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

Chalcone isomerase (CHI) is a key component of phenylalanine metabolism that can produce a variety of flavonoids. However, little information and no systematic analysis of CHI genes is available for cotton. Here, we identified 33 CHI genes in the complete genome sequences of four cotton species (Gossypium arboretum L., Gossypium raimondii L., Gossypium hirsutum L., and Gossypium barbadense L.). Cotton CHI proteins were classified into two main groups, and whole-genome/segmental and dispersed duplication events were important in CHI gene family expansion. qRT-PCR and semiquantitative RT-PCR results suggest that CHI genes exhibit temporal and spatial variation and respond to infection with Fusarium wilt race 7. A preliminary model of CHI gene involvement in cotton evolution was established. Pairwise comparison revealed that seven CHI genes showed higher expression in cultivar 06-146 than in cultivar Xinhai 14. Overall, this whole-genome identification unlocks a new approach to the comprehensive functional analysis of the CHI gene family, which may be involved in adaptation to plant pathogen stress.

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Genome-wide identification and characteristic analysis of the downstream melatonin metabolism gene GhM2H in Gossypium hirsutum L.

Biological Research ◽

10.1186/s40659-021-00358-y ◽

2021 ◽

Vol 54 (1) ◽

Author(s):

Yuexin Zhang ◽

Jing Wang ◽

Xiugui Chen ◽

Xuke Lu ◽

Delong Wang ◽

...

Keyword(s):

Abiotic Stress ◽

Gossypium Hirsutum ◽

Gene Family ◽

Structural Characteristics ◽

Whole Genome Sequence ◽

Whole Genome ◽

Characteristic Analysis ◽

Systematic Analysis ◽

Biological Stress ◽

Metabolism Gene

Abstract Background Melatonin 2-hydroxylase (M2H) is the first enzyme in the catabolism pathway of melatonin, which catalyzes the production of 2-hydroxymelatonin (2-OHM) from melatonin. The content of 2-hydroxymelatonin in plants is much higher than that of melatonin. So M2H may be a key enzyme in the metabolic pathway of melatonin. Method We conducted a systematic analysis of the M2H gene family in Gossypium hirsutum based on the whole genome sequence by integrating the structural characteristics, phylogenetic relationships, expression profile, and biological stress of the members of the Gossypium hirsutum M2H gene family. Result We identified 265 M2H genes in the whole genome of Gossypium hirsutum, which were divided into 7 clades (clades I-VII) according to phylogenetic analysis. Most M2H members in each group had similar motif composition and gene structure characteristics. More than half of GhM2H members contain ABA-responsive elements and MeJA-responsive elements. Under different stress conditions, the expression levels of the gene changed, indicating that GhM2H members were involved in the regulation of abiotic stress. Some genes in the GhM2H family were involved in regulating melatonin levels in cotton under salt stress, and some genes were regulated by exogenous melatonin. Conclusion This study is helpful to explore the function of GhM2H, the downstream metabolism gene of melatonin in cotton, and lay the foundation for better exploring the molecular mechanism of melatonin improving cotton's response to abiotic stress.

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Genome-Wide Analysis of LysM-Containing Gene Family in Wheat: Structural and Phylogenetic Analysis during Development and Defense

Genes ◽

10.3390/genes12010031 ◽

2020 ◽

Vol 12 (1) ◽

pp. 31

Author(s):

Zheng Chen ◽

Zijie Shen ◽

Da Zhao ◽

Lei Xu ◽

Lijun Zhang ◽

...

Keyword(s):

Gene Duplication ◽

Gene Family ◽

Plant Pathogens ◽

Plant Immunity ◽

Family Members ◽

Distribution Analysis ◽

Systematic Analysis ◽

Defense Proteins ◽

Duplication Events ◽

Bacteria And Fungi

The lysin motif (LysM) family comprise a number of defense proteins that play important roles in plant immunity. The LysM family includes LysM-containing receptor-like proteins (LYP) and LysM-containing receptor-like kinase (LYK). LysM generally recognizes the chitin and peptidoglycan derived from bacteria and fungi. Approximately 4000 proteins with the lysin motif (Pfam PF01476) are found in prokaryotes and eukaryotes. Our study identified 57 LysM genes and 60 LysM proteins in wheat and renamed these genes and proteins based on chromosome distribution. According to the phylogenetic and gene structure of intron–exon distribution analysis, the 60 LysM proteins were classified into seven groups. Gene duplication events had occurred among the LysM family members during the evolution process, resulting in an increase in the LysM gene family. Synteny analysis suggested the characteristics of evolution of the LysM family in wheat and other species. Systematic analysis of these species provided a foundation of LysM genes in crop defense. A comprehensive analysis of the expression and cis-elements of LysM gene family members suggested that they play an essential role in defending against plant pathogens. The present study provides an overview of the LysM family in the wheat genome as well as information on systematic, phylogenetic, gene duplication, and intron–exon distribution analyses that will be helpful for future functional analysis of this important protein family, especially in Gramineae species.

