Genome-Wide Identification and Characterization of Pectin Methylesterase Inhibitor Genes in Brassica oleracea

The activities of pectin methylesterases (PMEs) are regulated by pectin methylesterase inhibitors (PMEIs), which consequently control the pectin methylesterification status. However, the role of PMEI genes in Brassica oleracea, an economically important vegetable crop, is poorly understood. In this study, 95 B. oleracea PMEI (BoPMEI) genes were identified. A total of 77 syntenic ortholog pairs and 10 tandemly duplicated clusters were detected, suggesting that the expansion of BoPMEI genes was mainly attributed to whole-genome triplication (WGT) and tandem duplication (TD). During diploidization after WGT, BoPMEI genes were preferentially retained in accordance with the gene balance hypothesis. Most homologous gene pairs experienced purifying selection with ω (Ka/Ks) ratios lower than 1 in evolution. Five stamen-specific BoPMEI genes were identified by expression pattern analysis. By combining the analyses of expression and evolution, we speculated that nonfunctionalization, subfunctionalization, neofunctionalization, and functional conservation can occur in the long evolutionary process. This work provides insights into the characterization of PMEI genes in B. oleracea and contributes to the further functional studies of BoPMEI genes.

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Genome-Wide Identification and Characterization of the RCI2 Gene Family in Allotetraploid Brassica napus Compared with Its Diploid Progenitors

International Journal of Molecular Sciences ◽

10.3390/ijms23020614 ◽

2022 ◽

Vol 23 (2) ◽

pp. 614

Author(s):

Weiqi Sun ◽

Mengdi Li ◽

Jianbo Wang

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Gene Structure ◽

Stress Responses ◽

Stress Protein ◽

Purifying Selection ◽

Cis Acting ◽

Genome Wide ◽

Duplication Events

Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are suitable for studying the problems associated with polyploidization. As an important anti-stress protein, RCI2 proteins widely exist in various tissues of plants, and are crucial to plant growth, development, and stress response. In this study, the RCI2 gene family was comprehensively identified and analyzed, and 9, 9, and 24 RCI2 genes were identified in B. rapa, B. oleracea, and B. napus, respectively. Phylogenetic analysis showed that all of the identified RCI2 genes were divided into two groups, and further divided into three subgroups. Ka/Ks analysis showed that most of the identified RCI2 genes underwent a purifying selection after the duplication events. Moreover, gene structure analysis showed that the structure of RCI2 genes is largely conserved during polyploidization. The promoters of the RCI2 genes in B. napus contained more cis-acting elements, which were mainly involved in plant development and growth, plant hormone response, and stress responses. Thus, B. napus might have potential advantages in some biological aspects. In addition, the changes of RCI2 genes during polyploidization were also discussed from the aspects of gene number, gene structure, gene relative location, and gene expression, which can provide reference for future polyploidization analysis.

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Genome-Wide Identification and Characterization of theLRR-RLKGene Family in TwoVerniciaSpecies

International Journal of Genomics ◽

10.1155/2015/823427 ◽

2015 ◽

Vol 2015 ◽

pp. 1-17 ◽

Cited By ~ 2

Author(s):

Huiping Zhu ◽

Yangdong Wang ◽

Hengfu Yin ◽

Ming Gao ◽

Qiyan Zhang ◽

...

Keyword(s):

