Additional file 4: of Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture

Daoqian Yu (6050774)
Ghulam Qanmber (6050777)
Lili Lu (408133)
Lingling Wang (66269)
Jie Li (15030)
Zhaoen Yang (659918)
Zhao Liu (582169)
Yi Li (1144)
Quanjia Chen (3320355)
Venugopal Mendu (184563)
Fuguang Li (229466)
Zuoren Yang (518304)

Open link

Publication date

December 2018

DOI

10.6084/m9.figshare.7460066.v1

Abstract

Table S3. Comparison of characteristics of GH3s identified in two genome assemblies of G. hirsutum. (DOCX 19âkb

Extracted data

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Data Protection

Additional file 4: of Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture

Daoqian Yu (6050774)
Ghulam Qanmber (6050777)
Lili Lu (408133)
Lingling Wang (66269)
Jie Li (15030)
Zhaoen Yang (659918)
Zhao Liu (582169)
Yi Li (1144)
Quanjia Chen (3320355)
Venugopal Mendu (184563)
Fuguang Li (229466)
Zuoren Yang (518304)

Open link

Publication date

December 2018

DOI

10.6084/m9.figshare.7460066.v1

Abstract

Table S3. Comparison of characteristics of GH3s identified in two genome assemblies of G. hirsutum. (DOCX 19âkb

Extracted data

Lingling Wang (66269)
Zhaoen Yang (659918)
Bin Zhang (64682)
Daoqian Yu (6050774)
Ji Liu (110659)
Qian Gong (3710617)
Ghulam Qanmber (6050777)
Yi Li (1144)
Lili Lu (408133)
Yongjun Lin (161394)
Zuoren Yang (518304)
Fuguang Li (229466)

December 2018

Figure S3. Motif logos of 16 conserved motifs found in cotton GSK proteins. (PDF 817 kb

Additional file 3: of Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study

Xiongming Du (561554)
Shouye Liu (5384336)
Junling Sun (561545)
Gengyun Zhang (4118122)
Yinhua Jia (561544)
Zhaoe Pan (561546)
Haitao Xiang (3549005)
Shoupu He (561548)
Qiuju Xia (3549008)
Songhua Xiao (322277)
Weijun Shi (561549)
Zhiwu Quan (3548999)
Jianguang Liu (561553)
Jun Ma (9393)
Baoyin Pang (561551)
Liru Wang (561552)
Gaofei Sun (662300)
Wenfang Gong (193513)
Johnie Jenkins (3407099)
Xiangyang Lou (5384339)
Jun Zhu (84054)
Haiming Xu (178700)

June 2018

Table S3. The other genome-wide significant QTSs associated with five fatty acids. (DOC 185 kb

Additional file 16: of A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

Md Islam (257385)
Gregory Thyssen (531000)
Johnie Jenkins (3407099)
Linghe Zeng (3407102)
Christopher Delhom (3407096)
Jack McCarty (3407090)
Dewayne Deng (3407105)
Doug Hinchliffe (3407108)
Don Jones (3407093)
David Fang (3399707)

November 2016

Title: RT-qPCR gene expression analyses of selected genes related to cell wall activity during fiber...

Additional file 9: of Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture

Daoqian Yu (6050774)
Ghulam Qanmber (6050777)
Lili Lu (408133)
Lingling Wang (66269)
Jie Li (15030)
Zhaoen Yang (659918)
Zhao Liu (582169)
Yi Li (1144)
Quanjia Chen (3320355)
Venugopal Mendu (184563)
Fuguang Li (229466)
Zuoren Yang (518304)

December 2018

Table S5. The original RNA-seq data for GhGH3 expression pattern analysis. (XLSX 20âkb

Additional file 7: of Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture

Daoqian Yu (6050774)
Ghulam Qanmber (6050777)
Lili Lu (408133)
Lingling Wang (66269)
Jie Li (15030)
Zhaoen Yang (659918)
Zhao Liu (582169)
Yi Li (1144)
Quanjia Chen (3320355)
Venugopal Mendu (184563)
Fuguang Li (229466)
Zuoren Yang (518304)

December 2018

Figure S4. Chromosomal distribution of subfamily II GhGH3 genes together with putative subfamily I G...

Additional file 2: of Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture

Daoqian Yu (6050774)
Ghulam Qanmber (6050777)
Lili Lu (408133)
Lingling Wang (66269)
Jie Li (15030)
Zhaoen Yang (659918)
Zhao Liu (582169)
Yi Li (1144)
Quanjia Chen (3320355)
Venugopal Mendu (184563)
Fuguang Li (229466)
Zuoren Yang (518304)

December 2018

Figure S1. Three NJ phylogenetic trees for identification of GH3 genes in cotton. GH3s in G. arboreu...

