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)

Open link

Publication date

December 2018

DOI

10.6084/m9.figshare.7422119.v1

Abstract

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

Extracted data

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Data Protection

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)

Open link

Publication date

December 2018

DOI

10.6084/m9.figshare.7422119.v1

Abstract

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

Extracted data

Lingling Wang
Zhaoen Yang
Bin Zhang
Daoqian Yu
Ji Liu
Qian Gong
Ghulam Qanmber
Yi Li
Lili Lu
Yongjun Lin
Zuoren Yang
Fuguang Li

December 2018

Abstract Background The glycogen synthase kinase 3/shaggy kinase (GSK3) is a serine/threonine kinase...

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 5: of A genome-wide analysis of SWEET gene family in cotton and their expressions under different stresses

Lanjie ZHAO (5590889)
Jinbo YAO (5590892)
Wei CHEN (2902277)
Yan LI (5590895)
Youjun LĂ (5590898)
Yan GUO (5590901)
Junyi WANG (5590904)
Li YUAN (5590907)
Ziyang LIU (5590910)
Yongshan ZHANG (5590913)

August 2018

Table S4. The paralogous pairs of SWEET genes in G. arboreum, G. raimondii, G. hirsutum, and G. barb...

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 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...

Additional file 5: 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 S3. Motif logos of 16 conserved motifs found in cotton GSK proteins. (PDF 817 kb

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 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 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 12: 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 S7. 20 GhSKs expression patterns in response to BL treatment were analyzed by qRT-PCR. The re...

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 3: 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 S1. Multiple sequence alignments of the kinase domains of Arabidopsis, rice, and cotton. Amin...

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 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 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)

December 2018

Table S3. Comparison of characteristics of GH3s identified in two genome assemblies of G. hirsutum. ...

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
Zhaoen Yang
Bin Zhang
Daoqian Yu
Ji Liu
Qian Gong
Ghulam Qanmber
Yi Li
Lili Lu
Yongjun Lin
Zuoren Yang
Fuguang Li

December 2018

Abstract Background The glycogen synthase kinase 3/shaggy kinase (GSK3) is a serine/threonine kinase...

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 5: of A genome-wide analysis of SWEET gene family in cotton and their expressions under different stresses

Lanjie ZHAO (5590889)
Jinbo YAO (5590892)
Wei CHEN (2902277)
Yan LI (5590895)
Youjun LĂ (5590898)
Yan GUO (5590901)
Junyi WANG (5590904)
Li YUAN (5590907)
Ziyang LIU (5590910)
Yongshan ZHANG (5590913)

August 2018

Table S4. The paralogous pairs of SWEET genes in G. arboreum, G. raimondii, G. hirsutum, and G. barb...

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

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

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

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 S7. 20 GhSKs expression patterns in response to BL treatment were analyzed by qRT-PCR. The re...

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

Figure S1. Multiple sequence alignments of the kinase domains of Arabidopsis, rice, and cotton. Amin...

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 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 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)

December 2018

Table S3. Comparison of characteristics of GH3s identified in two genome assemblies of G. hirsutum. ...

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
Zhaoen Yang
Bin Zhang
Daoqian Yu
Ji Liu
Qian Gong
Ghulam Qanmber
Yi Li
Lili Lu
Yongjun Lin
Zuoren Yang
Fuguang Li

December 2018

Abstract Background The glycogen synthase kinase 3/shaggy kinase (GSK3) is a serine/threonine kinase...

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 5: of A genome-wide analysis of SWEET gene family in cotton and their expressions under different stresses

Lanjie ZHAO (5590889)
Jinbo YAO (5590892)
Wei CHEN (2902277)
Yan LI (5590895)
Youjun LĂ (5590898)
Yan GUO (5590901)
Junyi WANG (5590904)
Li YUAN (5590907)
Ziyang LIU (5590910)
Yongshan ZHANG (5590913)

August 2018

Table S4. The paralogous pairs of SWEET genes in G. arboreum, G. raimondii, G. hirsutum, and G. barb...

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

Abstract

Extracted data

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

Abstract

Extracted data

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