Expression Profiles ◽

Consensus Sequence ◽

Expression Patterns ◽

Functional Studies ◽

Industrial Oil ◽

Extensive Evaluation ◽

Genome Wide ◽

Pathogen Response ◽

Lrr Domain

Leucine-rich repeat receptor-like kinases (LRR-RLKs) make up the largest group of RLKs in plants and play important roles in many key biological processes such as pathogen response and signal transduction. To date, most studies on LRR-RLKs have been conducted on model plants. Here, we identified 236 and 230LRR-RLKsin two industrial oil-producing trees:Vernicia fordiiandVernicia montana, respectively. Sequence alignment analyses showed that the homology of the RLK domain (23.81%) was greater than that of the LRR domain (9.51%) among theVf/VmLRR-RLKs. The conserved motif of the LRR domain inVf/VmLRR-RLKsmatched well the known plant LRR consensus sequence but differed at the third last amino acid (W or L). Phylogenetic analysis revealed thatVf/VmLRR-RLKswere grouped into 16 subclades. We characterized the expression profiles ofVf/VmLRR-RLKsin various tissue types including root, leaf, petal, and kernel. Further investigation revealed thatVf/VmLRR-RLKorthologous genes mainly showed similar expression patterns in response to tree wilt disease, except 4 pairs ofVf/VmLRR-RLKsthat showed opposite expression trends. These results represent an extensive evaluation ofLRR-RLKsin two industrial oil trees and will be useful for further functional studies on these proteins.

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Genome-wide identification, phylogeny, and expression profile of the sucrose transporter multigene family in tobacco

Canadian Journal of Plant Science ◽

10.1139/cjps-2018-0187 ◽

2019 ◽

Vol 99 (3) ◽

pp. 312-323

Author(s):

Shanshan Wang ◽

Jun Yang ◽

Xiaodong Xie ◽

Feng Li ◽

Mingzhu Wu ◽

...

Keyword(s):

Expression Patterns ◽

Functional Characterization ◽

Nicotiana Sylvestris ◽

Multiple Roles ◽

Functional Conservation ◽

Sucrose Transporters ◽

Genome Wide ◽

Pi Starvation ◽

Profiling Analysis

The transportation and distribution of sucrose in plants is mediated by sucrose transporters (SUTs), which also participate in various plant developmental and resistance processes. However, no such study of the tobacco SUT family has been reported yet. In the present study, 11, 5, and 4 SUT genes were identified from the genomes of Nicotiana tabacum, Nicotiana sylvestris, and Nicotiana tomentosiformis, respectively. The exon–intron structures of the tobacco SUT genes were highly conserved in the three tobacco species. Gene loss, duplication, and chromosome exchange occurred in the NtSUT family during the formation of allotetraploid common tobacco. Expression profiling analysis revealed that the expression patterns of the NtSUT genes in common tobacco were closer to those in N. sylvestris plants. The NtSUT2s and NtSUT4 genes were ubiquitously expressed in various tobacco tissues, while the NtSUT1s gene was highly expressed in the maturing leaves, indicating their functional conservation and differentiation. The transcriptions of the NtSUT2t, NtSUT3s, NtSUT4, and NtSUT5s genes in tobacco plants were dramatically induced under Pi starvation, drought, and salinity stresses, but their highest expression levels occurred in different tissues, suggesting the multiple roles of NtSUTs in plant resistance to various abiotic stresses. This study provides useful information for the further functional characterization of SUT genes in tobacco.

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Genome-wide identification, expression profiles and regulatory network of MAPK cascade gene family in barley

10.21203/rs.2.10527/v1 ◽

2019 ◽

Author(s):

Licao Cui ◽

Guang Yang ◽

Jali Yan ◽

Yan Pan ◽

Xiaojun Nie

Keyword(s):

Regulatory Network ◽

Expression Profiles ◽

Purifying Selection ◽

Mapk Cascade ◽

Mitogen Activated Protein Kinase ◽

Systematic Analysis ◽

Functional Studies ◽

Genome Wide ◽

A Genome ◽

Duplication Events

Abstract Background Mitogen-activated protein kinase (MAPK) cascade is a conserved and universal signal transduction module in organism. Although it has been well characterized in many plants, no systematic analysis has been conducted in the model cereal crop barley. Results Here, we identified 20 MAPKs, 6 MAPKKs and 156 MAPKKKs through a genome-wide search method using the latest published barley genomic data. Phylogenetic analysis assigned all the MAPK cascade genes into three groups in accordance to MAPK, MAPKK and MAPKKK family. Gene duplication revealed that segmental and tandem duplication events contributed to the expansion of barley MAPK cascade genes and the duplicated gene pairs were found to undergone strong purifying selection. Expression profiles of the HvMAPK, HvMAPKK and HvMAPKKKs were then investigated in different organs and under diverse stresses using the available 132 RNA-seq datasets, and then the tissue-specific and stress-responsive ones were found. Finally, co-expression regulatory network of MAPK cascade genes was constructed by WGCNA tool, resulting in a complicated network composed of a total of 72 branches containing 46 HvMAPK cascade genes and 46 miRNAs. Conclusion This study provides the candidates for further functional studies and also contribute to better understand the MAPK cascade regulatory network in barley and beyond.

