A genome-wide identification of the BLH gene family reveals BLH1 involved in cotton fiber development

Abstract Background Cotton is the world’s largest and most important source of renewable natural fiber. BEL1-like homeodomain (BLH) genes are ubiquitous in plants and have been reported to contribute to plant development. However, there is no comprehensive characterization of this gene family in cotton. In this study, 32, 16, and 18 BLH genes were identified from the G. hirsutum, G. arboreum, and G. raimondii genome, respectively. In addition, we also studied the phylogenetic relationships, chromosomal location, gene structure, and gene expression patterns of the BLH genes. Results The results indicated that these BLH proteins were divided into seven distinct groups by phylogenetic analysis. Among them, 25 members were assigned to 15 chromosomes. Furthermore, gene structure, chromosomal location, conserved motifs, and expression level of BLH genes were investigated in G. hirsutum. Expression profiles analysis showed that four genes (GhBLH1_3, GhBLH1_4, GhBLH1_5, and GhBLH1_6) from BLH1 subfamily were highly expressed during the fiber cell elongation period. The expression levels of these genes were significantly induced by gibberellic acid and brassinosteroid, but not auxin. Exogenous application of gibberellic acid significantly enhanced GhBLH1_3, GhBLH1_4, and GhBLH1_5 transcripts. Expression levels of GhBLH1_3 and GhBLH1_4 genes were significantly increased under brassinosteroid treatment. Conclusions The BLH gene family plays a very important role in many biological processes during plant growth and development. This study deepens our understanding of the role of the GhBLH1 gene involved in fiber development and will help us in breeding better cotton varieties in the future.

Download Full-text

A genome-wide analysis of the cellulose synthase-like (Csl) gene family in maize (Zea mays)

10.7287/peerj.preprints.27374v1 ◽

2018 ◽

Author(s):

Yongkai Li ◽

Xiaojie Cheng ◽

Yaqin Fu ◽

Qinqin Wu ◽

Yuli Guo ◽

...

Keyword(s):

Gene Family ◽

Abiotic Stresses ◽

Early Stage ◽

Expression Profiles ◽

Expression Patterns ◽

Cellulose Synthase ◽

Biotic And Abiotic Stresses ◽

A Genome ◽

Evolutionary Features ◽

Different Tissues

Cell walls play an important role in the structure and morphology of plants as well as stress response, including various biotic and abiotic stresses. Although the comprehensive analysis of genes involved in cellulose synthase have been performed in model plants, such as Arabidopsis thaliana and rice, information regarding cellulose synthase-like (Csl) genes in maize is extremely limited. In this study, a total of 56 members of Csl gene family were identified in maize genome, which were classified into six subfamilies. Analysis of gene structure and conserved motif indicated functional similarities among the ZmCsl proteins within the same subfamily. Additionally, the 56 ZmCsl genes were dispersed on 10 chromosomes. The expression patterns of ZmCsl genes in different tissues using the transcriptome data revealed that most of ZmCsl genes had a relatively high expression in root and tassel tissues. Moreover, the expression profiles of ZmCsl genes under drought and re-watering indicated that the expression of ZmCsl genes were mainly responsive to early stage of drought stress. The protein-protein interaction network of ZmCsl genes proposed some potential interacted proteins. The data presented a comprehensive survey of Csl gene family in maize. The detailed description of maize Csl genes will be beneficial to understand their structural, functional, and evolutionary features. Importantly, we have described the differential expression profiles of these members across different tissues and under drought. This information will provide an important foundation for studying the roles of these ZmCsl genes in response to biotic and abiotic stresses.

Download Full-text

Genome-Wide Identification, Characterization and Expression Analysis of TCP Transcription Factors in Petunia

International Journal of Molecular Sciences ◽

10.3390/ijms21186594 ◽

2020 ◽

Vol 21 (18) ◽

pp. 6594

Author(s):

Shuting Zhang ◽

Qin Zhou ◽

Feng Chen ◽

Lan Wu ◽

Baojun Liu ◽

...

