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Shahzad A, Fan Y, Qian M, Khan SU, Mahmood U, Wei L, Qu C, Lu K. Genome-wide characterization of Related to ABI3/VP1 transcription factors among U's triangle Brassica species reveals a negative role for BnaA06.RAV3L in seed size. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108854. [PMID: 38901228 DOI: 10.1016/j.plaphy.2024.108854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/01/2024] [Accepted: 06/16/2024] [Indexed: 06/22/2024]
Abstract
The transcription factors Related to ABI3/VP1 (RAV) are crucial for various plant processes and stress responses. Although the U's triangle Brassica species genomes have been released, the knowledge regarding the RAV family is still limited. In this study, we identified 123 putative RAV genes across the six U's triangle Brassica species (Brassica rapa, 14; Brassica oleracea, 14; Brassica nigra, 13; Brassica carinata, 27; Brassica juncea, 28; Brassica napus, 27). Phylogenetic analysis categorized them into three groups. The RAV genes exhibited diversity in both functional and structural aspects, particularly in gene structure and cis-acting elements within their promoters. The expression analysis revealed that BnaRAV genes in Group 1/2 exhibited diverse expression patterns across various tissues, while those in Group 3 did not show expression except for BnaRAV3L-2 and BnaRAV3L-6, which were exclusively expressed in seeds. Furthermore, the seed-specific expression of BnaA06. RAV3L (BnaRAV3L-2) was confirmed through promoter-GUS staining. Subcellular localization studies demonstrated that BnaA06.RAV3L is localized to the nucleus. The overexpression of BnaA06. RAV3L in Arabidopsis led to a remarkable inhibition of seed-specific traits such as seed width, seed length, seed area, and seed weight. This study provides insights into the functional evolution of the RAV gene family in U triangle Brassica species. It establishes a foundation for uncovering the molecular mechanisms underlying the negative role of RAV3L in seed development.
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Affiliation(s)
- Ali Shahzad
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Yonghai Fan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Mingchao Qian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Shahid Ullah Khan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Umer Mahmood
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Lijuan Wei
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Cunmin Qu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Kun Lu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China; Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715, China.
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Ji Z, Wang R, Zhang M, Chen L, Wang Y, Hui J, Hao S, Lv B, Jiang Q, Cao Y. Genome-Wide Identification and Expression Analysis of BrBASS Genes in Brassica rapa Reveals Their Potential Roles in Abiotic Stress Tolerance. Curr Issues Mol Biol 2024; 46:6646-6664. [PMID: 39057038 PMCID: PMC11275500 DOI: 10.3390/cimb46070396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/15/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
The bile acid sodium symporter (BASS) family plays an important role in transporting substances and coordinating plants' salt tolerance. However, the function of BASS in Brassica rapa has not yet been elucidated. In this study, eight BrBASS genes distributed on five chromosomes were identified that belonged to four subfamilies. Expression profile analysis showed that BrBASS7 was highly expressed in roots, whereas BrBASS4 was highly expressed in flowers. The promoter element analysis also identified several typical homeopathic elements involved in abiotic stress tolerance and stress-related hormonal responses. Notably, under salt stress, the expression of BrBASS2 was significantly upregulated; under osmotic stress, that of BrBASS4 increased and then decreased; and under cold stress, that of BrBASS7 generally declined. The protein-protein interaction analysis revealed that the BrBASS2 homologous gene AtBASS2 interacted with Nhd1 (N-mediated heading date-1) to alleviate salt stress in plants, while the BrBASS4 homologous gene AtBASS3 interacted with BLOS1 (biogenesis of lysosome-related organelles complex 1 subunit 1) via co-regulation with SNX1 (sorting nexin 1) to mitigate an unfavorable growing environment for roots. Further, Bra-miR396 (Bra-microRNA396) targeting BrBASS4 and BrBASS7 played a role in the plant response to osmotic and cold stress conditions, respectively. This research demonstrates that BrBASS2, BrBASS4, and BrBASS7 harbor great potential for regulating abiotic stresses. The findings will help advance the study of the functions of the BrBASS gene family.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Yunyun Cao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China; (Z.J.)
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Ren X, Chen L, Deng L, Zhao Q, Yao D, Li X, Cong W, Zang Z, Zhao D, Zhang M, Yang S, Zhang J. Comparative transcriptomic analysis reveals the molecular mechanism underlying seedling heterosis and its relationship with hybrid contemporary seeds DNA methylation in soybean. FRONTIERS IN PLANT SCIENCE 2024; 15:1364284. [PMID: 38444535 PMCID: PMC10913200 DOI: 10.3389/fpls.2024.1364284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 01/31/2024] [Indexed: 03/07/2024]
Abstract
Heterosis is widely used in crop production, but phenotypic dominance and its underlying causes in soybeans, a significant grain and oil crop, remain a crucial yet unexplored issue. Here, the phenotypes and transcriptome profiles of three inbred lines and their resulting F1 seedlings were analyzed. The results suggest that F1 seedlings with superior heterosis in leaf size and biomass exhibited a more extensive recompilation in their transcriptional network and activated a greater number of genes compared to the parental lines. Furthermore, the transcriptional reprogramming observed in the four hybrid combinations was primarily non-additive, with dominant effects being more prevalent. Enrichment analysis of sets of differentially expressed genes, coupled with a weighted gene co-expression network analysis, has shown that the emergence of heterosis in seedlings can be attributed to genes related to circadian rhythms, photosynthesis, and starch synthesis. In addition, we combined DNA methylation data from previous immature seeds and observed similar recompilation patterns between DNA methylation and gene expression. We also found significant correlations between methylation levels of gene region and gene expression levels, as well as the discovery of 12 hub genes that shared or conflicted with their remodeling patterns. This suggests that DNA methylation in contemporary hybrid seeds have an impact on both the F1 seedling phenotype and gene expression to some extent. In conclusion, our study provides valuable insights into the molecular mechanisms of heterosis in soybean seedlings and its practical implications for selecting superior soybean varieties.
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Affiliation(s)
- Xiaobo Ren
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Liangyu Chen
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
- Zhanjiang City Key Laboratory for Tropical Crops Genetic Improvement, South Subtropical Crops Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Lin Deng
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Qiuzhu Zhao
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Dan Yao
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Xueying Li
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Weixuan Cong
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Zhenyuan Zang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Dingyi Zhao
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Miao Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Songnan Yang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Jun Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
- National Crop Variety Approval and Characteristic Identification Station, Jilin Agricultural University, Changchun, China
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Zhang JF, Chu HH, Liao D, Ma GJ, Tong YK, Liu YY, Li J, Ren F. Comprehensive Evolution and Expression anaLysis of PHOSPHATE 1 Gene Family in Allotetraploid Brassica napus and Its Diploid Ancestors. Biochem Genet 2023; 61:2330-2347. [PMID: 37036640 DOI: 10.1007/s10528-023-10375-z] [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: 01/15/2023] [Accepted: 03/29/2023] [Indexed: 04/11/2023]
Abstract
The members of PHOSPHATE 1 (PHO1) family play important roles in plant phosphate (Pi) transport and adaptation to Pi deficiency. The functions of PHO1 family proteins have been reported in several plant species, with the exception of Brassica species. Here, we identified 23, 23, and 44 putative PHO1 family genes in Brassica rapa, Brassica oleracea, and Brassica napus by whole genome analysis, respectively. The phylogenetic analysis divided PHO1 family proteins into eight groups, which represented the orthologous relationships among PHO1 members. The gene structure and the conserved motif analysis indicated that the most PHO1 family genes had similar gene structures and the PHO1 proteins shared mutual conserved motifs. The chromosome distribution analysis showed that the majority of BnPHO1 family genes distributed analogously at chromosomes with BrPHO1 and BoPHO1 family genes. The data showed that PHO1 family genes were highly conserved during evolution from diploid to tetraploid. Furthermore, the expression analysis showed that PHO1 family genes had different expression patterns in plant tissues, suggesting the diversity of gene functions in Brassica species. Meanwhile, the expression analysis also revealed that some PHO1 family genes were significantly responsive to Pi deficiency, suggesting that PHO1 family genes play critical roles in Pi uptake and homeostasis under low Pi stress. Altogether, the characteristics of PHO1 family genes provide a reliable groundwork for further dissecting their functions in Brassica species.
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Affiliation(s)
- Jian-Feng Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Hui-Hui Chu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Dan Liao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Guang-Jing Ma
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yi-Kai Tong
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Ying-Ying Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Jun Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Feng Ren
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
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Sun B, Zhao X, Gao J, Li J, Xin Y, Zhao Y, Liu Z, Feng H, Tan C. Genome-wide identification and expression analysis of the GASA gene family in Chinese cabbage (Brassica rapa L. ssp. pekinensis). BMC Genomics 2023; 24:668. [PMID: 37932701 PMCID: PMC10629197 DOI: 10.1186/s12864-023-09773-9] [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: 03/27/2023] [Accepted: 10/29/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND The Gibberellic Acid-Stimulated Arabidopsis (GASA) gene family is widely involved in the regulation of plant growth, development, and stress response. However, information on the GASA gene family has not been reported in Chinese cabbage (Brassica rapa L. ssp. pekinensis). RESULTS Here, we conducted genome-wide identification and analysis of the GASA genes in Chinese cabbage. In total, 15 GASA genes were identified in the Chinese cabbage genome, and the physicochemical property, subcellular location, and tertiary structure of the corresponding GASA proteins were elucidated. Phylogenetic analysis, conserved motif, and gene structure showed that the GASA proteins were divided into three well-conserved subfamilies. Synteny analysis proposed that the expansion of the GASA genes was influenced mainly by whole-genome duplication (WGD) and transposed duplication (TRD) and that duplication gene pairs were under negative selection. Cis-acting elements of the GASA promoters were involved in plant development, hormonal and stress responses. Expression profile analysis showed that the GASA genes were widely expressed in different tissues of Chinese cabbage, but their expression patterns appeared to diverse. The qRT-PCR analysis of nine GASA genes confirmed that they responded to salt stress, heat stress, and hormonal triggers. CONCLUSIONS Overall, this study provides a theoretical basis for further exploring the important role of the GASA gene family in the functional genome of Chinese cabbage.
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Affiliation(s)
- Bingxin Sun
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Xianlei Zhao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Jiahui Gao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Jie Li
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Yue Xin
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Yonghui Zhao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Zhiyong Liu
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Hui Feng
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Chong Tan
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China.
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Roy BC, Shukla N, Gachhui R, Mukherjee A. Genome-wide analysis of glutamate receptor gene family in allopolyploid Brassica napus and its diploid progenitors. Genetica 2023; 151:293-310. [PMID: 37624443 DOI: 10.1007/s10709-023-00192-y] [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: 04/16/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023]
Abstract
Ionotropic glutamate receptors are ligand-gated nonselective cation channels that mediate neurotransmission in the central nervous system of animals. Plants possess homologous proteins called glutamate receptor-like channels (GLRs) which are involved in vital physiological processes including seed germination, long-distance signaling, chemotaxis, Ca2+ signaling etc. Till now, a comprehensive genome-wide analysis of the GLR gene family members in different economically important species of Brassica is missing. Considering the origin of allotetraploid Brassica napus from the hybridization between the diploid Brassica oleracea and Brassica rapa, we have identified 11, 27 and 65 GLR genes in B. oleracea, B. rapa and B. napus, respectively showing an expansion of this gene family in B. napus. Chromosomal locations revealed several tandemly duplicated GLR genes in all the three species. Moreover, the gene family expanded in B. napus after allopolyploidization. The phylogenetic analysis showed that the 103 GLRs are classified into three main groups. The exon-intron structures of these genes are not very conserved and showed wide variation in intron numbers. However, protein sequences are much conserved as shown by the presence of ten short amino acid sequence motifs. Predicted cis-acting elements in 1 kb promoters of GLR genes are mainly involved in light, stress and hormone responses. RNA-seq analysis showed that in B. oleracea and B. rapa, some GLRs are more tissue specific than others. In B. napus, some GLRs are downregulated under cold stress, while others are upregulated. In summary, this bioinformatic study of the GLR gene family of the three Brassica species provides evidence for the expansion of this gene family in B. napus and also provided useful information for in-depth studies of their biological functions in Brassica.