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The Genome-Wide Analysis of RALF-Like Genes in Strawberry (Wild and Cultivated) and Five Other Plant Species (Rosaceae)

Genes ◽

10.3390/genes11020174 ◽

2020 ◽

Vol 11 (2) ◽

pp. 174

Author(s):

Hong Zhang ◽

Xiaotong Jing ◽

Ying Chen ◽

Zhe Liu ◽

Yuting Xin ◽

...

Keyword(s):

Evolutionary Process ◽

Purifying Selection ◽

Duplication Event ◽

Regulatory Elements ◽

Go Annotation ◽

Evolution Analysis ◽

Rosaceae Species ◽

Genome Wide ◽

Tandem Duplication Event ◽

Rapid Alkalinization Factor

The rapid alkalinization factor (RALF) gene family is essential for the plant growth and development. However, there is little known about these genes among Rosaceae species. Here, we identify 124 RALF-like genes from seven Rosaceae species, and 39 genes from Arabidopsis, totally 163 genes, divided into four clades according to the phylogenetic analysis, which includes 45 mature RALF genes from Rosaceae species. The YISY motif and RRXL cleavage site are typical features of true RALF genes, but some variants were detected in our study, such as YISP, YIST, NISY, YINY, YIGY, YVGY, FIGY, YIAY, and RRVM. Motif1 is widely distributed among all the clades. According to screening of cis-regulatory elements, GO annotation, expression sequence tags (EST), RNA-seq, and RT-qPCR, we reported that 24 RALF genes coding mature proteins related to tissue development, fungal infection, and hormone response. Purifying selection may play an important role in the evolutionary process of RALF-like genes among Rosaceae species according to the result from ka/ks. The tandem duplication event just occurs in four gene pairs (Fv-RALF9 and Fv-RALF10, Md-RALF7 and Md-RALF8, Pm-RALF2 and Pm-RALF8, and Pp-RALF11 and Pp-RALF14) from four Rosaceae species. Our research provides a wide overview of RALF-like genes in seven Rosaceae species involved in identification, classification, structure, expression, and evolution analysis.

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Identification, Classification, and Expression Analysis of the Triacylglycerol Lipase (TGL) Gene Family Related to Abiotic Stresses in Tomato

International Journal of Molecular Sciences ◽

10.3390/ijms22031387 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1387

Author(s):

Qi Wang ◽

Xin Xu ◽

Xiaoyu Cao ◽

Tixu Hu ◽

Dongnan Xia ◽

...

Keyword(s):

Abiotic Stress ◽

Gene Family ◽

Stress Responses ◽

Structural Characteristics ◽

Limited Information ◽

Triacylglycerol Lipase ◽

Functional Studies ◽

Solanum Lycopersicum L ◽

Genome Wide

Triacylglycerol Lipases (TGLs) are the major enzymes involved in triacylglycerol catabolism. TGLs hydrolyze long-chain fatty acid triglycerides, which are involved in plant development and abiotic stress responses. Whereas most studies of TGLs have focused on seed oil metabolism and biofuel in plants, limited information is available regarding the genome-wide identification and characterization of the TGL gene family in tomato (Solanum lycopersicum L.). Based on the latest published tomato genome annotation ITAG4.0, 129 SlTGL genes were identified and classified into 5 categories according to their structural characteristics. Most SlTGL genes were distributed on 3 of 12 chromosomes. Segment duplication appeared to be the driving force underlying expansion of the TGL gene family in tomato. The promoter analysis revealed that the promoters of SlTGLs contained many stress responsiveness cis-elements, such as ARE, LTR, MBS, WRE3, and WUN-motifs. Expression of the majority of SlTGL genes was suppressed following exposure to chilling and heat, while it was induced under drought stress, such as SlTGLa9, SlTGLa6, SlTGLa25, SlTGLa26, and SlTGLa13. These results provide valuable insights into the roles of the SlTGL genes family and lay a foundation for further functional studies on the linkage between triacylglycerol catabolism and abiotic stress responses in tomato.

