Genome-Wide Identification and Analysis of the Metallothionein Genes in Oryza Genus

Metallothionein (MT) proteins are low molecular mass, cysteine-rich, and metal-binding proteins that play an important role in maintaining metal homeostasis and stress response. However, the evolutionary relationships and functional differentiation of MT in the Oryza genus remain unclear. Here we identified 53 MT genes from six Oryza genera, including O. sativa ssp. japonica, O. rufipogon, O. sativa ssp. indica, O. nivara, O. glumaepatula, and O. barthii. The MT genes were clustered into four groups based on phylogenetic analysis. MT genes are unevenly distributed on chromosomes; almost half of the MT genes were clustered on chromosome 12, which may result from a fragment duplication containing the MT genes on chromosome 12. Five pairs of segmental duplication events and ten pairs of tandem duplication events were found in the rice MT family. The Ka/Ks values of the fifteen duplicated MT genes indicated that the duplicated MT genes were under a strong negative selection during evolution. Next, combining the promoter activity assay with gene expression analysis revealed different expression patterns of MT genes. In addition, the expression of OsMT genes was induced under different stresses, including NaCl, CdCl2, ABA, and MeJ treatments. Additionally, we found that OsMT genes were mainly located in chloroplasts. These results imply that OsMT genes play different roles in response to these stresses. All results provide important insights into the evolution of the MT gene family in the Oryza genus, and will be helpful to further study the function of MT genes.

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Genome-Wide Identification and Analysis of Class III Peroxidases in Betula pendula

10.21203/rs.3.rs-29021/v1 ◽

2020 ◽

Author(s):

Kewei Cai ◽

Song Chen ◽

Xiyang Zhao ◽

Su Chen

Keyword(s):

Stress Responses ◽

Betula Pendula ◽

Tandem Duplication ◽

Expression Patterns ◽

Class Iii ◽

Physiological Processes ◽

Genome Wide ◽

Plant Life Cycle ◽

Class Iii Peroxidases ◽

Comprehensive Study

Abstract Background: Class III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the plant life cycle. However, little is known about the POD genes in Betula pendula, although it has been characterized in Arabidopsis, rice and maize. The POD genes remain to be determined in Betula pendula.Results: A total of 90 nonredundant POD genes were identified in Betula pendula. (designated BpPODs). These POD genes were divided into twelve groups based on their phylogenetic relationships. The BpPODs are unevenly distributed on the 14 chromosomes. In addition, some BpPOD genes were located sequentially in tandem on chromosomes, inferred that tandem duplication contributes to the expansion of the POD genes family in Betula pendula. Analysis of the distribution of conserved domains of BpPOD proteins showed that all these proteins contain highly conserved motifs. We also investigated their expression patterns in different tissues, the results show that some BpPOD genes might play significant roles in root, xylem, leaf and flower. Furthermore, under low temperature conditions, some BpPOD genes showed different expression patterns at different times.Conclusions: Comprehensive study of the POD genes suggests that their functional diversity during Betula pendula growth and development. Our findings provide a basis for further functional analysis on POD genes family in Betula pendula.

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Genome-wide identification and expression analysis of the JAZ gene family in turnip

Scientific Reports ◽

10.1038/s41598-021-99593-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kai Jia ◽

Cunyao Yan ◽

Jing Zhang ◽

Yunxia Cheng ◽

Wenwen Li ◽

...

Keyword(s):

Gene Family ◽

Expression Analysis ◽

Tandem Duplication ◽

Expression Profiles ◽

Purifying Selection ◽

Specific Protein ◽

Gene Pairs ◽

Genome Wide ◽

Duplication Events ◽

Gene Structure And Expression

AbstractJAZ is a plant-specific protein family involved in the regulation of plant development, abiotic stresses, and responses to phytohormone treatments. In this study, we carried out a bioinformatics analysis of JAZ genes in turnip by determining the phylogenetic relationship, chromosomal location, gene structure and expression profiles analysis under stresses. The 36 JAZ genes were identified and classified into four subfamilies (ZML, JAZ, PPD and TIFY). The JAZ genes were located on 10 chromosomes. Two gene pairs were involved in tandem duplication events. We identified 44 collinear JAZ gene pairs in the turnip genome. Analysis of the Ka/Ks ratios indicated that the paralogs of the BrrJAZ family principally underwent purifying selection. Expression analysis suggested JAZ genes may be involved in the formation of turnip tuberous root, and they also participated in the response to ABA, SA, MeJA, salt stress and low-temperature stress. The results of this study provided valuable information for further exploration of the JAZ gene family in turnip.