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Genome-Wide Analysis of the COBRA-Like Gene Family Supports Gene Expansion through Whole-Genome Duplication in Soybean (Glycine max)

Plants ◽

10.3390/plants10010167 ◽

2021 ◽

Vol 10 (1) ◽

pp. 167

Author(s):

Sara Sangi ◽

Paula M. Araújo ◽

Fernanda S. Coelho ◽

Rajesh K. Gazara ◽

Fabrício Almeida-Silva ◽

...

Keyword(s):

Cell Wall ◽

Gene Family ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Expression Patterns ◽

Whole Genome ◽

Comprehensive Overview ◽

Genome Wide ◽

Duplication Events ◽

Cell Wall Expansion

The COBRA-like (COBL) gene family has been associated with the regulation of cell wall expansion and cellulose deposition. COBL mutants result in reduced levels and disorganized deposition of cellulose causing defects in the cell wall and inhibiting plant development. In this study, we report the identification of 24 COBL genes (GmCOBL) in the soybean genome. Phylogenetic analysis revealed that the COBL proteins are divided into two groups, which differ by about 170 amino acids in the N-terminal region. The GmCOBL genes were heterogeneously distributed in 14 of the 20 soybean chromosomes. This study showed that segmental duplication has contributed significantly to the expansion of the COBL family in soybean during all Glycine-specific whole-genome duplication events. The expression profile revealed that the expression of the paralogous genes is highly variable between organs and tissues of the plant. Only 20% of the paralogous gene pairs showed similar expression patterns. The high expression levels of some GmCOBLs suggest they are likely essential for regulating cell expansion during the whole soybean life cycle. Our comprehensive overview of the COBL gene family in soybean provides useful information for further understanding the evolution and diversification of COBL genes in soybean.

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Genome-Wide Identification and Evolutionary Analysis of AOMT Gene Family in Pomegranate (Punica granatum)

Agronomy ◽

10.3390/agronomy11020318 ◽

2021 ◽

Vol 11 (2) ◽

pp. 318

Author(s):

Xinhui Zhang ◽

Weicheng Yuan ◽

Yujie Zhao ◽

Yuan Ren ◽

Xueqing Zhao ◽

...

Keyword(s):

Gene Family ◽

Gene Evolution ◽

Punica Granatum ◽

Gene Family Evolution ◽

Raw Material ◽

Whole Genome ◽

Evolutionary Analysis ◽

New Genes ◽

Genome Wide ◽

Duplication Events

Gene duplication is the major resource with which to generate new genes, which provide raw material for novel functions evolution. Thus, to elucidate the gene family evolution after duplication events is of vital importance. Anthocyanin O-methyltransferases (AOMTs) have been recognized as being capable of anthocyanin methylation, which increases anthocyanin diversity and stability and improves the protection of plants from environmental stress. Meanwhile, no detailed identification or genome-wide analysis of the AOMT gene family members in pomegranate (Punicagranatum) have been reported. Three published pomegranate genome sequences offer substantial resources with which to explore gene evolution based on the whole genome. Altogether, 58 identified OMTs from pomegranate and five other species were divided into the AOMT group and the OMT group, according to their phylogenetic tree and AOMTs derived from OMTs. AOMTs in the same subclade have a similar gene structure and protein conserved motifs. The PgAOMT family evolved and expanded primarily via whole-genome duplication (WGD) and tandem duplication. PgAOMTs expression pattern in peel and aril development by qRT-PCR verification indicated that PgAOMTs had tissue-specific patterns. The main fates of AOMTs were neo- or non-functionalization after duplication events. High expression genes of PgOMT04 and PgOMT09 were speculated to contribute to “Taishanhong” pomegranate’s bright red peel color. Finally, we integrated the above analysis in order to infer the evolutionary scenario of AOMT family.