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Affiliation(s)
- Bidhan Chandra Roy
- Department of Botany, Dinabandhu Mahavidyalaya, North 24 Parganas, Bongaon, West Bengal, 743235, India
- Department of Life Science & Biotechnology, Jadavpur University, 188 Raja S.C. Mullick Road, Kolkata, West Bengal, 700032, India
| | - Nikita Shukla
- Department of Life Science & Biotechnology, Jadavpur University, 188 Raja S.C. Mullick Road, Kolkata, West Bengal, 700032, India
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, 500007, India
| | - Ratan Gachhui
- Department of Life Science & Biotechnology, Jadavpur University, 188 Raja S.C. Mullick Road, Kolkata, West Bengal, 700032, India
| | - Ashutosh Mukherjee
- Department of Botany, Vivekananda College, 269, Diamond Harbour Road, Thakurpukur, Kolkata, West Bengal, 700063, India.
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Cui S, Liu H, Wu Y, Zhang L, Nie S. Genome-Wide Identification of BrCAX Genes and Functional Analysis of BrCAX1 Involved in Ca 2+ Transport and Ca 2+ Deficiency-Induced Tip-Burn in Chinese Cabbage ( Brassica rapa L. ssp. pekinensis). Genes (Basel) 2023; 14:1810. [PMID: 37761950 PMCID: PMC10531375 DOI: 10.3390/genes14091810] [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: 09/02/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Calcium (Ca2+) plays essential roles in plant growth and development. Ca2+ deficiency causes a physiological disorder of tip-burn in Brassiceae crops and is involved in the regulation of cellular Ca2+ homeostasis. Although the functions of Ca2+/H+ exchanger antiporters (CAXs) in mediating transmembrane transport of Ca2+ have been extensively characterized in multiple plant species, the potential roles of BrCAX genes remain unclear in Chinese cabbage. In this study, eight genes of the BrCAX family were genome-widely identified in Chinese cabbage. These BrCAX proteins contained conserved Na_Ca_ex domain and belonged to five members of the CAX family. Molecular evolutionary analysis and sequence alignment revealed the evolutionary conservation of BrCAX family genes. Expression profiling demonstrated that eight BrCAX genes exhibited differential expression in different tissues and under heat stress. Furthermore, Ca2+ deficiency treatment induced the typical symptoms of tip-burn in Chinese cabbage seedlings and a significant decrease in total Ca2+ content in both roots and leaves. The expression changes in BrCAX genes were related to the response to Ca2+ deficiency-induced tip-burn of Chinese cabbage. Specially, BrCAX1-1 and BrCAX1-2 genes were highly expressed gene members of the BrCAX family in the leaves and were significantly differentially expressed under Ca2+ deficiency stress. Moreover, overexpression of BrCAX1-1 and BrCAX1-2 genes in yeast and Chinese cabbage cotyledons exhibited a higher Ca2+ tolerance, indicating the Ca2+ transport capacity of BrCAX1-1 and BrCAX1-2. In addition, suppression expression of BrCAX1-1 and BrCAX1-2 genes reduced cytosolic Ca2+ levels in the root tips of Chinese cabbage. These results provide references for functional studies of BrCAX genes and to investigate the regulatory mechanisms underlying Ca2+ deficiency disorder in Brassiceae vegetables.
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Affiliation(s)
| | | | | | | | - Shanshan Nie
- State Key Laboratory of Crop Stress Biology for Arid Area, College of Horticulture, Northwest A&F University, Xianyang 712100, China; (S.C.); (H.L.); (Y.W.); (L.Z.)
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Li T, Luo K, Wang C, Wu L, Pan J, Wang M, Liu J, Li Y, Yao J, Chen W, Zhu S, Zhang Y. GhCKX14 responding to drought stress by modulating antioxi-dative enzyme activity in Gossypium hirsutum compared to CKX family genes. BMC PLANT BIOLOGY 2023; 23:409. [PMID: 37658295 PMCID: PMC10474641 DOI: 10.1186/s12870-023-04419-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023]
Abstract
BACKGROUND Cytokinin oxidase/dehydrogenase (CKX) plays a vital role in response to abiotic stress through modulating the antioxidant enzyme activities. Nevertheless, the biological function of the CKX gene family has yet to be reported in cotton. RESULT In this study, a total of 27 GhCKXs were identified by the genome-wide investigation and distributed across 18 chromosomes. Phylogenetic tree analysis revealed that CKX genes were clustered into four clades, and most gene expansions originated from segmental duplications. The CKXs gene structure and motif analysis displayed remarkably well conserved among the four groups. Moreover, the cis-acting elements related to the abiotic stress, hormones, and light response were identified within the promoter regions of GhCKXs. Transcriptome data and RT-qPCR showed that GhCKX genes demonstrated higher expression levels in various tissues and were involved in cotton's abiotic stress and phytohormone response. The protein-protein interaction network indicates that the CKX family probably participated in redox regulation, including oxidoreduction or ATP levels, to mediate plant growth and development. Functionally identified via virus-induced gene silencing (VIGS) found that the GhCKX14 gene improved drought resistance by modulating the antioxidant-related activitie. CONCLUSIONS In this study, the CKX gene family members were analyzed by bioinformatics, and validates the response of GhCKX gene to various phytohormone treatment and abiotic stresses. Our findings established the foundation of GhCKXs in responding to abiotic stress and GhCKX14 in regulating drought resistance in cotton.
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Affiliation(s)
- Tengyu Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Kun Luo
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China
| | - Chenlei Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Lanxin Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jingwen Pan
- College of Plant Science, Tarim University, Alar, 843300, Xinjiang, China
| | - Mingyang Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan, Zhengzhou, 450001, China
| | - Jinwei Liu
- College of Plant Science, Tarim University, Alar, 843300, Xinjiang, China
| | - Yan Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jinbo Yao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Wei Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Shouhong Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Yongshan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- College of Plant Science, Tarim University, Alar, 843300, Xinjiang, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan, Zhengzhou, 450001, China.
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9
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Bian X, Cao Y, Zhi X, Ma N. Genome-Wide Identification and Analysis of the Plant Cysteine Oxidase (PCO) Gene Family in Brassica napus and Its Role in Abiotic Stress Response. Int J Mol Sci 2023; 24:11242. [PMID: 37511002 PMCID: PMC10379087 DOI: 10.3390/ijms241411242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Plant Cysteine Oxidase (PCO) is a plant O2-sensing enzyme catalyzing the oxidation of cysteine to Cys-sulfinic acid at the N-termini of target proteins. To better understand the Brassica napus PCO gene family, PCO genes in B. napus and related species were analyzed. In this study, 20, 7 and 8 PCO genes were identified in Brassica napus, Brassica rapa and Brassica oleracea, respectively. According to phylogenetic analysis, the PCOs were divided into five groups: PCO1, PCO2, PCO3, PCO4 and PCO5. Gene organization and motif distribution analysis suggested that the PCO gene family was relatively conserved during evolution. According to the public expression data, PCO genes were expressed in different tissues at different developmental stages. Moreover, qRT-PCR data showed that most of the Bna/Bra/BoPCO5 members were expressed in leaves, roots, flowers and siliques, suggesting an important role in both vegetative and reproductive development. Expression of BnaPCO was induced by various abiotic stress, especially waterlogging stress, which was consistent with the result of cis-element analysis. In this study, the PCO gene family of Brassicaceae was analyzed for the first time, which contributes to a comprehensive understanding of the origin and evolution of PCO genes in Brassicaceae and the function of BnaPCO in abiotic stress responses.
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Affiliation(s)
- Xiaohua Bian
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Yifan Cao
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Ximin Zhi
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ni Ma
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
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Chen L, Yang W, Liu S, Meng Y, Zhu Z, Liang R, Cao K, Xie Y, Li X. Genome-wide analysis and identification of light-harvesting chlorophyll a/b binding (LHC) gene family and BSMV-VIGS silencing TaLHC86 reduced salt tolerance in wheat. Int J Biol Macromol 2023; 242:124930. [PMID: 37236564 DOI: 10.1016/j.ijbiomac.2023.124930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 04/24/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023]
Abstract
The discovery and identification of gene families by using wide-genome and public databases is an effective way to gain initial insight into gene function, which also is one of the current hot spots of research. Chlorophyll ab-binding proteins (LHC) are important for photosynthesis and widely involved in plant adversity stress. However, the study in wheat has not been reported. In this study, we identified 127 TaLHC members from common wheat which were unevenly distributed on all chromosomes except 3B and 3D. All members divided into three subfamilies, LHC a, LHC b and the LHC t which was only discovered in wheat. All of them had maximum expression in leaves and contained multiple light-responsive cis-acting element, which were evidence of the extensive involvement of LHC families in photosynthesis. In addition, we also analyzed their collinear relationship, targeting relationship with miRNA and their responses under different stresses. Based on these analyses, it was found that TaLHC86 was an excellent candidate gene for stress resistance. The full-length ORF of TaLHC86 was 792 bp and was localized on the chloroplasts. The salt tolerance of wheat was reduced when BSMV-VIGS silenced TaLHC86, and the photosynthetic rate and electron transport were also seriously affected. This study made a comprehensive analysis of the TaLHC family and found that TaLHC86 was a good gene for salt tolerance.
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Affiliation(s)
- Liuping Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weibing Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Shuqing Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ying Meng
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhanhua Zhu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Rui Liang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kaiyan Cao
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanzhou Xie
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xuejun Li
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
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11
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Identification of NPF Family Genes in Brassica rapa Reveal Their Potential Functions in Pollen Development and Response to Low Nitrate Stress. Int J Mol Sci 2023; 24:ijms24010754. [PMID: 36614198 PMCID: PMC9821126 DOI: 10.3390/ijms24010754] [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: 11/04/2022] [Revised: 12/25/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
Nitrate Transporter 1/Peptide Transporter Family (NPF) genes encode membrane transporters involved in the transport of diverse substrates. However, little is known about the diversity and functions of NPFs in Brassica rapa. In this study, 85 NPFs were identified in B. rapa (BrNPFs) which comprised eight subfamilies. Gene structure and conserved motif analysis suggested that BrNFPs were conserved throughout the genus. Stress and hormone-responsive cis-acting elements and transcription factor binding sites were identified in BrNPF promoters. Syntenic analysis suggested that tandem duplication contributed to the expansion of BrNPFs in B. rapa. Transcriptomic profiling analysis indicated that BrNPF2.6, BrNPF2.15, BrNPF7.6, and BrNPF8.9 were expressed in fertile floral buds, suggesting important roles in pollen development. Thirty-nine BrNPFs were responsive to low nitrate availability in shoots or roots. BrNPF2.10, BrNPF2.19, BrNPF2.3, BrNPF5.12, BrNPF5.16, BrNPF5.8, and BrNPF6.3 were only up-regulated in roots under low nitrate conditions, indicating that they play positive roles in nitrate absorption. Furthermore, many genes were identified in contrasting genotypes that responded to vernalization and clubroot disease. Our results increase understanding of BrNPFs as candidate genes for genetic improvement studies of B. rapa to promote low nitrate availability tolerance and for generating sterile male lines based on gene editing methods.
