Conservation and Divergence of the CONSTANS-Like (COL) Genes Related to Flowering and Circadian Rhythm in Brassica napus

The CONSTANS-LIKE (COL) genes are important signaling component in the photoperiod pathway and flowering regulation pathway. However, people still know little about their role in Brassica napus. To achieve a better understanding of the members of the BnaCOL gene family, reveal their evolutionary relationship and related functions involved in photoperiod regulation, we systematically analyzed the BnaCOL family members in B. napus genome. A total of 33 BnaCOL genes distributed unevenly on 16 chromosomes were identified in B. napus and could be classified into three subfamilies. The same subfamilies have relatively conservative gene structures, three-dimensional protein structures and promoter motifs such as light-responsive cis-elements. The collinearity analysis detected 37 pairs of repetitive genes in B. napus genome. A 67.7% of the BnaCOL genes were lost after B. napus genome polyploidization. In addition, the BnaCOL genes showed different tissue-specific expression patterns. A 81.8% of the BnaCOL genes were mainly expressed in leaves, indicating that they may play a conservative role in leaves. Subsequently, we tested the circadian expression profiles of nine homologous genes that regulate flowering in Arabidopsis. Most BnaCOL genes exhibit several types of circadian rhythms, indicating that these BnaCOL genes are involved in the photoperiod pathway. As such, our research has laid the foundation for understanding the exact role of the BnaCOL family in the growth and development of rapeseed, especially in flowering.

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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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Comprehensive Analysis of the SUV Gene Family in Allopolyploid Brassica napus and Its Diploid Ancestors

Genes ◽

10.3390/genes12121848 ◽

2021 ◽

Vol 12 (12) ◽

pp. 1848

Author(s):

Meimei Hu ◽

Mengdi Li ◽

Jianbo Wang

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Expression Patterns ◽

Protein Structures ◽

Evolutionary Process ◽

Orthologous Gene ◽

Evolutionary Relationships ◽

Protein Motifs ◽

Gene Pairs ◽

Gene Structures

SUV (the Suppressor of variegation [Su(var)] homologs and related) gene family is a subgroup of the SET gene family. According to the SRA domain and WIYLD domain distributions, it can be divided into two categories, namely SUVH (the Suppressor of variegation [Su(var)] homologs) and SUVR (the Suppressor of variegation [Su(var)] related). In this study, 139 SUV genes were identified in allopolyploid Brassica napus and its diploid ancestors, and their evolutionary relationships, protein properties, gene structures, motif distributions, transposable elements, cis-acting elements and gene expression patterns were analyzed. Our results showed that the SUV gene family of B. napus was amplified during allopolyploidization, in which the segmental duplication and TRD played critical roles. After the separation of Brassica and Arabidopsis lineages, orthologous gene analysis showed that many SUV genes were lost during the evolutionary process in B. rapa, B. oleracea and B. napus. The analysis of the gene and protein structures and expression patterns of 30 orthologous gene pairs which may have evolutionary relationships showed that most of them were conserved in gene structures and protein motifs, but only four gene pairs had the same expression patterns.

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Insight into the B3Transcription Factor Superfamily and Expression Profiling of B3 Genes in Axillary Buds after Topping in Tobacco(Nicotiana tabacum L.)

Genes ◽

10.3390/genes10020164 ◽

2019 ◽

Vol 10 (2) ◽

pp. 164 ◽

Cited By ~ 3

Author(s):

Fei Xia ◽

Tingting Sun ◽

Shuangjuan Yang ◽

Xiao Wang ◽

Jiangtao Chao ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Expression Patterns ◽

Protein Structures ◽

Axillary Buds ◽

Comparative Genome Analysis ◽

Specific Expression ◽

Protein Motifs ◽

Nicotiana Tabacum L ◽

Gene Structures ◽

Insight Into

Members of the plant-specific B3 transcription factor superfamily play important roles in various growth and developmental processes in plants. Even though there are many valuable studies on B3 genes in other species, little is known about the B3 superfamily in tobacco. We identified 114 B3 proteins from tobacco using comparative genome analysis. These proteins were classified into four subfamilies based on their phylogenetic relationships, and include the ARF, RAV, LAV, and REM subfamilies. The chromosomal locations, gene structures, conserved protein motifs, and sub-cellular localizations of the tobacco B3 proteins were analyzed. The patterns of exon-intron numbers and arrangement and the protein structures of the tobacco B3 proteins were in general agreement with their phylogenetic relationships. The expression patterns of 114 B3 genes revealed that many B3 genes show tissue-specific expression. The expression levels of B3 genes in axillary buds after topping showed that the REM genes are mainly up-regulated in response to topping, while the ARF genes are down-regulated after topping.