Keyword(s):

Transcription Factors ◽

Plant Growth ◽

Gene Family ◽

Stress Responses ◽

Expression Profiles ◽

Expression Patterns ◽

Leaf Morphogenesis ◽

Systematic Analysis ◽

Genome Wide ◽

A Genome

The plant-specific TCP transcription factors are well-characterized in both monocots and dicots, which have been implicated in multiple aspects of plant biological processes such as leaf morphogenesis and senescence, lateral branching, flower development and hormone crosstalk. However, no systematic analysis of the petunia TCP gene family has been described. In this work, a total of 66 petunia TCP genes (32 PaTCP genes in P. axillaris and 34 PiTCP genes in P. inflata) were identified. Subsequently, a systematic analysis of 32 PaTCP genes was performed. The phylogenetic analysis combined with structural analysis clearly distinguished the 32 PaTCP proteins into two classes—class Ι and class Ⅱ. Class Ⅱ was further divided into two subclades, namely, the CIN-TCP subclade and the CYC/TB1 subclade. Plenty of cis-acting elements responsible for plant growth and development, phytohormone and/or stress responses were identified in the promoter of PaTCPs. Distinct spatial expression patterns were determined among PaTCP genes, suggesting that these genes may have diverse regulatory roles in plant growth development. Furthermore, differential temporal expression patterns were observed between the large- and small-flowered petunia lines for most PaTCP genes, suggesting that these genes are likely to be related to petal development and/or petal size in petunia. The spatiotemporal expression profiles and promoter analysis of PaTCPs indicated that these genes play important roles in petunia diverse developmental processes that may work via multiple hormone pathways. Moreover, three PaTCP-YFP fusion proteins were detected in nuclei through subcellular localization analysis. This is the first comprehensive analysis of the petunia TCP gene family on a genome-wide scale, which provides the basis for further functional characterization of this gene family in petunia.

Download Full-text

Magnetic Bead Adsorption Extraction of Xyloglucan Endoglucosidase/Hydrolase Gene and Its Expression Analysis in Land Cotton

Journal of Biobased Materials and Bioenergy ◽

10.1166/jbmb.2021.2091 ◽

2021 ◽

Vol 15 (4) ◽

pp. 478-490

Author(s):

Xianliang Li ◽

Hang Liu ◽

Zhichang Zhao

Keyword(s):

Gene Family ◽

Developmental Stages ◽

Expression Profiles ◽

Expression Patterns ◽

Magnetic Bead ◽

Evolutionary Significance ◽

Cotton Fibers ◽

Expression Levels ◽

Duplication Events ◽

And Function

The xyloglucan Endotransglucosylase/hydrolase (XTH) genes are proposed to encode enzymes responsible for cleaving and reattaching xyloglucan polymers. Despite prior identification of the XTH gene family in Arabidopsis and rice, the XTH family in upland cotton, a tetraploid plant whose fiber cell is an excellent model for the study of plant cell elongation, is yet uncharacterized. In this study, iron tetroxide based magnetic nanobead (Fe3O4 NPs) was successfully prepared and applied to extract xyloglucan endoglucosidase/hydrolase genes. Analysis of the genes can provide insight into the evolutionary significance and function of the XTH gene family. A total of 41 XTH genes found by searching the phytozomev 10 database were classified into three groups based on their phylogeny and the motifs of individual genes. The 25 and 5 GhXTH genes occurred as clusters resulting from the segmental and tandem duplication. More frequent duplication events in cotton contributed to the expansion of the family. Global microarray analysis of GhXTH gene expression in cotton fibers showed that 18 GhXTH genes could be divided into two clusters and four subclusters based on their expression patterns. Accumulated expression levels were relatively high at the elongation stages of the cotton fibers, suggesting that cotton fiber elongation requires high amounts of the GhXTH protein. The expression profiles of GhXTH3 and GhXTH4 showed by quantitative realtime PCR were similar to those determined by microarray. Additionally, the expression levels of GhXTH3 and GhXTH4 in Gossypium barbadense were higher than those in Gossypium hirsutum at developmental stages, indicating that expression levels of GhXTH3 and GhXTH4 in fibers varied among cultivars differing in fiber length.

Download Full-text

A genome-wide analysis of the cellulose synthase-like (Csl) gene family in maize (Zea mays)

10.7287/peerj.preprints.27374 ◽

2018 ◽

Author(s):

Yongkai Li ◽

Xiaojie Cheng ◽

Yaqin Fu ◽

Qinqin Wu ◽

Yuli Guo ◽

...