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12
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Comprehensive Analyses of the Histone Deacetylases Tuin (HDT) Gene Family in Brassicaceae Reveals Their Roles in Stress Response. Int J Mol Sci 2022; 24:ijms24010525. [PMID: 36613968 PMCID: PMC9820156 DOI: 10.3390/ijms24010525] [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: 11/21/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022] Open
Abstract
Histone deacetylases tuin (HDT) is a plant-specific protein subfamily of histone deacetylation enzymes (HDAC) which has a variety of functions in plant development, hormone signaling and stress response. Although the HDT family's genes have been studied in many plant species, they have not been characterized in Brassicaceae. In this study, 14, 8 and 10 HDT genes were identified in Brassica napus, Brassica rapa and Brassica oleracea, respectively. According to phylogenetic analysis, the HDTs were divided into four groups: HDT1(HD2A), HDT2(HD2B), HDT3(HD2C) and HDT4(HD2D). There was an expansion of HDT2 orthologous genes in Brassicaceae. Most of the HDT genes were intron-rich and conserved in gene structure, and they coded for proteins with a nucleoplasmin-like (NPL) domain. Expression analysis showed that B. napus, B. rapa, and B. oleracea HDT genes were expressed in different organs at different developmental stages, while different HDT subgroups were specifically expressed in specific organs and tissues. Interestingly, most of the Bna/Br/BoHDT2 members were expressed in flowers, buds and siliques, suggesting they have an important role in the development of reproductive organs in Brassicaceae. Expression of BnaHDT was induced by various hormones, such as ABA and ethylene treatment, and some subgroups of genes were responsive to heat treatment. The expression of most HDT members was strongly induced by cold stress and freezing stress after non-cold acclimation, while it was slightly induced after cold acclimation. In this study, the HDT gene family of Brassicaceae was analyzed for the first time, which helps in understanding the function of BnaHDT in regulating plant responses to abiotic stresses, especially freezing stresses.
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Zhou J, Song T, Zhou H, Zhang M, Li N, Xiang J, Zhang X. Genome-wide identification, characterization, evolution, and expression pattern analyses of the typical thioredoxin gene family in wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1020584. [PMID: 36618641 PMCID: PMC9813791 DOI: 10.3389/fpls.2022.1020584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Typical thioredoxin (TRX) plays an important role in maintaining redox balance in plants. However, the typical TRX genes in wheat still need to be comprehensively and deeply studied. In this research, a total of 48 typical TaTRX genes belonging to eight subtypes were identified via a genome-wide search in wheat, and the gene structures, protein conserved motifs, and protein 3D structures of the same subtype were very similar. Evolutionary analysis showed that there are two pairs of tandem duplication genes and 14 clusters of segmental duplication genes in typical TaTRX family members; TaTRX15, TaTRX36, and TaTRX42 had positive selection compared with the orthologs of their ancestral species; rice and maize have 11 and 13 orthologous typical TRXs with wheat, respectively. Gene Ontology (GO) analysis indicated that typical TaTRXs were involved in maintaining redox homeostasis in wheat cells. Estimation of ROS content, determination of antioxidant enzyme activity, and gene expression analysis in a line overexpressing one typical TaTRX confirmed that TRX plays an important role in maintaining redox balance in wheat. A predictive analysis of cis-acting elements in the promoter region showed that typical TaTRXs were extensively involved in various hormone metabolism and response processes to stress. The results predicted using public databases or verified using RT-qPCR show that typical TaTRXs were able to respond to biotic and abiotic stresses, and their expression in wheat was spatiotemporal. A total of 16 wheat proteins belonging to four different families interacting with typical TaTRXs were predicted. The above comprehensive analysis of typical TaTRX genes can enrich our understanding of this gene family in wheat and provide valuable insights for further gene function research.
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Affiliation(s)
- Jianfei Zhou
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Tianqi Song
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Hongwei Zhou
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Mingfei Zhang
- Academy of Agricultural Sciences/Key Laboratory of Agro-Ecological Protection & Exploitation and Utilization of Animal and Plant Resources, ChiFeng University, Chifeng, Inner Mongolia, China
| | - Nan Li
- Academy of Agricultural Sciences/Key Laboratory of Agro-Ecological Protection & Exploitation and Utilization of Animal and Plant Resources, ChiFeng University, Chifeng, Inner Mongolia, China
| | - Jishan Xiang
- Academy of Agricultural Sciences/Key Laboratory of Agro-Ecological Protection & Exploitation and Utilization of Animal and Plant Resources, ChiFeng University, Chifeng, Inner Mongolia, China
| | - Xiaoke Zhang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
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14
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Wu X, Pan L, Guo X, Li T, Li J, Duan Q, Huang J. Genome-wide identification and expression analysis of BrAGC genes in Brassica rapa reveal their potential roles in sexual reproduction and abiotic stress tolerance. Front Genet 2022; 13:1044853. [PMID: 36386810 PMCID: PMC9644056 DOI: 10.3389/fgene.2022.1044853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/14/2022] [Indexed: 11/25/2022] Open
Abstract
AGC protein kinases play important roles in regulating plant growth, immunity, and cell death. However, the function of AGC in Brassica rapa has not yet been clarified. In this study, 62 BrAGC genes were identified, and these genes were distributed on 10 chromosomes and divided into six subfamilies. Analysis of gene structure and conserved motifs showed that the activation segment of BrAGC genes was highly conserved, and genes of the same subfamily showed higher sequence and structural similarity. Collinearity analysis revealed that BrAGCs were more closely related to AtAGCs than to OsAGCs. Expression profile analysis revealed that BrAGCs were preferentially expressed in flowers and BrAGC26, BrAGC33, and BrAGC04 were preferentially expressed in the stigma; the expression of these genes was significantly upregulated after self-incompatibility pollination, and the expression of BrAGC13 and BrAGC32 was significantly upregulated after cross-pollination. In addition, several typical cis-elements involved in the stress response were identified in BrAGC promoters. The expression levels of BrAGC37 and BrAGC44 significantly varied under different types of abiotic stress. Collectively, we identified that BrAGC26, BrAGC33, and BrAGC44 have the greatest potential in regulating pollen-pistil interaction and abiotic stress tolerance, respectively. Our findings will aid future functional investigations of BrAGCs in B. rapa.
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Affiliation(s)
- Xiaoyu Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, Shandong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
| | - Lianhui Pan
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, Shandong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
| | - Xinping Guo
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, Shandong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
| | - Ting Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, Shandong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
| | - Jiali Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
| | - Qiaohong Duan
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, Shandong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
| | - Jiabao Huang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, Shandong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
- *Correspondence: Jiabao Huang,
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15
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Chen L, Song B, Yu C, Zhang J, Zhang J, Bi R, Li X, Ren X, Zhu Y, Yao D, Song Y, Yang S, Zhao R. Identifying Soybean Pod Borer ( Leguminivora glycinivorella) Resistance QTLs and the Mechanism of Induced Defense Using Linkage Mapping and RNA-Seq Analysis. Int J Mol Sci 2022; 23:ijms231810910. [PMID: 36142822 PMCID: PMC9504297 DOI: 10.3390/ijms231810910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
The soybean pod borer (Leguminivora glycinivorella) (SPB) is a major cause of soybean (Glycine max L.) yield losses in northeast Asia, thus it is desirable to elucidate the resistance mechanisms involved in soybean response to the SPB. However, few studies have mapped SPB-resistant quantitative trait loci (QTLs) and deciphered the response mechanism in soybean. Here, we selected two soybean varieties, JY93 (SPB-resistant) and K6 (SPB-sensitive), to construct F2 and F2:3 populations for QTL mapping and collected pod shells before and after SPB larvae chewed on the two parents to perform RNA-Seq, which can identify stable QTLs and explore the response mechanism of soybean to the SPB. The results show that four QTLs underlying SPB damage to seeds were detected on chromosomes 4, 9, 13, and 15. Among them, qESP-9-1 was scanned in all environments, hence it can be considered a stable QTL. All QTLs explained 0.79 to 6.09% of the phenotypic variation. Meanwhile, 2298 and 3509 DEGs were identified for JY93 and K6, respectively, after the SPB attack, and most of these genes were upregulated. Gene Ontology enrichment results indicated that the SPB-induced and differently expressed genes in both parents are involved in biological processes such as wound response, signal transduction, immune response, and phytohormone pathways. Interestingly, secondary metabolic processes such as flavonoid synthesis were only significantly enriched in the upregulated genes of JY93 after SPB chewing compared with K6. Finally, we identified 18 candidate genes related to soybean pod borer resistance through the integration of QTL mapping and RNA-Seq analysis. Seven of these genes had similar expression patterns to the mapping parents in four additional soybean germplasm after feeding by the SPB. These results provide additional knowledge of the early response and induced defense mechanisms against the SPB in soybean, which could help in breeding SPB-resistant soybean accessions.
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Affiliation(s)
- Liangyu Chen
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Baixing Song
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Cheng Yu
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Jun Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
- National Crop Variety Approval and Characteristic Identification Station, Jilin Agricultural University, Changchun 130118, China
| | - Jian Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
- Department Biology, University of British Columbia-Okanagan, Kelowna, BC V1V 1V7, Canada
| | - Rui Bi
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Xueying Li
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Xiaobo Ren
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Yanyu Zhu
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Dan Yao
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Yang Song
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Songnan Yang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (S.Y.); (R.Z.)
| | - Rengui Zhao
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (S.Y.); (R.Z.)
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16
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Karamat U, Yang R, Ren Y, Lu Y, Li N, Zhao J. Comprehensive In Silico Characterization and Expression Pro-Filing of DA1/DAR Family Genes in Brassica rapa. Genes (Basel) 2022; 13:genes13091577. [PMID: 36140744 PMCID: PMC9498896 DOI: 10.3390/genes13091577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/24/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
The DA1/DAR family genes have been shown to play important roles in regulating organ size and plant biomass in the model plant Arabidopsis and several crops. However, this family has not been characterized in Brassica rapa (B. rapa). In this study, we identified 17 DA1&DAR genes from B. rapa. Phylogenetic analysis indicated that these genes are classified into four groups. Structural and motif analysis of BrDA1&DARs discovered that the genes within the same group have similar exon-intron structures and share an equal number of conserved motifs except for BrDAR6.3 from group IV, which contains two conserved motifs. Cis-regulatory elements identified four phytohormones (Salicylic acid, Abscisic acid, Gibberellin, and auxin) and three major abiotic (Light, Low temperature, and drought) responsive elements. Further, six br-miRNAs named br-miR164a, br-miR164b, br-miR164c, br-miR164d, br-miRN360, and br-miRN366 were found which target BrDAR6.1, BrDA1.4, and BrDA1.5. BrDA1&DAR genes were highly expressed in stem, root, silique, flower, leaf, and callus tissues. Moreover, qRT-PCR analyses indicated that some of these genes were responsive to abiotic stresses or phytohormone treatments. Our findings provide a foundation for further genetic and physiological studies of BrDA1&DARs in B. rapa.
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17
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Palos K, Nelson Dittrich AC, Yu L, Brock JR, Railey CE, Wu HYL, Sokolowska E, Skirycz A, Hsu PY, Gregory BD, Lyons E, Beilstein MA, Nelson ADL. Identification and functional annotation of long intergenic non-coding RNAs in Brassicaceae. THE PLANT CELL 2022; 34:3233-3260. [PMID: 35666179 PMCID: PMC9421480 DOI: 10.1093/plcell/koac166] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 05/05/2022] [Indexed: 06/01/2023]
Abstract
Long intergenic noncoding RNAs (lincRNAs) are a large yet enigmatic class of eukaryotic transcripts that can have critical biological functions. The wealth of RNA-sequencing (RNA-seq) data available for plants provides the opportunity to implement a harmonized identification and annotation effort for lincRNAs that enables cross-species functional and genomic comparisons as well as prioritization of functional candidates. In this study, we processed >24 Tera base pairs of RNA-seq data from >16,000 experiments to identify ∼130,000 lincRNAs in four Brassicaceae: Arabidopsis thaliana, Camelina sativa, Brassica rapa, and Eutrema salsugineum. We used nanopore RNA-seq, transcriptome-wide structural information, peptide data, and epigenomic data to characterize these lincRNAs and identify conserved motifs. We then used comparative genomic and transcriptomic approaches to highlight lincRNAs in our data set with sequence or transcriptional conservation. Finally, we used guilt-by-association analyses to assign putative functions to lincRNAs within our data set. We tested this approach on a subset of lincRNAs associated with germination and seed development, observing germination defects for Arabidopsis lines harboring T-DNA insertions at these loci. LincRNAs with Brassicaceae-conserved putative miRNA binding motifs, small open reading frames, or abiotic-stress modulated expression are a few of the annotations that will guide functional analyses into this cryptic portion of the transcriptome.