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Expansion and Molecular Characterization of AP2/ERF Gene Family in Wheat (Triticum aestivum L.)

Frontiers in Genetics ◽

10.3389/fgene.2021.632155 ◽

2021 ◽

Vol 12 ◽

Author(s):

Muhammad Waheed Riaz ◽

Jie Lu ◽

Liaqat Shah ◽

Liu Yang ◽

Can Chen ◽

...

Keyword(s):

Triticum Aestivum ◽

Gene Family ◽

Expression Profiles ◽

Functional Divergence ◽

Triticum Aestivum L ◽

Vital Role ◽

Systematic Analysis ◽

Wheat Seedlings ◽

A Genome ◽

Duplication Events

The AP2/ERF is a large protein family of transcription factors, playing an important role in signal transduction, plant growth, development, and response to various stresses. AP2/ERF super-family is identified and functionalized in a different plant but no comprehensive and systematic analysis in wheat (Triticum aestivum L.) has been reported. However, a genome-wide and functional analysis was performed and identified 322 TaAP2/ERF putative genes from the wheat genome. According to the phylogenetic and structural analysis, TaAP2/ERF genes were divided into 12 subfamilies (Ia, Ib, Ic, IIa, IIb, IIc, IIIa, IIIb, IIIc, IVa, IVb, and IVc). Furthermore, conserved motifs and introns/exons analysis revealed may lead to functional divergence within clades. Cis-Acting analysis indicated that many elements were involved in stress-related and plant development. Chromosomal location showed that 320 AP2/ERF genes were distributed among 21 chromosomes and 2 genes were present in a scaffold. Interspecies microsynteny analysis revealed that maximum orthologous between Arabidopsis, rice followed by wheat. Segment duplication events have contributed to the expansion of the AP2/ERF family and made this family larger than rice and Arabidopsis. Additionally, AP2/ERF genes were differentially expressed in wheat seedlings under the stress treatments of heat, salt, and drought, and expression profiles were verified by qRT-PCR. Remarkably, the RNA-seq data exposed that AP2/ERF gene family might play a vital role in stress-related. Taken together, our findings provided useful and helpful information to understand the molecular mechanism and evolution of the AP2/ERF gene family in wheat.

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Whole-Genome Sequence Characterization of Primary Auxin-Responsive Aux/IAA Gene Family in Sorghum (Sorghum bicolor L.)

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2010.00688 ◽

2010 ◽

Vol 36 (4) ◽

pp. 688-694

Author(s):

Yi-Jun WANG ◽

Yan-Ping LÜ ◽

Qin XIE ◽

De-Xiang DENG ◽

Yun-Long BIAN

Keyword(s):

Sorghum Bicolor ◽

Gene Family ◽

Genome Sequence ◽

Whole Genome Sequence ◽

Whole Genome ◽

Sequence Characterization ◽

I Gene

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Genome-wide identification and expression analysis of the Brassica oleracea L. chitin-binding genes and response to pathogens infections

Planta ◽

10.1007/s00425-021-03596-2 ◽

2021 ◽

Vol 253 (4) ◽

Author(s):

Mingzhao Zhu ◽

Shujin Lu ◽

Mu Zhuang ◽

Yangyong Zhang ◽

Honghao Lv ◽

...

Keyword(s):

Powdery Mildew ◽

Gene Family ◽

Brassica Oleracea ◽

Downy Mildew ◽

Fusarium Wilt ◽

Black Spot ◽

Housekeeping Genes ◽

Chitinase Gene ◽

Genome Wide ◽

A Genome

Abstract Main conclusion Chitinase family genes were involved in the response of Brassica oleracea to Fusarium wilt, powdery mildew, black spot and downy mildew. Abstract Abstract Chitinase, a category of pathogenesis-related proteins, is believed to play an important role in defending against external stress in plants. However, a comprehensive analysis of the chitin-binding gene family has not been reported to date in cabbage (Brassica oleracea L.), especially regarding the roles that chitinases play in response to various diseases. In this study, a total of 20 chitinase genes were identified using a genome-wide search method. Phylogenetic analysis was employed to classify these genes into two groups. The genes were distributed unevenly across six chromosomes in cabbage, and all of them contained few introns (≤ 2). The results of collinear analysis showed that the cabbage genome contained 1–5 copies of each chitinase gene (excluding Bol035470) identified in Arabidopsis. The heatmap of the chitinase gene family showed that these genes were expressed in various tissues and organs. Two genes (Bol023322 and Bol041024) were relatively highly expressed in all of the investigated tissues under normal conditions, exhibiting the expression characteristics of housekeeping genes. In addition, under four different stresses, namely, Fusarium wilt, powdery mildew, black spot and downy mildew, we detected 9, 5, 8 and 8 genes with different expression levels in different treatments, respectively. Our results may help to elucidate the roles played by chitinases in the responses of host plants to various diseases.

