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Hu F, Ye Z, Zhang W, Fang D, Cao J. Decipher the molecular evolution and expression patterns of Cupin family genes in oilseed rape. Int J Biol Macromol 2023; 227:437-452. [PMID: 36549611 DOI: 10.1016/j.ijbiomac.2022.12.150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
Cupin proteins are involved in plant growth and development as well as in response to various stresses. Here, a total of 173 Cupin genes were identified in Brassica napus, and their molecular evolution and expression patterns were analyzed. These genes were classified into ten groups. Motif and exon-intron structure indicated a high degree of conservation within each group during evolution. BnaCupins were distributed on 19 chromosomes and their expansion is mainly contributed by whole-genome duplication (WGD) and segmental duplication events. BnaCupins have undergone severe purifying selection during a long evolutionary process. Meanwhile, some positive selection sites were identified. Expression patterns and cis-element analysis indicated that BnaCupins play significant roles in plant growth and stress responses. In addition, the expression levels of some BnCupins were significantly altered when treated with different conditions (cold, salt, drought, IAA, ABA, and 6-BA). Some BnaCupin interacting proteins, such as glycosyl hydrolase5 (GHs5), carbohydrate kinase (CHKs), ATP-dependent 6-phosphofructokinase (ATP-PFK), S-adenosylmethionine synthase (S-MAT), and aldolase class II (ALD II), were identified by the protein-protein interaction network. It will contribute to enriching our knowledge of the Cupin gene family in B. napus and provide a basis for further studies of their functions.
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Affiliation(s)
- Fei Hu
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Ziyi Ye
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Weimeng Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Da Fang
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Jun Cao
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu, China.
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Bretani G, Rossini L, Ferrandi C, Russell J, Waugh R, Kilian B, Bagnaresi P, Cattivelli L, Fricano A. Segmental duplications are hot spots of copy number variants affecting barley gene content. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1073-1088. [PMID: 32338390 PMCID: PMC7496488 DOI: 10.1111/tpj.14784] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 04/10/2020] [Accepted: 04/14/2020] [Indexed: 05/31/2023]
Abstract
Copy number variants (CNVs) are pervasive in several animal and plant genomes and contribute to shaping genetic diversity. In barley, there is evidence that changes in gene copy number underlie important agronomic traits. The recently released reference sequence of barley represents a valuable genomic resource for unveiling the incidence of CNVs that affect gene content and for identifying sequence features associated with CNV formation. Using exome sequencing and read count data, we detected 16 605 deletions and duplications that affect barley gene content by surveying a diverse panel of 172 cultivars, 171 landraces, 22 wild relatives and other 32 uncategorized domesticated accessions. The quest for segmental duplications (SDs) in the reference sequence revealed many low-copy repeats, most of which overlap predicted coding sequences. Statistical analyses revealed that the incidence of CNVs increases significantly in SD-rich regions, indicating that these sequence elements act as hot spots for the formation of CNVs. The present study delivers a comprehensive genome-wide study of CNVs affecting barley gene content and implicates SDs in the molecular mechanisms that lead to the formation of this class of CNVs.
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Affiliation(s)
- Gianluca Bretani
- Università degli Studi di Milano – DiSAAVia Celoria 220133MilanoItaly
| | - Laura Rossini
- Università degli Studi di Milano – DiSAAVia Celoria 220133MilanoItaly
| | - Chiara Ferrandi
- Parco Tecnologico PadanoLoc. C.na CodazzaVia Einstein26900LodiItaly
| | | | - Robbie Waugh
- James Hutton Institute, InvergowrieDundeeDD2 5DAUK
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstrasse 306466GaterslebenGermany
- Global Crop Diversity TrustPlatz der Vereinten Nationen 753113BonnGermany
| | - Paolo Bagnaresi
- Council for Agricultural Research and Economics – Research Centre for Genomics & BioinformaticsVia San Protaso 30229017Fiorenzuola d'Arda (PC)Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics – Research Centre for Genomics & BioinformaticsVia San Protaso 30229017Fiorenzuola d'Arda (PC)Italy
| | - Agostino Fricano
- Council for Agricultural Research and Economics – Research Centre for Genomics & BioinformaticsVia San Protaso 30229017Fiorenzuola d'Arda (PC)Italy
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Kong L, Zhao K, Gao Y, Miao L, Chen C, Deng H, Liu Z, Yu X. Comparative analysis of cytokinin response factors in Brassica diploids and amphidiploids and insights into the evolution of Brassica species. BMC Genomics 2018; 19:728. [PMID: 30285607 PMCID: PMC6171139 DOI: 10.1186/s12864-018-5114-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 09/25/2018] [Indexed: 12/31/2022] Open
Abstract
Background Cytokinin is a classical phytohormone that plays important roles in numerous plant growth and development processes. In plants, cytokinin signals are transduced by a two-component system, which involves many genes, including cytokinin response factors (CRFs). Although CRFs take vital part in the growth of Arabidopsis thaliana and Solanum lycopersicum, little information of the CRFs in the Brassica U-triangle species has been known yet. Results We identified and compared 141 CRFs in the diploids and amphidiploids of Brassica species, including B. rapa, B. oleracea, B. nigra, B. napus, and B. juncea. For all the 141 CRFs, the sequence and structure analysis, physiological and biochemical characteristics analysis were performed. Meanwhile, the Ka/Ks ratios of orthologous and paralogous gene pairs were calculated, which indicated the natural selective pressure upon the overall length or a certain part of the CRFs. The expression profiles of CRFs in different tissues and under various stresses were analyzed in B. oleracea, B. nigra, and B. napus. The similarities and differences in gene sequences and expression profiles among the homologous genes of these species were discussed. In addition, AtCRF11 and its ortholog BrCRF11a were identified to be related to primary root growth in Arabidopsis. Conclusion This study performed a genome-wide comparative analysis of the CRFs in the diploids and amphidiploids of the Brassica U-triangle species. Many similarities and differences in gene sequences and expression profiles existed among the CRF homologous genes of these species. In the bioinformatics analysis, we found the close relativity of the CRF homologous genes in the Brassica A and C genomes and the distinctiveness of those in the B genome, and the CRF homologous genes in B subgenome were considerably influenced by the A subgenome of B. juncea. In addition, we identified a new function of the Clade V CRFs related to root growth, which also clarified the functional conservation between Arabidopsis and B. rapa. These results not only offer useful information on the functional analysis of CRFs but also provide new insights into the evolution of Brassica species. Electronic supplementary material The online version of this article (10.1186/s12864-018-5114-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lijun Kong
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Key Laboratory of Horticultural Plant Growth, Development, and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, Zhejiang, China
| | - Kun Zhao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Key Laboratory of Horticultural Plant Growth, Development, and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, Zhejiang, China
| | - Yingying Gao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Key Laboratory of Horticultural Plant Growth, Development, and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, Zhejiang, China
| | - Liming Miao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Key Laboratory of Horticultural Plant Growth, Development, and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, Zhejiang, China
| | - Chaoquan Chen
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Key Laboratory of Horticultural Plant Growth, Development, and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, Zhejiang, China
| | - Hang Deng
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Key Laboratory of Horticultural Plant Growth, Development, and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, Zhejiang, China
| | - Zhenning Liu
- College of Agriculture and Forestry Sciences, Linyi University, Linyi, 276000, Shandong, China
| | - Xiaolin Yu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China. .,Key Laboratory of Horticultural Plant Growth, Development, and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, Zhejiang, China.
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