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Zuo D, Yan Y, Ma J, Zhao P. Genome-Wide Analysis of Transcription Factor R2R3-MYB Gene Family and Gene Expression Profiles during Anthocyanin Synthesis in Common Walnut ( Juglans regia L.). Genes (Basel) 2024; 15:587. [PMID: 38790216 PMCID: PMC11121633 DOI: 10.3390/genes15050587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
The R2R3-MYB gene family, encoding plant transcriptional regulators, participates in many metabolic pathways of plant physiology and development, including flavonoid metabolism and anthocyanin synthesis. This study proceeded as follows: the JrR2R3-MYB gene family was analyzed genome-wide, and the family members were identified and characterized using the high-quality walnut reference genome "Chandler 2.0". All 204 JrR2R3-MYBs were established and categorized into 30 subgroups via phylogenetic analysis. JrR2R3-MYBs were unevenly distributed over 16 chromosomes. Most JrR2R3-MYBs had similar structures and conservative motifs. The cis-acting elements exhibit multiple functions of JrR2R3-MYBs such as light response, metabolite response, and stress response. We found that the expansion of JrR2R3-MYBs was mainly caused by WGD or segmental duplication events. Ka/Ks analysis indicated that these genes were in a state of negative purifying selection. Transcriptome results suggested that JrR2R3-MYBs were widely entangled in the process of walnut organ development and differentially expressed in different colored varieties of walnuts. Subsequently, we identified 17 differentially expressed JrR2R3-MYBs, 9 of which may regulate anthocyanin biosynthesis based on the results of a phylogenetic analysis. These genes were present in greater expression levels in 'Zijing' leaves than in 'Lvling' leaves, as revealed by the results of qRT-PCR experiments. These results contributed to the elucidation of the functions of JrR2R3-MYBs in walnut coloration. Collectively, this work provides a foundation for exploring the functional characteristics of the JrR2R3-MYBs in walnuts and improving the nutritional value and appearance quality of walnuts.
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Affiliation(s)
| | | | | | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (D.Z.); (Y.Y.); (J.M.)
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Liang M, Du Z, Yang Z, Luo T, Ji C, Cui H, Li R. Genome-wide characterization and expression analysis of MADS-box transcription factor gene family in Perilla frutescens. FRONTIERS IN PLANT SCIENCE 2024; 14:1299902. [PMID: 38259943 PMCID: PMC10801092 DOI: 10.3389/fpls.2023.1299902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024]
Abstract
MADS-box transcription factors are widely involved in the regulation of plant growth, developmental processes, and response to abiotic stresses. Perilla frutescens, a versatile plant, is not only used for food and medicine but also serves as an economical oil crop. However, the MADS-box transcription factor family in P. frutescens is still largely unexplored. In this study, a total of 93 PfMADS genes were identified in P. frutescens genome. These genes, including 37 Type I and 56 Type II members, were randomly distributed across 20 chromosomes and 2 scaffold regions. Type II PfMADS proteins were found to contain a greater number of motifs, indicating more complex structures and diverse functions. Expression analysis revealed that most PfMADS genes (more than 76 members) exhibited widely expression model in almost all tissues. The further analysis indicated that there was strong correlation between some MIKCC-type PfMADS genes and key genes involved in lipid synthesis and flavonoid metabolism, which implied that these PfMADS genes might play important regulatory role in the above two pathways. It was further verified that PfMADS47 can effectively mediate the regulation of lipid synthesis in Chlamydomonas reinhardtii transformants. Using cis-acting element analysis and qRT-PCR technology, the potential functions of six MIKCC-type PfMADS genes in response to abiotic stresses, especially cold and drought, were studied. Altogether, this study is the first genome-wide analysis of PfMADS. This result further supports functional and evolutionary studies of PfMADS gene family and serves as a benchmark for related P. frutescens breeding studies.
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Affiliation(s)
- Mengjing Liang
- Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Zhongyang Du
- Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Ze Yang
- Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Tao Luo
- Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Chunli Ji
- Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Hongli Cui
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, China
| | - Runzhi Li
- Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Jinzhong, Shanxi, China
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Zhang X, Li J, Cao Y, Huang J, Duan Q. Genome-Wide Identification and Expression Analysis under Abiotic Stress of BrAHL Genes in Brassica rapa. Int J Mol Sci 2023; 24:12447. [PMID: 37569822 PMCID: PMC10420281 DOI: 10.3390/ijms241512447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
The AT-hook motif nuclear localized (AHL) gene family is a highly conserved transcription factor critical for the growth, development, and stress tolerance of plants. However, the function of the AHL gene family in Brassica rapa (B. rapa) remains unclear. In this study, 42 AHL family members were identified from the B. rapa genome and mapped to nine B. rapa chromosomes. Two clades have formed in the evolution of the AHL gene family. The results showed that most products encoded by AHL family genes are located in the nucleus. Gene duplication was common and expanded the BrAHL gene family. According to the analysis of cis-regulatory elements, the genes interact with stress responses (osmotic, cold, and heavy metal stress), major hormones (abscisic acid), and light responses. In addition, the expression profiles revealed that BrAHL genes are widely expressed in different tissues. BrAHL16 was upregulated at 4 h under drought stress, highly expressed under cadmium conditions, and downregulated in response to cold conditions. BrAHL02 and BrAHL24 were upregulated at the initial time point and peaked at 12 h under cold and cadmium stress, respectively. Notably, the interactions between AHL genes and proteins under drought, cold, and heavy metal stresses were observed when predicting the protein-protein interaction network.
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Affiliation(s)
| | | | | | - Jiabao Huang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China; (X.Z.); (J.L.); (Y.C.)
| | - Qiaohong Duan
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China; (X.Z.); (J.L.); (Y.C.)
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Luo D, Mei D, Wei W, Liu J. Identification and Phylogenetic Analysis of the R2R3-MYB Subfamily in Brassica napus. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12040886. [PMID: 36840234 PMCID: PMC9962269 DOI: 10.3390/plants12040886] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 05/22/2023]
Abstract
The R2R3-MYB sub-family proteins are composed of most members of MYB (v-Myb avian myeloblastosis viral oncogene homolog) protein, a plant-specific transcription factor (TF) that is classified into four classes depending on the number of MYB repeats. R2R3-MYB TFs are involved in physiological and biochemical processes. However, the functions of the Brassica napus R2R3-MYB genes are still mainly unknown. In this study, 35 Brassica napus MYB (BnaMYB) genes were screened in the genome of Brassica napus, and details about their physical and chemical characteristics, evolutionary relationships, chromosome locations, gene structures, three-dimensional protein structures, cis-acting promoter elements, and gene duplications were uncovered. The BnaMYB genes have undergone segmental duplications and positive selection pressure, according to evolutionary studies. The same subfamilies have similar intron-exon patterns and motifs, according to the genes' structure and conserved motifs. Additionally, through cis-element analysis, many drought-responsive and other stress-responsive cis-elements have been found in the promoter regions of the BnaMYB genes. The expression of the BnaMYB gene displays a variety of tissue-specific patterns. Ten lignin-related genes were chosen for drought treatment. Our research screened four genes that showed significant upregulation under drought stress, and thus may be important drought-responsive genes. The findings lay a new foundation for understanding the complex mechanisms of BnaMYB in multiple developmental stages and pathways related to drought stress in rapeseed.
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Affiliation(s)
- Dingfan Luo
- College of Agriculture, Yangtze University, Jingzhou 434023, China
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No. 2 Xudong 2nd Rd., Wuhan 430062, China
| | - Desheng Mei
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No. 2 Xudong 2nd Rd., Wuhan 430062, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Wenliang Wei
- College of Agriculture, Yangtze University, Jingzhou 434023, China
- Correspondence: (W.W.); (J.L.)
| | - Jia Liu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No. 2 Xudong 2nd Rd., Wuhan 430062, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
- Correspondence: (W.W.); (J.L.)