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Genome-Wide Analysis of the HSP20 Gene Family and Expression Patterns of HSP20 Genes in Response to Abiotic Stresses in Cynodon transvaalensis

Frontiers in Genetics ◽

10.3389/fgene.2021.732812 ◽

2021 ◽

Vol 12 ◽

Author(s):

Fengchao Cui ◽

Geli Taier ◽

Xiangfeng Wang ◽

Kehua Wang

Keyword(s):

Abiotic Stresses ◽

Expression Profiles ◽

Expression Patterns ◽

Three Dimensional ◽

Evolutionary Relationship ◽

Warm Season ◽

Dimensional Structure ◽

Grass Species ◽

Group I ◽

Cynodon Transvaalensis

African bermudagrass (Cynodon transvaalensis Burtt–Davy) is an important warm-season turfgrass and forage grass species. Heat shock protein 20 (HSP20) is a diverse, ancient, and important protein family. To date, HSP20 genes have not been characterized genome-widely in African bermudagrass. Here, we confirmed 41 HSP20 genes in African bermudagrass genome. On the basis of the phylogenetic tree and cellular locations, the HSP20 proteins were classified into 12 subfamilies. Motif composition was consistent with the phylogeny. Moreover, we identified 15 pairs of paralogs containing nine pairs of tandem duplicates and six pairs of WGD/segmental duplicates of HSP20 genes. Unsurprisingly, the syntenic genes revealed that African bermudagrass had a closer evolutionary relationship with monocots (maize and rice) than dicots (Arabidopsis and soybean). The expression patterns of HSP20 genes were identified with the transcriptome data under abiotic stresses. According to the expression profiles, HSP20 genes could be clustered into three groups (Groups I, II, and III). Group I was the largest, and these genes were up-regulated in response to heat stress as expected. In Group II, one monocot-specific HSP20, CtHSP20-14 maintained higher expression levels under optimum temperature and low temperature, but not high temperature. Moreover, a pair of WGD/segmental duplicates CtHSP20-9 and CtHSP20-10 were among the most conserved HSP20s across different plant species, and they seemed to be positively selected in response to extreme temperatures during evolution. A total of 938 cis-elements were captured in the putative promoters of HSP20 genes. Almost half of the cis-elements were stress responsive, indicating that the expression pattern of HSP20 genes under abiotic stresses might be largely regulated by the cis-elements. Additionally, three-dimensional structure simulations and protein–protein interaction networks were incorporated to resolve the function mechanism of HSP20 proteins. In summary, the findings fulfilled the HSP20 family analysis and could provide useful information for further functional investigations of the specific HSP20s (e.g., CtHSP20-9, CtHSP20-10, and CtHSP20-14) in African bermudagrass.

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Genome-Wide Identification of JRL Genes in Moso Bamboo and Their Expression Profiles in Response to Multiple Hormones and Abiotic Stresses

Frontiers in Plant Science ◽

10.3389/fpls.2021.809666 ◽

2022 ◽

Vol 12 ◽

Author(s):

Zhijun Zhang ◽

Bin Huang ◽

Jialu Chen ◽

Yang Jiao ◽

Hui Guo ◽

...

Keyword(s):

Structure Prediction ◽

Expression Profiles ◽

Brachypodium Distachyon ◽

Expression Patterns ◽

Three Dimensional ◽

Moso Bamboo ◽

Dimensional Structure ◽

Abiotic Stress Response ◽

Specific Expression

Jacalin-related lectins (JRLs) are a new subfamily of plant lectins that has recently been recognized and plays an important role in plant growth, development, and abiotic stress response. Although moso bamboo (Phyllostachys edulis) is an economically and industrially important bamboo worldwide, there has been no systematic identification of JRLs in this species. Here, we identified 25 JRL genes in moso bamboo, and these genes are unequally distributed among 10 genome scaffolds. Phylogenetic analysis showed that the moso bamboo JRLs were clustered into four JRL subgroups: I, II, V, and VII. Numerous stress-responsive and hormone-regulated cis-elements were detected in the upstream promoter regions of the JRLs. Genome collinearity analyses showed that the JRL genes of moso bamboo are more closely related to those of Brachypodium distachyon than to those of Oryza sativa and Zea mays. Sixty-four percent of the PeJRL genes are present as segmental and tandem duplicates. qRT-PCR expression analysis showed that JRL genes in the same subgroup were significantly downregulated in response to salicylic acid (SA), abscisic acid (ABA), and methyl jasmonate (MeJA) treatments and significantly upregulated under low temperature, drought, and salt stress; they also exhibited tissue-specific expression patterns. Subcellular localization experiments revealed that PeJRL04 and PeJRL13 were localized to the cell membrane, nucleus, and cytoplasm. Three dimensional structure prediction and yeast two-hybrid assays were used to verify that PeJRL13 exists as a self-interacting homodimer in vivo. These findings provide an important reference for understanding the functions of specific moso bamboo JRL genes and for the effective selection of stress-related genes.

