publication . Article . 2016

Evolutionary Conservation and Divergence of Gene Coexpression Networks in Gossypium (Cotton) Seeds

Guanjing Hu; Ran Hovav; Corrinne E. Grover; Adi Faigenboim-Doron; Noa Kadmon; Justin T. Page; Joshua A. Udall; Jonathan F. Wendel;
Open Access English
  • Published: 01 Dec 2016 Journal: Genome Biology and Evolution, volume 8, issue 12, pages 3,765-3,783 (eissn: 1759-6653, Copyright policy)
  • Publisher: Oxford University Press
Abstract
The cotton genus (Gossypium) provides a superior system for the study of diversification, genome evolution, polyploidization, and human-mediated selection. To gain insight into phenotypic diversification in cotton seeds, we conducted coexpression network analysis of developing seeds from diploid and allopolyploid cotton species and explored network properties. Key network modules and functional associations were identified related to seed oil content and seed weight. We compared species-specific networks to reveal topological changes, including rewired edges and differentially coexpressed genes, associated with speciation, polyploidy, and cotton domestication. N...
Subjects
free text keywords: Research Article, Gossypium, oil seed, polyploid evolution, domestication, gene coexpression network, Genetics, Ecology, Evolution, Behavior and Systematics, Gene coexpression, biology.organism_classification, biology, Conserved sequence, Divergence
68 references, page 1 of 5

Alexa A Rahnenfuhrer J.2010. topGO: enrichment analysis for gene ontology. R package version 2.16.0.

Angelovici R Galili G Fernie AR Fait A.2010 Seed desiccation: a bridge between maturation and germination. Trends Plant Sci.15(4):211–218.20138563 [OpenAIRE] [PubMed]

Ashokkumar K Ravikesavan R.2013 Genetic variation and heterotic effects for seed oil, seed protein and yield attributing traits in upland cotton (Gossypium hirsutum L.). Afr J Biotechnol. 12(33):5183–5191. [OpenAIRE]

Basnet RK, 2013 Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes. BMC Genomics 14:840.24289287 [OpenAIRE] [PubMed]

Baud S Boutin J-P Miquel M Lepiniec L Rochat C.2002 An integrated overview of seed development in Arabidopsis thaliana ecotype WS. Plant Physiol Biochem.40(2):151–160.

Baud S Lepiniec L.2009 Regulation of de novo fatty acid synthesis in maturing oilseeds of Arabidopsis. Plant Physiol Biochem.47(6):448–455.19136270 [OpenAIRE] [PubMed]

Benjamini Y Hochberg Y.1995 Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 57:289–300.

Bewley JD.2006 Cotton - an oilseed In: Bewley JD Black M Halmer P, editor. The encyclopedia of seeds: science, technology and uses. London: CAB international p. 106–109.

Buggs RJ, 2014 The legacy of diploid progenitors in allopolyploid gene expression patterns. Philos Trans R Soc Lond B Biol Sci.369(1648):20130354.24958927 [OpenAIRE] [PubMed]

Cañas RA, 2015 Understanding developmental and adaptive cues in pine through metabolite profiling and co-expression network analysis. J Exp Bot. 66(11):3113–3127.25873654 [OpenAIRE] [PubMed]

Chia TYP Pike MJ Rawsthorne S.2005 Storage oil breakdown during embryo development of Brassica napus (L.). J Exp Bot. 56(415):1285–1296.15767324 [PubMed]

Dowd MK.2015 Seed In: Fang DD Percy RG, editor. Cotton. Madison, WI: American Society of Agronomy, Inc., Crop Science Society of America, Inc., and Soil Science Society of America, Inc p. 745–782.