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Molecular Phylogenetic Analysis of the AIG Family in Vertebrates

Genes ◽

10.3390/genes12081190 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1190

Author(s):

Yuqi Huang ◽

Minghao Sun ◽

Lenan Zhuang ◽

Jin He

Keyword(s):

Phylogenetic Analysis ◽

Gene Family ◽

Functional Characterization ◽

Vertebrate Evolution ◽

Molecular Phylogenetic Analysis ◽

Whole Genome Duplications ◽

Genome Duplications ◽

Molecular Phylogenetic ◽

Duplication Events ◽

Inducible Genes

Androgen-inducible genes (AIGs), which can be regulated by androgen level, constitute a group of genes characterized by the presence of the AIG/FAR-17a domain in its protein sequence. Previous studies on AIGs demonstrated that one member of the gene family, AIG1, is involved in many biological processes in cancer cell lines and that ADTRP is associated with cardiovascular diseases. It has been shown that the numbers of AIG paralogs in humans, mice, and zebrafish are 2, 2, and 3, respectively, indicating possible gene duplication events during vertebrate evolution. Therefore, classifying subgroups of AIGs and identifying the homologs of each AIG member are important to characterize this novel gene family further. In this study, vertebrate AIGs were phylogenetically grouped into three major clades, ADTRP, AIG1, and AIG-L, with AIG-L also evident in an outgroup consisting of invertebrsate species. In this case, AIG-L, as the ancestral AIG, gave rise to ADTRP and AIG1 after two rounds of whole-genome duplications during vertebrate evolution. Then, the AIG family, which was exposed to purifying forces during evolution, lost or gained some of its members in some species. For example, in eutherians, Neognathae, and Percomorphaceae, AIG-L was lost; in contrast, Salmonidae and Cyprinidae acquired additional AIG copies. In conclusion, this study provides a comprehensive molecular phylogenetic analysis of vertebrate AIGs, which can be employed for future functional characterization of AIGs.

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Genome-wide identification and expression analysis of the GhIQD gene family in upland cotton (Gossypium hirsutum L.)

Journal of Cotton Research ◽

10.1186/s42397-021-00079-3 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Lingling DOU ◽

Limin LV ◽

Yangyang KANG ◽

Ruijie TIAN ◽

Deqing HUANG ◽

...

Keyword(s):

Gossypium Hirsutum ◽

Gene Family ◽

Segmental Duplication ◽

Gene Expression Pattern ◽

Cell Development ◽

Fiber Cell ◽

Fiber Cells ◽

Genome Wide ◽

Duplication Events ◽

Signaling Receptors

Abstract Background Calmodulin (CaM) is one of the most important Ca2+ signaling receptors because it regulates diverse physiological and biochemical reactions in plants. CaM functions by interacting with CaM-binding proteins (CaMBPs) to modulate Ca2+ signaling. IQ domain (IQD) proteins are plant-specific CaMBPs that bind to CaM by their specific CaM binding sites. Results In this study, we identified 102 GhIQD genes in the Gossypium hirsutum L. genome. The GhIQD gene family was classified into four clusters (I, II, III, and IV), and we then mapped the GhIQD genes to the G. hirsutum L. chromosomes. Moreover, we found that 100 of the 102 GhIQD genes resulted from segmental duplication events, indicating that segmental duplication is the main force driving GhIQD gene expansion. Gene expression pattern analysis showed that a total of 89 GhIQD genes expressed in the elongation stage and second cell wall biosynthesis stage of the fiber cells, suggesting that GhIQD genes may contribute to fiber cell development in cotton. In addition, we found that 20 selected GhIQD genes were highly expressed in various tissues. Exogenous application of MeJA significantly enhanced the expression levels of GhIQD genes. Conclusions Our study shows that GhIQD genes are involved in fiber cell development in cotton and are also widely induced by MeJA. Thw results provide bases to systematically characterize the evolution and biological functions of GhIQD genes, as well as clues to breed better cotton varieties in the future.

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