The Chalcone Isomerase Family in Cotton: Whole-Genome Bioinformatic and Expression Analyses of the Gossypium barbadense L. Response to Fusarium Wilt Infection

Zu, Qianli; Qu, Yanying; Zheng, Kai; Chen, Qin; Chen, Quanjia

doi:10.3390/genes10121006

Cited by 14 publications

(5 citation statements)

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“…In seven gene candidates encoding the OsCHIs gene family, OsCHI3 and OsCHI5 contained three introns and OsCHI1 , OsCHI6 and OsCHI7 had four introns, which was similar to other CHI genes, as they are generally composed of three or four introns ( Figure 2 ). Notably, OsCHI2 and OsCHI4 had as many as nine introns, which is a rare phenomenon among gene structures but is similar to findings in cotton species [ 125 ]. Interestingly, we also found the distribution of 85 rice flavonoid-related genes on Chrs displayed a certain physical positon with bias to Chr4, Chr7, Chr9 and Chr10.…”

Section: Discussionsupporting

confidence: 69%

Genome-Wide Identification and Expression Profiles of 13 Key Structural Gene Families Involved in the Biosynthesis of Rice Flavonoid Scaffolds

Wang

Zhang

2022

Genes

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Flavonoids are a class of key polyphenolic secondary metabolites with broad functions in plants, including stress defense, growth, development and reproduction. Oryza sativa L. (rice) is a well-known model plant for monocots, with a wide range of flavonoids, but the key flavonoid biosynthesis-related genes and their molecular features in rice have not been comprehensively and systematically characterized. Here, we identified 85 key structural gene candidates associated with flavonoid biosynthesis in the rice genome. They belong to 13 families potentially encoding chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavonol synthase (FLS), leucoanthocyanidin dioxygenase (LDOX), anthocyanidin synthase (ANS), flavone synthase II (FNSII), flavanone 2-hydroxylase (F2H), flavonoid 3′-hydroxylase (F3′H), flavonoid 3′,5′-hydroxylase (F3′5′H), dihydroflavonol 4-reductase (DFR), anthocyanidin reductase (ANR) and leucoanthocyanidin reductase (LAR). Through structural features, motif analyses and phylogenetic relationships, these gene families were further grouped into five distinct lineages and were examined for conservation and divergence. Subsequently, 22 duplication events were identified out of a total of 85 genes, among which seven pairs were derived from segmental duplication events and 15 pairs were from tandem duplications, demonstrating that segmental and tandem duplication events play important roles in the expansion of key flavonoid biosynthesis-related genes in rice. Furthermore, these 85 genes showed spatial and temporal regulation in a tissue-specific manner and differentially responded to abiotic stress (including six hormones and cold and salt treatments). RNA-Seq, microarray analysis and qRT-PCR indicated that these genes might be involved in abiotic stress response, plant growth and development. Our results provide a valuable basis for further functional analysis of the genes involved in the flavonoid biosynthesis pathway in rice.

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Section: Discussionsupporting

confidence: 69%

Genome-Wide Identification and Expression Profiles of 13 Key Structural Gene Families Involved in the Biosynthesis of Rice Flavonoid Scaffolds

Wang

Zhang

2022

Genes

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“…Functional diversification after gene expansion could occur at the transcriptional level. To date, 12 differentially expressed CHIs in G. max [ 25 ], 5 tissue-specific CHIs in A. thaliana [ 15 ], 33 CHIs in cotton [ 32 ], 7 CHIs in rice [ 33 , 34 ], 30 CHIs in six Citrus species [ 35 ], 31 CHIs in liverwort and Selaginella species [ 18 ], 56 CHIs in fern species [ 26 ], and 11 CHIs in D. cambodiana [ 36 ], have been reported. These observations showed that CHIs usually have tissue-specific expression in various tissues, and often respond to various environmental stressors.…”