Keyword(s):

Gene Family ◽

Abiotic Stresses ◽

Early Stage ◽

Expression Profiles ◽

Expression Patterns ◽

Cellulose Synthase ◽

Biotic And Abiotic Stresses ◽

A Genome ◽

Evolutionary Features ◽

Different Tissues

Download Full-text

Sucrose synthase gene family in Brassica juncea: genomic organization, evolutionary comparisons, and expression regulation

PeerJ ◽

10.7717/peerj.10878 ◽

2021 ◽

Vol 9 ◽

pp. e10878

Author(s):

Mengyao Li ◽

Qi He ◽

Ying Huang ◽

Ya Luo ◽

Yong Zhang ◽

...

Keyword(s):

Gene Family ◽

Brassica Juncea ◽

Sucrose Synthase ◽

Expression Profiles ◽

Expression Patterns ◽

Sucrose Metabolism ◽

Stress Factors ◽

Expression Levels ◽

Abiotic Stress Factors ◽

Stem Development

Sucrose synthase (SUS) plays an important role in sucrose metabolism and plant development. The SUS gene family has been identified in many plants, however, there is no definitive study of SUS gene in Brassica juncea. In this study, 14 SUS family genes were identified and comprehensively analyzed using bioinformatics tools. The analyzed parameters included their family member characteristics, chromosomal locations, gene structures and phylogenetic as well as transcript expression profiles. Phylogenetic analysis revealed that the 14 members could be allocated into three groups: SUS I, SUS II and SUS III. Comparisons of the exon/intron structure of the mustard SUS gene indicated that its structure is highly conserved. The conserved structure is attributed to purification selection during evolution. Expansion of the SUS gene family is associated with fragment and tandem duplications of the mustard SUS gene family. Collinearity analysis among species revealed that the SUS gene family could be lost or mutated to varying degrees after the genome was doubled, or when Brassica rapa and Brassica nigra hybridized to form Brassica juncea. The expression patterns of BjuSUSs vary among different stages of mustard stem swelling. Transcriptomics revealed that the BjuSUS01-04 expression levels were the most elevated. It has been hypothesized that they play an important role in sucrose metabolism during stem development. The expression levels of some BjuSUSs were significantly up-regulated when they were treated with plant hormones. However, when subjected to abiotic stress factors, their expression levels were suppressed. This study establishes SUS gene functions during mustard stem development and stress.

Download Full-text

Genome-wide identification, characterisation and functional evaluation of WRKY genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.) G. Don. under abiotic stresses

BMC Genetics ◽

10.1186/s12863-019-0789-x ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 4

Author(s):

Yuxia Li ◽

Lei Zhang ◽

Panpan Zhu ◽

Qinghe Cao ◽

Jian Sun ◽

...

Keyword(s):

Gene Family ◽

Sweet Potato ◽

Gene Structure ◽

Abiotic Stresses ◽

Expression Profiles ◽

Functional Evaluation ◽

Ipomoea Trifida ◽

Wild Ancestor ◽

Genome Wide ◽

A Genome

Abstract Background WRKY DNA-binding protein (WRKY) is a large gene family involved in plant responses and adaptation to salt, drought, cold and heat stresses. Sweet potato from the genus Ipomoea is a staple food crop, but the WRKY genes in Ipomoea species remain unknown to date. Hence, we carried out a genome-wide analysis of WRKYs in Ipomoea trifida (H.B.K.) G. Don., the wild ancestor of sweet potato. Results A total of 83 WRKY genes encoding 96 proteins were identified in I. trifida, and their gene distribution, duplication, structure, phylogeny and expression patterns were studied. ItfWRKYs were distributed on 15 chromosomes of I. trifida. Gene duplication analysis showed that segmental duplication played an important role in the WRKY gene family expansion in I. trifida. Gene structure analysis showed that the intron-exon model of the ItfWRKY gene was highly conserved. Meanwhile, the ItfWRKYs were divided into five groups (I, IIa + IIb, IIc, IId + IIe and III) on the basis of the phylogenetic analysis on I. trifida and Arabidopsis thaliana WRKY proteins. In addition, gene expression profiles confirmed by quantitative polymerase chain reaction showed that ItfWRKYs were highly up-regulated or down-regulated under salt, drought, cold and heat stress conditions, implying that these genes play important roles in response and adaptation to abiotic stresses. Conclusions In summary, genome-wide identification, gene structure, phylogeny and expression analysis of WRKY gene in I. trifida provide basic information for further functional studies of ItfWRKYs and for the molecular breeding of sweet potato.