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Genome-wide characterization, expression analyses, and functional prediction of the NPF family in Brassica napus

BMC Genomics ◽

10.1186/s12864-020-07274-7 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Jing Wen ◽

Peng-Feng Li ◽

Feng Ran ◽

Peng-Cheng Guo ◽

Jia-Tian Zhu ◽

...

Keyword(s):

Brassica Napus ◽

Expression Profiles ◽

Expression Patterns ◽

Protein Structures ◽

Small Scale ◽

Preferential Expression ◽

Qrt Pcr ◽

Genome Wide ◽

Duplication Events ◽

Small Scale Duplication

Abstract Background NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER (NRT1/PTR) family (NPF) members are essential transporters for many substrates in plants, including nitrate, hormones, peptides, and secondary metabolites. Here, we report the global characterization of NPF in the important oil crop Brassica napus, including that for phylogeny, gene/protein structures, duplications, and expression patterns. Results A total of 199 B. napus (BnaNPFs) NPF-coding genes were identified. Phylogenetic analyses categorized these genes into 11 subfamilies, including three new ones. Sequence feature analysis revealed that members of each subfamily contain conserved gene and protein structures. Many hormone−/abiotic stress-responsive cis-acting elements and transcription factor binding sites were identified in BnaNPF promoter regions. Chromosome distribution analysis indicated that BnaNPFs within a subfamily tend to cluster on one chromosome. Syntenic relationship analysis showed that allotetraploid creation by its ancestors (Brassica rapa and Brassica oleracea) (57.89%) and small-scale duplication events (39.85%) contributed to rapid BnaNPF expansion in B. napus. A genome-wide spatiotemporal expression survey showed that NPF genes of each Arabidopsis and B. napus subfamily have preferential expression patterns across developmental stages, most of them are expressed in a few organs. RNA-seq analysis showed that many BnaNPFs (32.66%) have wide exogenous hormone-inductive profiles, suggesting important hormone-mediated patterns in diverse bioprocesses. Homologs in a clade or branch within a given subfamily have conserved organ/spatiotemporal and hormone-inductive profiles, indicating functional conservation during evolution. qRT-PCR-based comparative expression analysis of the 12 BnaNPFs in the NPF2–1 subfamily between high- and low-glucosinolate (GLS) content B. napus varieties revealed that homologs of AtNPF2.9 (BnaNPF2.12, BnaNPF2.13, and BnaNPF2.14), AtNPF2.10 (BnaNPF2.19 and BnaNPF2.20), and AtNPF2.11 (BnaNPF2.26 and BnaNPF2.28) might be involved in GLS transport. qRT-PCR further confirmed the hormone-responsive expression profiles of these putative GLS transporter genes. Conclusion We identified 199 B. napus BnaNPFs; these were divided into 11 subfamilies. Allopolyploidy and small-scale duplication events contributed to the immense expansion of BnaNPFs in B. napus. The BnaNPFs had preferential expression patterns in different tissues/organs and wide hormone-induced expression profiles. Four BnaNPFs in the NPF2–1 subfamily may be involved in GLS transport. Our results provide an abundant gene resource for further functional analysis of BnaNPFs.

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Genome-Wide Analysis of OPR Family Genes in Cotton Identified a Role for GhOPR9 in Verticillium dahliae Resistance

Genes ◽

10.3390/genes11101134 ◽

2020 ◽

Vol 11 (10) ◽

pp. 1134

Author(s):

Shichao Liu ◽

Ruibin Sun ◽

Xiaojian Zhang ◽

Zili Feng ◽

Feng Wei ◽

...

Keyword(s):

Expression Patterns ◽

Regulatory Elements ◽

Virus Induced Gene Silencing ◽

Biotic And Abiotic Stresses ◽

Cis Acting ◽

Protein Motifs ◽

Genome Wide ◽

Duplication Events ◽

Polyethylene Glycol 6000 ◽

Similar Gene

The 12-oxo-phytodienoic acid reductases (OPRs) have been proven to play a major role in plant development and growth. Although the classification and functions of OPRs have been well understood in Arabidopsis, tomato, rice, maize, and wheat, the information of OPR genes in cotton genome and their responses to biotic and abiotic stresses have not been reported. In this study, we found 10 and 9 OPR genes in Gossypium hirsutum and Gossypium barbadense, respectively. They were classified into three groups, based on the similar gene structure and conserved protein motifs. These OPR genes just located on chromosome 01, chromosome 05, and chromosome 06. In addition, the whole genome duplication (WGD) or segmental duplication events contributed to the evolution of the OPR gene family. The analyses of cis-acting regulatory elements of GhOPRs showed that the functions of OPR genes in cotton might be related to growth, development, hormone, and stresses. Expression patterns showed that GhOPRs were upregulated under salt treatment and repressed by polyethylene glycol 6000 (PEG6000). The expression patterns of GhOPRs were different in leaf, root, and stem under V. dahliae infection. GhOPR9 showed a higher expression level than other OPR genes in cotton root. The virus-induced gene silencing (VIGS) analysis suggested that knockdown of GhOPR9 could increase the susceptibility of cotton to V. dahliae infection. Furthermore, GhOPR9 also modulated the expressions of jasmonic acid (JA) pathway-regulated genes under the V. dahliae infection. Overall, our results provided the evolution and potential functions of the OPR genes in cotton. These findings suggested that GhOPR9 might play an important role in cotton resistance to V. dahliae.

