Genome-Wide Identification of GDSL-Type Esterase/Lipase Gene Family in Dasypyrum villosum L. Reveals That DvGELP53 Is Related to BSMV Infection

GDSL-type esterase/lipase proteins (GELPs) characterized by a conserved GDSL motif at their N-terminus belong to the lipid hydrolysis enzyme superfamily. In plants, GELPs play an important role in plant growth, development and stress response. The studies of the identification and characterization of the GELP gene family in Triticeae have not been reported. In this study, 193 DvGELPs were identified in Dasypyrum villosum and classified into 11 groups (clade A–K) by means of phylogenetic analysis. Most DvGELPs contain only one GDSL domain, only four DvGELPs contain other domains besides the GDSL domain. Gene structure analysis indicated 35.2% DvGELP genes have four introns and five exons. In the promoter regions of the identified DvGELPs, we detected 4502 putative cis-elements, which were associated with plant hormones, plant growth, environmental stress and light responsiveness. Expression profiling revealed 36, 44 and 17 DvGELPs were highly expressed in the spike, the root and the grain, respectively. Further investigation of a root-specific expressing GELP, DvGELP53, indicated it was induced by a variety of biotic and abiotic stresses. The knockdown of DvGELP53 inhibited long-distance movement of BSMV in the tissue of D. villosum. This research provides a genome-wide glimpse of the D. villosum GELP genes and hints at the participation of DvGELP53 in the interaction between virus and plants.

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Genome-Wide Analysis of the TCP Gene Family in Switchgrass (Panicum virgatum L.)

International Journal of Genomics ◽

10.1155/2019/8514928 ◽

2019 ◽

Vol 2019 ◽

pp. 1-13 ◽

Cited By ~ 2

Author(s):

Yuzhu Huo ◽

Wangdan Xiong ◽

Kunlong Su ◽

Yu Li ◽

Yawen Yang ◽

...

Keyword(s):

Salt Stress ◽

Plant Growth ◽

Gene Family ◽

Stress Responses ◽

Panicum Virgatum ◽

Expression Profiles ◽

Specific Expression ◽

Genome Wide Analysis ◽

Genome Wide ◽

A Genome

The plant-specific transcription factor TCPs play multiple roles in plant growth, development, and stress responses. However, a genome-wide analysis of TCP proteins and their roles in salt stress has not been declared in switchgrass (Panicum virgatum L.). In this study, 42 PvTCP genes (PvTCPs) were identified from the switchgrass genome and 38 members can be anchored to its chromosomes unevenly. Nine PvTCPs were predicted to be microRNA319 (miR319) targets. Furthermore, PvTCPs can be divided into three clades according to the phylogeny and conserved domains. Members in the same clade have the similar gene structure and motif localization. Although all PvTCPs were expressed in tested tissues, their expression profiles were different under normal condition. The specific expression may indicate their different roles in plant growth and development. In addition, approximately 20 cis-acting elements were detected in the promoters of PvTCPs, and 40% were related to stress response. Moreover, the expression profiles of PvTCPs under salt stress were also analyzed and 29 PvTCPs were regulated after NaCl treatment. Taken together, the PvTCP gene family was analyzed at a genome-wide level and their possible functions in salt stress, which lay the basis for further functional analysis of PvTCPs in switchgrass.

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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.

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Genome-Wide Identification and Characterization of Soybean GmLOR Gene Family and Expression Analysis in Response to Abiotic Stresses

International Journal of Molecular Sciences ◽

10.3390/ijms222212515 ◽

2021 ◽

Vol 22 (22) ◽

pp. 12515

Author(s):

Yisheng Fang ◽

Dong Cao ◽

Hongli Yang ◽

Wei Guo ◽

Wenqi Ouyang ◽

...

