scholarly journals Genome-Wide Identification, Characterization, and Expression Analyses of P-Type ATPase Superfamily Genes in Soybean

Agronomy ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 71
Author(s):  
Bingqian Zhao ◽  
Haicheng Wu ◽  
Wenjing Xu ◽  
Wei Zhang ◽  
Xi Chen ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Root Hairs ◽  
Phosphate Starvation ◽  
Promoter Regions ◽  
Specific Expression ◽  
Relationship Analysis ◽  
Genome Wide ◽  
Wide Range ◽  
Almost All ◽  
P Type

P-type ATPases are transmembrane pumps of cations and phospholipids. They are energized by hydrolysis of ATP and play important roles in a wide range of fundamental cellular and physiological processes during plant growth and development. However, the P-type ATPase superfamily genes have not been characterized in soybean. Here, we performed genome-wide bioinformatic and expression analyses of the P-type ATPase superfamily genes in order to explore the potential functions of P-type ATPases in soybean. A total of 105 putative P-type ATPase genes were identified in the soybean genome. Phylogenetic relationship analysis of the P-type ATPase genes indicated that they can be divided into five subfamilies including P1B, P2A/B, P3A, P4 and P5. Proteins belonging to the same subfamily shared conserved domains. Forty-seven gene pairs were related to segmental duplication, which contributed to the expansion of the P-type ATPase genes during the evolution of soybean. Most of the P-type ATPase genes contained hormonal- and/or stress-related cis-elements in their promoter regions. Expression analysis by retrieving RNA-sequencing datasets suggested that almost all of the P-type ATPase genes could be detected in soybean tissues, and some genes showed tissue-specific expression patterns. Nearly half of the P-type ATPase genes were found to be significantly induced or repressed under stresses like salt, drought, cold, flooding, and/or phosphate starvation. Four genes were significantly affected by rhizobia inoculation in root hairs. The induction of two P2B-ATPase genes, GmACA1 and GmACA2, by phosphate starvation was confirmed by quantitative RT-PCR. This study provides information for understanding the evolution and biological functions of the P-type ATPase superfamily genes in soybean.

scholarly journals Genome-wide characterization and expression patterns of chitinase genes in the pigeonpea (Cajanus cajan (L.) Millsp.) genome

Plant Omics ◽  
2019 ◽  
pp. 109-119
Author(s):  
Ajay Kumar Mahato ◽  
Ajay Kumar Sharm ◽  
Nagendra Kumar Singh
Keyword(s):  
Developmental Stages ◽  
Insect Pests ◽  
Expression Patterns ◽  
Functional Domain ◽  
Specific Expression ◽  
Genome Wide ◽  
Wide Range ◽  
Version 2.0 ◽  
Chitinase Genes ◽  
Plant Chitinases

Plant chitinases are involved in defense as well as a wide range of physiological functions in plants, including germination, embryogenesis, flowering, and senescence. This study was conducted to identify and annotate the chitinase-related genes from the pigeonpea genome version 2.0, their chromosomal localization and phylogenetic relationship with chitinase genes from 13 different plant species. Here, we report the identification of 34 putative chitinase genes in the pigeonpea genome. These 34 genes encode proteins belonging to two functional domain families, and are subdivided into four classes matching four of the five chitinase classes in Arabidopsis. These chitinase genes are present in clusters on the chromosome. We investigated the expression patterns of these chitinases in 29 different tissues at five developmental stages. There was clear clustering of the chitinase genes into three groups based on their expression patterns in tissues. We identified two chitinase genes C_caj-24 and C_caj-25 that were highly expressed in all tissues as well as other chitinase genes with tissue-specific expression, which suggests that they play important roles in plant defense at specific developmental stages. This information on pigeonpea chitinases could be useful for the development of pigeonpea varieties that are resistant to insect pests and fungal diseases.

scholarly journals Genome-wide identification, characterization and expression analysis of BES1 gene family in tomato