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Genome-wide identification and expression analysis of the cytokinin gene family in Brassica oleracea L. reveals its role in clubroot resistance

10.21203/rs.2.17992/v1 ◽

2019 ◽

Author(s):

Mingzhao Zhu ◽

Yu Ning ◽

Longxiang Yan ◽

Wenxue Cao ◽

Congcong Kong ◽

...

Keyword(s):

Gene Family ◽

Brassica Oleracea ◽

Plant Immunity ◽

Homologous Gene ◽

Element Analysis ◽

Clubroot Disease ◽

Genome Wide ◽

A Genome ◽

Genome Wide Search

Abstract Background: cytokinins have important functions in regulating plant growth and response to abiotic stress. cytokinin family genes have been described in several plant species, but a comprehensive analysis of the cytokinin family genes in Brassica oleracea has not been reported to date, especially their roles in dealing with the invasion of P. brassicae. Results: Cytokinins are a class of phytohormones that promote cell division and differentiation and are thought to affect plant immunity to multiple pathogens. To reveal the mechanisms of the Brassica oleracea cytokinin family genes in response to clubroot disease, a total of 36 cytokinin genes were identified using a genome-wide search method. Phylogenetic analysis classified these genes into three groups. They were distributed unevenly across nine chromosomes in B. oleracea, and 15 of them did not contain introns. The results of colinear analysis showed that each cytokinin gene in the B. oleracea genome had at least one homologous gene in the Arabidopsis genome. A cis-element analysis indicated that these genes possessed several stress response cis-elements. The heatmap of the cytokinin gene family showed that these genes were expressed in various tissues and organs. Five and eight genes were up- and downregulated, respectively, in the susceptible material after inoculation. In addition, two and one genes were up- and downregulated, respectively, in resistant material. This may indicate that these cytokinin genes play important roles in the host plant response to clubroot disease. In addition, the results provide insights for better understanding the role of cytokinin in the B. oleracea–P. brassicae interaction. Conclusions: Our results are helpful to elucidate the role of cytokinin family genes in cabbage response to infection by P. brassicae, and lay a foundation for further study on the function of these genes. Keywords: Brassica oleracea, genome-wide, cytokinin family genes, clubroot

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Genome-Wide Identification and Characterization of JAZ Protein Family in Two Petunia Progenitors

Plants ◽

10.3390/plants8070203 ◽

2019 ◽

Vol 8 (7) ◽

pp. 203 ◽

Cited By ~ 1

Author(s):

Shaoze Tian ◽

Siyu Liu ◽

Yu Wang ◽

Kun Wang ◽

Chaoqun Yin ◽

...

Keyword(s):

Expression Patterns ◽

Purifying Selection ◽

Protein Family ◽

Pcr Analysis ◽

Petunia Inflata ◽

Flower Bud ◽

Genome Wide ◽

Meja Treatment ◽

Jaz Proteins

Jasmonate ZIM-domain (JAZ) family proteins are the key repressors in the jasmonate signaling pathway and play crucial roles in plant development, defenses, and responses to stresses. However, our knowledge about the JAZ protein family in petunia is limited. This research respectively identified 12 and 16 JAZ proteins in two Petunia progenitors, Petunia axillaris and Petunia inflata. Phylogenetic analysis showed that the 28 proteins could be divided into four groups (Groups A–D) and further classified into six subgroups (A1, A2, B1, B3, C, and D1); members in the same subgroup shared some similarities in motif composition and sequence structure. The Ka/Ks ratios of seven paralogous pairs were less than one, suggesting the petunia JAZ family might have principally undergone purifying selection. Quantitative real-time PCR (qRT-PCR) analysis revealed that PaJAZ genes presented differential expression patterns during the development of flower bud and anther in petunia, and the expression of PaJAZ5, 9, 12 genes was generally up-regulated after MeJA treatment. Subcellular localization assays demonstrated that proteins PaJAZ5, 9, 12 were localized in nucleus. Yeast two hybrid (Y2H) elucidated most PaJAZ proteins (PaJAZ1-7, 9, 12) might interact with transcription factor MYC2. This study provides insights for further investigation of functional analysis in petunia JAZ family proteins.