Keyword(s):

Abiotic Stress ◽

Gene Family ◽

Abiotic Stresses ◽

Expression Patterns ◽

Plant Tolerance ◽

Promoter Regions ◽

Real Time Quantitative Pcr ◽

Related Family ◽

Genome Wide ◽

A Genome

The LOR (LURP-one related) family genes encode proteins containing a conserved LOR domain. Several members of the LOR family genes are required for defense against Hyaloperonospora parasitica (Hpa) in Arabidopsis. However, there are few reports of LOR genes in response to abiotic stresses in plants. In this study, a genome-wide survey and expression levels in response to abiotic stresses of 36 LOR genes from Glycine max were conducted. The results indicated that the GmLOR gene family was divided into eight subgroups, distributed on 14 chromosomes. A majority of members contained three extremely conservative motifs. There were four pairs of tandem duplicated GmLORs and nineteen pairs of segmental duplicated genes identified, which led to the expansion of the number of GmLOR genes. The expansion patterns of the GmLOR family were mainly segmental duplication. A heatmap of soybean LOR family genes showed that 36 GmLOR genes exhibited various expression patterns in different tissues. The cis-acting elements in promoter regions of GmLORs include abiotic stress-responsive elements, such as dehydration-responsive elements and drought-inducible elements. Real-time quantitative PCR was used to detect the expression level of GmLOR genes, and most of them were expressed in the leaf or root except that GmLOR6 was induced by osmotic and salt stresses. Moreover, GmLOR4/10/14/19 were significantly upregulated after PEG and salt treatments, indicating important roles in the improvement of plant tolerance to abiotic stress. Overall, our study provides a foundation for future investigations of GmLOR gene functions in soybean.

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Genome-wide identification, genomic organization, and expression profiling of the CONSTANS-like (COL) gene family in petunia under multiple stresses

10.21203/rs.3.rs-307371/v1 ◽

2021 ◽

Author(s):

Khadiza Khatun ◽

Sourav Debnath ◽

Arif Hasan Khan Robin ◽

Antt Htet Wai ◽

Ujjal Kumar Nath ◽

...

Keyword(s):

Stress Response ◽

Plant Growth ◽

Gene Family ◽

Plant Development ◽

Expression Patterns ◽

Functional Characterization ◽

Flowering Plants ◽

Genome Wide ◽

A Genome ◽

Photoperiod Sensitive

Abstract BackgroundCONSTANS-like (CO-like, COL) is a putative zinc-finger transcription factor family that plays a key role in the control of flowering time in photoperiod-sensitive plants. Besides, the COL family protein is also involved in plant development, responses to stresses. However, information on plant development and stress response related function has not been previously performed in any solanaceous crop. In this study, a genome-wide analysis of COL gene family was conducted in Petunia hybrida cv. Mirage Rose to elucidate their roles in organ development and stress response.ResultsA total of 15 COL genes were identified in petunia. Based on their amino acid sequence identity and domain composition they were phylogenetically classified into three groups those are conserved among the flowering plants. Similar gene structure and motif distribution were observed in the same group. Subcellular localization assays demonstrated that all PaCOL proteins were localized in nucleus. Furthermore, differential expression patterns of PaCOL genes were observed in various tissues. The expression patterns of PaCOL genes were observed under various abiotic and phytohormone treatment to explore their relatedness in different stresses. Moreover, several stress and light-responsive cis-elements were detected for different PaCOL genes.ConclusionThe COL genes of petunia genome, those were clustered into three distinct groups, are conserved among flowering plants, were expressed in different tissues and induced under multiple abiotic stress treatments indicating their involvement in plant growth and development and stress response mechanism. This work laid the significant foundation for functional characterization of PaCOL gene family to uncover their biological roles in plant growth, development and in stress response.

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Genome-wide identification of cyclin-dependent kinase (CDK) genes affecting adipocyte differentiation in cattle

BMC Genomics ◽

10.1186/s12864-021-07653-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Cuili Pan ◽

Zhaoxiong Lei ◽

Shuzhe Wang ◽

Xingping Wang ◽

Dawei Wei ◽

...

Keyword(s):