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The β- Amylase Gene Family in Brassica Napus: Genome Wide Analysis and Expression Profiles in Response to Abiotic Stresses

10.21203/rs.3.rs-70066/v1 ◽

2020 ◽

Author(s):

Yan Lv ◽

Dan Luo ◽

Ziqi Jia ◽

Yong Cheng ◽

Xiling Zou

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Abiotic Stresses ◽

Sequence Similarity ◽

Expression Profiles ◽

Expression Patterns ◽

Chromosomal Distribution ◽

Brassica Crops ◽

Genome Wide ◽

Gene Structures

Abstract Background: The β amylase (BAM) gene family, known for their property of catalytic ability to hydrolyze starch to maltose units, has been recognized to play critical roles in metabolism and gene regulation. To date, BAM genes have not been characterized in oil crops.Results: In this study, the genome wide survey revealed the identification of 30 BnaBAM genes in Brassica napus (B. napus), 11 BraBAM genes in Brassica rapa (B. rapa), 20 BoBAM genes in Brassica oleracea (B. oleracea), which were divided into 4 subfamilies according to the sequence similarity and phylogenetic relationships. All the BAM genes identified in the allotetraploid genome of B. napus, as well as two parental related species (B. rapa and B. oleracea), were analyzed for the gene structures, chromosomal distribution and collinearity, the sequence alignment of the core glucosyl hydrolase domains was further applied. 30 BnaBAMs, 11 BraBAMs and 17 BoBAMs exhibited uneven distribution on chromosomes of Brassica crops. The similar structural compositions of BAM genes in the same subfamily suggested that they were relatively conserved. Abiotic stresses pose one of the major constraints to plant growth and productivity worldwide. Thus, the responsiveness of BnaBAM genes under abiotic stresses were analyzed in B. napus. The expression patterns revealed a stress responsive behavior of all members, of which BnaBAM3s were more prominent. These differential expression patterns suggested an intricate regulation of BnaBAMs elicited by environmental stimuli. Conclusion: Altogether, the present study provides first insights into the BAM gene family of Brassica crops, which lays the foundation for investigating the roles of stress--responsive BnaBAM candidates in B. napus.

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The Divergent Roles of the Rice bcl-2 Associated Athanogene (BAG) Genes in Plant Development and Environmental Responses

Plants ◽

10.3390/plants10102169 ◽

2021 ◽

Vol 10 (10) ◽

pp. 2169

Author(s):

Hailian Zhou ◽

Jiaying Li ◽

Xueyuan Liu ◽

Xiaoshuang Wei ◽

Ziwei He ◽

...

Keyword(s):

Plant Development ◽

Stress Responses ◽

Expression Profiles ◽

Expression Patterns ◽

Brown Planthopper ◽

Protein Structures ◽

Secondary Growth ◽

Primary Cell Wall ◽

Biological Functions ◽

Group I

Bcl-2-associated athanogene (BAG), a group of proteins evolutionarily conserved and functioned as co-chaperones in plants and animals, is involved in various cell activities and diverse physiological processes. However, the biological functions of this gene family in rice are largely unknown. In this study, we identified a total of six BAG members in rice. These genes were classified into two groups, OsBAG1, -2, -3, and -4 are in group I with a conserved ubiquitin-like structure and OsBAG5 and -6 are in group Ⅱ with a calmodulin-binding domain, in addition to a common BAG domain. The BAG genes exhibited diverse expression patterns, with OsBAG4 showing the highest expression level, followed by OsBAG1 and OsBAG3, and OsBAG6 preferentially expressed in the panicle, endosperm, and calli. The co-expression analysis and the hierarchical cluster analysis indicated that the OsBAG1 and OsBAG3 were co-expressed with primary cell wall-biosynthesizing genes, OsBAG4 was co-expressed with phytohormone and transcriptional factors, and OsBAG6 was co-expressed with disease and shock-associated genes. β-glucuronidase (GUS) staining further indicated that OsBAG3 is mainly involved in primary young tissues under both primary and secondary growth. In addition, the expression of the BAG genes under brown planthopper (BPH) feeding, N, P, and K deficiency, heat, drought and plant hormones treatments was investigated. Our results clearly showed that OsBAGs are multifunctional molecules as inferred by their protein structures, subcellular localizations, and expression profiles. BAGs in group I are mainly involved in plant development, whereas BAGs in group II are reactive in gene regulations and stress responses. Our results provide a solid basis for the further elucidation of the biological functions of plant BAG genes.