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Luo T, Song Y, Gao H, Wang M, Cui H, Ji C, Wang J, Yuan L, Li R. Genome-wide identification and functional analysis of Dof transcription factor family in Camelina sativa. BMC Genomics 2022; 23:812. [PMID: 36476342 PMCID: PMC9730592 DOI: 10.1186/s12864-022-09056-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Dof transcription factors (TFs) containing C2-C2 zinc finger domains are plant-specific regulatory proteins, playing crucial roles in a variety of biological processes. However, little is known about Dof in Camelina sativa, an important oil crop worldwide, with high stress tolerance. In this study, a genome-wide characterization of Dof proteins is performed to examine their basic structural characteristics, phylogenetics, expression patterns, and functions to identify the regulatory mechanism underlying lipid/oil accumulation and the candidate Dofs mediating stress resistance regulation in C. sativa. RESULTS Total of 103 CsDof genes unevenly distributed on 20 chromosomes were identified from the C. sativa genome, and they were classified into four groups (A, B, C and D) based on the classification of Arabidopsis Dof gene family. All of the CsDof proteins contained the highly-conserved typic CX2C-X21-CX2C structure. Segmental duplication and purifying selection were detected for CsDof genes. 61 CsDof genes were expressed in multiple tissues, and 20 of them showed tissue-specific expression patterns, suggesting that CsDof genes functioned differentially in different tissues of C. sativa. Remarkably, a set of CsDof members were detected to be possible involved in regulation of oil/lipid biosynthesis in C. sativa. Six CsDof genes exhibited significant expression changes in seedlings under salt stress treatment. CONCLUSIONS The present data reveals that segmental duplication is the key force responsible for the expansion of CsDof gene family, and a strong purifying pressure plays a crucial role in CsDofs' evolution. Several CsDof TFs may mediate lipid metabolism and stress responses in C. sativa. Several CsDof TFs may mediate lipid metabolism and stress responses in C. sativa. Collectively, our findings provide a foundation for deep understanding the roles of CsDofs and genetic improvements of oil yield and salt stress tolerance in this species and the related crops.
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Affiliation(s)
- Tao Luo
- grid.412545.30000 0004 1798 1300Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Taigu, 030801 China
| | - Yanan Song
- grid.412545.30000 0004 1798 1300Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Taigu, 030801 China
| | - Huiling Gao
- grid.412545.30000 0004 1798 1300Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Taigu, 030801 China
| | - Meng Wang
- grid.412545.30000 0004 1798 1300Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Taigu, 030801 China
| | - Hongli Cui
- grid.412545.30000 0004 1798 1300Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Taigu, 030801 China
| | - Chunli Ji
- grid.412545.30000 0004 1798 1300Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Taigu, 030801 China
| | - Jiping Wang
- grid.412545.30000 0004 1798 1300Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Taigu, 030801 China
| | - Lixia Yuan
- grid.495248.60000 0004 1778 6134College of Biological Science and Technology, Jinzhong University, Jinzhong, 030600 Shanxi China
| | - Runzhi Li
- grid.412545.30000 0004 1798 1300Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Taigu, 030801 China
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Li Z, Li M, Wu X, Wang J. The characteristics of mRNA m 6A methylomes in allopolyploid Brassica napus and its diploid progenitors. HORTICULTURE RESEARCH 2022; 10:uhac230. [PMID: 36643749 PMCID: PMC9832873 DOI: 10.1093/hr/uhac230] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/30/2022] [Indexed: 06/17/2023]
Abstract
Genome duplication events, comprising whole-genome duplication and single-gene duplication, produce a complex genomic context leading to multiple levels of genetic changes. However, the characteristics of m6A modification, the most widespread internal eukaryotic mRNA modification, in polyploid species are still poorly understood. This study revealed the characteristics of m6A methylomes within the early formation and following the evolution of allopolyploid Brassica napus. We found a complex relationship between m6A modification abundance and gene expression level depending on the degree of enrichment or presence/absence of m6A modification. Overall, the m6A genes had lower gene expression levels than the non-m6A genes. Allopolyploidization may change the expression divergence of duplicated gene pairs with identical m6A patterns and diverged m6A patterns. Compared with duplicated genes, singletons with a higher evolutionary rate exhibited higher m6A modification. Five kinds of duplicated genes exhibited distinct distributions of m6A modifications in transcripts and gene expression level. In particular, tandem duplication-derived genes showed unique m6A modification enrichment around the transcript start site. Active histone modifications (H3K27ac and H3K4me3) but not DNA methylation were enriched around genes of m6A peaks. These findings provide a new understanding of the features of m 6A modification and gene expression regulation in allopolyploid plants with sophisticated genomic architecture.
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Affiliation(s)
- Zeyu Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, China
| | - Mengdi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan 430062, China
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Xu Y, Zhang H, Zhong Y, Jiang N, Zhong X, Zhang Q, Chai S, Li H, Zhang Z. Comparative genomics analysis of bHLH genes in cucurbits identifies a novel gene regulating cucurbitacin biosynthesis. HORTICULTURE RESEARCH 2022; 9:uhac038. [PMID: 35184192 PMCID: PMC9071377 DOI: 10.1093/hr/uhac038] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/22/2022] [Accepted: 01/30/2022] [Indexed: 05/08/2023]
Abstract
The basic helix-loop-helix (bHLH) family of transcription factors (TFs) participate in a variety of biological regulatory processes in plants, and have undergone significant expansion during land plant evolution by gene duplications. In cucurbit crops, several bHLH genes have been found to be responsible for the agronomic traits such as bitterness. However, the characterization of bHLH genes across the genomes of cucurbit species has not been reported, and how they have evolved and diverged remains largely unanswered. Here we identified 1160 bHLH genes in seven cucurbit crops and performed a comprehensive comparative genomics analysis. We determined orthologous and paralogous bHLH genes across cucurbit crops by syntenic analysis between or within species. Orthology and phylogenetic analysis of the tandem-duplicated bHLH genes in the Bt cluster which regulate the biosynthesis of cucurbitacins suggest that this cluster is derived from three ancestral genes after the cucurbit-common tetraploidization event. Interestingly, we identified a new conserved cluster paralogous to the Bt cluster that includes two tandem bHLH genes, and the evolutionary history and expression profiles of these two genes in the new cluster suggest the involvement of one gene (Brp) in the regulation of cucurbitacin biosynthesis in roots. Further biochemical and transgenic assays in melon hairy roots support the function of Brp. This study provides useful information for further investigating the functions of bHLH TFs and novel insights into the regulation of cucurbitacin biosynthesis in cucurbit crops and other plants.
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Affiliation(s)
- Yuanchao Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huimin Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Yang Zhong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Naiyu Jiang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaoyun Zhong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qiqi Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sen Chai
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Hongbo Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhonghua Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
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Wen Y, Raza A, Chu W, Zou X, Cheng H, Hu Q, Liu J, Wei W. Comprehensive In Silico Characterization and Expression Profiling of TCP Gene Family in Rapeseed. Front Genet 2021; 12:794297. [PMID: 34868279 PMCID: PMC8635964 DOI: 10.3389/fgene.2021.794297] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
TCP proteins are plant-specific transcription factors that have multipurpose roles in plant developmental procedures and stress responses. Therefore, a genome-wide analysis was performed to categorize the TCP genes in the rapeseed genome. In this study, a total of 80 BnTCP genes were identified in the rapeseed genome and grouped into two main classes (PCF and CYC/TB1) according to phylogenetic analysis. The universal evolutionary analysis uncovered that BnTCP genes had experienced segmental duplications and positive selection pressure. Gene structure and conserved motif examination presented that Class I and Class II have diverse intron-exon patterns and motifs numbers. Overall, nine conserved motifs were identified and varied from 2 to 7 in all TCP genes; and some of them were gene-specific. Mainly, Class II (PCF and CYC/TB1) possessed diverse structures compared to Class I. We identified four hormone- and four stress-related responsive cis-elements in the promoter regions. Moreover, 32 bna-miRNAs from 14 families were found to be targeting 21 BnTCPs genes. Gene ontology enrichment analysis presented that the BnTCP genes were primarily related to RNA/DNA binding, metabolic processes, transcriptional regulatory activities, etc. Transcriptome-based tissue-specific expression analysis showed that only a few genes (mainly BnTCP9, BnTCP22, BnTCP25, BnTCP48, BnTCP52, BnTCP60, BnTCP66, and BnTCP74) presented higher expression in root, stem, leaf, flower, seeds, and silique among all tested tissues. Likewise, qRT-PCR-based expression analysis exhibited that BnTCP36, BnTCP39, BnTCP53, BnTCP59, and BnTCP60 showed higher expression at certain time points under various hormones and abiotic stress conditions but not by drought and MeJA. Our results opened the new groundwork for future understanding of the intricate mechanisms of BnTCP in various developmental processes and abiotic stress signaling pathways in rapeseed.