Gene Family ◽

Expression Analysis ◽

Adipocyte Differentiation ◽

Bos Taurus ◽

Adipogenic Differentiation ◽

Critical Role ◽

Bos Indicus ◽

Specific Expression ◽

Genome Wide ◽

A Genome

Abstract Background Cyclin-dependent kinases (CDKs) are protein kinases regulating important cellular processes such as cell cycle and transcription. Many CDK genes also play a critical role during adipogenic differentiation, but the role of CDK gene family in regulating bovine adipocyte differentiation has not been studied. Therefore, the present study aims to characterize the CDK gene family in bovine and study their expression pattern during adipocyte differentiation. Results We performed a genome-wide analysis and identified a number of CDK genes in several bovine species. The CDK genes were classified into 8 subfamilies through phylogenetic analysis. We found that 25 bovine CDK genes were distributed in 16 different chromosomes. Collinearity analysis revealed that the CDK gene family in Bos taurus is homologous with Bos indicus, Hybrid-Bos taurus, Hybrid Bos indicus, Bos grunniens and Bubalus bubalis. Several CDK genes had higher expression levels in preadipocytes than in differentiated adipocytes, as shown by RNA-seq analysis and qPCR, suggesting a role in the growth of emerging lipid droplets. Conclusion In this research, 185 CDK genes were identified and grouped into eight distinct clades in Bovidae, showing extensively homology. Global expression analysis of different bovine tissues and specific expression analysis during adipocytes differentiation revealed CDK4, CDK7, CDK8, CDK9 and CDK14 may be involved in bovine adipocyte differentiation. The results provide a basis for further study to determine the roles of CDK gene family in regulating adipocyte differentiation, which is beneficial for beef quality improvement.

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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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Genome- Wide Identification, Structure Characterization and Expression Pattern Profiling of the Aquaporin Gene Family in Betula pendula

International Journal of Molecular Sciences ◽

10.3390/ijms22147269 ◽

2021 ◽

Vol 22 (14) ◽

pp. 7269

Author(s):

Jean-Stéphane Venisse ◽

Eele Õunapuu-Pikas ◽

Maxime Dupont ◽

Aurélie Gousset-Dupont ◽

Mouadh Saadaoui ◽

...

Keyword(s):

Cold Stress ◽

Gene Family ◽

Betula Pendula ◽

Large Family ◽

Biochemical Properties ◽

Silver Birch ◽

Structure Characterization ◽

Transcriptional Expression ◽

Genome Wide ◽

A Genome

Aquaporin water channels (AQPs) constitute a large family of transmembrane proteins present throughout all kingdoms of life. They play key roles in the flux of water and many solutes across the membranes. The AQP diversity, protein features, and biological functions of silver birch are still unknown. A genome analysis of Betula pendula identified 33 putative genes encoding full-length AQP sequences (BpeAQPs). They are grouped into five subfamilies, representing ten plasma membrane intrinsic proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), eight NOD26-like intrinsic proteins (NIPs), four X intrinsic proteins (XIPs), and three small basic intrinsic proteins (SIPs). The BpeAQP gene structure is conserved within each subfamily, with exon numbers ranging from one to five. The predictions of the aromatic/arginine selectivity filter (ar/R), Froger’s positions, specificity-determining positions, and 2D and 3D biochemical properties indicate noticeable transport specificities to various non-aqueous substrates between members and/or subfamilies. Nevertheless, overall, the BpePIPs display mostly hydrophilic ar/R selective filter and lining-pore residues, whereas the BpeTIP, BpeNIP, BpeSIP, and BpeXIP subfamilies mostly contain hydrophobic permeation signatures. Transcriptional expression analyses indicate that 23 BpeAQP genes are transcribed, including five organ-related expressions. Surprisingly, no significant transcriptional expression is monitored in leaves in response to cold stress (6 °C), although interesting trends can be distinguished and will be discussed, notably in relation to the plasticity of this pioneer species, B. pendula. The current study presents the first detailed genome-wide analysis of the AQP gene family in a Betulaceae species, and our results lay a foundation for a better understanding of the specific functions of the BpeAQP genes in the responses of the silver birch trees to cold stress.

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Genome-wide identification, evolution, and expression analysis of the NPR1-like gene family in pears

PeerJ ◽

10.7717/peerj.12617 ◽

2021 ◽

Vol 9 ◽

pp. e12617

Author(s):

Yarui Wei ◽

Shuliang Zhao ◽

Na Liu ◽

Yuxing Zhang

Keyword(s):