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Deding Su ◽  
Wei Xiang ◽  
Ling Wen ◽  
Wang Lu ◽  
Yuan Shi ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Patterns ◽  
Transcriptional Repressors ◽  
Promoter Regions ◽  
Specific Expression ◽  
Genome Wide ◽  
Development Processes ◽  
Genomic Characterization ◽  
Functional Features

Abstract Background As the key regulators in BR signaling, BES1 family genes regulate thousands of target genes involved in various development processes. So far, the functions of BES1 family are poorly understood in tomato, and a comprehensive genomic and expressional analysis is worth to conduct for this family. Results Here, nine SlBES1 family members were identified in tomato and classified into five groups based on the conserved motif, gene structure and phylogenetic analysis. Synteny among tomato, Arabidopsis, pepper and rice were further analyzed to obtain insights into evolutionary characteristics. Several cis-elements related to hormone, stress and plant development were exhibited in the promoter regions of SlBES1 family genes. Subcellular localization showed seven members localized both in the nucleus and cytoplasm, implying the presence of dephosphorylated and phosphorylated form of these seven proteins, furthermore, five of them possessed transcription activation activity whereas the left two functioned as transcriptional repressors. Another two members, however, neither localized in the nucleus nor had transactivation activity. Besides, SlBES1.8 showed flower-specific expression while other members expressed ubiquitously in all organs. Moreover, SlBES1 genes exhibited variational expression in response to nine principal plant hormones. Notably, the expression levels of SlBES1 genes presented a dominant downregulated trend in response to stresses. Conclusions In this study, we systematically analyzed the genomic characterization of SlBES1 family, together with the analyses of protein functional features and expression patterns, our results lay a foundation for the functional research of SlBES1 family.

scholarly journals Catalase (CAT) Gene Family in Wheat (Triticum aestivum L.): Evolution, Expression Pattern and Function Analysis

2022 ◽  
Vol 23 (1) ◽  
pp. 542
Author(s):  
Yan Zhang ◽  
Lanjie Zheng ◽  
Liu Yun ◽  
Li Ji ◽  
Guanhui Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Function Analysis ◽  
Expression Patterns ◽  
Triticum Aestivum L ◽  
Duplication Event ◽  
Oxygen Deficit ◽  
Promoter Regions ◽  
Relationship Analysis ◽  
Living Organisms ◽  
Almost All

Catalases (CATs) are present in almost all living organisms and play important roles in plant development and response to various stresses. However, there is relatively little information on CAT genes in wheat and related Triticeae species. A few studies on CAT family genes in wheat have been reported. In this study, ten CAT proteins (TaCATs) were identified in wheat and classified into three groups based on their phylogenetic features and sequence analysis. The analysis of the structure and motif composition of the TaCAT proteins suggested that a segmental duplication event occurred in the TaCAT gene family. Collinearity relationship analysis among different species showed that there were three orthologous CAT genes in rice and in maize. By analyzing the cis-elements in the promoter regions, we speculated that TaCAT genes expression might be regulated by light, oxygen deficit, methyl jasmonate and abscisic acid, and by transcription factors such as MYB. A Gene Ontology (GO)-based analysis showed that TaCAT proteins may be related to the response to various stresses, are cytoplasm localized, and may function as antioxidant enzymes. RT-qPCR and transcriptome data analyses exhibited distinct expression patterns of TaCAT genes in different tissues and in response to various treatments. In this study, a comprehensive analysis of wheat CAT genes was performed, enriching our knowledge of CAT genes and providing a foundation for further functional analyses of this gene family in wheat.

scholarly journals Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8358 ◽  
Author(s):  
Yong Zhou ◽  
Yuan Cheng ◽  
Chunpeng Wan ◽  
Jingwen Li ◽  
Youxin Yang ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Patterns ◽  
Future Research ◽  
Promoter Regions ◽  
Syntenic Relationship ◽  
Specific Expression ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Intron Structure