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Affiliation(s)
- Kyle Palos
- The Boyce Thompson Institute, Cornell University, Ithaca, New York, USA
| | | | - Li’ang Yu
- The Boyce Thompson Institute, Cornell University, Ithaca, New York, USA
| | - Jordan R Brock
- Department of Horticulture, Michigan State University, East Lansing, Michigan, USA
| | - Caylyn E Railey
- The Boyce Thompson Institute, Cornell University, Ithaca, New York, USA
| | - Hsin-Yen Larry Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | | | | | - Polly Yingshan Hsu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Eric Lyons
- The School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Mark A Beilstein
- The School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
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18
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Corona-Gomez JA, Coss-Navarrete EL, Garcia-Lopez IJ, Klapproth C, Pérez-Patiño JA, Fernandez-Valverde SL. Transcriptome-guided annotation and functional classification of long non-coding RNAs in Arabidopsis thaliana. Sci Rep 2022; 12:14063. [PMID: 35982083 PMCID: PMC9388643 DOI: 10.1038/s41598-022-18254-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/08/2022] [Indexed: 11/16/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a prominent class of eukaryotic regulatory genes. Despite the numerous available transcriptomic datasets, the annotation of plant lncRNAs remains based on dated annotations that have been historically carried over. We present a substantially improved annotation of Arabidopsis thaliana lncRNAs, generated by integrating 224 transcriptomes in multiple tissues, conditions, and developmental stages. We annotate 6764 lncRNA genes, including 3772 that are novel. We characterize their tissue expression patterns and find 1425 lncRNAs are co-expressed with coding genes, with enriched functional categories such as chloroplast organization, photosynthesis, RNA regulation, transcription, and root development. This improved transcription-guided annotation constitutes a valuable resource for studying lncRNAs and the biological processes they may regulate.
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Affiliation(s)
| | | | | | - Christopher Klapproth
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center of Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107, Leipzig, Germany.,ScaDS.AI Leipzig (Center for Scalable Data Analytics and Artificial Intelligence), Humboldstrasse 25, 04105, Leipzig, Germany
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19
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Xu S, Hao Z, Li Y, Zhou Y, Shao R, Chen R, Zheng M, Xu Y, Wang H. Biochemical toxicity and transcriptome aberration induced by dinotefuran in Bombyx mori. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 307:119562. [PMID: 35659910 DOI: 10.1016/j.envpol.2022.119562] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/20/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
Dinotefuran is a third-generation neonicotinoid pesticide and is increasingly used in agricultural production, which has adverse effects on nontarget organisms. However, the research on the impact of dinotefuran on nontarget organisms is still limited. Here the toxic effects of dinotefuran on an important economic species and a model lepidopteran insect, Bombyx mori, were investigated. Exposure to different doses of dinotefuran caused physiological disorders or death. Cytochrome P450, glutathione S-transferase, carboxylesterase, and UDP glycosyl-transferase activities were induced in the fat body at early stages after dinotefuran exposure. By contrast, only glutathione S-transferase activity was increased in the midgut. To overcome the lack of sensitivity of the biological assays at the individual organism level, RNA sequencing was performed to measure differential expressions of mRNA from silkworm larvae after dinotefuran exposure. Differential gene expression profiling revealed that various detoxification enzyme genes were significantly increased after dinotefuran exposure, which was consistent with the upregulation of the detoxifying enzyme. The global transcriptional pattern showed that the physiological responses induced by dinotefuran toxicity involved multiple cellular processes, including energy metabolism, oxidative stress, detoxification, and other fundamental physiological processes. Many metabolism processes, such as carbon metabolism, fatty acid biosynthesis, pyruvate metabolism, and the citrate cycle, were partially repressed in the midgut or fat body. Furthermore, dinotefuran significantly activated the MAPK/CREB, CncC/Keap1, PI3K/Akt, and Toll/IMD pathways. The links between physiological, biochemical toxicity and comparative transcriptomic analysis facilitated the systematic understanding of the integrated biological toxicity of dinotefuran. This study provides a holistic view of the toxicity and detoxification metabolism of dinotefuran in silkworm and other organisms.
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Affiliation(s)
- Shiliang Xu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhihua Hao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yinghui Li
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanyan Zhou
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ruixi Shao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Rui Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Meidan Zheng
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yusong Xu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Huabing Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
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20
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HSP70 Gene Family in Brassica rapa: Genome-Wide Identification, Characterization, and Expression Patterns in Response to Heat and Cold Stress. Cells 2022; 11:cells11152316. [PMID: 35954158 PMCID: PMC9367284 DOI: 10.3390/cells11152316] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/04/2022] [Accepted: 07/17/2022] [Indexed: 02/05/2023] Open
Abstract
Heat shock proteins protect plants from abiotic stress, such as salt, drought, heat, and cold stress. HSP70 is one of the major members of the heat shock protein family. To explore the mechanism of HSP70 in Brassica rapa, we identified 28 putative HSP70 gene family members using state-of-the-art bioinformatics-based tools and methods. Based on chromosomal mapping, HSP70 genes were the most differentially distributed on chromosome A03 and the least distributed on chromosome A05. Ka/Ks analysis revealed that B. rapa evolution was subjected to intense purifying selection of the HSP70 gene family. RNA-sequencing data and expression profiling showed that heat and cold stress induced HSP70 genes. The qRT-PCR results verified that the HSP70 genes in Chinese cabbage (Brassica rapa ssp. pekinensis) are stress-inducible under both cold and heat stress. The upregulated expression pattern of these genes indicated the potential of HSP70 to mitigate environmental stress. These findings further explain the molecular mechanism underlying the responses of HSP70 to heat and cold stress.
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Gu BJ, Tong YK, Wang YY, Zhang ML, Ma GJ, Wu XQ, Zhang JF, Xu F, Li J, Ren F. Genome-wide evolution and expression analysis of the MYB-CC gene family in Brassica spp. PeerJ 2022; 10:e12882. [PMID: 35237467 PMCID: PMC8884064 DOI: 10.7717/peerj.12882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 01/13/2022] [Indexed: 01/11/2023] Open
Abstract
The MYB-CC family is a subtype within the MYB superfamily. This family contains an MYB domain and a predicted coiled-coil (CC) domain. Several MYB-CC transcription factors are involved in the plant's adaptability to low phosphate (Pi) stress. We identified 30, 34, and 55 MYB-CC genes in Brassica rapa, Brassica oleracea, and Brassica napus, respectively. The MYB-CC genes were divided into nine groups based on phylogenetic analysis. The analysis of the chromosome distribution and gene structure revealed that most MYB-CC genes retained the same relative position on the chromosomes and had similar gene structures during allotetraploidy. Evolutionary analysis showed that the ancestral whole-genome triplication (WGT) and the recent allopolyploidy are critical for the expansion of the MYB-CC gene family. The expression patterns of MYB-CC genes were found to be diverse in different tissues of the three Brassica species. Furthermore, the gene expression analysis under low Pi stress revealed that MYB-CC genes may be related to low Pi stress responses. These results may increase our understanding of MYB-CC gene family diversification and provide the basis for further analysis of the specific functions of MYB-CC genes in Brassica species.
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Affiliation(s)
- Bin-Jie Gu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Yi-Kai Tong
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - You-Yi Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Mei-Li Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Guang-Jing Ma
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture and Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xiao-Qin Wu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Jian-Feng Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Fan Xu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Jun Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Feng Ren
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
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22
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Yu T, Bai Y, Liu Z, Wang Z, Yang Q, Wu T, Feng S, Zhang Y, Shen S, Li Q, Gu L, Song X. Large-scale analyses of heat shock transcription factors and database construction based on whole-genome genes in horticultural and representative plants. HORTICULTURE RESEARCH 2022; 9:uhac035. [PMID: 35184193 PMCID: PMC9123238 DOI: 10.1093/hr/uhac035] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/18/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Heat shock transcription factor (Hsf) plays a critical role in regulating heat resistance. Here, 2950 Hsf family genes were identified from 111 horticultural and representative plants. More Hsf genes were detected in higher plants than lower plants. Based on all Hsf genes, we constructed a phylogenetic tree, which indicated that Hsf genes of each branch evolved independently after species differentiation. Furthermore, we uncovered the evolutionary trajectories of Hsf genes by motif analysis. There were only 6 motifs (M1 to M6) in lower plants, and then 4 novel motifs (M7-M10) appeared in higher plants. However, the motifs of some Hsf genes were lost in higher plant, indicating that Hsf genes have undergone sequence variation during the evolution. The number of Hsf gene loss was more than duplication after whole-genome duplication in higher plants. The heat response network was constructed using 24 Hsf genes, 2421 downstream, and 222 upstream genes of Arabidopsis. Further enrichment analysis revealed that Hsf genes and other transcription factors interacted with each other to response heat resistance. The global expression maps were illustrated for Hsf genes under various abiotic, biotic stresses, and several developmental stages in Arabidopsis. The syntenic and phylogenetic analyses were conducted using Hsf genes of Arabidopsis and Pan-genome of 18 Brassica rapa accessions. We also performed the expression pattern analysis of Hsf and six Hsp family genes using expression values from different tissues and heat treatments in B. rapa. The interaction network between Hsf and Hsp gene families was constructed in B. rapa, and several core genes were detected in the network. Finally, we constructed a Hsf database (http://hsfdb.bio2db.com) for researchers to retrieve Hsf gene family information. Therefore, our study will provide rich resources for the evolution and functional study of Hsf genes.
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Affiliation(s)
- Tong Yu
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Yun Bai
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Zhuo Liu
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Zhiyuan Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Qihang Yang
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Tong Wu
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Shuyan Feng
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Yu Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Shaoqin Shen
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Qiang Li
- Faculty of Life Science, Tangshan Normal University, Tangshan 063000, Hebei, China
| | - Liqiang Gu
- Faculty of Life Science, Tangshan Normal University, Tangshan 063000, Hebei, China
| | - Xiaoming Song
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, Hebei, China
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
- Food Science and Technology Department, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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23
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Ma L, Qi W, Bai J, Li H, Fang Y, Xu J, Xu Y, Zeng X, Pu Y, Wang W, Liu L, Li X, Sun W, Wu J. Genome-Wide Identification and Analysis of the Ascorbate Peroxidase (APX) Gene Family of Winter Rapeseed (Brassica rapa L.) Under Abiotic Stress. Front Genet 2022; 12:753624. [PMID: 35126448 PMCID: PMC8814366 DOI: 10.3389/fgene.2021.753624] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/24/2021] [Indexed: 11/29/2022] Open
Abstract
Winter Brassica rapa (B. rapa) is an important oilseed crop in northern China, but the mechanism of its cold resistance remains unclear. Ascorbate peroxidase (APX) plays important roles in the response of this plant to abiotic stress and in scavenging free radicals. In this study, the roles of APX proteins in the cold response and superoxide metabolism pathways in rapeseed species were investigated, and a comprehensive analysis of phylogeny, chromosome distribution, motif identification, sequence structure, gene duplication, and RNA-seq expression profiles in the APX gene family was conducted. Most BrAPX genes were specifically expressed under cold stress and behaved significantly differently in cold-tolerant and weakly cold-resistant varieties. Quantitative real-time-PCR (qRT-PCR) was also used to verify the differences in expression between these two varieties under cold, freezing, drought and heat stress. The expression of five BrAPX genes was significantly upregulated in growth cones at 3 h of cold stress, while their expression was significantly lower at 24 h than at 3 h. The expression of Bra015403 and Bra003918 was significantly higher in “Longyou-7” growth cones than in other treatments. Five BrAPXs (Bra035235, Bra003918, Bra033040, Bra017120, and Bra031934) were closely associated with abiotic stress responses in B. rapa. These candidate genes may play important roles in the response of B. rapa to low temperature stress and provide new information for the elucidation of the cold resistance mechanism in B. rapa.