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Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat

BMC Plant Biology ◽

10.1186/s12870-020-02576-0 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Ting Zhu ◽

Yue Liu ◽

Liting Ma ◽

Xiaoying Wang ◽

Dazhong Zhang ◽

...

Keyword(s):

Abscisic Acid ◽

Gene Family ◽

Gene Structure ◽

Expression Patterns ◽

Wheat Yield ◽

Chromosomal Distribution ◽

Positive Role ◽

Qrt Pcr ◽

Genome Wide ◽

Duplication Events

Abstract Background Members of the plant-specific SPL gene family (squamosa promoter-binding protein -like) contain the SBP conserved domain and are involved in the regulation of plant growth and development, including the development of plant flowers and plant epidermal hair, the plant stress response, and the synthesis of secondary metabolites. This family has been identified in various plants. However, there is no systematic analysis of the SPL gene family at the genome-wide level of wheat. Results In this study, 56 putative TaSPL genes were identified using the comparative genomics method; we renamed them TaSPL001 - TaSPL056 on their chromosomal distribution. According to the un-rooted neighbor joining phylogenetic tree, gene structure and motif analyses, the 56 TaSPL genes were divided into 8 subgroups. A total of 81 TaSPL gene pairs were designated as arising from duplication events and 64 interacting protein branches were identified as involve in the protein interaction network. The expression patterns of 21 randomly selected TaSPL genes in different tissues (roots, stems, leaves and inflorescence) and under 4 treatments (abscisic acid, gibberellin, drought and salt) were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Conclusions The wheat genome contains 56 TaSPL genes and those in same subfamily share similar gene structure and motifs. TaSPL gene expansion occurred through segmental duplication events. Combining the results of transcriptional and qRT-PCR analyses, most of these TaSPL genes were found to regulate inflorescence and spike development. Additionally, we found that 13 TaSPLs were upregulated by abscisic acid, indicating that TaSPL genes play a positive role in the abscisic acid-mediated pathway of the seedling stage. This study provides comprehensive information on the SPL gene family of wheat and lays a solid foundation for elucidating the biological functions of TaSPLs and improvement of wheat yield.

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Genome-Wide Identification of YABBY Genes in Orchidaceae and Their Expression Patterns in Phalaenopsis Orchid

Genes ◽

10.3390/genes11090955 ◽

2020 ◽

Vol 11 (9) ◽

pp. 955

Author(s):

You-Yi Chen ◽

Yu-Yun Hsiao ◽

Song-Bin Chang ◽

Diyang Zhang ◽

Si-Ren Lan ◽

...

Keyword(s):

Expression Patterns ◽

Functional Differentiation ◽

Reproductive Organs ◽

Development Stage ◽

Early Developmental Stage ◽

Orchid Species ◽

Helix Loop Helix ◽

Lateral Organs ◽

Genome Wide ◽

Yabby Gene

The plant YABBY transcription factors are key regulators in the lamina development of lateral organs. Orchid is one of the largest families in angiosperm and known for their unique floral morphology, reproductive biology, and diversified lifestyles. However, nothing is known about the role of YABBY genes in orchids, although biologists have never lost their fascination with orchids. In this study, a total of 54 YABBY genes, including 15 genes in CRC/DL, eight in INO, 17 in YAB2, and 14 in FIL clade, were identified from the eight orchid species. A sequence analysis showed that all protein sequences encoded by these YABBY genes share the highly conserved C2C2 zinc-finger domain and YABBY domain (a helix-loop-helix motif). A gene structure analysis showed that the number of exons is highly conserved in the same clades. The genes in YAB2 clade have six exons, and genes in CRC/DL, INO, and FIL have six or seven exons. A phylogenetic analysis showed all 54 orchid YABBY genes could be classified into four major clades, including CRC/DL, INO, FIL, and YAB2. Many of orchid species maintain more than one member in CRC/DL, FIL, and YAB2 clades, implying functional differentiation among these genes, which is supported by sequence diversification and differential expression. An expression analysis of PhalaenopsisYABBY genes revealed that members in the CRC/DL clade have concentrated expressions in the early floral development stage and gynostemium, the fused male and female reproductive organs. The expression of PeINO is consistent with the biological role it played in ovule integument morphogenesis. Transcripts of members in the FIL clade could be obviously detected at the early developmental stage of the flowers. The expression of three genes, PeYAB2,PeYAB3, and PeYAB4, in the YAB2 clade could be revealed both in vegetative and reproductive tissues, and PeYAB4 was transcribed at a relatively higher level than that of PeYAB2 and PeYAB3. Together, this comprehensive analysis provides the basic information for understanding the function of the YABBY gene in Orchidaceae.