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Genome-Wide Identification of Banana Csl Gene Family and Their Different Responses to Low Temperature between Chilling-Sensitive and Tolerant Cultivars

Plants ◽

10.3390/plants10010122 ◽

2021 ◽

Vol 10 (1) ◽

pp. 122

Author(s):

Weina Yuan ◽

Jing Liu ◽

Tomáš Takáč ◽

Houbin Chen ◽

Xiaoquan Li ◽

...

Keyword(s):

Low Temperature ◽

Expression Patterns ◽

Rna Seq ◽

Plant Tolerance ◽

Quantitative Real Time Pcr ◽

Genomic Features ◽

Functional Studies ◽

Genome Wide ◽

Gene Structures

The cell wall plays an important role in responses to various stresses. The cellulose synthase-like gene (Csl) family has been reported to be involved in the biosynthesis of the hemicellulose backbone. However, little information is available on their involvement in plant tolerance to low-temperature (LT) stress. In this study, a total of 42 Csls were identified in Musa acuminata and clustered into six subfamilies (CslA, CslC, CslD, CslE, CslG, and CslH) according to phylogenetic relationships. The genomic features of MaCsl genes were characterized to identify gene structures, conserved motifs and the distribution among chromosomes. A phylogenetic tree was constructed to show the diversity in these genes. Different changes in hemicellulose content between chilling-tolerant and chilling-sensitive banana cultivars under LT were observed, suggesting that certain types of hemicellulose are involved in LT stress tolerance in banana. Thus, the expression patterns of MaCsl genes in both cultivars after LT treatment were investigated by RNA sequencing (RNA-Seq) technique followed by quantitative real-time PCR (qPCR) validation. The results indicated that MaCslA4/12, MaCslD4 and MaCslE2 are promising candidates determining the chilling tolerance of banana. Our results provide the first genome-wide characterization of the MaCsls in banana, and open the door for further functional studies.

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Expansion of Imaginal Disc Growth Factor Gene Family in Diptera Reflects the Evolution of Novel Functions

Insects ◽

10.3390/insects10100365 ◽

2019 ◽

Vol 10 (10) ◽

pp. 365 ◽

Cited By ~ 2

Author(s):

Martina Zurovcova ◽

Vladimir Benes ◽

Michal Zurovec ◽

Lucie Kucerova

Keyword(s):

Imaginal Disc ◽

Purifying Selection ◽

Growth Stimulation ◽

Single Copy ◽

Factor Gene ◽

Multiple Functions ◽

Functional Studies ◽

Growth Factor Gene ◽

Intron Structure

Imaginal disc growth factors (IDGFs) are a small protein family found in insects. They are related to chitinases and implicated in multiple functions, including cell growth stimulation, antimicrobial activity, insect hemolymph clotting, and maintenance of the extracellular matrix. A number of new IDGFs have been found in several insect species and their detailed phylogenetic analysis provides a good basis for further functional studies. To achieve this goal, we sequenced Idgf cDNAs from several lepidopteran and trichopteran species and supplemented our data with sequences retrieved from public databases. A comparison of Idgf genes in different species showed that Diptera typically contain several Idgf paralogs with a simple exon-intron structure (2–3 exons), whereas lepidopteran Idgfs appear as a single copy per genome and contain a higher number of exons (around 9). Our results show that, while lepidopteran Idgfs, having single orthologs, are characterized by low divergence and stronger purifying selection over most of the molecule, the duplicated Idgf genes in Diptera, Idgf1 and Idgf4, exhibit signs of positive selection. This characterization of IDGF evolution provides, to our knowledge, the first information on the changes that formed these important molecules.

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