Additional file 6: of Genome-wide characterization and phylogenetic analysis of GSK gene family in three species of cotton: evidence for a role of some GSKs in fiber development and responses to stress

Lingling Wang (66269)
Zhaoen Yang (659918)
Bin Zhang (64682)
Daoqian Yu (6050774)
Ji Liu (110659)
Qian Gong (3710617)
Ghulam Qanmber (6050777)
Yi Li (1144)
Lili Lu (408133)
Yongjun Lin (161394)
Zuoren Yang (518304)
Fuguang Li (229466)

December 2018

Table S3. Orthologous GSK genes identified in G. hirsutum, G. arboreum and G. raimondii. Orthologous...

Additional file 3: of Comparative fiber property and transcriptome analyses reveal key genes potentially related to high fiber strength in cotton (Gossypium hirsutum L.) line MD52ne

Md Islam (257385)
David Fang (3399707)
Gregory Thyssen (531000)
Chris Delhom (2290288)
Yongliang Liu (561185)
Hee Kim (2025640)

February 2016

Differentially expressed genes at 20 DPA between MD52ne and MD90ne. This table contains 1080 allotet...

Additional file 4: of Genome-wide characterization and phylogenetic analysis of GSK gene family in three species of cotton: evidence for a role of some GSKs in fiber development and responses to stress

Lingling Wang (66269)
Zhaoen Yang (659918)
Bin Zhang (64682)
Daoqian Yu (6050774)
Ji Liu (110659)
Qian Gong (3710617)
Ghulam Qanmber (6050777)
Yi Li (1144)
Lili Lu (408133)
Yongjun Lin (161394)
Zuoren Yang (518304)
Fuguang Li (229466)

December 2018

Figure S2. Phylogenetic analysis of GSK3 proteins in Arabidopsis, rice, and species of cotton. 10 At...

Additional file 1: of Genome-wide characterization and phylogenetic analysis of GSK gene family in three species of cotton: evidence for a role of some GSKs in fiber development and responses to stress

Lingling Wang (66269)
Zhaoen Yang (659918)
Bin Zhang (64682)
Daoqian Yu (6050774)
Ji Liu (110659)
Qian Gong (3710617)
Ghulam Qanmber (6050777)
Yi Li (1144)
Lili Lu (408133)
Yongjun Lin (161394)
Zuoren Yang (518304)
Fuguang Li (229466)

December 2018

Table S1.1 Gene accession numbers and sample information of transcriptome data used in our research....

Additional file 11: of Genome-wide characterization and phylogenetic analysis of GSK gene family in three species of cotton: evidence for a role of some GSKs in fiber development and responses to stress

Lingling Wang (66269)
Zhaoen Yang (659918)
Bin Zhang (64682)
Daoqian Yu (6050774)
Ji Liu (110659)
Qian Gong (3710617)
Ghulam Qanmber (6050777)
Yi Li (1144)
Lili Lu (408133)
Yongjun Lin (161394)
Zuoren Yang (518304)
Fuguang Li (229466)

December 2018

Table S5.1 GO annotations of the co-expressed genes involved in the weighted gene co-expression sub-...

Additional file 9: of Genome-wide characterization and phylogenetic analysis of GSK gene family in three species of cotton: evidence for a role of some GSKs in fiber development and responses to stress

Lingling Wang (66269)
Zhaoen Yang (659918)
Bin Zhang (64682)
Daoqian Yu (6050774)
Ji Liu (110659)
Qian Gong (3710617)
Ghulam Qanmber (6050777)
Yi Li (1144)
Lili Lu (408133)
Yongjun Lin (161394)
Zuoren Yang (518304)
Fuguang Li (229466)

December 2018

Figure S5. The GO (a) and KEGG (b) enrichment of weighted co-expressed genes of the brown module (Gh...

Additional file 2: of Genome-wide characterization and phylogenetic analysis of GSK gene family in three species of cotton: evidence for a role of some GSKs in fiber development and responses to stress

Lingling Wang (66269)
Zhaoen Yang (659918)
Bin Zhang (64682)
Daoqian Yu (6050774)
Ji Liu (110659)
Qian Gong (3710617)
Ghulam Qanmber (6050777)
Yi Li (1144)
Lili Lu (408133)
Yongjun Lin (161394)
Zuoren Yang (518304)
Fuguang Li (229466)

December 2018

Table S2. FPKM values of different tissues obtained from published transcriptome data. (XLSX 16 kb

Additional file 10: of Genome-wide characterization and phylogenetic analysis of GSK gene family in three species of cotton: evidence for a role of some GSKs in fiber development and responses to stress

Lingling Wang (66269)
Zhaoen Yang (659918)
Bin Zhang (64682)
Daoqian Yu (6050774)
Ji Liu (110659)
Qian Gong (3710617)
Ghulam Qanmber (6050777)
Yi Li (1144)
Lili Lu (408133)
Yongjun Lin (161394)
Zuoren Yang (518304)
Fuguang Li (229466)

December 2018

Figure S6. The weighted gene co-expression analysis sub-network of GhSK32 and GhSK34 were visualized...