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Affiliation(s)
- Li Ma
- State Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Weiliang Qi
- College of Agriculture and Forestry, Longdong University, Qingyang, China
| | - Jing Bai
- Zhangye Academy of Agricultural Sciences, Zhangye, China
| | - Haiyun Li
- Collaborative Innovation Center for Western Ecological Safety, Lanzhou University, Lanzhou, China
| | - Yan Fang
- State Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Jia Xu
- State Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Yaozhao Xu
- College of Agronomy and Biotechnology, Hexi University, Zhangye, China
| | - Xiucun Zeng
- College of Agronomy and Biotechnology, Hexi University, Zhangye, China
| | - Yuanyuan Pu
- State Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Wangtian Wang
- State Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Lijun Liu
- State Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xuecai Li
- State Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Wancang Sun
- State Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Wancang Sun, ; Junyan Wu,
| | - Junyan Wu
- State Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Wancang Sun, ; Junyan Wu,
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24
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Chen H, Ji K, Li Y, Gao Y, Liu F, Cui Y, Liu Y, Ge W, Wang Z. Triplication is the main evolutionary driving force of NLP transcription factor family in Chinese cabbage and related species. Int J Biol Macromol 2022; 201:492-506. [PMID: 35051503 DOI: 10.1016/j.ijbiomac.2022.01.082] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/09/2022] [Accepted: 01/12/2022] [Indexed: 11/25/2022]
Abstract
The NODULE-INCEPTION-like protein (NLP) is a plant-specific transcription factor (TF) family that plays an important role in both signal transduction and nitrate assimilation. However, the NLP gene family in Chinese cabbage (Brassica rapa) has yet to be studied. Here we identified 17, 16, and 32 NLP genes in Chinese cabbage, Brassica oleracea, and Brassica napus, respectively. We found that duplication of those NLP genes almost always originated from genome-wide duplication events. Further analysis (using Arabidopsis as a reference) revealed that the NLP family in Chinese cabbage and B. oleracea was characterized by direct expansion caused by whole-genome duplication. By contrast, indirect expansion characterized B. napus, which arose from hybridization and fusion of the two species. In addition, phylogenetic and homology analyses showed that the Brassica NLP gene family has been highly conserved in evolution. Finally, we also identified optimal codons for four studied species. Altogether, through comparative genome analysis methods, we presented compelling evidence that triplication is the main driving force for the NLP TF family's evolution in Chinese cabbage and related Brassica plants, a process evidently highly conserved. This work will help in better understanding the impact of genome-wide duplication on gene families of plants.
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Affiliation(s)
- Huilong Chen
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China; School of Information Science and Technology, Yanching Institute of Technology, Langfang, Hebei 065000, China
| | - Kexin Ji
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Yuxian Li
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Yaliu Gao
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Fang Liu
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Yutong Cui
- College of Management, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Ying Liu
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Weina Ge
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China.
| | - Zhenyi Wang
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China.
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25
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Zhang Z, Guo J, Cai X, Li Y, Xi X, Lin R, Liang J, Wang X, Wu J. Improved Reference Genome Annotation of Brassica rapa by Pacific Biosciences RNA Sequencing. FRONTIERS IN PLANT SCIENCE 2022; 13:841618. [PMID: 35371168 PMCID: PMC8968949 DOI: 10.3389/fpls.2022.841618] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/17/2022] [Indexed: 05/05/2023]
Abstract
The species Brassica rapa includes several important vegetable crops. The draft reference genome of B. rapa ssp. pekinensis was completed in 2011, and it has since been updated twice. The pangenome with structural variations of 18 B. rapa accessions was published in 2021. Although extensive genomic analysis has been conducted on B. rapa, a comprehensive genome annotation including gene structure, alternative splicing (AS) events, and non-coding genes is still lacking. Therefore, we used the Pacific Biosciences (PacBio) single-molecular long-read technology to improve gene models and produced the annotated genome version 3.5. In total, we obtained 753,041 full-length non-chimeric (FLNC) reads and collapsed these into 92,810 non-redundant consensus isoforms, capturing 48% of the genes annotated in the B. rapa reference genome annotation v3.1. Based on the isoform data, we identified 830 novel protein-coding genes that were missed in previous genome annotations, defined the untranslated regions (UTRs) of 20,340 annotated genes and corrected 886 wrongly spliced genes. We also identified 28,564 AS events and 1,480 long non-coding RNAs (lncRNAs). We produced a relatively complete and high-quality reference transcriptome for B. rapa that can facilitate further functional genomic research.
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26
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Baloch AA, Raza AM, Rana SSA, Ullah S, Khan S, Zaib-un-Nisa, Zahid H, Malghani GK, Kakar KU. BrCNGC gene family in field mustard: genome-wide identification, characterization, comparative synteny, evolution and expression profiling. Sci Rep 2021; 11:24203. [PMID: 34921218 PMCID: PMC8683401 DOI: 10.1038/s41598-021-03712-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/03/2021] [Indexed: 12/30/2022] Open
Abstract
CNGCs are ligand-gated calcium signaling channels, which participate in important biological processes in eukaryotes. However, the CNGC gene family is not well-investigated in Brassica rapa L. (i.e., field mustard) that is economically important and evolutionary model crop. In this study, we systematically identified 29 member genes in BrCNGC gene family, and studied their physico-chemical properties. The BrCNGC family was classified into four major and two sub phylogenetic groups. These genes were randomly localized on nine chromosomes, and dispersed into three sub-genomes of B. rapa L. Both whole-genome triplication and gene duplication (i.e., segmental/tandem) events participated in the expansion of the BrCNGC family. Using in-silico bioinformatics approaches, we determined the gene structures, conserved motif compositions, protein interaction networks, and revealed that most BrCNGCs can be regulated by phosphorylation and microRNAs of diverse functionality. The differential expression patterns of BrCNGC genes in different plant tissues, and in response to different biotic, abiotic and hormonal stress types, suggest their strong role in plant growth, development and stress tolerance. Notably, BrCNGC-9, 27, 18 and 11 exhibited highest responses in terms of fold-changes against club-root pathogen Plasmodiophora brassicae, Pseudomonas syringae pv. maculicola, methyl-jasmonate, and trace elements. These results provide foundation for the selection of candidate BrCNGC genes for future breeding of field mustard.
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Affiliation(s)
- Akram Ali Baloch
- grid.440526.10000 0004 0609 3164Department of Biotechnology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering, and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Agha Muhammad Raza
- grid.440526.10000 0004 0609 3164Department of Microbiology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Shahjahan Shabbir Ahmed Rana
- grid.440526.10000 0004 0609 3164Department of Biotechnology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering, and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Saad Ullah
- grid.440526.10000 0004 0609 3164Department of Microbiology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Samiullah Khan
- grid.440526.10000 0004 0609 3164Department of Biotechnology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering, and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Zaib-un-Nisa
- grid.411555.10000 0001 2233 7083Department of Botany, GC University Lahore, Lahore, Pakistan
| | - Humera Zahid
- grid.413062.2Department of Zoology, University of Balochistan, Quetta, Pakistan
| | - Gohram Khan Malghani
- grid.440526.10000 0004 0609 3164Department of Environmental Sciences, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Kaleem U. Kakar
- grid.440526.10000 0004 0609 3164Department of Microbiology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
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27
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Lu YH, Alam I, Yang YQ, Yu YC, Chi WC, Chen SB, Chalhoub B, Jiang LX. Evolutionary Analysis of the YABBY Gene Family in Brassicaceae. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122700. [PMID: 34961171 PMCID: PMC8704796 DOI: 10.3390/plants10122700] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
The YABBY gene family is one of the plant transcription factors present in all seed plants. The family members were extensively studied in various plants and shown to play important roles in plant growth and development, such as the polarity establishment in lateral organs, the formation and development of leaves and flowers, and the response to internal plant hormone and external environmental stress signals. In this study, a total of 364 YABBY genes were identified from 37 Brassicaceae genomes, of which 15 were incomplete due to sequence gaps, and nine were imperfect (missing C2C2 zinc-finger or YABBY domain) due to sequence mutations. Phylogenetic analyses resolved these YABBY genes into six compact clades except for a YAB3-like gene identified in Aethionema arabicum. Seventeen Brassicaceae species each contained a complete set of six basic YABBY genes (i.e., 1 FIL, 1 YAB2, 1 YAB3, 1 YAB5, 1 INO and 1 CRC), while 20 others each contained a variable number of YABBY genes (5-25) caused mainly by whole-genome duplication/triplication followed by gene losses, and occasionally by tandem duplications. The fate of duplicate YABBY genes changed considerably according to plant species, as well as to YABBY gene type. These YABBY genes were shown to be syntenically conserved across most of the Brassicaceae species, but their functions might be considerably diverged between species, as well as between paralogous copies, as demonstrated by the promoter and expression analysis of YABBY genes in two Brassica species (B. rapa and B. oleracea). Our study provides valuable insights for understanding the evolutionary story of YABBY genes in Brassicaceae and for further functional characterization of each YABBY gene across the Brassicaceae species.
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Affiliation(s)
- Yun-Hai Lu
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.-C.Y.); (B.C.); (L.-X.J.)
| | - Intikhab Alam
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (I.A.); (Y.-Q.Y.)
| | - Yan-Qing Yang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (I.A.); (Y.-Q.Y.)
| | - Ya-Cen Yu
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.-C.Y.); (B.C.); (L.-X.J.)
| | - Wen-Chao Chi
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou 350108, China; (W.-C.C.); (S.-B.C.)
| | - Song-Biao Chen
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou 350108, China; (W.-C.C.); (S.-B.C.)
| | - Boulos Chalhoub
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.-C.Y.); (B.C.); (L.-X.J.)
| | - Li-Xi Jiang
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.-C.Y.); (B.C.); (L.-X.J.)
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28
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Guo Y, Liu J, Wang X, Li Y, Hou X, Du J. Distribution, expression and methylation analysis of positively selected genes provides insights into the evolution in Brassica rapa. PLoS One 2021; 16:e0256120. [PMID: 34624037 PMCID: PMC8500406 DOI: 10.1371/journal.pone.0256120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 07/29/2021] [Indexed: 11/18/2022] Open
Abstract
It is believed that positive selection is one of the major evolutionary forces underlying organism phenotypic diversification. Nevertheless, the characteristics of positively selected genes (PSGs), have not been well investigated. In this study, we performed a genome-wide analysis of orthologous genes between Brassica rapa (B. rapa) and Brassica oleracea (B. oleracea), and identified 468 putative PSGs. Our data show that, (1) PSGs are enriched in plant hormone signal transduction pathway and the transcription factor family; (2) PSGs are significantly lower expressed than randomly selected non-PSGs; (3) PSGs with tissue specificity are significantly higher expressed in the callus and reproductive tissues (flower and silique) than in vegetable tissues (root, stem and leaf); (4) the proportion of PSGs is positively correlated with the number of retained triplication gene copies, but the expression level of PSGs decay with the increasing of triplication gene copies; (5) the CG and CHG methylation levels of PSGs are significantly higher in introns and UTRs than in the promoter and exon regions; (6) the percent of transposable element is in proportion to the methylation level, and DNA methylation (especially in the CG content) has the tendency to reduce the expression of PSGs. This study provides insights into the characteristics, evolution, function, expression and methylation of PSGs in B. rapa.
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Affiliation(s)
- Yue Guo
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People’s Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jing Liu
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xingna Wang
- Institute of Farm Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jianchang Du
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- * E-mail:
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29
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Singh S, Chhapekar SS, Ma Y, Rameneni JJ, Oh SH, Kim J, Lim YP, Choi SR. Genome-Wide Identification, Evolution, and Comparative Analysis of B-Box Genes in Brassica rapa, B. oleracea, and B. napus and Their Expression Profiling in B. rapa in Response to Multiple Hormones and Abiotic Stresses. Int J Mol Sci 2021; 22:ijms221910367. [PMID: 34638707 PMCID: PMC8509055 DOI: 10.3390/ijms221910367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/19/2021] [Accepted: 09/22/2021] [Indexed: 11/23/2022] Open
Abstract
The B-box zinc-finger transcription factors are important for plant growth, development, and various physiological processes such as photomorphogenesis, light signaling, and flowering, as well as for several biotic and abiotic stress responses. However, there is relatively little information available regarding Brassica B-box genes and their expression. In this study, we identified 51, 52, and 101 non-redundant genes encoding B-box proteins in Brassica rapa (BrBBX genes), B. oleracea (BoBBX genes), and B. napus (BnBBX genes), respectively. A whole-genome identification, characterization, and evolutionary analysis (synteny and orthology) of the B-box gene families in the diploid species B. rapa (A genome) and B. oleracea (C genome) and in the allotetraploid species B. napus (AC genome) revealed segmental duplications were the major contributors to the expansion of the BrassicaBBX gene families. The BrassicaBBX genes were classified into five subgroups according to phylogenetic relationships, gene structures, and conserved domains. Light-responsive cis-regulatory elements were detected in many of the BBX gene promoters. Additionally, BrBBX expression profiles in different tissues and in response to various abiotic stresses (heat, cold, salt, and drought) or hormones (abscisic acid, methyl jasmonate, and gibberellic acid) were analyzed by qRT-PCR. The data indicated that many B-box genes (e.g., BrBBX13, BrBBX15, and BrBBX17) may contribute to plant development and growth as well as abiotic stress tolerance. Overall, the identified BBX genes may be useful as functional genetic markers for multiple stress responses and plant developmental processes.