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Affiliation(s)
- Yunfei Wen
- College of Agriculture, Yangtze University, Jingzhou, China.,Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Ali Raza
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Wen Chu
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Xiling Zou
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Hongtao Cheng
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Qiong Hu
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Jia Liu
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Wenliang Wei
- College of Agriculture, Yangtze University, Jingzhou, China
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9
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Liu J, Wang J, Wang M, Zhao J, Zheng Y, Zhang T, Xue L, Lei J. Genome-Wide Analysis of the R2R3-MYB Gene Family in Fragaria × ananassa and Its Function Identification During Anthocyanins Biosynthesis in Pink-Flowered Strawberry. FRONTIERS IN PLANT SCIENCE 2021; 12:702160. [PMID: 34527006 PMCID: PMC8435842 DOI: 10.3389/fpls.2021.702160] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/29/2021] [Indexed: 05/14/2023]
Abstract
The strawberry (Fragaria × ananassa) is an economically important fruit throughout the world. The large R2R3-MYB gene family participates in a variety of plant functions, including anthocyanin biosynthesis. The present study is the first genome-wide analysis of the MYB gene family in the octoploid strawberry and describes the identification and characterization of the family members using the recently sequenced F. × ananassa genome. Specifically, we aimed to identify the key MYBs involved in petal coloration in the pink-flowered strawberry, which increases its ornamental value. A comprehensive, genome-wide analysis of F. × ananassa R2R3-FaMYBs was performed, investigating gene structures, phylogenic relationships, promoter regions, chromosomal locations, and collinearity. A total of 393 R2R3-FaMYB genes were identified in the F. × ananassa genome and divided into 36 subgroups based on phylogenetic analysis. Most genes with similar functions in the same subgroup exhibited similar exon-intron structures and motif compositions. These R2R3-FaMYBs were unevenly distributed over 28 chromosomes. The expansion of the R2R3-FaMYB gene family in the F. × ananassa genome was found to be caused mainly by segmental duplication. The Ka/Ks analysis indicated that duplicated R2R3-FaMYBs mostly experienced purifying selection and showed limited functional divergence after the duplication events. To elucidate which R2R3-FaMYB genes were associated with anthocyanin biosynthesis in the petals of the pink-flowered strawberry, we compared transcriptional changes in different flower developmental stages using RNA-seq. There were 131 differentially expressed R2R3-FaMYB genes identified in the petals, of which three genes, FaMYB28, FaMYB54, and FaMYB576, appeared likely, based on the phylogenetic analysis, to regulate anthocyanin biosynthesis. The qRT-PCR showed that these three genes were more highly expressed in petals than in other tissues (fruit, leaf, petiole and stolon) and their expressions were higher in red compared to pink and white petals. These results facilitate the clarification on the roles of the R2R3-FaMYB genes in petal coloration in the pink-flowered strawberry. This work provides useful information for further functional analysis on the R2R3-FaMYB gene family in F. × ananassa.
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Affiliation(s)
- Jiaxin Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Jian Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Mingqian Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Jun Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Yang Zheng
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Tian Zhang
- Genepioneer Biotechnologies Co. Ltd, Nanjing, China
| | - Li Xue
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Jiajun Lei
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
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10
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Wen Y, Raza A, Chu W, Zou X, Cheng H, Hu Q, Liu J, Wei W. Comprehensive In Silico Characterization and Expression Profiling of TCP Gene Family in Rapeseed. Front Genet 2021. [PMID: 34868279 DOI: 10.3389/fgene2021.794297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
TCP proteins are plant-specific transcription factors that have multipurpose roles in plant developmental procedures and stress responses. Therefore, a genome-wide analysis was performed to categorize the TCP genes in the rapeseed genome. In this study, a total of 80 BnTCP genes were identified in the rapeseed genome and grouped into two main classes (PCF and CYC/TB1) according to phylogenetic analysis. The universal evolutionary analysis uncovered that BnTCP genes had experienced segmental duplications and positive selection pressure. Gene structure and conserved motif examination presented that Class I and Class II have diverse intron-exon patterns and motifs numbers. Overall, nine conserved motifs were identified and varied from 2 to 7 in all TCP genes; and some of them were gene-specific. Mainly, Class II (PCF and CYC/TB1) possessed diverse structures compared to Class I. We identified four hormone- and four stress-related responsive cis-elements in the promoter regions. Moreover, 32 bna-miRNAs from 14 families were found to be targeting 21 BnTCPs genes. Gene ontology enrichment analysis presented that the BnTCP genes were primarily related to RNA/DNA binding, metabolic processes, transcriptional regulatory activities, etc. Transcriptome-based tissue-specific expression analysis showed that only a few genes (mainly BnTCP9, BnTCP22, BnTCP25, BnTCP48, BnTCP52, BnTCP60, BnTCP66, and BnTCP74) presented higher expression in root, stem, leaf, flower, seeds, and silique among all tested tissues. Likewise, qRT-PCR-based expression analysis exhibited that BnTCP36, BnTCP39, BnTCP53, BnTCP59, and BnTCP60 showed higher expression at certain time points under various hormones and abiotic stress conditions but not by drought and MeJA. Our results opened the new groundwork for future understanding of the intricate mechanisms of BnTCP in various developmental processes and abiotic stress signaling pathways in rapeseed.
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Affiliation(s)
- Yunfei Wen
- College of Agriculture, Yangtze University, Jingzhou, China
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Ali Raza
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
- Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Wen Chu
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Xiling Zou
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Hongtao Cheng
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Qiong Hu
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Jia Liu
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Wenliang Wei
- College of Agriculture, Yangtze University, Jingzhou, China
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11
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Das Laha S, Dutta S, Schäffner AR, Das M. Gene duplication and stress genomics in Brassicas: Current understanding and future prospects. JOURNAL OF PLANT PHYSIOLOGY 2020; 255:153293. [PMID: 33181457 DOI: 10.1016/j.jplph.2020.153293] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 09/09/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
Polyploidy or whole genome duplication (WGD) is an evolutionary phenomenon that happened in all angiosperms multiple times over millions of years. Extensive studies on the model plant Arabidopsis thaliana genome have revealed that it has undergone five rounds of WGDs followed, in the Brassicaceae tribe, by a characteristic whole genome triplication (WGT). In addition, small-scale events such as tandem or segmental duplications and retrotransposition also enable plants to reshape their genomes. Over the decades, extensive research efforts have been undertaken to understand the evolutionary significance of polyploidy. On the other hand, much less attention has been paid to understanding the impact of gene duplication on the diversification of important stress response genes. The main objective of this review is to discuss key aspects of gene and genome duplications with a focus on genes primarily regulated by osmotic stresses. The focal family is the Brassicaceae, since it (i) underwent multiple rounds of WGDs plus WGTs, (ii) hosts many economically important crops and wild relatives that are tolerant to a range of stresses, and (iii) comprises many species that have already been sequenced. Diverse molecular mechanisms that lead to structural and regulatory alterations of duplicated genes are discussed. Examples are drawn from recent literature to elucidate expanded, stress responsive gene families identified from different Brassica crops. A combined bioinformatic and transcriptomic method has been proposed and tested on a known stress-responsive gene pair to prove that stress-responsive duplicated allelic variants can be identified by this method. Finally, future prospects for engineering these genes into crops to enhance stress tolerance are discussed, and important resources for Brassica genome research are provided.
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Affiliation(s)
- Shayani Das Laha
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Smritikana Dutta
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Anton R Schäffner
- Institute of Biochemical Plant Pathology, Department of Environmental Sciences, Helmholtz Zentrum München, München, Germany
| | - Malay Das
- Department of Life Sciences, Presidency University, Kolkata, India.