Download Full-text

Genome-wide Identification and Expression Analysis of the Cucumber PP2C Genes Family

10.21203/rs.3.rs-1133107/v1 ◽

2021 ◽

Author(s):

Guobin Zhang ◽

Zeyu Zhang ◽

Shilei Luo ◽

Xia Li ◽

Jian Lyu ◽

...

Keyword(s):

Gene Family ◽

Gene Structure ◽

Expression Patterns ◽

Cold Treatment ◽

Negative Regulator ◽

Motif Analysis ◽

Response Elements ◽

Genome Wide ◽

A Genome ◽

Duplication Events

Abstract Background: Type 2C protein phosphatase (PP2Cs) is a negative regulator of ABA signaling pathway, which play important roles in stress signal transduction in plants. However, cucumber (Cucumis sativus L.), as an important economic vegetable, has little research on its PP2C genes family. Results: This study conducted a genome-wide investigation of CsPP2C gene family. Through bioinformatics analysis, 56 CsPP2C genes were identified in cucumber. Based on phylogenetic analysis, the PP2C genes of cucumber and Arabidopsis were divided into 13 groups. Gene structure and conserved motif analysis showed that CsPP2C genes in the same group had similar gene structure and conserved domains. Collinearity analysis showed that segmental duplication events played a key role in the expansion of cucumber PP2C genes family. In addition, the expression of CsPP2Cs under different abiotic treatments was analyzed by qRT-PCR. The results showed that CsPP2C family genes showed different expression patterns under ABA, drought, salt and cold treatment, and a significantly responsive gene CsPP2Cs was obtained (CsPP2C3). By predicting the cis-elements in the promoter, we found that all CsPP2C members contained ABA response elements (ABRE) and drought response elements (MYC). Additionally, the expression patterns of CsPP2C genes were specific in different tissues. Conclusions: The results of this study provide a reference for the genome-wide identification of PP2C gene family in other species, and provide a basis for future studies on the function of PP2C gene in cucumber.

Download Full-text

Genome-wide analysis and expression patterns of lipid phospholipid phospholipase gene family in Brassica napus L.

BMC Genomics ◽

10.1186/s12864-021-07862-1 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Wei Su ◽

Ali Raza ◽

Liu Zeng ◽

Ang Gao ◽

Yan Lv ◽

...

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Expression Profiles ◽

Expression Patterns ◽

Stress Conditions ◽

Motif Analysis ◽

Genome Wide Analysis ◽

Group I ◽

Genome Wide ◽

A Genome

Abstract Background Lipid phosphate phosphatases (LPP) are critical for regulating the production and degradation of phosphatidic acid (PA), an essential signaling molecule under stress conditions. Thus far, the LPP family genes have not been reported in rapeseed (Brassica napus L.). Results In this study, a genome-wide analysis was carried out to identify LPP family genes in rapeseed that respond to different stress conditions. Eleven BnLPPs genes were identified in the rapeseed genome. Based on phylogenetic and synteny analysis, BnLPPs were classified into four groups (Group I-Group IV). Gene structure and conserved motif analysis showed that similar intron/exon and motifs patterns occur in the same group. By evaluating cis-elements in the promoters, we recognized six hormone- and seven stress-responsive elements. Further, six putative miRNAs were identified targeting three BnLPP genes. Gene ontology analysis disclosed that BnLPP genes were closely associated with phosphatase/hydrolase activity, membrane parts, phosphorus metabolic process, and dephosphorylation. The qRT-PCR based expression profiles of BnLPP genes varied in different tissues/organs. Likewise, several gene expression were significantly up-regulated under NaCl, PEG, cold, ABA, GA, IAA, and KT treatments. Conclusions This is the first report to describe the comprehensive genome-wide analysis of the rapeseed LPP gene family. We identified different phytohormones and abiotic stress-associated genes that could help in enlightening the plant tolerance against phytohormones and abiotic stresses. The findings unlocked new gaps for the functional verification of the BnLPP gene family during stresses, leading to rapeseed improvement.