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Affiliation(s)
- Sonam Singh
- Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea; (S.S.); (S.S.C.); (Y.M.); (J.J.R.); (S.H.O.)
| | - Sushil Satish Chhapekar
- Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea; (S.S.); (S.S.C.); (Y.M.); (J.J.R.); (S.H.O.)
| | - Yinbo Ma
- Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea; (S.S.); (S.S.C.); (Y.M.); (J.J.R.); (S.H.O.)
| | - Jana Jeevan Rameneni
- Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea; (S.S.); (S.S.C.); (Y.M.); (J.J.R.); (S.H.O.)
| | - Sang Heon Oh
- Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea; (S.S.); (S.S.C.); (Y.M.); (J.J.R.); (S.H.O.)
| | - Jusang Kim
- Breeding Research Institute, Dayi International Seed Co., Ltd., 16-35 Ssiat-gil, Baeksan-myeon, Gimje 54324, Jeollabuk-do, Korea;
| | - Yong Pyo Lim
- Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea; (S.S.); (S.S.C.); (Y.M.); (J.J.R.); (S.H.O.)
- Correspondence: (Y.P.L.); (S.R.C.); Tel.: +82-42-821-8846 (Y.P.L. & S.R.C.); Fax: +82-42-821-8847 (Y.P.L. & S.R.C.)
| | - Su Ryun Choi
- Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea; (S.S.); (S.S.C.); (Y.M.); (J.J.R.); (S.H.O.)
- Correspondence: (Y.P.L.); (S.R.C.); Tel.: +82-42-821-8846 (Y.P.L. & S.R.C.); Fax: +82-42-821-8847 (Y.P.L. & S.R.C.)
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Functional divergence of Brassica napus BnaABI1 paralogs in the structurally conserved PP2CA gene subfamily of Brassicaceae. Genomics 2021; 113:3185-3197. [PMID: 34182082 DOI: 10.1016/j.ygeno.2021.06.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 05/26/2021] [Accepted: 06/23/2021] [Indexed: 11/21/2022]
Abstract
Group A PP2C (PP2CA) genes form a gene subfamily whose members play an important role in regulating many biological processes by dephosphorylation of target proteins. In this study we examined the effects of evolutionary changes responsible for functional divergence of BnaABI1 paralogs in Brassica napus against the background of the conserved PP2CA gene subfamily in Brassicaceae. We performed comprehensive phylogenetic analyses of 192 PP2CA genes in 15 species in combination with protein structure homology modeling. Fundamentally, the number of PP2CA genes remained relatively constant in these taxa, except in the Brassica genus and Camelina sativa. The expansion of this gene subfamily in these species has resulted from whole genome duplication. We demonstrated a high degree of structural conservation of the PP2CA genes, with a few minor variations between the different PP2CA groups. Furthermore, the pattern of conserved sequence motifs in the PP2CA proteins and their secondary and 3D structures revealed strong conservation of the key ion-binding sites. Syntenic analysis of triplicated regions including ABI1 paralogs revealed significant structural rearrangements of the Brassica genomes. The functional and syntenic data clearly show that triplication of BnaABI1 in B. napus has had an impact on its functions, as well as the positions of adjacent genes in the corresponding chromosomal regions. The expression profiling of BnaABI1 genes showed functional divergence, i.e. subfunctionalization, potentially leading to neofunctionalization. These differences in expression are likely due to changes in the promoters of the BnaABI1 paralogs. Our results highlight the complexity of PP2CA gene subfamily evolution in Brassicaceae.
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Zhang Y, Liang J, Cai X, Chen H, Wu J, Lin R, Cheng F, Wang X. Divergence of three BRX homoeologs in Brassica rapa and its effect on leaf morphology. HORTICULTURE RESEARCH 2021; 8:68. [PMID: 33790228 PMCID: PMC8012600 DOI: 10.1038/s41438-021-00504-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/28/2020] [Accepted: 01/17/2021] [Indexed: 05/26/2023]
Abstract
The leafy head characteristic is a special phenotype of Chinese cabbage resulting from artificial selection during domestication and breeding. BREVIS RADIX (BRX) has been suggested to control root elongation, shoot growth, and tiller angle in Arabidopsis and rice. In Brassica rapa, three BrBRX homoeologs have been identified, but only BrBRX.1 and BrBRX.2 were found to be under selection in leaf-heading accessions, indicating their functional diversification in leafy head formation. Here, we show that these three BrBRX genes belong to a plant-specific BRX gene family but that they have significantly diverged from other BRX-like members on the basis of different phylogenetic classifications, motif compositions and expression patterns. Moreover, although the expression of these three BrBRX genes differed, compared with BrBRX.3, BrBRX.1, and BrBRX.2 displayed similar expression patterns. Arabidopsis mutant complementation studies showed that only BrBRX.1 could rescue the brx root phenotype, whereas BrBRX.2 and BrBRX.3 could not. However, overexpression of each of the three BrBRX genes in Arabidopsis resulted in similar pleiotropic leaf phenotypes, including epinastic leaf morphology, with an increase in leaf number and leaf petiole length and a reduction in leaf angle. These leaf traits are associated with leafy head formation. Further testing of a SNP (T/C) in BrBRX.2 confirmed that this allele in the heading accessions was strongly associated with the leaf-heading trait of B. rapa. Our results revealed that all three BrBRX genes may be involved in the leaf-heading trait, but they may have functionally diverged on the basis of their differential expression.
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Affiliation(s)
- Yuanyuan Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - Jianli Liang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - Xu Cai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - Haixu Chen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - Runmao Lin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China.
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Wu P, Zhang Y, Zhao S, Li L. Comprehensive Analysis of Evolutionary Characterization and Expression for Monosaccharide Transporter Family Genes in Nelumbo nucifera. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.537398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Sugar transporters, an important class of transporters for sugar function, regulate many processes associated with growth, maturation, and senescence processes in plants. In this study, a total of 35 NuMSTs were identified in the Nelumbo nucifera genome and grouped by conserved domains and phylogenetic analysis. Additionally, we identified 316 MST genes in 10 other representative plants and performed a comparative analysis with Nelumbo nucifera genes, including evolutionary trajectory, gene duplication, and expression pattern. A large number of analyses across plants and algae indicated that the MST family could have originated from STP and Glct, expanding to form STP and SFP by dispersed duplication. Finally, a quantitative real-time polymerase chain reaction and cis-element analysis showed that some of them may be regulated by plant hormones (e.g., abscisic acid), biotic stress factors, and abiotic factors (e.g., drought, excessive cold, and light). We found that under the four abiotic stress conditions, only NuSTP5 expression was upregulated, generating a stress response, and ARBE and LTR were present in NuSTP5. In summary, our findings are significant for understanding and exploring the molecular evolution and mechanisms of NuMSTs in plants.
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Liu B, Iwata-Otsubo A, Yang D, Baker RL, Liang C, Jackson SA, Liu S, Ma J, Zhao M. Analysis of CACTA transposase genes unveils the mechanism of intron loss and distinct small RNA silencing pathways underlying divergent evolution of Brassica genomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:34-48. [PMID: 33098166 DOI: 10.1111/tpj.15037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/19/2020] [Accepted: 10/13/2020] [Indexed: 06/11/2023]
Abstract
In comparison with retrotransposons, DNA transposons make up a smaller proportion of most plant genomes. However, these elements are often proximal to genes to affect gene expression depending on the activity of the transposons, which is largely reflected by the activity of the transposase genes. Here, we show that three AT-rich introns were retained in the TNP2-like transposase genes of the Bot1 (Brassica oleracea transposon 1) CACTA transposable elements in Brassica oleracea, but were lost in the majority of the Bot1 elements in Brassica rapa. A recent burst of transposition of Bot1 was observed in B. oleracea, but not in B. rapa. This burst of transposition is likely related to the activity of the TNP2-like transposase genes as the expression values of the transposase genes were higher in B. oleracea than in B. rapa. In addition, distinct populations of small RNAs (21, 22 and 24 nt) were detected from the Bot1 elements in B. oleracea, but the vast majority of the small RNAs from the Bot1 elements in B. rapa are 24 nt in length. We hypothesize that the different activity of the TNP2-like transposase genes is likely associated with the three introns, and intron loss is likely reverse transcriptase mediated. Furthermore, we propose that the Bot1 family is currently undergoing silencing in B. oleracea, but has already been silenced in B. rapa. Taken together, our data provide new insights into the differentiation of transposons and their role in the asymmetric evolution of these two closely related Brassica species.
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Affiliation(s)
- Beibei Liu
- Department of Biology, Miami University, Oxford, OH, 45056, USA
| | - Aiko Iwata-Otsubo
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602,, USA
| | - Diya Yang
- Department of Biology, Miami University, Oxford, OH, 45056, USA
| | - Robert L Baker
- Department of Biology, Miami University, Oxford, OH, 45056, USA
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH, 45056, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602,, USA
| | - Shengyi Liu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Meixia Zhao
- Department of Biology, Miami University, Oxford, OH, 45056, USA
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Mehraj H, Takahashi S, Miyaji N, Akter A, Suzuki Y, Seki M, Dennis ES, Fujimoto R. Characterization of Histone H3 Lysine 4 and 36 Tri-methylation in Brassica rapa L. FRONTIERS IN PLANT SCIENCE 2021; 12:659634. [PMID: 34163501 PMCID: PMC8215614 DOI: 10.3389/fpls.2021.659634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/08/2021] [Indexed: 05/10/2023]
Abstract
Covalent modifications of histone proteins act as epigenetic regulators of gene expression. We report the distribution of two active histone marks (H3K4me3 and H3K36me3) in 14-day leaves in two lines of Brassica rapa L. by chromatin immunoprecipitation sequencing. Both lines were enriched with H3K4me3 and H3K36me3 marks at the transcription start site, and the transcription level of a gene was associated with the level of H3K4me3 and H3K36me3. H3K4me3- and H3K36me3-marked genes showed low tissue-specific gene expression, and genes with both H3K4me3 and H3K36me3 had a high level of expression and were constitutively expressed. Bivalent active and repressive histone modifications such as H3K4me3 and H3K27me3 marks or antagonistic coexistence of H3K36me3 and H3K27me3 marks were observed in some genes. Expression may be susceptible to changes by abiotic and biotic stresses in genes having both H3K4me3 and H3K27me3 marks. We showed that the presence of H3K36me3 marks was associated with different gene expression levels or tissue specificity between paralogous paired genes, suggesting that H3K36me3 might be involved in subfunctionalization of the subgenomes.