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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 ◽

10.1139/gen-2017-0163 ◽

2018 ◽

Vol 61 (2) ◽

pp. 121-130 ◽

Cited By ~ 4

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.

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Genome-Wide Analysis of Basic Helix–Loop–Helix Superfamily Members Reveals Organization and Chilling-Responsive Patterns in Cabbage (Brassica oleracea var. capitata L.)

Genes ◽

10.3390/genes10110914 ◽

2019 ◽

Vol 10 (11) ◽

pp. 914

Author(s):

Shan ◽

Zhang ◽

Yu ◽

Wang ◽

Li ◽

...

Keyword(s):

Brassica Oleracea ◽

Expression Profiles ◽

Phylogenetic Analyses ◽

Chilling Stress ◽

Expression Patterns ◽

Comprehensive Analysis ◽

Bhlh Transcription Factor ◽

Specific Expression ◽

Basic Helix Loop Helix ◽

Helix Loop Helix

Basic helix–loop–helix (bHLH) transcription factor (TF) family is commonly found in eukaryotes, which is one of the largest families of regulator proteins. It plays an important role in plant growth and development, as well as various biotic and abiotic stresses. However, a comprehensive analysis of the bHLH family has not been reported in Brassica oleracea. In this study, we systematically describe the BobHLHs in the phylogenetic relationships, expression patterns in different organs/tissues, and in response to chilling stress, and gene and protein characteristics. A total of 234 BobHLH genes were identified in the B. oleracea genome and were further clustered into twenty-three subfamilies based on the phylogenetic analyses. A large number of BobHLH genes were unevenly located on nine chromosomes of B. oleracea. Analysis of RNA-Seq expression profiles revealed that 21 BobHLH genes exhibited organ/tissue-specific expression. Additionally, the expression of six BobHLHs (BobHLH003, -048, -059, -093, -109, and -148) were significantly down-regulated in chilling-sensitive cabbage (CS-D9) and chilling-tolerant cabbage (CT-923). At 24h chilling stress, BobHLH054 was significantly down-regulated and up-regulated in chilling-treated CS-D9 and CT-923. Conserved motif characterization and exon/intron structural patterns showed that BobHLH genes had similar structures in the same subfamily. This study provides a comprehensive analysis of BobHLH genes and reveals several candidate genes involved in chilling tolerance of B. oleracea, which may be helpful to clarify the roles of bHLH family members and understand the regulatory mechanisms of BobHLH genes in response to the chilling stress of cabbage.

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Genome-Wide Characterization of PDI Gene Family in Medicago truncatula and their Roles in Response to ER stress

Genome ◽

10.1139/gen-2020-0064 ◽

2020 ◽

Author(s):

Zhe Meng ◽

Yuwei Zhao ◽

Lijie Liu ◽

Xihua Du

Keyword(s):

Protein Folding ◽

Er Stress ◽

Gene Family ◽

Medicago Truncatula ◽

Environmental Changes ◽

Expression Profiles ◽

Expression Patterns ◽

Protein Structures ◽

Pcr Analysis ◽

Model Legume

Protein disulfide isomerases (PDIs) are pivotal protein folding catalysts in the endoplasmic reticulum (ER) through formation of disulfide bond, isomerization, and inhibition of misfolded protein aggregation. When protein folding capacity is overwhelmed by the demands during transitions between growth phases or under environmental changes, the accumulation of unfolded or misfolded proteins in the ER triggers ER stress. However, little is known about PDI gene family in the model legume, Medicago truncatula, especially the responses to ER stress. Therefore, we identified 17 putative PDIs from the genome of M. truncatula and presented their gene and protein structures, phylogenetic relationships, chromosomal distributions, and synteny analysis with the orthologs in other four eudicot species inculding A. thaliana, G. max, B. rapa, and V. vinifera. Moreover, expression profiles derived from transcriptome data showed distinct expression patterns of MtPDI genes among plant organs, while real-time quantitative PCR analysis and data from the proteome revealed the potential roles of MtPDIs in response to ER stress. Our study provides a foundation for further investigations of the biological roles of PDIs in Medicago, especially their roles in response to ER stress.

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