Lingling Wang (66269)
Zhaoen Yang (659918)
Bin Zhang (64682)
Daoqian Yu (6050774)
Ji Liu (110659)
Qian Gong (3710617)
Ghulam Qanmber (6050777)
Yi Li (1144)
Lili Lu (408133)
Yongjun Lin (161394)
Zuoren Yang (518304)
Fuguang Li (229466)

December 2018

Figure S3. Motif logos of 16 conserved motifs found in cotton GSK proteins. (PDF 817 kb

Additional file 3: of Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study

Xiongming Du (561554)
Shouye Liu (5384336)
Junling Sun (561545)
Gengyun Zhang (4118122)
Yinhua Jia (561544)
Zhaoe Pan (561546)
Haitao Xiang (3549005)
Shoupu He (561548)
Qiuju Xia (3549008)
Songhua Xiao (322277)
Weijun Shi (561549)
Zhiwu Quan (3548999)
Jianguang Liu (561553)
Jun Ma (9393)
Baoyin Pang (561551)
Liru Wang (561552)
Gaofei Sun (662300)
Wenfang Gong (193513)
Johnie Jenkins (3407099)
Xiangyang Lou (5384339)
Jun Zhu (84054)
Haiming Xu (178700)

June 2018

Table S3. The other genome-wide significant QTSs associated with five fatty acids. (DOC 185 kb

Additional file 16: of A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

Md Islam (257385)
Gregory Thyssen (531000)
Johnie Jenkins (3407099)
Linghe Zeng (3407102)
Christopher Delhom (3407096)
Jack McCarty (3407090)
Dewayne Deng (3407105)
Doug Hinchliffe (3407108)
Don Jones (3407093)
David Fang (3399707)

November 2016

Title: RT-qPCR gene expression analyses of selected genes related to cell wall activity during fiber...

Additional file 9: of Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture

Daoqian Yu (6050774)
Ghulam Qanmber (6050777)
Lili Lu (408133)
Lingling Wang (66269)
Jie Li (15030)
Zhaoen Yang (659918)
Zhao Liu (582169)
Yi Li (1144)
Quanjia Chen (3320355)
Venugopal Mendu (184563)
Fuguang Li (229466)
Zuoren Yang (518304)

December 2018

Table S5. The original RNA-seq data for GhGH3 expression pattern analysis. (XLSX 20âkb

Additional file 7: of Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture

Daoqian Yu (6050774)
Ghulam Qanmber (6050777)
Lili Lu (408133)
Lingling Wang (66269)
Jie Li (15030)
Zhaoen Yang (659918)
Zhao Liu (582169)
Yi Li (1144)
Quanjia Chen (3320355)
Venugopal Mendu (184563)
Fuguang Li (229466)
Zuoren Yang (518304)

December 2018

Figure S4. Chromosomal distribution of subfamily II GhGH3 genes together with putative subfamily I G...

Additional file 2: of Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture

Daoqian Yu (6050774)
Ghulam Qanmber (6050777)
Lili Lu (408133)
Lingling Wang (66269)
Jie Li (15030)
Zhaoen Yang (659918)
Zhao Liu (582169)
Yi Li (1144)
Quanjia Chen (3320355)
Venugopal Mendu (184563)
Fuguang Li (229466)
Zuoren Yang (518304)

December 2018

Figure S1. Three NJ phylogenetic trees for identification of GH3 genes in cotton. GH3s in G. arboreu...

Lingling Wang (66269)
Zhaoen Yang (659918)
Bin Zhang (64682)
Daoqian Yu (6050774)
Ji Liu (110659)
Qian Gong (3710617)
Ghulam Qanmber (6050777)
Yi Li (1144)
Lili Lu (408133)
Yongjun Lin (161394)
Zuoren Yang (518304)
Fuguang Li (229466)

December 2018

Table S3. Orthologous GSK genes identified in G. hirsutum, G. arboreum and G. raimondii. Orthologous...

Additional file 3: of Comparative fiber property and transcriptome analyses reveal key genes potentially related to high fiber strength in cotton (Gossypium hirsutum L.) line MD52ne

Md Islam (257385)
David Fang (3399707)
Gregory Thyssen (531000)
Chris Delhom (2290288)
Yongliang Liu (561185)
Hee Kim (2025640)

February 2016

Differentially expressed genes at 20 DPA between MD52ne and MD90ne. This table contains 1080 allotet...