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Affiliation(s)
- Hasan Mehraj
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | | | - Naomi Miyaji
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Ayasha Akter
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
- Department of Horticulture, Faculty of Agriculture, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Motoaki Seki
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- RIKEN Cluster for Pioneering Research, Saitama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Elizabeth S. Dennis
- CSIRO Agriculture and Food, Canberra, ACT, Australia
- School of Life Sciences, Faculty of Science University of Technology, Sydney, NSW, Australia
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
- *Correspondence: Ryo Fujimoto,
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Wang Z, Zhang R, Cheng Y, Lei P, Song W, Zheng W, Nie X. Genome-Wide Identification, Evolution, and Expression Analysis of LBD Transcription Factor Family in Bread Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:721253. [PMID: 34539714 PMCID: PMC8446603 DOI: 10.3389/fpls.2021.721253] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 08/09/2021] [Indexed: 05/04/2023]
Abstract
The lateral organ boundaries domain (LBD) genes, as the plant-specific transcription factor family, play a crucial role in controlling plant architecture and stress tolerance. Although it has been thoroughly characterized in many species, the LBD family was not well studied in wheat. Here, the wheat LBD family was systematically investigated through an in silico genome-wide search method. A total of 90 wheat LBD genes (TaLBDs) were identified, which were classified into class I containing seven subfamilies, and class II containing two subfamilies. Exon-intron structure, conserved protein motif, and cis-regulatory elements analysis showed that the members in the same subfamily shared similar gene structure organizations, supporting the classification. Furthermore, the expression patterns of these TaLBDs in different types of tissues and under diverse stresses were identified through public RNA-seq data analysis, and the regulation networks of TaLBDs involved were predicted. Finally, the expression levels of 12 TaLBDs were validated by quantitative PCR (qPCR) analysis and the homoeologous genes showed differential expression. Additionally, the genetic diversity of TaLBDs in the landrace population showed slightly higher than that of the genetically improved germplasm population while obvious asymmetry at the subgenome level. This study not only provided the potential targets for further functional analysis but also contributed to better understand the roles of LBD genes in regulating development and stress tolerance in wheat and beyond.
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Affiliation(s)
- Zhenyu Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, China
| | - Ruoyu Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, China
| | - Yue Cheng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, China
| | - Pengzheng Lei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, China
| | - Weining Song
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, China
- Australia-China Joint Research Centre for Abiotic and Biotic Stress Management in Agriculture, Horticulture and Forestry, Yangling, China
| | - Weijun Zheng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, China
- *Correspondence: Weijun Zheng
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, China
- Xiaojun Nie
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Wu D, Liu A, Qu X, Liang J, Song M. Genome-wide identification, and phylogenetic and expression profiling analyses, of XTH gene families in Brassica rapa L. and Brassica oleracea L. BMC Genomics 2020; 21:782. [PMID: 33176678 PMCID: PMC7656703 DOI: 10.1186/s12864-020-07153-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/14/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Xyloglucan endotransglucosylase/hydrolase genes (XTHs) are a multigene family and play key roles in regulating cell wall extensibility in plant growth and development. Brassica rapa and Brassica oleracea contain XTHs, but detailed identification and characterization of the XTH family in these species, and analysis of their tissue expression profiles, have not previously been carried out. RESULTS In this study, 53 and 38 XTH genes were identified in B. rapa and B. oleracea respectively, which contained some novel members not observed in previous studies. All XTHs of B. rapa, B. oleracea and Arabidopsis thaliana could be classified into three groups, Group I/II, III and the Early diverging group, based on phylogenetic relationships. Gene structures and motif patterns were similar within each group. All XTHs in this study contained two characteristic conserved domains (Glyco_hydro and XET_C). XTHs are located mainly in the cell wall but some are also located in the cytoplasm. Analyses of the mechanisms of gene family expansion revealed that whole-genome triplication (WGT) events and tandem duplication (TD) may have been the major mechanisms accounting for the expansion of the XTH gene family. Interestingly, TD genes all belonged to Group I/II, suggesting that TD was the main reason for the largest number of genes being in these groups. B. oleracea had lost more of the XTH genes, the conserved domain XET_C and the conserved active-site motif EXDXE compared with B. rapa, consistent with asymmetrical evolution between the two Brassica genomes. A majority of XTH genes exhibited different tissue-specific expression patterns based on RNA-seq data analyses. Moreover, there was differential expression of duplicated XTH genes in the two species, indicating that their functional differentiation occurred after B. rapa and B. oleracea diverged from a common ancestor. CONCLUSIONS We carried out the first systematic analysis of XTH gene families in B. rapa and B. oleracea. The results of this investigation can be used for reference in further studies on the functions of XTH genes and the evolution of this multigene family.
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Affiliation(s)
- Di Wu
- Qufu Normal University, College of Life Science, Qufu, 273165, P.R. China
| | - Anqi Liu
- Qufu Normal University, College of Life Science, Qufu, 273165, P.R. China
| | - Xiaoyu Qu
- Qufu Normal University, College of Life Science, Qufu, 273165, P.R. China
| | - Jiayi Liang
- Qufu Normal University, College of Life Science, Qufu, 273165, P.R. China
| | - Min Song
- Qufu Normal University, College of Life Science, Qufu, 273165, P.R. China.
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Kim W, Prokchorchik M, Tian Y, Kim S, Jeon H, Segonzac C. Perception of unrelated microbe-associated molecular patterns triggers conserved yet variable physiological and transcriptional changes in Brassica rapa ssp. pekinensis. HORTICULTURE RESEARCH 2020; 7:186. [PMID: 33328480 PMCID: PMC7603518 DOI: 10.1038/s41438-020-00410-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 05/12/2023]
Abstract
Pattern-triggered immunity (PTI) includes the different transcriptional and physiological responses that enable plants to ward off microbial invasion. Surface-localized pattern-recognition receptors (PRRs) recognize conserved microbe-associated molecular patterns (MAMPs) and initiate a branched signaling cascade that culminate in an effective restriction of pathogen growth. In the model species Arabidopsis thaliana, early PTI events triggered by different PRRs are broadly conserved although their nature or intensity is dependent on the origin and features of the detected MAMP. In order to provide a functional basis for disease resistance in leafy vegetable crops, we surveyed the conservation of PTI events in Brassica rapa ssp. pekinensis. We identified the PRR homologs present in B. rapa genome and found that only one of the two copies of the bacterial Elongation factor-Tu receptor (EFR) might function. We also characterized the extent and unexpected specificity of the transcriptional changes occurring when B. rapa seedlings are treated with two unrelated MAMPs, the bacterial flagellin flg22 peptide and the fungal cell wall component chitin. Finally, using a MAMP-induced protection assay, we could show that bacterial and fungal MAMPs elicit a robust immunity in B. rapa, despite significant differences in the kinetic and amplitude of the early signaling events. Our data support the relevance of PTI for crop protection and highlight specific functional target for disease resistance breeding in Brassica crops.
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Affiliation(s)
- Wanhui Kim
- Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea
| | - Maxim Prokchorchik
- Life Sciences Department, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Yonghua Tian
- Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seulgi Kim
- Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyelim Jeon
- Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, Republic of Korea
| | - Cécile Segonzac
- Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea.
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, Republic of Korea.
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Chai L, Zhang J, Li H, Zheng B, Jiang J, Cui C, Jiang L. Investigation for a multi-silique trait in Brassica napus by alternative splicing analysis. PeerJ 2020; 8:e10135. [PMID: 33083151 PMCID: PMC7548069 DOI: 10.7717/peerj.10135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 09/18/2020] [Indexed: 12/13/2022] Open
Abstract
Background Flower and fruit development are vital stages of the angiosperm lifecycle. We previously investigated the multi-silique trait in the rapeseed (Brassica napus) line zws-ms on a genomic and transcriptomic level, leading to the identification of two genomic regions and several candidate genes associated with this trait. However, some events on the transcriptome level, like alternative splicing, were poorly understood. Methods Plants from zws-ms and its near-isogenic line (NIL) zws-217 were both grown in Xindu with normal conditions and a colder area Ma'erkang. Buds from the two lines were sampled and RNA was isolated to perform the transcriptomic sequencing. The numbers and types of alternative splicing (AS) events from the two lines were counted and classified. Genes with AS events and expressed differentially between the two lines, as well as genes with AS events which occurred in only one line were emphasized. Their annotations were further studied. Results From the plants in Xindu District, an average of 205,496 AS events, which could be sorted into five AS types, were identified. zws-ms and zws-217 shared highly similar ratios of each AS type: The alternative 5' and 3' splice site types were the most common, while the exon skipping type was observed least often. Eleven differentially expressed AS genes were identified, of which four were upregulated and seven were downregulated in zws-ms. Their annotations implied that five of these genes were directly associated with the multi-silique trait. While samples from colder area Ma'erkang generated generally reduced number of each type of AS events except for Intron Retention; but the number of differentially expressed AS genes increased significantly. Further analysis found that among the 11 differentially expressed AS genes from Xindu, three of them maintained the same expression models, while the other eight genes did not show significant difference between the two lines in expression level. Additionally, the 205 line-specific expressed AS genes were analyzed, of which 187 could be annotated, and two were considered to be important. Discussion This study provides new insights into the molecular mechanism of the agronomically important multi-silique trait in rapeseed on the transcriptome level and screens out some environment-responding candidate genes.
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Affiliation(s)
- Liang Chai
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan Province, China
| | - Jinfang Zhang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan Province, China
| | - Haojie Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan Province, China
| | - Benchuan Zheng
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan Province, China
| | - Jun Jiang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan Province, China
| | - Cheng Cui
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan Province, China
| | - Liangcai Jiang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan Province, China
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39
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Shen C, Yuan J. Genome-Wide Investigation and Expression Analysis of K +-Transport-Related Gene Families in Chinese Cabbage (Brassica rapa ssp. pekinensis). Biochem Genet 2020; 59:256-282. [PMID: 32990910 DOI: 10.1007/s10528-020-10004-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/18/2020] [Indexed: 10/23/2022]
Abstract
Potassium (K+) transport and channel systems play vital roles in plant growth, development and responses to various stresses. In this study, 44 putative K+-transport-related genes (18K+ uptake permease (KUP)/high-affinity K+ (HAK)/K+ transporter (KT) family genes and 26 channel genes, including 18 Shaker family genes and 8K+ channel outward (KCO) family genes) were identified in the genome of Chinese cabbage (Brassica rapa ssp. pekinensis). To clarify the molecular evolution of each family in Chinese cabbage, phylogenetic analysis and assessments of the gene structures, conserved motifs, chromosomal locations, gene duplications, expression patterns and cis-acting elements of the 44 putative K+-transport-related genes were performed. The phylogenetic analysis showed that these genes could be classified into five clades [KUP/HAK/KTs, KCOs, Kout, Kin (KAT) and Kin (AKT)] and that the members of a given clade shared conserved exon-intron distributions and motif compositions. These K+-transport-related genes were unevenly distributed over all ten chromosomes, including four duplicated gene pairs that implied an expansion of K+-transport-related genes in Chinese cabbage. Analyses of Illumina RNA-seq data for these 44K+-transport-related genes indicated tissue-/organ-specific expression patterns. In addition, an overall evaluation showed that the expression levels of KUP/HAK/KT genes were significantly higher than those of potassium channel genes in six tissues. Promoter cis-acting element analysis revealed that these 44K+-transport-related genes may be associated with responses to 10 abiotic stresses, primarily light, methyl jasmonate (MeJA) and abscisic acid (ABA). Our results provide a systematic and comprehensive overview of K+-transport-related gene families in Chinese cabbage and establish a foundation for further research on K+ absorption and transport functions.
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Affiliation(s)
- Changwei Shen
- School of Resources and Environmental Sciences, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Jingping Yuan
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, 453003, China.
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Zhang Z, Tong T, Fang Y, Zheng J, Zhang X, Niu C, Li J, Zhang X, Xue D. Genome-Wide Identification of Barley ABC Genes and Their Expression in Response to Abiotic Stress Treatment. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9101281. [PMID: 32998428 PMCID: PMC7599588 DOI: 10.3390/plants9101281] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 05/15/2023]
Abstract
Adenosine triphosphate-binding cassette transporters (ABC transporters) participate in various plant growth and abiotic stress responses. In the present study, 131 ABC genes in barley were systematically identified using bioinformatics. Based on the classification method of the family in rice, these members were classified into eight subfamilies (ABCA-ABCG, ABCI). The conserved domain, amino acid composition, physicochemical properties, chromosome distribution, and tissue expression of these genes were predicted and analyzed. The results showed that the characteristic motifs of the barley ABC genes were highly conserved and there were great diversities in the homology of the transmembrane domain, the number of exons, amino acid length, and the molecular weight, whereas the span of the isoelectric point was small. Tissue expression profile analysis suggested that ABC genes possess non-tissue specificity. Ultimately, 15 differentially expressed genes exhibited diverse expression responses to stress treatments including drought, cadmium, and salt stress, indicating that the ABCB and ABCG subfamilies function in the response to abiotic stress in barley.