Section: Discussionmentioning

confidence: 99%

“…With the sequencing of plant genomes and transcriptomes, more and more plant CHI family genes have been discovered from many species, including primitive seedless plants and higher seed plants. To date, 12 CHIs in Glycine max [ 25 ], 5 CHIs in Arabidopsis thaliana [ 15 ], 33 CHIs in cotton [ 32 ], 7 CHIs in Oryza sativa [ 33 , 34 ], 30 CHIs in six Citrus species [ 35 ], 31 CHIs in liverwort and Selaginella species [ 18 ], 56 CHIs in fern species [ 26 ], and 11 CHIs in Dracaena cambodiana [ 36 ], have been identified based on their corresponding genomic or transcriptomic data. Acquisition of CHI enzymatic activity in plants during evolution is an intriguing topic, because both type III and type IV CHIs are devoid of bona fide CHI catalytic activity.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Classification and Evolutionary Analysis Reveal Diverged Patterns of Chalcone Isomerase in Plants

et al. 2022

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Flavonoids as a class of important secondary metabolites are widely present in land plants, and chalcone isomerase (CHI) is the key rate-limiting enzyme that participates in catalyzing the stereospecific isomerization of chalcones to yield their corresponding flavanones. However, the phylogenetic dynamics and functional divergence of CHI family genes during the evolutionary path of green plants remains poorly understood. Here, a total of 122 CHI genes were identified by performing a genome-wide survey of 15 representative green plants from the most ancestral basal plant chlorophyte algae to higher angiosperm plants. Phylogenetic, orthologous groups (OG) classification, and genome structure analysis showed that the CHI family genes have evolved into four distinct types (types I–IV) containing eight OGs after gene duplication, and further studies indicated type III CHIs consist of three subfamilies (FAP1, FAP2, and FAP3). The phylogeny showed FAP3 CHIs as an ancestral out-group positioned on the outer layers of the main branch, followed by type IV CHIs, which are placed in an evolutionary intermediate between FAP3 CHIs and bona fide CHIs (including type I and type II). The results imply a potential intrinsic evolutionary connection between CHIs existing in the green plants. The amino acid substitutions occurring in several residues have potentially affected the functional divergence between CHI proteins. This is supported by the analysis of transcriptional divergence and cis-acting element analysis. Evolutionary dynamics analyses revealed that the differences in the total number of CHI family genes in each plant are primarily attributed to the lineage-specific expansion by natural selective forces. The current studies provide a deeper understanding of the phylogenetic relationships and functional diversification of CHI family genes in green plants, which will guide further investigation on molecular characteristics and biological functions of CHIs.

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“…Murat et al (2012) showed that one method of the development of adaptive phenotypes in crops may be genome-wide replication (Murat et al 2012). At the same time, it may be considered that these genes encoding specific interaction products between biological and nonbiological exogenous factors have retained their corresponding structure and function after replication (Murat et al 2012;Zu et al 2019). During the process of plant evolution, the polyploidization mode will cause many repeated genes to appear in the plant genome (Otto et al 2000).…”

Section: Discussionmentioning

confidence: 99%

“…This will cause many changes in gene expression and gene organization in plant tissues (Adams et al 2007). Therefore, in the process of plant evolution, the polyploidization of plants provides the basic material for this process (Zu et al 2019). The phylogenetic analysis showed that the homologous RF genes were classified on the same branch (Fig.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and expression analysis of the 2OG-Fe(II) oxygenase gene family in upland cotton (Gossypium hirsutum L.)

Sun

Chen

et al. 2021

Physiol Mol Biol Plants

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The 2OG-Fe(II) oxygenase (RF) family of enzyme proteins can affect bulliform cells and cause leaf curling. However, there are few studies related to this family in cotton, and there has been no systematic analysis of RF genes. Here, we determined 25 RF genes in the complete genome sequence of upland cotton (Gossypium hirsutum L.) and 11 RF genes in the complete genome sequence of Arabidopsis thaliana. Cotton RF proteins can be divided into three categories. Whole genome/fragment and scattered replication events played an important role in the expansion of the RF gene family. qRT-PCR analysis results showed that RF genes respond to drought stress Pairwise comparison results showed that the expression of RF genes in Shi yuan 321 was higher than that in Kui 85–174. Overall, genome-wide identification approach was used to further analyze the related functions of the RF gene family, which may include the response to drought stress, in cotton.

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The Chalcone Isomerase Family in Cotton: Whole-Genome Bioinformatic and Expression Analyses of the Gossypium barbadense L. Response to Fusarium Wilt Infection

Cited by 14 publications

References 65 publications

Genome-Wide Identification and Expression Profiles of 13 Key Structural Gene Families Involved in the Biosynthesis of Rice Flavonoid Scaffolds

Genome-Wide Identification and Expression Profiles of 13 Key Structural Gene Families Involved in the Biosynthesis of Rice Flavonoid Scaffolds

Genome-Wide Classification and Evolutionary Analysis Reveal Diverged Patterns of Chalcone Isomerase in Plants

Genome-wide identification and expression analysis of the 2OG-Fe(II) oxygenase gene family in upland cotton (Gossypium hirsutum L.)

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