Gene Family ◽

Stress Responses ◽

Systemic Acquired Resistance ◽

Acquired Resistance ◽

Signal Transduction Pathway ◽

Promoter Regions ◽

Systematic Analysis ◽

Genome Wide ◽

Pathogenesis Related ◽

Genome Level

The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) plays a master regulatory role in the salicylic acid (SA) signal transduction pathway and plant systemic acquired resistance (SAR). Members of the NPR1-like gene family have been reported to the associated with biotic/abiotic stress in many plants, however the genome-wide characterization of NPR1-like genes has not been carried out in Chinese pear (Pyrus bretschneideri Reld). In this study, a systematic analysis was conducted on the characteristics of the NPR1-like genes in P. bretschneideri Reld at the whole-genome level. A total nine NPR1-like genes were detected which eight genes were located on six chromosomes and one gene was mapped to scaffold. Based on the phylogenetic analysis, the nine PbrNPR1-like proteins were divided into three clades (Clades I–III) had similar gene structure, domain and conserved motifs. We sorted the cis-acting elements into three clades, including plant growth and development, stress responses, and hormone responses in the promoter regions of PbrNPR1-like genes. The result of qPCR analysis showed that expression diversity of PbrNPR1-like genes in various tissues. All the genes were up-regulated after SA treatment in leaves except for Pbrgene8896. PbrNPR1-like genes showed circadian rhythm and significantly different expression levels after inoculation with Alternaria alternata. These findings provide a solid insight for understanding the functions and evolution of PbrNPR1-like genes in Chinese pear.

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Genome-wide identification and analysis of cystatin family genes in Sorghum (Sorghum bicolor (L.) Moench)

PeerJ ◽

10.7717/peerj.10617 ◽

2021 ◽

Vol 9 ◽

pp. e10617

Author(s):

Jie Li ◽

Xinhao Liu ◽

Qingmei Wang ◽

Junyan Sun ◽

Dexian He

Keyword(s):

Gene Family ◽

Seed Development ◽

Stress Responses ◽

Abiotic Stresses ◽

Expression Profiles ◽

Seed Formation ◽

Aphid Infestation ◽

Genome Wide ◽

A Genome ◽

Cystatin Family

To set a systematic study of the Sorghum cystatins (SbCys) gene family, a genome-wide analysis of the SbCys family genes was performed by bioinformatics-based methods. In total, 18 SbCys genes were identified in Sorghum, which were distributed unevenly on chromosomes, and two genes were involved in a tandem duplication event. All SbCys genes had similar exon/intron structure and motifs, indicating their high evolutionary conservation. Transcriptome analysis showed that 16 SbCys genes were expressed in different tissues, and most genes displayed higher expression levels in reproductive tissues than in vegetative tissues, indicating that the SbCys genes participated in the regulation of seed formation. Furthermore, the expression profiles of the SbCys genes revealed that seven cystatin family genes were induced during Bipolaris sorghicola infection and only two genes were responsive to aphid infestation. In addition, quantitative real-time polymerase chain reaction (qRT-PCR) confirmed that 17 SbCys genes were induced by one or two abiotic stresses (dehydration, salt, and ABA stresses). The interaction network indicated that SbCys proteins were associated with several biological processes, including seed development and stress responses. Notably, the expression of SbCys4 was up-regulated under biotic and abiotic stresses, suggesting its potential roles in mediating the responses of Sorghum to adverse environmental impact. Our results provide new insights into the structural and functional characteristics of the SbCys gene family, which lay the foundation for better understanding the roles and regulatory mechanism of Sorghum cystatins in seed development and responses to different stress conditions.

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High similarity among ChEC-seq datasets

10.1101/2021.02.04.429774 ◽

2021 ◽

Author(s):

Chitvan Mittal ◽

Matthew J. Rossi ◽

B. Franklin Pugh

Keyword(s):

Rna Polymerase Ii ◽

Transcriptional Regulators ◽

Micrococcal Nuclease ◽

High Similarity ◽

Dna Interactions ◽

Promoter Regions ◽

Genome Wide ◽

A Genome ◽

Protein Dna Interactions ◽

Negative Controls

AbstractChEC-seq is a method used to identify protein-DNA interactions across a genome. It involves fusing micrococcal nuclease (MNase) to a protein of interest. In principle, specific genome-wide interactions of the fusion protein with chromatin result in local DNA cleavages that can be mapped by DNA sequencing. ChEC-seq has been used to draw conclusions about broad gene-specificities of certain protein-DNA interactions. In particular, the transcriptional regulators SAGA, TFIID, and Mediator are reported to generally occupy the promoter/UAS of genes transcribed by RNA polymerase II in yeast. Here we compare published yeast ChEC-seq data performed with a variety of protein fusions across essentially all genes, and find high similarities with negative controls. We conclude that ChEC-seq patterning for SAGA, TFIID, and Mediator differ little from background at most promoter regions, and thus cannot be used to draw conclusions about broad gene specificity of these factors.

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