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12
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Genome-wide characterization of ALDH Superfamily in Brassica rapa and enhancement of stress tolerance in heterologous hosts by BrALDH7B2 expression. Sci Rep 2019; 9:7012. [PMID: 31065035 PMCID: PMC6505040 DOI: 10.1038/s41598-019-43332-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 04/22/2019] [Indexed: 12/17/2022] Open
Abstract
Aldehyde dehydrogenase (ALDH) carries out oxidation of toxic aldehydes using NAD+/NADP+ as cofactors. In the present study, we performed a genome-wide identification and expression analysis of genes in the ALDH gene family in Brassica rapa. A total of 23 ALDH genes in the superfamily have been identified according to the classification of ALDH Gene Nomenclature Committee (AGNC). They were distributed unevenly across all 10 chromosomes. All the 23 Brassica rapa ALDH (BrALDH) genes exhibited varied expression patterns during treatments with abiotic stress inducers and hormonal treatments. The relative expression profiles of ALDH genes in B. rapa showed that they are predominantly expressed in leaves and stem suggesting their function in the vegetative tissues. BrALDH7B2 showed a strong response to abiotic stress and hormonal treatments as compared to other ALDH genes; therefore, it was overexpressed in heterologous hosts, E. coli and yeast to study its possible function under abiotic stress conditions. Over-expression of BrALDH7B2 in heterologous systems, E. coli and yeast cells conferred significant tolerance to abiotic stress treatments. Results from this work demonstrate that BrALDH genes are a promising and untapped genetic resource for crop improvement and could be deployed further in the development of drought and salinity tolerance in B. rapa and other economically important crops.
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Comprehensive genomic survey, structural classification and expression analysis of C2H2 zinc finger protein gene family in Brassica rapa L. PLoS One 2019; 14:e0216071. [PMID: 31059545 PMCID: PMC6502316 DOI: 10.1371/journal.pone.0216071] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/12/2019] [Indexed: 12/20/2022] Open
Abstract
C2H2 zinc finger protein (ZFP) genes have been extensively studied in many organisms and can function as transcription factors and be involved in many biological processes including plant growth and development and stress responses. In the current study, a comprehensive genomics analysis of the C2H2-ZFP genes in B. rapa was performed. A total of 301 B. rapa putative C2H2-ZFP (BrC2H2-ZFP) genes were identified from the available Brassica genome databases, and further characterized through analysis of conserved amino acid residues in C2H2-ZF domains and their organization, subcellular localization, phylogeny, additional domain, chromosomal location, synteny relationship, Ka/Ks ratio, and expression pattern. We also analyzed the expression patterns of eight B. rapa C2H2-ZFP genes under salt and drought stress conditions by using qRT-PCR technique. Our results showed that about one-third of these B. rapa C2H2-ZFP genes were originated from segmental duplication caused by the WGT around 13 to 17 MYA, one-third of them were highly and consecutively expressed in all tested tissues, and 92% of them were located in nucleus by prediction supporting then their functional roles as transcription factors, of which some may play important roles in plant growth and development. The Ka/Ks ratios of 264 orthologous C2H2-ZFP gene pairs between A. thaliana and B. rapa were all, except two, inferior to 1 (varied from 0.0116 to 1.4919, with an average value of 0.3082), implying that these genes had mainly experienced purifying selection during species evolution. The estimated divergence times of the same set of gene pairs ranged from 6.23 to 38.60 MY, with an average value of 18.29 MY, indicating that these gene members have undergone different selective pressures resulting in different evolutionary rates during species evolution. In addition, a few of these B. rapa C2H2-ZFPs were shown to be involved in stress responses in a similar way as their orthologs in A. thaliana. Comparison between A. thaliana and B. rapa orthologous C2H2-ZFP genes showed that the majority of these C2H2-ZFP gene members encodes proteins with conserved subcellular localization and functional domains between the two species but differed in their expression patterns in five tissues or organs. Thus, our study provides valuable information for further functional determination of each C2H2-ZFP gene across the Brassica species, and may help to select the appropriate gene targets for further in-depth studies, and genetic engineering and improvement of Brassica crops.
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14
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Koramutla MK, Ram C, Bhatt D, Annamalai M, Bhattacharya R. Genome-wide identification and expression analysis of sucrose synthase genes in allotetraploid Brassica juncea. Gene 2019; 707:126-135. [PMID: 31026572 DOI: 10.1016/j.gene.2019.04.059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/20/2019] [Accepted: 04/22/2019] [Indexed: 12/23/2022]
Abstract
Sucrose plays pivotal role in energy metabolism and regulating gene expression of several physiological processes in higher plants. Here, fourteen sucrose synthase (SUS) genes have been identified in the allotetraploid genome of Indian mustard, Brassica juncea. The identified SUS genes in B. juncea (BjSUS) were derived from the two-progenitor species, B. rapa and B. nigra. Intron-exon analysis indicated loss or gain of 1-3 introns in diversification of SUS gene family. Phylogenetic analysis revealed discrete evolutionary paths for the BjSUS genes, originating from three ancestor groups, SUS I, SUS II and SUS III. Gene expression study revealed significant variability in expression of the BjSUS paralogs across the different tissues. BjSUS genes showed transcriptional activation in response to defense hormones and a late response to wounding. Tissue and temporal specificity of expression revealed importance of specific SUS paralogs at different developmental stages and under different stress conditions. The study highlighted differential involvement of SUS paralogs in sucrose metabolism across the tissues and stress-responses, in a major oilseed crop B. juncea.
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Affiliation(s)
- Murali Krishna Koramutla
- ICAR-National Institute for Plant Biotechnology, Indian Agricultural Research Institute Campus, New Delhi 110012, India
| | - Chet Ram
- ICAR-National Institute for Plant Biotechnology, Indian Agricultural Research Institute Campus, New Delhi 110012, India
| | - Deepa Bhatt
- ICAR-National Institute for Plant Biotechnology, Indian Agricultural Research Institute Campus, New Delhi 110012, India
| | - Muthuganeshan Annamalai
- ICAR-National Institute for Plant Biotechnology, Indian Agricultural Research Institute Campus, New Delhi 110012, India
| | - Ramcharan Bhattacharya
- ICAR-National Institute for Plant Biotechnology, Indian Agricultural Research Institute Campus, New Delhi 110012, India.
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15
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Liu T, Yu H, Xiong X, Yu Y, Yue X, Liu J, Cao J. Genome-Wide Identification and Characterization of Pectin Methylesterase Inhibitor Genes in Brassica oleracea. Int J Mol Sci 2018; 19:ijms19113338. [PMID: 30373125 PMCID: PMC6274938 DOI: 10.3390/ijms19113338] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/11/2018] [Accepted: 10/23/2018] [Indexed: 11/16/2022] Open
Abstract
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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Affiliation(s)
- Tingting Liu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China.
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
| | - Hui Yu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China.
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
| | - Xingpeng Xiong
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China.
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
| | - Youjian Yu
- Department of Horticulture, College of Agriculture and Food Science, Zhejiang A & F University, Lin'an 311300, China.
| | - Xiaoyan Yue
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China.
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
| | - Jinlong Liu
- Laboratory of Molecular Biology and Gene Engineering, School of Life Sciences, Nanchang University, Nanchang 330031, China.
| | - Jiashu Cao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China.
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
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Microsynteny analysis to understand evolution and impact of polyploidization on MIR319 family within Brassicaceae. Dev Genes Evol 2018; 228:227-242. [PMID: 30242472 DOI: 10.1007/s00427-018-0620-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 09/14/2018] [Indexed: 10/28/2022]
Abstract
The availability of a large number of whole-genome sequences allows comparative genomic analysis to reveal and understand evolution of regulatory regions and elements. The role played by events such as whole-genome and segmental duplications followed by genome fractionation in shaping genomic landscape and in expansion of gene families is crucial toward developing insights into evolutionary trends and consequences such as sequence and functional diversification. Members of Brassicaceae are known to have experienced several rounds of whole-genome duplication (WGD) that have been termed as paleopolyploidy, mesopolyploidy, and neopolyploidy. Such repeated events led to the creation and expansion of a large number of gene families. MIR319 is reported to be one of the most ancient and conserved plant MIRNA families and plays a role in growth and development including leaf development, seedling development, and embryo patterning. We have previously reported functional diversification of members of miR319 in Brassica oleracea affecting leaf architecture; however, the evolutionary history of the MIR319 gene family across Brassicaceae remains unknown and requires investigation. We therefore identified homologous and homeologous segments of ca. 100 kb, with or without MIR319, performed comparative synteny analysis and genome fractionation studies. We detected variable rates of gene retention across members of Brassicaceae when genomic blocks of MIR319a, MIR319b, and MIR319c were compared either between themselves or against Arabidopsis thaliana genome which was taken as the base genome. The highest levels of shared genes were found between A. thaliana and Capsella rubella in both MIR319b- and MIR319c-containing genomic segments, and with the closest species of A. thaliana, A. lyrata, only in MIR319a-containing segment. Synteny analysis across 12 genomes (with 30 sub-genomes) revealed MIR319c to be the most conserved MIRNA loci (present in 27 genomes/sub-genomes) followed by MIR319a (present in 23 genomes/sub-genomes); MIR319b was found to be frequently lost (present in 20 genomes/sub-genomes) and thus is under least selection pressure for retention. Genome fractionation revealed extensive and differential loss of MIRNA homeologous loci and flanking genes from various sub-genomes of Brassica species that is in accordance with their older history of polyploidy when compared to Camelina sativa, a recent neopolyploid, where the effect of genome fractionation was least. Finally, estimation of phylogenetic relationship using precursor sequences of MIR319 reveals MIR319a and MIR319b form sister clades, with MIR319c forming a separate clade. An intra-species synteny analysis between MIR319a-, MIR319b-, and MIR319c-containing genomic segments suggests segmental duplications at the base of Brassicaceae to be responsible for the origin of MIR319a and MIR319b.