Lingling Wang (66269)
Zhaoen Yang (659918)
Bin Zhang (64682)
Daoqian Yu (6050774)
Ji Liu (110659)
Qian Gong (3710617)
Ghulam Qanmber (6050777)
Yi Li (1144)
Lili Lu (408133)
Yongjun Lin (161394)
Zuoren Yang (518304)
Fuguang Li (229466)

December 2018

Figure S2. Phylogenetic analysis of GSK3 proteins in Arabidopsis, rice, and species of cotton. 10 At...

Lingling Wang (66269)
Zhaoen Yang (659918)
Bin Zhang (64682)
Daoqian Yu (6050774)
Ji Liu (110659)
Qian Gong (3710617)
Ghulam Qanmber (6050777)
Yi Li (1144)
Lili Lu (408133)
Yongjun Lin (161394)
Zuoren Yang (518304)
Fuguang Li (229466)

December 2018

Table S1.1 Gene accession numbers and sample information of transcriptome data used in our research....

Lingling Wang (66269)
Zhaoen Yang (659918)
Bin Zhang (64682)
Daoqian Yu (6050774)
Ji Liu (110659)
Qian Gong (3710617)
Ghulam Qanmber (6050777)
Yi Li (1144)
Lili Lu (408133)
Yongjun Lin (161394)
Zuoren Yang (518304)
Fuguang Li (229466)

December 2018

Table S5.1 GO annotations of the co-expressed genes involved in the weighted gene co-expression sub-...

Lingling Wang (66269)
Zhaoen Yang (659918)
Bin Zhang (64682)
Daoqian Yu (6050774)
Ji Liu (110659)
Qian Gong (3710617)
Ghulam Qanmber (6050777)
Yi Li (1144)
Lili Lu (408133)
Yongjun Lin (161394)
Zuoren Yang (518304)
Fuguang Li (229466)

December 2018

Figure S5. The GO (a) and KEGG (b) enrichment of weighted co-expressed genes of the brown module (Gh...

Lingling Wang (66269)
Zhaoen Yang (659918)
Bin Zhang (64682)
Daoqian Yu (6050774)
Ji Liu (110659)
Qian Gong (3710617)
Ghulam Qanmber (6050777)
Yi Li (1144)
Lili Lu (408133)
Yongjun Lin (161394)
Zuoren Yang (518304)
Fuguang Li (229466)

December 2018

Table S2. FPKM values of different tissues obtained from published transcriptome data. (XLSX 16 kb

Lingling Wang (66269)
Zhaoen Yang (659918)
Bin Zhang (64682)
Daoqian Yu (6050774)
Ji Liu (110659)
Qian Gong (3710617)
Ghulam Qanmber (6050777)
Yi Li (1144)
Lili Lu (408133)
Yongjun Lin (161394)
Zuoren Yang (518304)
Fuguang Li (229466)

December 2018

Figure S6. The weighted gene co-expression analysis sub-network of GhSK32 and GhSK34 were visualized...

Lingling Wang (66269)
Zhaoen Yang (659918)
Bin Zhang (64682)
Daoqian Yu (6050774)
Ji Liu (110659)
Qian Gong (3710617)
Ghulam Qanmber (6050777)
Yi Li (1144)
Lili Lu (408133)
Yongjun Lin (161394)
Zuoren Yang (518304)
Fuguang Li (229466)

December 2018

Figure S3. Motif logos of 16 conserved motifs found in cotton GSK proteins. (PDF 817 kb

Additional file 3: of Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study

Xiongming Du (561554)
Shouye Liu (5384336)
Junling Sun (561545)
Gengyun Zhang (4118122)
Yinhua Jia (561544)
Zhaoe Pan (561546)
Haitao Xiang (3549005)
Shoupu He (561548)
Qiuju Xia (3549008)
Songhua Xiao (322277)
Weijun Shi (561549)
Zhiwu Quan (3548999)
Jianguang Liu (561553)
Jun Ma (9393)
Baoyin Pang (561551)
Liru Wang (561552)
Gaofei Sun (662300)
Wenfang Gong (193513)
Johnie Jenkins (3407099)
Xiangyang Lou (5384339)
Jun Zhu (84054)
Haiming Xu (178700)

June 2018

Table S3. The other genome-wide significant QTSs associated with five fatty acids. (DOC 185 kb

Additional file 16: of A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

Md Islam (257385)
Gregory Thyssen (531000)
Johnie Jenkins (3407099)
Linghe Zeng (3407102)
Christopher Delhom (3407096)
Jack McCarty (3407090)
Dewayne Deng (3407105)
Doug Hinchliffe (3407108)
Don Jones (3407093)
David Fang (3399707)

November 2016

Title: RT-qPCR gene expression analyses of selected genes related to cell wall activity during fiber...

Additional file 4: of Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture

Abstract

Extracted data

Additional file 4: of Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture

Abstract

Extracted data

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