The plant DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors that play vital roles in many biological processes and stress responses. In the present study, a total of 36 ClDof genes were identified in the watermelon genome, which were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the ClDof proteins could be divided into nine groups, and the members in a particular group had similar motif arrangement and exon–intron structure. Synteny analysis indicated the presence of a large number of syntenic relationship events between watermelon and cucumber. In promoter analysis, five kinds of stress-related and nine kinds of hormone-related cis-elements were identified in the promoter regions of ClDof genes. We then analyzed the expression patterns of nine selected ClDof genes in eight specific tissues by qRT-PCR, and the results showed that they have tissue-specific expression patterns. We also evaluated the expression levels of 12 selected ClDof genes under salt stress and ABA treatments using qRT-PCR. As a result, they showed differential expression under these treatments, suggesting their important roles in stress response. Taken together, our results provide a basis for future research on the biological functions of Dof genes in watermelon.

scholarly journals Genome-Wide Characterization of OFP Family Genes in Wheat (Triticum aestivum L.) Reveals That TaOPF29a-A Promotes Drought Tolerance

2020 ◽  
Vol 2020 ◽  
pp. 1-17
Author(s):  
Dezhou Wang ◽  
Zhichen Cao ◽  
Weiwei Wang ◽  
Wengen Zhu ◽  
Xiaocong Hao ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Drought Tolerance ◽  
Expression Patterns ◽  
Triticum Aestivum L ◽  
Promoter Regions ◽  
Specific Expression ◽  
Genome Wide ◽  
A Genome ◽  
Starting Point ◽  
Genetically Engineer

OVATE family proteins (OFPs) are plant-specific transcription factors that play important roles in plant development. Although common wheat (Triticum aestivum L.) is a major staple food worldwide, OFPs have not been systematically analyzed in this important crop. Here, we performed a genome-wide survey of OFP genes in wheat and identified 100 genes belonging to 34 homoeologous groups. Arabidopsis thaliana, rice (Oryza sativa), and wheat OFP genes were divided into four subgroups based on their phylogenetic relationships. Structural analysis indicated that only four TaOFPs contain introns. We mapped the TaOFP genes onto the wheat chromosomes and determined that TaOFP17 was duplicated in this crop. A survey of cis-acting elements along the promoter regions of TaOFP genes suggested that subfunctionalization of homoeologous genes might have occurred during evolution. The TaOFPs were highly expressed in wheat, with tissue- or organ-specific expression patterns. In addition, these genes were induced by various hormone and stress treatments. For instance, TaOPF29a-A was highly expressed in roots in response to drought stress. Wheat plants overexpressing TaOPF29a-A had longer roots and higher dry weights than nontransgenic plants under drought conditions, suggesting that this gene improves drought tolerance. Our findings provide a starting point for further functional analysis of this important transcription factor family and highlight the potential of using TaOPF29a-A to genetically engineer drought-tolerant crops.

Genome-wide identification, characterization and expression analysis of BES1 gene family in tomato

2021 ◽  
Author(s):  
Deding Su ◽  
Wei Xiang ◽  
Ling Wen ◽  
Wang Lu ◽  
Yuan Shi ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Patterns ◽  
Transcriptional Repressors ◽  
Promoter Regions ◽  
Specific Expression ◽  
Genome Wide ◽  
Development Processes ◽  
Genomic Characterization ◽  
Functional Features

Abstract Background: As the key regulators in BR signaling, BES1 family genes regulate thousands of target genes involved in various development processes. So far, the functions of BES1 family are poorly understood in tomato, and a comprehensive genomic and expressional analysis is worth to conduct for this family.Results: Here, nine SlBES1 family members were identified in tomato and classified into five groups based on the conserved motif, gene structure and phylogenetic analysis. Synteny among tomato, Arabidopsis, pepper and rice were further analyzed to obtain insights into evolutionary characteristics. Several cis-elements related to hormone, stress and plant development were exhibited in the promoter regions of SlBES1 family genes. Subcellular localization showed seven members localized both in the nucleus and cytoplasm, implying the presence of dephosphorylated and phosphorylated form of these seven proteins, furthermore, five of them possessed transcription activation activity whereas the left two functioned as transcriptional repressors. Another two members, however, neither localized in the nucleus nor had transactivation activity. Besides, SlBES1.8 showed flower-specific expression while other members expressed ubiquitously in all organs. Moreover, SlBES1 genes exhibited variational expression in response to nine principal plant hormones. Notably, the expression levels of SlBES1 genes presented a dominant downregulated trend in response to stresses.Conclusions: In this study, we systematically analyzed the genomic characterization of SlBES1 family, together with the analyses of protein functional features and expression patterns, our results lay a foundation for the functional research of SlBES1 family.