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17
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Genome-Wide Identification, Molecular Evolution, and Expression Profiling Analysis of Pectin Methylesterase Inhibitor Genes in Brassica campestris ssp. chinensis. Int J Mol Sci 2018; 19:ijms19051338. [PMID: 29724020 PMCID: PMC5983585 DOI: 10.3390/ijms19051338] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 02/08/2023] Open
Abstract
Pectin methylesterase inhibitor genes (PMEIs) are a large multigene family and play crucial roles in cell wall modifications in plant growth and development. Here, a comprehensive analysis of the PMEI gene family in Brassicacampestris, an important leaf vegetable, was performed. We identified 100 BrassicacampestrisPMEI genes (BcPMEIs), among which 96 BcPMEIs were unevenly distributed on 10 chromosomes and nine tandem arrays containing 20 BcPMEIs were found. We also detected 80 pairs of syntenic PMEI orthologs. These findings indicated that whole-genome triplication (WGT) and tandem duplication (TD) were the main mechanisms accounting for the current number of BcPMEIs. In evolution, BcPMEIs were retained preferentially and biasedly, consistent with the gene balance hypothesis and two-step theory, respectively. The molecular evolution analysis of BcPMEIs manifested that they evolved through purifying selection and the divergence time is in accordance with the WGT data of B. campestris. To obtain the functional information of BcPMEIs, the expression patterns in five tissues and the cis-elements distributed in promoter regions were investigated. This work can provide a better understanding of the molecular evolution and biological function of PMEIs in B. campestris.
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Perumal S, Waminal NE, Lee J, Lee J, Choi BS, Kim HH, Grandbastien MA, Yang TJ. Elucidating the major hidden genomic components of the A, C, and AC genomes and their influence on Brassica evolution. Sci Rep 2017; 7:17986. [PMID: 29269833 PMCID: PMC5740159 DOI: 10.1038/s41598-017-18048-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/04/2017] [Indexed: 11/09/2022] Open
Abstract
Decoding complete genome sequences is prerequisite for comprehensive genomics studies. However, the currently available reference genome sequences of Brassica rapa (A genome), B. oleracea (C) and B. napus (AC) cover 391, 540, and 850 Mbp and represent 80.6, 85.7, and 75.2% of the estimated genome size, respectively, while remained are hidden or unassembled due to highly repetitive nature of these genome components. Here, we performed the first comprehensive genome-wide analysis using low-coverage whole-genome sequences to explore the hidden genome components based on characterization of major repeat families in the B. rapa and B. oleracea genomes. Our analysis revealed 10 major repeats (MRs) including a new family comprising about 18.8, 10.8, and 11.5% of the A, C and AC genomes, respectively. Nevertheless, these 10 MRs represented less than 0.7% of each assembled reference genome. Genomic survey and molecular cytogenetic analyses validates our insilico analysis and also pointed to diversity, differential distribution, and evolutionary dynamics in the three Brassica species. Overall, our work elucidates hidden portions of three Brassica genomes, thus providing a resource for understanding the complete genome structures. Furthermore, we observed that asymmetrical accumulation of the major repeats might be a cause of diversification between the A and C genomes.
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Affiliation(s)
- Sampath Perumal
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada.,Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Nomar Espinosa Waminal
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.,Department of Life Science, Plant Biotechnology Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Jonghoon Lee
- Joeun Seed, Goesan-Gun, Chungcheongbuk-Do, 28051, Republic of Korea
| | - Junki Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Beom-Soon Choi
- Phyzen Genomics Institute, Seongnam, 13558, Republic of Korea
| | - Hyun Hee Kim
- Department of Life Science, Plant Biotechnology Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | | | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea. .,Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, 232-916, Republic of Korea.
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19
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Jin X, Zhu L, Yao Q, Meng X, Ding G, Wang D, Xie Q, Tong Z, Tao C, Yu L, Li H, Wang X. Expression Profiling of Mitogen-Activated Protein Kinase Genes Reveals Their Evolutionary and Functional Diversity in Different Rubber Tree (Hevea brasiliensis) Cultivars. Genes (Basel) 2017; 8:genes8100261. [PMID: 28984837 PMCID: PMC5664111 DOI: 10.3390/genes8100261] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/19/2017] [Accepted: 09/19/2017] [Indexed: 12/03/2022] Open
Abstract
Rubber tree (Heveabrasiliensis) is the only commercially cultivated plant for producing natural rubber, one of the most essential industrial raw materials. Knowledge of the evolutionary and functional characteristics of kinases in H. brasiliensis is limited because of the long growth period and lack of well annotated genome information. Here, we reported mitogen-activated protein kinases in H. brasiliensis (HbMPKs) by manually checking and correcting the rubber tree genome. Of the 20 identified HbMPKs, four members were validated by proteomic data. Protein motif and phylogenetic analyses classified these members into four known groups comprising Thr-Glu-Tyr (TEY) and Thr-Asp-Tyr (TDY) domains, respectively. Evolutionary and syntenic analyses suggested four duplication events: HbMPK3/HbMPK6, HbMPK8/HbMPK9/HbMPK15, HbMPK10/HbMPK12 and HbMPK11/HbMPK16/HbMPK19. Expression profiling of the identified HbMPKs in roots, stems, leaves and latex obtained from three cultivars with different latex yield ability revealed tissue- and variety-expression specificity of HbMPK paralogues. Gene expression patterns under osmotic, oxidative, salt and cold stresses, combined with cis-element distribution analyses, indicated different regulation patterns of HbMPK paralogues. Further, Ka/Ks and Tajima analyses suggested an accelerated evolutionary rate in paralogues HbMPK10/12. These results revealed HbMPKs have diverse functions in natural rubber biosynthesis, and highlighted the potential possibility of using MPKs to improve stress tolerance in future rubber tree breeding.
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Affiliation(s)
- Xiang Jin
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
- College of Life Sciences, Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi 832003, China.
| | - Liping Zhu
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
- College of Life Sciences, Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi 832003, China.
| | - Qi Yao
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Xueru Meng
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Guohua Ding
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Dan Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Quanliang Xie
- College of Life Sciences, Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi 832003, China.
| | - Zheng Tong
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Chengcheng Tao
- College of Life Sciences, Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi 832003, China.
| | - Li Yu
- College of Life Sciences, Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi 832003, China.
| | - Hongbin Li
- College of Life Sciences, Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi 832003, China.
| | - Xuchu Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
- College of Life Sciences, Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi 832003, China.
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Pont C, Salse J. Wheat paleohistory created asymmetrical genomic evolution. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:29-37. [PMID: 28182971 DOI: 10.1016/j.pbi.2017.01.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/12/2016] [Accepted: 01/04/2017] [Indexed: 05/26/2023]
Abstract
Following the triplication reported in Brassiceae ∼10million years ago, and at the basis of rosids ∼100million years ago, bias in organization and regulation, known as subgenome dominance, has been reported between the three post-polyploidy compartments referenced to as less fractionated (LF), medium fractionated (MF1) and more fractionated (MF2), that have been proposed to derive from an hexaploidization event involving ancestors of 7-14-21 chromosomes. Modern bread wheat experienced similar paleohistory during the last half million year of evolution opening a new hypothesis where the wheat genome is at the earliest stages on the road of diploidization through subgenome dominance driving asymmetry in gene content, gene expression abundance, transposable element content as dynamics and epigenetic control between the A, B and D subgenomes.