Download Full-text

Genomic Analysis of Sugar Transporter Gene Family in Cultivated Peanut (Arachis Hypogaea): Evolution, Expression Profiles and Gene Variation

10.21203/rs.3.rs-41476/v1 ◽

2020 ◽

Author(s):

zhijun Xu ◽

Sheng Zhao ◽

Xiaowen Hu ◽

Xiaoli Wu ◽

Yang Liu

Keyword(s):

Gene Family ◽

Arachis Hypogaea ◽

Expression Profiles ◽

Expression Patterns ◽

Crop Improvement ◽

Functional Characterization ◽

Structure Evolution ◽

Gene Variation ◽

A Genome ◽

Cultivated Peanut

Abstract BackgroundSugar transporter (STP) gene family, belonging to the major facilitator superfamily, plays significant roles in monosaccharide distribution and many aspects of physiological processes. However, little information was available about the STP genes in cultivated peanut (Arachis hypogaea), an important edible and oil crop. The recent release of the whole-genome sequence of cultivated peanut allowed us to perform a genome-wide investigation into the phylogeny and expression profiling of peanut STP genes.ResultsA total of thirty-six STP genes containing the Sugar_tr conserved motifs were identified from the A. hypogaea genome and all the genes were renamed on the basis of their respective chromosome distribution. According to their phylogenetic features, the STPs were classified into four groups. The structure of the STP genes and their encoded proteins were examined. Synteny analysis and phylogenetic comparison of the STP genes provided deep insight into the evolutionary characteristics of peanut STP genes. The segmental duplication events played a major role in the expansion of the peanut STP gene family and homeologous chromosomes rearrangement may lead to the exchange of STP genes between the A and B sub-genome. Expression profiles derived from transcriptome data exhibited distinct expression patterns of AhSTP genes in various tissues. Among them, four AhSTP genes, AhSTP3, AhSTP9, AhSTP19, AhSTP28, exhibited high expression in early stage of pod formulate in subsp. hypogaea, and in developing phase of seed in subsp. fastigiate, suggesting these genes may be involved in the development of pod and seed. Gene variation analysis of the four genes utilizing the subspecies genome sequences indicated multiple variations occurred in gene sequence or promoter region, and provided valuable clues for the different expression profiles of the four genes during seed development in subsp. hypogaea and subsp. fastigiate.ConclusionThirty-six STP genes were identified in cultivated peanut and their protein character,structure,evolution characteristics, expression patterns and gene variation were analyzed.This study provided a foundation for further functional characterization of STP genes with an aim of cultivated peanut crop improvement.

Download Full-text

Genome-Wide Analysis of the GRAS Gene Family Exhibited Expansion Model and Functional Differentiation in Sea Buckthorn

10.21203/rs.3.rs-55445/v1 ◽

2020 ◽

Author(s):

Liyang Yu ◽

Guoyun Zhang ◽

Zhongrui Lyu ◽

Caiyun He ◽

Jianguo Zhang

Keyword(s):

Gene Family ◽

Expression Profiles ◽

Expression Patterns ◽

Sea Buckthorn ◽

Gene Pairs ◽

Genome Wide ◽

A Genome ◽

Expansion Model ◽

Duplication Models ◽

Gras Gene

Abstract Background: GRAS proteins comprise a large family of transcription factors that experienced extensive replication, and play important roles in many aspects of growth regulatory and environmental signals. However, limited information was available about the GRAS genes in sea buckthorn of Elaeagnaceae. We perform a genome-wide investigation into the expansion model and tissue expression profiling of sea buckthorn GRAS genes based on the comparative genomes methods.Results: In this study, 62 sea buckthorn GRAS (HrGRAS) genes were identified and renamed based on their respective chromosome distribution. Fifty-nine HrGRASs were further classified into nine subgroups and three HrGRASs did not belong to any of the subfamilies according to their phylogenetic features. HrGRAS genes tend to have a representative GRAS domain, few introns and unevenly distributed on chromosomes. Collinear homology dotplot and the median synonymous substitution sites of collinearity blocks distinguished gene pairs with different duplication models and found that segmental duplication was the main driver of the GRAS gene family expansion in sea buckthorn, followed by whole genome duplication and tandem duplication. The all gene pairs from the different duplication models may experience strong purifying selection pressure during evolution processes according to the Ka/Ks ratios. Expression profiles derived from transcriptome data exhibited distinct expression patterns of HrGRAS genes in various tissues and fruit developmental stages. The interaction network analysis of HrGRAS protein found that some HrGRAS proteins interacted with more proteins and retained more copies in sea buckthorn, which indicate that the products of these genes play more important roles in the growth and development of sea buckthorn.Conclusions: Sea buckthorn GRAS gene family was first comprehensively analyzed in this study. This systematic analysis provided a foundation to further understand the expansion and potential functions of GRAS genes with an aim of sea buckthorn crop improvement.

Download Full-text