scholarly journals Genome-Wide Identification and Expression Analyses of CONSTANS-Like Family Genes in Cucumber (Cucumis sativus L.)

2021 ◽  
Author(s):  
Zhen Tian ◽  
Xiaodong Qin ◽  
Hui Wang ◽  
Ji Li ◽  
Jinfeng Chen
Keyword(s):  
Floral Induction ◽  
Structural Characteristics ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Biological Functions ◽  
Promoter Regions ◽  
Cucumis Sativus L ◽  
Cis Acting ◽  
Genome Wide ◽  
Induction Process

AbstractThe CONSTANS-like (COL) gene family is one of the plant-specific transcription factor families that play important roles in plant growth and development. However, the knowledge of COLs related in cucumber is limited, and their biological functions, especially in the photoperiod-dependent flowering process, are still unclear. In this study, twelve CsaCOL genes were identified in the cucumber genome. Phylogenetic and conserved motif analyses provided insights into the evolutionary relationship between the CsaCOLs. Further, the comparative genome analysis revealed that COL genes are conserved in different plant species, especially collinearity gene pairs related to CsaCOL5. Ten kinds of cis-acting elements were vividly detected in CsaCOLs promoter regions, including five light-responsive elements, which echo the diurnal rhythm expression patterns of seven CsaCOL genes under SD and LD photoperiod regimes. Combined with the expression data of developmental stage, three CsaCOL genes are involved in the flowering network and play pivotal roles for the floral induction process. Our results provide useful information for further elucidating the structural characteristics, expression patterns, and biological functions of COL family genes in many plants

Genome-wide identification and expression analysis of the CaLAX and CaPIN gene families in pepper (Capsicum annuum L.) under various abiotic stresses and hormone treatments

Genome ◽  
2018 ◽  
Vol 61 (2) ◽  
pp. 121-130 ◽  
Author(s):  
Chenghao Zhang ◽  
Wenqi Dong ◽  
Zong-an Huang ◽  
MyeongCheoul Cho ◽  
Qingcang Yu ◽  
...  
Keyword(s):  
Capsicum Annuum ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Families ◽  
Environmental Stresses ◽  
Transcriptional Level ◽  
Specific Expression ◽  
Capsicum Annuum L ◽  
Genome Wide

Auxin plays key roles in regulating plant growth and development as well as in response to environmental stresses. The intercellular transport of auxin is mediated by the following four gene families: ATP-binding cassette family B (ABCB), auxin resistant1/like aux1 (AUX/LAX), PIN-formed (PIN), and PIN-like (PILS). Here, the latest assembled pepper (Capsicum annuum L.) genome was used to characterise and analyse the CaLAX and CaPIN gene families. Genome-wide investigations into these families, including chromosomal distributions, phytogenic relationships, and intron/exon structures, were performed. In total, 4 CaLAX and 10 CaPIN genes were mapped to 10 chromosomes. Most of these genes exhibited varied tissue-specific expression patterns assessed by quantitative real-time PCR. The expression profiles of the CaLAX and CaPIN genes under various abiotic stresses (salt, drought, and cold), exogenous phytohormones (IAA, 6-BA, ABA, SA, and MeJA), and polar auxin transport inhibitor treatments were evaluated. Most CaLAX and CaPIN genes were altered by abiotic stress at the transcriptional level in both shoots and roots, and many CaLAX and CaPIN genes were regulated by exogenous phytohormones. Our study helps to identify candidate auxin transporter genes and to further analyse their biological functions in pepper development and in its adaptation to environmental stresses.