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Affiliation(s)
- Caroline Pont
- INRA/UCA UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Laboratory PaleoEVO 'Paleogenomics & Evolution', 5 chemin de Beaulieu, 63100 Clermont Ferrand, France
| | - Jérôme Salse
- INRA/UCA UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Laboratory PaleoEVO 'Paleogenomics & Evolution', 5 chemin de Beaulieu, 63100 Clermont Ferrand, France*.
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Ren Y, Wu J, Zhao J, Hao L, Zhang L. Identification of SSR markers closely linked to the yellow seed coat color gene in heading Chinese cabbage ( Brassica rapa L. ssp. pekinensis). Biol Open 2017; 6:278-282. [PMID: 28069590 PMCID: PMC5312096 DOI: 10.1242/bio.021592] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Research on the yellow-seeded variety of heading Chinese cabbage will aid in broadening its germplasm resources and lay a foundation for AA genome research in Brassica crops. Here, an F2 segregating population of 1575 individuals was constructed from two inbred lines (brown-seeded ‘92S105’ and yellow-seeded ‘91-125’). This population was used to identify the linkage molecular markers of the yellow seed coat trait using simple sequence repeat (SSR) techniques combined with a bulk segregant analysis (BSA). Of the 144 SSR primer pairs on the A01-A10 chromosomes from the Brassica database (http://brassicadb.org/brad/), two pairs located on the A06 chromosome showed polymorphic bands between the bulk DNA pools of eight brown-seeded and eight yellow-seeded F2 progeny. Based on the genome sequence, 454 SSR markers were designed to A06 to detect these polymorphic bands and were synthesized. Six SSR markers linked to the seed coat color gene were successfully selected for fine linkage genetic map construction, in which the two closest flanking markers, SSR449a and SSR317, mapped the Brsc-ye gene to a 40.2 kb region with distances of 0.07 and 0.06 cM, respectively. The molecular markers obtained in this report will assist in the marker-assisted selection and breeding of yellow-seeded lines in Brassica rapa L. and other close species. Summary: Genetic mapping of the yellow seed coat gene Brsc-ye to a 40.2 kb region of the Chinese cabbage (Brassica rapa ssp. pekinensis) genome will allow marker-assisted selection and breeding of yellow-seeded lines.
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Affiliation(s)
- Yanjing Ren
- State Key Laboratory of Crop Stress Biology for Arid Area, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Junqing Wu
- State Key Laboratory of Crop Stress Biology for Arid Area, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Jing Zhao
- State Key Laboratory of Crop Stress Biology for Arid Area, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Lingyu Hao
- State Key Laboratory of Crop Stress Biology for Arid Area, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Lugang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Area, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
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El Baidouri M, Murat F, Veyssiere M, Molinier M, Flores R, Burlot L, Alaux M, Quesneville H, Pont C, Salse J. Reconciling the evolutionary origin of bread wheat (Triticum aestivum). THE NEW PHYTOLOGIST 2017; 213:1477-1486. [PMID: 27551821 DOI: 10.1111/nph.14113] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 06/18/2016] [Indexed: 05/26/2023]
Abstract
The origin of bread wheat (Triticum aestivum; AABBDD) has been a subject of controversy and of intense debate in the scientific community over the last few decades. In 2015, three articles published in New Phytologist discussed the origin of hexaploid bread wheat (AABBDD) from the diploid progenitors Triticum urartu (AA), a relative of Aegilops speltoides (BB) and Triticum tauschii (DD). Access to new genomic resources since 2013 has offered the opportunity to gain novel insights into the paleohistory of modern bread wheat, allowing characterization of its origin from its diploid progenitors at unprecedented resolution. We propose a reconciled evolutionary scenario for the modern bread wheat genome based on the complementary investigation of transposable element and mutation dynamics between diploid, tetraploid and hexaploid wheat. In this scenario, the structural asymmetry observed between the A, B and D subgenomes in hexaploid bread wheat derives from the cumulative effect of diploid progenitor divergence, the hybrid origin of the D subgenome, and subgenome partitioning following the polyploidization events.
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Affiliation(s)
- Moaine El Baidouri
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Florent Murat
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Maeva Veyssiere
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Mélanie Molinier
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Raphael Flores
- INRA UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, 78026, France
| | - Laura Burlot
- INRA UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, 78026, France
| | - Michael Alaux
- INRA UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, 78026, France
| | - Hadi Quesneville
- INRA UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, 78026, France
| | - Caroline Pont
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Jérôme Salse
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
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23
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Murat F, Louis A, Maumus F, Armero A, Cooke R, Quesneville H, Roest Crollius H, Salse J. Understanding Brassicaceae evolution through ancestral genome reconstruction. Genome Biol 2015; 16:262. [PMID: 26653025 PMCID: PMC4675067 DOI: 10.1186/s13059-015-0814-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 10/27/2015] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Brassicaceae is a family of green plants of high scientific and economic interest, including thale cress (Arabidopsis thaliana), cruciferous vegetables (cabbages) and rapeseed. RESULTS We reconstruct an evolutionary framework of Brassicaceae composed of high-resolution ancestral karyotypes using the genomes of modern A. thaliana, Arabidopsis lyrata, Capsella rubella, Brassica rapa and Thellungiella parvula. The ancestral Brassicaceae karyotype (Brassicaceae lineages I and II) is composed of eight protochromosomes and 20,037 ordered and oriented protogenes. After speciation, it evolved into the ancestral Camelineae karyotype (eight protochromosomes and 22,085 ordered protogenes) and the proto-Calepineae karyotype (seven protochromosomes and 21,035 ordered protogenes) genomes. CONCLUSIONS The three inferred ancestral karyotype genomes are shown here to be powerful tools to unravel the reticulated evolutionary history of extant Brassicaceae genomes regarding the fate of ancestral genes and genomic compartments, particularly centromeres and evolutionary breakpoints. This new resource should accelerate research in comparative genomics and translational research by facilitating the transfer of genomic information from model systems to species of agronomic interest.
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Affiliation(s)
- Florent Murat
- INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 5 Chemin de Beaulieu, 63100, Clermont Ferrand, France
| | - Alexandra Louis
- Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris, F-75005, France.,Inserm, U1024, Paris, F-75005, France.,CNRS, UMR 8197, Paris, F-75005, France
| | - Florian Maumus
- INRA UMR 1164 URGI Route de Saint Cyr, Versailles, 78026, France
| | - Alix Armero
- INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 5 Chemin de Beaulieu, 63100, Clermont Ferrand, France
| | - Richard Cooke
- CNRS/UPVD UMR 5096 LGDP, 58 avenue P. Alduy, 66860, Perpignan, Cedex, France
| | - Hadi Quesneville
- INRA UMR 1164 URGI Route de Saint Cyr, Versailles, 78026, France
| | - Hugues Roest Crollius
- Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris, F-75005, France.,Inserm, U1024, Paris, F-75005, France.,CNRS, UMR 8197, Paris, F-75005, France
| | - Jerome Salse
- INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 5 Chemin de Beaulieu, 63100, Clermont Ferrand, France.
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Genome-wide identification and expression profiling of annexins in Brassica rapa and their phylogenetic sequence comparison with B. juncea and A. thaliana annexins. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.plgene.2015.10.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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25
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Lu K, Guo W, Lu J, Yu H, Qu C, Tang Z, Li J, Chai Y, Liang Y. Genome-Wide Survey and Expression Profile Analysis of the Mitogen-Activated Protein Kinase (MAPK) Gene Family in Brassica rapa. PLoS One 2015; 10:e0132051. [PMID: 26173020 PMCID: PMC4501733 DOI: 10.1371/journal.pone.0132051] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 06/09/2015] [Indexed: 12/29/2022] Open
Abstract
Mitogen-activated protein kinase (MAPK) cascades are fundamental signal transduction modules in plants, controlling cell division, development, hormone signaling, and biotic and abiotic stress responses. Although MAPKs have been investigated in several plant species, a comprehensive analysis of the MAPK gene family has hitherto not been performed in Brassica rapa. In this study, we identified 32 MAPKs in the B. rapa genome by conducting BLASTP and syntenic block analyses, and screening for the essential signature motif (TDY or TEY) of plant MAPK proteins. Of the 32 BraMAPK genes retrieved from the Brassica Database, 13 exhibited exon splicing errors, excessive splicing of the 5' sequence, excessive retention of the 5' sequence, and sequencing errors of the 3' end. Phylogenetic trees of the 32 corrected MAPKs from B. rapa and of MAPKs from other plants generated by the neighbor-joining and maximum likelihood methods suggested that BraMAPKs could be divided into four groups (groups A, B, C, and D). Gene number expansion was observed for BraMAPK genes in groups A and D, which may have been caused by the tandem duplication and genome triplication of the ancestral genome of the Brassica progenitor. Except for five members of the BraMAPK10 subfamily, the identified BraMAPKs were expressed in most of the tissues examined, including callus, root, stem, leaf, flower, and silique. Quantitative real-time PCR demonstrated that at least six and five BraMAPKs were induced or repressed by various abiotic stresses and hormone treatments, respectively, suggesting their potential roles in the abiotic stress response and various hormone signal transduction pathways in B. rapa. This study provides valuable insight into the putative physiological and biochemical functions of MAPK genes in B. rapa.