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Genome-wide identification and expression analysis of the B-box transcription factor gene family in grapevine (Vitis vinifera L.)

BMC Genomics ◽

10.1186/s12864-021-07479-4 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Xiuming Zhang ◽

Li Zhang ◽

Miaomiao Ji ◽

Yifei Wu ◽

Songlin Zhang ◽

...

Keyword(s):

Vitis Vinifera ◽

Gene Family ◽

Evolutionary History ◽

Potential Role ◽

Expression Patterns ◽

Vitis Vinifera L ◽

Genome Wide ◽

Duplication Events ◽

Powdery Mildew Infection ◽

Transcription Factor Gene Family

Abstract Background B-box (BBX) zinc-finger transcription factors play important roles in plant growth, development, and stress response. Although these proteins have been studied in model plants such as Arabidopsis thaliana or Oryza sativa, little is known about the evolutionary history or expression patterns of BBX proteins in grapevine (Vitis vinifera L.). Results We identified a total of 25 VviBBX genes in the grapevine genome and named them according to the homology with Arabidopsis. These proteins were classified into five groups on the basis of their phylogenetic relationships, number of B-box domains, and presence or absence of a CCT domain or VP motif. BBX proteins within the same group showed similar exon-intron structures and were unevenly distributed in grapevine chromosomes. Synteny analyses suggested that only segmental duplication events contributed to the expansion of the VviBBX gene family in grapevine. The observed syntenic relationships between some BBX genes from grapevine and Arabidopsis suggest that they evolved from a common ancestor. Transcriptional analyses showed that the grapevine BBX genes were regulated distinctly in response to powdery mildew infection and various phytohormones. Moreover, the expression levels of a subset of BBX genes in ovules were much higher in seedless grapevine cultivars compared with seeded cultivars during ovule development, implying a potential role in seed abortion. Additionally, VviBBX8, VquBBX15a and VquBBX29b were all located in the nucleus and had transcriptional activity except for VquBBX29b. Conclusions The results of this study establish the genome-wide analysis of the grapevine BBX family and provide a framework for understanding the biological roles of BBX genes in grapevine.

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Genome-Wide Identification of the CrRLK1L Subfamily and Comparative Analysis of Its Role in the Legume-Rhizobia Symbiosis

Genes ◽

10.3390/genes11070793 ◽

2020 ◽

Vol 11 (7) ◽

pp. 793

Author(s):

Jorge Solis-Miranda ◽

Citlali Fonseca-García ◽

Noreide Nava ◽

Ronal Pacheco ◽

Carmen Quinto

Keyword(s):

Plant Species ◽

Expression Patterns ◽

Phaseolus Vulgaris L ◽

Genome Wide ◽

Receptor Like Kinase ◽

Duplication Events ◽

Gene Structure And Expression ◽

Wide Group ◽

Shed Light ◽

Kinase Subfamily

The plant receptor-like-kinase subfamily CrRLK1L has been widely studied, and CrRLK1Ls have been described as crucial regulators in many processes in Arabidopsis thaliana (L.), Heynh. Little is known, however, about the functions of these proteins in other plant species, including potential roles in symbiotic nodulation. We performed a phylogenetic analysis of CrRLK1L subfamily receptors of 57 different plant species and identified 1050 CrRLK1L proteins, clustered into 11 clades. This analysis revealed that the CrRLK1L subfamily probably arose in plants during the transition from chlorophytes to embryophytes and has undergone several duplication events during its evolution. Among the CrRLK1Ls of legumes and A. thaliana, protein structure, gene structure, and expression patterns were highly conserved. Some legume CrRLK1L genes were active in nodules. A detailed analysis of eight nodule-expressed genes in Phaseolus vulgaris L. showed that these genes were differentially expressed in roots at different stages of the symbiotic process. These data suggest that CrRLK1Ls are both conserved and underwent diversification in a wide group of plants, and shed light on the roles of these genes in legume–rhizobia symbiosis.

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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 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.

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