elongation stage", "Z 263", "Different Fiber Color", "line Z 128", "fiber quality", "pigmentation formation", "line Z 263", "dpa", "fiber cell", "Z 128.", "cotton lines"], "article_id"=>1244223, "categories"=>["Uncategorised"], "users"=>["Wenfang Gong", "Shoupu He", "Jiahuan Tian", "Junling Sun", "Zhaoe Pan", "Yinhua Jia", "Gaofei Sun", "Xiongming Du"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112966.t001", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_primers_used_in_this_study_/1244223", "title"=>"The primers used in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-11-17 03:20:03"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"11", "full-text"=>"8", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}

Relative Metric

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Agriculture", "average_usage"=>[282]}, {"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[282]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[306, 482]}]}
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