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Affiliation(s)
- Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, PR China
- Chongqing Rapeseed Engineering Research Center, Southwest University, Beibei, Chongqing 400715, PR China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Beibei, Chongqing 400715, PR China
- * E-mail: (KL); (YL)
| | - Wenjin Guo
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, PR China
| | - Junxing Lu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, PR China
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Hao Yu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, PR China
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, PR China
- Chongqing Rapeseed Engineering Research Center, Southwest University, Beibei, Chongqing 400715, PR China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Beibei, Chongqing 400715, PR China
| | - Zhanglin Tang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, PR China
- Chongqing Rapeseed Engineering Research Center, Southwest University, Beibei, Chongqing 400715, PR China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Beibei, Chongqing 400715, PR China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, PR China
- Chongqing Rapeseed Engineering Research Center, Southwest University, Beibei, Chongqing 400715, PR China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Beibei, Chongqing 400715, PR China
| | - Yourong Chai
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, PR China
- Chongqing Rapeseed Engineering Research Center, Southwest University, Beibei, Chongqing 400715, PR China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Beibei, Chongqing 400715, PR China
| | - Ying Liang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, PR China
- Chongqing Rapeseed Engineering Research Center, Southwest University, Beibei, Chongqing 400715, PR China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Beibei, Chongqing 400715, PR China
- * E-mail: (KL); (YL)
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Large-Scale Evolutionary Analysis of Genes and Supergene Clusters from Terpenoid Modular Pathways Provides Insights into Metabolic Diversification in Flowering Plants. PLoS One 2015; 10:e0128808. [PMID: 26046541 PMCID: PMC4457800 DOI: 10.1371/journal.pone.0128808] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/30/2015] [Indexed: 12/31/2022] Open
Abstract
An important component of plant evolution is the plethora of pathways producing more than 200,000 biochemically diverse specialized metabolites with pharmacological, nutritional and ecological significance. To unravel dynamics underlying metabolic diversification, it is critical to determine lineage-specific gene family expansion in a phylogenomics framework. However, robust functional annotation is often only available for core enzymes catalyzing committed reaction steps within few model systems. In a genome informatics approach, we extracted information from early-draft gene-space assemblies and non-redundant transcriptomes to identify protein families involved in isoprenoid biosynthesis. Isoprenoids comprise terpenoids with various roles in plant-environment interaction, such as pollinator attraction or pathogen defense. Combining lines of evidence provided by synteny, sequence homology and Hidden-Markov-Modelling, we screened 17 genomes including 12 major crops and found evidence for 1,904 proteins associated with terpenoid biosynthesis. Our terpenoid genes set contains evidence for 840 core terpene-synthases and 338 triterpene-specific synthases. We further identified 190 prenyltransferases, 39 isopentenyl-diphosphate isomerases as well as 278 and 219 proteins involved in mevalonate and methylerithrol pathways, respectively. Assessing the impact of gene and genome duplication to lineage-specific terpenoid pathway expansion, we illustrated key events underlying terpenoid metabolic diversification within 250 million years of flowering plant radiation. By quantifying Angiosperm-wide versatility and phylogenetic relationships of pleiotropic gene families in terpenoid modular pathways, our analysis offers significant insight into evolutionary dynamics underlying diversification of plant secondary metabolism. Furthermore, our data provide a blueprint for future efforts to identify and more rapidly clone terpenoid biosynthetic genes from any plant species.
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27
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Cao J, Li X, Lv Y, Ding L. Comparative analysis of the phytocyanin gene family in 10 plant species: a focus on Zea mays. FRONTIERS IN PLANT SCIENCE 2015; 6:515. [PMID: 26217366 PMCID: PMC4499708 DOI: 10.3389/fpls.2015.00515] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/26/2015] [Indexed: 05/18/2023]
Abstract
Phytocyanins (PCs) are plant-specific blue copper proteins, which play essential roles in electron transport. While the origin and expansion of this gene family is not well-investigated in plants. Here, we investigated their evolution by undertaking a genome-wide identification and comparison in 10 plants: Arabidopsis, rice, poplar, tomato, soybean, grape, maize, Selaginella moellendorffii, Physcomitrella patens, and Chlamydomonas reinhardtii. We found an expansion process of this gene family in evolution. Except PCs in Arabidopsis and rice, which have described in previous researches, a structural analysis of PCs in other eight plants indicated that 292 PCs contained N-terminal secretion signals and 217 PCs were expected to have glycosylphosphatidylinositol-anchor signals. Moreover, 281 PCs had putative arabinogalactan glycomodules and might be AGPs. Chromosomal distribution and duplication patterns indicated that tandem and segmental duplication played dominant roles for the expansion of PC genes. In addition, gene organization and motif compositions are highly conserved in each clade. Furthermore, expression profiles of maize PC genes revealed diversity in various stages of development. Moreover, all nine detected maize PC genes (ZmUC10, ZmUC16, ZmUC19, ZmSC2, ZmUC21, ZmENODL10, ZmUC22, ZmENODL13, and ZmENODL15) were down-regulated under salt treatment, and five PCs (ZmUC19, ZmSC2, ZmENODL10, ZmUC22, and ZmENODL13) were down-regulated under drought treatment. ZmUC16 was strongly expressed after drought treatment. This study will provide a basis for future understanding the characterization of this family.
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Affiliation(s)
- Jun Cao
- *Correspondence: Jun Cao, Institute of Life Sciences, Jiangsu University, Xuefu Road 301, Jiangsu, Zhenjiang 212013, China,
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28
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Hofberger JA, Zhou B, Tang H, Jones JDG, Schranz ME. A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants. BMC Genomics 2014; 15:966. [PMID: 25380807 PMCID: PMC4289383 DOI: 10.1186/1471-2164-15-966] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 10/06/2014] [Indexed: 01/10/2023] Open
Abstract
Background Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene family curation is often only inferred from DNA sequence homology and lacks insights into evolutionary processes contributing to gene family dynamics. In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters composed of multi-domain resistance (R)-proteins of the NB-LRR type (for NUCLEOTIDE BINDING/LEUCINE-RICH REPEATS), that are involved in plant innate immunity. Results To assess the diversity of R-proteins within and between species, we screened twelve eudicot plant genomes including six major crops and found a total of 2,363 NB-LRR genes. Our curated R-proteins set shows a 50% average for tandem duplicates and a 22% fraction of gene copies retained from ancient polyploidy events (ohnologs). We provide evidence for strong positive selection and show significant differences in molecular evolution rates (Ka/Ks-ratio) among tandem- (mean = 1.59), ohnolog (mean = 1.36) and singleton (mean = 1.22) R-gene duplicates. To foster the process of gene-edited plant breeding, we report species-specific presence/absence of all 140 NB-LRR genes present in the model plant Arabidopsis and describe four distinct clusters of NB-LRR “gatekeeper” loci sharing syntenic orthologs across all analyzed genomes. Conclusion By curating a near-complete set of multi-domain R-protein clusters in an eudicot-wide scale, our analysis offers significant insight into evolutionary dynamics underlying diversification of the plant innate immune system. Furthermore, our methods provide a blueprint for future efforts to identify and more rapidly clone functional NB-LRR genes from any plant species. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-966) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - M Eric Schranz
- Wageningen University & Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, Gelderland, The Netherlands.