Doyle JJ, 2008 Evolutionary genetics of genome merger and doubling in plants. Annu Rev Genet.42:443–461.18983261 [PubMed]

Emerson JJ Li WH.2010 The genetic basis of evolutionary change in gene expression levels. Philos Trans R Soc Lond B Biol Sci.365(1552):2581–2590.20643748 [OpenAIRE] [PubMed]

Fukushima A.2013 DiffCorr: an R package to analyze and visualize differential correlations in biological networks. Gene 518(1):209.23246976 [OpenAIRE] [PubMed]

68 references, page 1 of 5
Abstract
The cotton genus (Gossypium) provides a superior system for the study of diversification, genome evolution, polyploidization, and human-mediated selection. To gain insight into phenotypic diversification in cotton seeds, we conducted coexpression network analysis of developing seeds from diploid and allopolyploid cotton species and explored network properties. Key network modules and functional associations were identified related to seed oil content and seed weight. We compared species-specific networks to reveal topological changes, including rewired edges and differentially coexpressed genes, associated with speciation, polyploidy, and cotton domestication. N...
Subjects
free text keywords: Research Article, Gossypium, oil seed, polyploid evolution, domestication, gene coexpression network, Genetics, Ecology, Evolution, Behavior and Systematics, Gene coexpression, biology.organism_classification, biology, Conserved sequence, Divergence
68 references, page 1 of 5

Alexa A Rahnenfuhrer J.2010. topGO: enrichment analysis for gene ontology. R package version 2.16.0.

Angelovici R Galili G Fernie AR Fait A.2010 Seed desiccation: a bridge between maturation and germination. Trends Plant Sci.15(4):211–218.20138563 [OpenAIRE] [PubMed]

Ashokkumar K Ravikesavan R.2013 Genetic variation and heterotic effects for seed oil, seed protein and yield attributing traits in upland cotton (Gossypium hirsutum L.). Afr J Biotechnol. 12(33):5183–5191. [OpenAIRE]

Basnet RK, 2013 Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes. BMC Genomics 14:840.24289287 [OpenAIRE] [PubMed]

Baud S Boutin J-P Miquel M Lepiniec L Rochat C.2002 An integrated overview of seed development in Arabidopsis thaliana ecotype WS. Plant Physiol Biochem.40(2):151–160.

Baud S Lepiniec L.2009 Regulation of de novo fatty acid synthesis in maturing oilseeds of Arabidopsis. Plant Physiol Biochem.47(6):448–455.19136270 [OpenAIRE] [PubMed]

Benjamini Y Hochberg Y.1995 Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 57:289–300.

Bewley JD.2006 Cotton - an oilseed In: Bewley JD Black M Halmer P, editor. The encyclopedia of seeds: science, technology and uses. London: CAB international p. 106–109.

Buggs RJ, 2014 The legacy of diploid progenitors in allopolyploid gene expression patterns. Philos Trans R Soc Lond B Biol Sci.369(1648):20130354.24958927 [OpenAIRE] [PubMed]

Cañas RA, 2015 Understanding developmental and adaptive cues in pine through metabolite profiling and co-expression network analysis. J Exp Bot. 66(11):3113–3127.25873654 [OpenAIRE] [PubMed]

Chia TYP Pike MJ Rawsthorne S.2005 Storage oil breakdown during embryo development of Brassica napus (L.). J Exp Bot. 56(415):1285–1296.15767324 [PubMed]

Dowd MK.2015 Seed In: Fang DD Percy RG, editor. Cotton. Madison, WI: American Society of Agronomy, Inc., Crop Science Society of America, Inc., and Soil Science Society of America, Inc p. 745–782.

Doyle JJ, 2008 Evolutionary genetics of genome merger and doubling in plants. Annu Rev Genet.42:443–461.18983261 [PubMed]

Emerson JJ Li WH.2010 The genetic basis of evolutionary change in gene expression levels. Philos Trans R Soc Lond B Biol Sci.365(1552):2581–2590.20643748 [OpenAIRE] [PubMed]

Fukushima A.2013 DiffCorr: an R package to analyze and visualize differential correlations in biological networks. Gene 518(1):209.23246976 [OpenAIRE] [PubMed]

68 references, page 1 of 5
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publication . Article . 2016

Evolutionary Conservation and Divergence of Gene Coexpression Networks in Gossypium (Cotton) Seeds

Guanjing Hu; Ran Hovav; Corrinne E. Grover; Adi Faigenboim-Doron; Noa Kadmon; Justin T. Page; Joshua A. Udall; Jonathan F. Wendel;