scholarly journals Genome-wide identification, phylogenetic and biochemical analysis of the APYRASE family members, and gene expression analysis in response to the abiotic and biotic stresses in bread wheat (Triticum aestivum)

2019 ◽  
Author(s):  
Wenbo Liu ◽  
Jun Ni ◽  
Faheem Shah ◽  
Kaiqin Ye ◽  
Hao Hu ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Time Course ◽  
Tertiary Structure ◽  
Expression Patterns ◽  
Family Members ◽  
High Stress ◽  
High Catalytic Activity ◽  
Specific Expression ◽  
Wheat Seedlings ◽  
Genome Wide

APYRASEs, which directly regulated the intra- and extra-cellular ATP homeostasis, plays a pivotal role in the regulation of the adaptations to various stresses in mammals, bacteria and plants. In the present study, we identified and characterized the wheat APYRASE family members at the genomic level. The results showed that a total of eight APY homologs with conserved ACR domains were identified. The wheat APYs were further analyzed bioinformatically of their sequence alignment, phylogenetic relations and conserved motifs. Although they share highly conserved secondary structure and tertiary structure, the wheat APYs could be mainly categorized into three groups, according to the phylogenetic and structural analysis. Further, these APYs exhibited similar expression patterns in the root and shoot, among which TaAPY3-1 and TaAPY3-3 had the highest expression level. The time-course expression patterns of the eight APYs in the wheat seedlings in response to the biotic stress and abiotic stress were also investigated. TaAPY3-2, TaAPY3-3, and TaAPY6 exhibited strong sensitivity to all kinds of stresses in the leaves. Some APYs showed specific expression responses, such as TaAPY6 to the heavy metal stress, and TaAPY7 to the heat and salt stress. These results suggested that the stress-inducible APYs could have potential roles in the regulation of the adaptation to the environmental stresses. Moreover, the catalytic activity of TaAPY3-1 was further analyzed in the in vitro system. The results showed that TaAPY3-1 protein exhibited high catalytic activity in degradation of ATP and ADP, but not GTP, CTP and TTP. It also has an extensive range of temperature adaptability, but rather preferred relative acid pH conditions. In this study, the genome-wide identification and characterization of the APYs in wheat could be useful for further genetic modifications to generate high-stress tolerant wheat cultivars.

scholarly journals Genome-Wide Analysis of Allele-Specific Expression Patterns in Seventeen Tissues of Korean Cattle (Hanwoo)

Animals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 727
Author(s):  
Kyu-Sang Lim ◽  
Sun-Sik Chang ◽  
Bong-Hwan Choi ◽  
Seung-Hwan Lee ◽  
Kyung-Tai Lee ◽  
...  
Keyword(s):  
Phenotypic Variation ◽  
Expression Patterns ◽  
Monoallelic Expression ◽  
Specific Expression ◽  
Adult Cattle ◽  
Korean Cattle ◽  
Family Trio ◽  
Epigenetic Effects ◽  
Genome Wide ◽  
Allele Specific

The functional hemizygosity could be caused by the MAE of a given gene and it can be one of the sources to affect the phenotypic variation in cattle. We aimed to identify MAE genes across the transcriptome in Korean cattle (Hanwoo). For three Hanwoo family trios, the transcriptome data of 17 tissues were generated in three offspring. Sixty-two MAE genes had a monoallelic expression in at least one tissue. Comparing genotypes among each family trio, the preferred alleles of 18 genes were identified (maternal expression, n = 9; paternal expression, n = 9). The MAE genes are involved in gene regulation, metabolic processes, and immune responses, and in particular, six genes encode transcription factors (FOXD2, FOXM1, HTATSF1, SCRT1, NKX6-2, and UBN1) with tissue-specific expression. In this study, we report genome-wide MAE genes in seventeen tissues of adult cattle. These results could help to elucidate epigenetic effects on phenotypic variation in Hanwoo.

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