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Guo N, Cheng F, Wu J, Liu B, Zheng S, Liang J, Wang X. Anthocyanin biosynthetic genes in Brassica rapa. BMC Genomics 2014; 15:426. [PMID: 24893600 PMCID: PMC4072887 DOI: 10.1186/1471-2164-15-426] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/27/2014] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Anthocyanins are a group of flavonoid compounds. As a group of important secondary metabolites, they perform several key biological functions in plants. Anthocyanins also play beneficial health roles as potentially protective factors against cancer and heart disease. To elucidate the anthocyanin biosynthetic pathway in Brassica rapa, we conducted comparative genomic analyses between Arabidopsis thaliana and B. rapa on a genome-wide level. RESULTS In total, we identified 73 genes in B. rapa as orthologs of 41 anthocyanin biosynthetic genes in A. thaliana. In B. rapa, the anthocyanin biosynthetic genes (ABGs) have expanded and most genes exist in more than one copy. The anthocyanin biosynthetic structural genes have expanded through whole genome and tandem duplication in B. rapa. More structural genes located upstream of the anthocyanin biosynthetic pathway have been retained than downstream. More negative regulatory genes are retained in the anthocyanin biosynthesis regulatory system of B. rapa. CONCLUSIONS These results will promote an understanding of the genetic mechanism of anthocyanin biosynthesis, as well as help the improvement of the nutritional quality of B. rapa through the breeding of high anthocyanin content varieties.
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Affiliation(s)
- Ning Guo
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No.12, Haidian district Beijing, 100081 P. R. China
| | - Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No.12, Haidian district Beijing, 100081 P. R. China
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No.12, Haidian district Beijing, 100081 P. R. China
| | - Bo Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No.12, Haidian district Beijing, 100081 P. R. China
| | - Shuning Zheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No.12, Haidian district Beijing, 100081 P. R. China
| | - Jianli Liang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No.12, Haidian district Beijing, 100081 P. R. China
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie No.12, Haidian district Beijing, 100081 P. R. China
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30
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Shapiro JA. Epigenetic control of mobile DNA as an interface between experience and genome change. Front Genet 2014; 5:87. [PMID: 24795749 PMCID: PMC4007016 DOI: 10.3389/fgene.2014.00087] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/01/2014] [Indexed: 12/29/2022] Open
Abstract
Mobile DNA in the genome is subject to RNA-targeted epigenetic control. This control regulates the activity of transposons, retrotransposons and genomic proviruses. Many different life history experiences alter the activities of mobile DNA and the expression of genetic loci regulated by nearby insertions. The same experiences induce alterations in epigenetic formatting and lead to trans-generational modifications of genome expression and stability. These observations lead to the hypothesis that epigenetic formatting directed by non-coding RNA provides a molecular interface between life history events and genome alteration.
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Affiliation(s)
- James A. Shapiro
- Department of Biochemistry and Molecular Biology, University of ChicagoChicago, IL, USA
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31
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Wang Y, Wu F, Bai J, He Y. BrpSPL9 (Brassica rapa ssp. pekinensis SPL9) controls the earliness of heading time in Chinese cabbage. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:312-21. [PMID: 24237584 DOI: 10.1111/pbi.12138] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 10/10/2013] [Accepted: 10/15/2013] [Indexed: 05/21/2023]
Abstract
The leafy heads of cabbage (Brassica oleracea), Chinese cabbage (Brassica rapa ssp. pekinensis), Brussels sprouts (B. oleracea ssp. gemmifera) and lettuce (Lactuca sativa) comprise extremely incurved leaves that are edible vegetable products. The heading time is important for high quality and yield of these crops. Here, we report that BrpSPL9-2 (B. rapa ssp. pekinensis SQUAMOSA PROMOTER BINDING-LIKE 9-2), a target gene of microRNA brp-miR156, controls the heading time of Chinese cabbage. Quantitative measurements of leaf shapes, sizes, colour and curvature indicated that heading is a late adult phase of vegetative growth. During the vegetative period, miR156 levels gradually decreased from the seedling stage to the heading one, whereas BrpSPL9-2 and BrpSPL15-1 mRNAs increased progressively and reached the highest levels at the heading stage. Overexpression of a mutated miR156-resistant form of BrpSPL9-2 caused the significant earliness of heading, concurrent with shortening of the seedling and rosette stages. By contrast, overexpression of miR156 delayed the folding time, concomitant with prolongation of the seedling and rosette stages. Morphological analysis reveals that the significant earliness of heading in the transgenic plants overexpressing BrpSPL9-2 gene was produced because the juvenile phase was absent and the early adult phase shortened, whereas the significant delay of folding in the transgenic plants overexpressing Brp-MIR156a was due to prolongation of the juvenile and early adult phases. Thus, miR156 and BrpSPL9 genes are potentially important for genetic improvement of earliness of Chinese cabbage and other crops.
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Affiliation(s)
- Yali Wang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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Yang R, Jarvis DE, Chen H, Beilstein MA, Grimwood J, Jenkins J, Shu S, Prochnik S, Xin M, Ma C, Schmutz J, Wing RA, Mitchell-Olds T, Schumaker KS, Wang X. The Reference Genome of the Halophytic Plant Eutrema salsugineum. FRONTIERS IN PLANT SCIENCE 2013; 4:46. [PMID: 23518688 PMCID: PMC3604812 DOI: 10.3389/fpls.2013.00046] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 02/24/2013] [Indexed: 05/02/2023]
Abstract
Halophytes are plants that can naturally tolerate high concentrations of salt in the soil, and their tolerance to salt stress may occur through various evolutionary and molecular mechanisms. Eutrema salsugineum is a halophytic species in the Brassicaceae that can naturally tolerate multiple types of abiotic stresses that typically limit crop productivity, including extreme salinity and cold. It has been widely used as a laboratorial model for stress biology research in plants. Here, we present the reference genome sequence (241 Mb) of E. salsugineum at 8× coverage sequenced using the traditional Sanger sequencing-based approach with comparison to its close relative Arabidopsis thaliana. The E. salsugineum genome contains 26,531 protein-coding genes and 51.4% of its genome is composed of repetitive sequences that mostly reside in pericentromeric regions. Comparative analyses of the genome structures, protein-coding genes, microRNAs, stress-related pathways, and estimated translation efficiency of proteins between E. salsugineum and A. thaliana suggest that halophyte adaptation to environmental stresses may occur via a global network adjustment of multiple regulatory mechanisms. The E. salsugineum genome provides a resource to identify naturally occurring genetic alterations contributing to the adaptation of halophytic plants to salinity and that might be bioengineered in related crop species.
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Affiliation(s)
- Ruolin Yang
- School of Plant Sciences, University of ArizonaTucson, AZ, USA
| | - David E. Jarvis
- School of Plant Sciences, University of ArizonaTucson, AZ, USA
| | - Hao Chen
- School of Plant Sciences, University of ArizonaTucson, AZ, USA
| | | | - Jane Grimwood
- Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
- HudsonAlpha Institute of BiotechnologyHuntsville, AL, USA
| | - Jerry Jenkins
- Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
- HudsonAlpha Institute of BiotechnologyHuntsville, AL, USA
| | - ShengQiang Shu
- Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | - Simon Prochnik
- Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | - Mingming Xin
- School of Plant Sciences, University of ArizonaTucson, AZ, USA
| | - Chuang Ma
- School of Plant Sciences, University of ArizonaTucson, AZ, USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
- HudsonAlpha Institute of BiotechnologyHuntsville, AL, USA
| | - Rod A. Wing
- School of Plant Sciences, University of ArizonaTucson, AZ, USA
| | | | - Karen S. Schumaker
- School of Plant Sciences, University of ArizonaTucson, AZ, USA
- *Correspondence: Karen S. Schumaker and Xiangfeng Wang, School of Plant Sciences, University of Arizona, 303 Forbes Hall, 1140 E. South Campus Drive, Tucson, AZ 85721-0036, USA. e-mail: ;
| | - Xiangfeng Wang
- School of Plant Sciences, University of ArizonaTucson, AZ, USA
- *Correspondence: Karen S. Schumaker and Xiangfeng Wang, School of Plant Sciences, University of Arizona, 303 Forbes Hall, 1140 E. South Campus Drive, Tucson, AZ 85721-0036, USA. e-mail: ;
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