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Duan W, Huang Z, Li Y, Song X, Sun X, Jin C, Wang Y, Wang J. Molecular Evolutionary and Expression Pattern Analysis of AKR Genes Shed New Light on GalUR Functional Characteristics in Brassica rapa. Int J Mol Sci 2020; 21:ijms21175987. [PMID: 32825292 PMCID: PMC7503288 DOI: 10.3390/ijms21175987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 12/31/2022] Open
Abstract
The aldo-keto reductase (AKR) superfamily plays a major role in oxidation-reduction in plants. D-galacturonic acid reductase (GalUR), an ascorbic acid (AsA) biosynthetic enzyme, belongs to this superfamily. However, the phylogenetic relationship and evolutionary history of the AKR gene family in plants has not yet been clarified. In this study, a total of 1268 AKR genes identified in 36 plant species were used to determine this phylogenetic relationship. The retention, structural characteristics, and expression patterns of AKR homologous genes in Brassica rapa and Arabidopsis thaliana were analyzed to further explore their evolutionary history. We found that the AKRs originated in algae and could be divided into A and B groups according to the bootstrap value; GalURs belonged to group A. Group A AKR genes expanded significantly before the origin of angiosperms. Two groups of AKR genes demonstrated functional divergence due to environmental adaptability, while group A genes were more conservative than those in group B. All 12 candidate GalUR genes were cloned, and their expression patterns under stress were analyzed, in Pak-choi. These genes showed an obvious expression divergence under multiple stresses, and BrcAKR22 exhibited a positive correlation between its expression trend and AsA content. Our findings provide new insights into the evolution of the AKR superfamily and help build a foundation for further investigations of GalUR’s functional characteristics.
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Affiliation(s)
- Weike Duan
- College of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China; (W.D.); (X.S.); (C.J.); (Y.W.); (J.W.)
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture of Nanjing Agricultural University, Nanjing 210095, China
| | - Zhinan Huang
- College of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China; (W.D.); (X.S.); (C.J.); (Y.W.); (J.W.)
- Correspondence: (Z.H.); (Y.L.); Tel.: +86-0517-8355-9216 (Z.H.); +86-025-8439-5756 (Y.L.)
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture of Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (Z.H.); (Y.L.); Tel.: +86-0517-8355-9216 (Z.H.); +86-025-8439-5756 (Y.L.)
| | - Xiaoming Song
- School of Life Science and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan 063210, China;
| | - Xiaochuan Sun
- College of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China; (W.D.); (X.S.); (C.J.); (Y.W.); (J.W.)
| | - Cong Jin
- College of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China; (W.D.); (X.S.); (C.J.); (Y.W.); (J.W.)
| | - Yunpeng Wang
- College of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China; (W.D.); (X.S.); (C.J.); (Y.W.); (J.W.)
| | - Jizhong Wang
- College of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China; (W.D.); (X.S.); (C.J.); (Y.W.); (J.W.)
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Transcriptome Analysis and Metabolic Profiling of Green and Red Mizuna ( Brassica rapa L. var. japonica). Foods 2020; 9:foods9081079. [PMID: 32784373 PMCID: PMC7466343 DOI: 10.3390/foods9081079] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 11/17/2022] Open
Abstract
Mizuna (Brassica rapa L. var. japonica), a member of the family Brassicaceae, is rich in various health-beneficial phytochemicals, such as glucosinolates, phenolics, and anthocyanins. However, few studies have been conducted on genes associated with metabolic traits in mizuna. Thus, this study provides a better insight into the metabolic differences between green and red mizuna via the integration of transcriptome and metabolome analyses. A mizuna RNAseq analysis dataset showed 257 differentially expressed unigenes (DEGs) with a false discovery rate (FDR) of <0.05. These DEGs included the biosynthesis genes of secondary metabolites, such as anthocyanins, glucosinolates, and phenolics. Particularly, the expression of aliphatic glucosinolate biosynthetic genes was higher in the green cultivar. In contrast, the expression of most genes related to indolic glucosinolates, phenylpropanoids, and flavonoids was higher in the red cultivar. Furthermore, the metabolic analysis showed that 14 glucosinolates, 12 anthocyanins, five phenolics, and two organic acids were detected in both cultivars. The anthocyanin levels were higher in red than in green mizuna, while the glucosinolate levels were higher in green than in red mizuna. Consistent with the results of phytochemical analyses, the transcriptome data revealed that the expression levels of the phenylpropanoid and flavonoid biosynthesis genes were significantly higher in red mizuna, while those of the glucosinolate biosynthetic genes were significantly upregulated in green mizuna. A total of 43 metabolites, such as amino acids, carbohydrates, tricarboxylic acid (TCA) cycle intermediates, organic acids, and amines, was identified and quantified in both cultivars using gas chromatography coupled with time-of-flight mass spectrometry (GC-TOFMS). Among the identified metabolites, sucrose was positively correlated with anthocyanins, as previously reported.
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Lu X, Cheng Y, Gao M, Li M, Xu X. Molecular Characterization, Expression Pattern and Function Analysis of Glycine-Rich Protein Genes Under Stresses in Chinese Cabbage ( Brassica rapa L. ssp. pekinensis). Front Genet 2020; 11:774. [PMID: 32849790 PMCID: PMC7396569 DOI: 10.3389/fgene.2020.00774] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/30/2020] [Indexed: 11/15/2022] Open
Abstract
Plant Glycine-rich proteins (GRP), a superfamily with a glycine-rich domain, play an important role in various stresses such as high or low temperature stress and drought stress. GRP genes have been studied in many plants, but seldom in Chinese cabbage (Brassica rapa L. ssp. pekinensis). In this study, a total of 64 GRP genes were identified in Chinese cabbage by homology comparative analysis. The physical and chemical characteristics predicted by ProtParam tool revealed that 62.5% of BrGRPs were alkaline, 53.1% were stable, and 79.7% were hydrophilic. Conserved domain analysis by MEME and TBtools showed that 64 BrGRPs contained 20 of the same conserved motifs, based on which BrGRPs were classified into five main classes and four subclasses in class IV to clarify their evolutionary relationship. Our results demonstrated that The BrGRP genes were located on ten chromosomes and in three different subgenomes of Chinese cabbage, and 43 pairs of orthologous GRP genes were found between Chinese cabbage and Arabidopsis. According to the transcriptome data, 64 BrGRP genes showed abnormal expression under high temperature stress, 52 under low temperature stress, 39 under drought stress, and 23 responses to soft rot. A large number of stress-related cis-acting elements, such as DRE, MYC, MYB, and ABRE were found in their promoter regions by PlantCare, which corresponded with differential expressions. Two BrGRP genes-w546 (Bra030284) and w1409 (Bra014000), both belonging to the subfamily Subclass IVa RBP-GRP (RNA binding protein-glycine rich protein), were up-regulated under 150 mmol⋅L-1 NaCl stress in Chinese cabbage. However, the overexpressed w546 gene could significantly inhibit seed germination, while w1409 significantly accelerated seed germination under 100 mmol⋅L-1 NaCl or 300 mmol⋅L-1 mannitol stresses. In short, most BrGRP genes showed abnormal expression under adversity stress, and some were involved in multiple stress responses, suggesting a potential capacity to resist multiple biotic and abiotic stresses, which is worthy of further study. Our study provides a systematic investigation of the molecular characteristics and expression patterns of BrGRP genes and promotes for further work on improving stress resistance of Chinese cabbage.
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Affiliation(s)
| | | | | | | | - Xiaoyong Xu
- College of Horticulture, Shanxi Agricultural University; and Collaborative Innovation Center for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi, Taigu, China
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Mooney BC, Graciet E. A simple and efficient Agrobacterium-mediated transient expression system to dissect molecular processes in Brassica rapa and Brassica napus. PLANT DIRECT 2020; 4:e00237. [PMID: 32775949 PMCID: PMC7403836 DOI: 10.1002/pld3.237] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/05/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
The family Brassicaceae is a source of important crop species, including Brassica napus (oilseed rape), Brassica oleracea, and B. rapa, that is used globally for oil production or as a food source (e.g., pak choi or turnip). However, despite advances in recent years, including genome sequencing, a lack of established tools tailored to the study of Brassica crop species has impeded efforts to understand their molecular processes in greater detail. Here, we describe the use of a simple Agrobacterium-mediated transient expression system adapted to B. rapa and B. napus that could facilitate study of molecular and biochemical events in these species. We also demonstrate the use of this method to characterize the N-degron pathway of protein degradation in B. rapa. The N-degron pathway is a subset of the ubiquitin-proteasome system and represents a mechanism through which proteins may be targeted for degradation based on the identity of their N-terminal amino acid residue. Interestingly, N-degron-mediated processes in plants have been implicated in the regulation of traits with potential agronomic importance, including the responses to pathogens and to abiotic stresses such as flooding tolerance. The stability of transiently expressed N-degron reporter proteins in B. rapa indicates that its N-degron pathway is highly conserved with that of Arabidopsis thaliana. These findings highlight the utility of Agrobacterium-mediated transient expression in B. rapa and B. napus and establish a framework to investigate the N-degron pathway and its roles in regulating agronomical traits in these species. SIGNIFICANCE STATEMENT We describe an Agrobacterium-mediated transient expression system applicable to Brassica crops and demonstrate its utility by identifying the destabilizing residues of the N-degron pathway in B. rapa. As the N-degron pathway functions as an integrator of environmental signals, this study could facilitate efforts to improve the robustness of Brassica crops.
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Affiliation(s)
| | - Emmanuelle Graciet
- Department of BiologyMaynooth UniversityMaynoothIreland
- Kathleen Lonsdale Institute for Human Health ResearchMaynooth UniversityMaynoothIreland
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45
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Chen G, Wang J, Wang H, Wang C, Tang X, Li J, Zhang L, Song J, Hou J, Yuan L. Genome-wide analysis of proline-rich extension-like receptor protein kinase (PERK) in Brassica rapa and its association with the pollen development. BMC Genomics 2020; 21:401. [PMID: 32539701 PMCID: PMC7296749 DOI: 10.1186/s12864-020-06802-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 06/02/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Proline-rich extension-like receptor protein kinases (PERKs) are an important class of receptor kinases located in the plasma membrane, most of which play a vital role in pollen development. RESULTS Our study identified 25 putative PERK genes from the whole Brassica rapa genome (AA). Phylogenetic analysis of PERK protein sequences from 16 Brassicaceae species divided them into four subfamilies. The biophysical properties of the BrPERKs were investigated. Gene duplication and synteny analyses and the calculation of Ka/Ks values suggested that all 80 orthologous/paralogous gene pairs between B. rapa and A. thaliana, B. nigra and B. oleracea have experienced strong purifying selection. RNA-Seq data and qRT-PCR analyses showed that several BrPERK genes were expressed in different tissues, while some BrPERKs exhibited high expression levels only in buds. Furthermore, comparative transcriptome analyses from six male-sterile lines of B. rapa indicated that 7 BrPERK genes were downregulated in all six male-sterile lines. Meanwhile, the interaction networks of the BrPERK genes were constructed and 13 PERK coexpressed genes were identified, most of which were downregulated in the male sterile buds. CONCLUSION Combined with interaction networks, coexpression and qRT-PCR analyses, these results demonstrated that two BrPERK genes, Bra001723.1 and Bra037558.1 (the orthologs of AtPERK6 (AT3G18810)), were downregulated beginning in the meiosis II period of male sterile lines and involved in anther development. Overall, this comprehensive analysis of some BrPERK genes elucidated their roles in male sterility.
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Affiliation(s)
- Guohu Chen
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China. .,Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei, 230036, China. .,Wanjiang Vegetable Industrial Technology Institute, Maanshan, 238200, China.
| | - Jian Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China.,Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei, 230036, China
| | - Hao Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Chenggang Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China. .,Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei, 230036, China. .,Wanjiang Vegetable Industrial Technology Institute, Maanshan, 238200, China.
| | - Xiaoyan Tang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China.,Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei, 230036, China
| | - Jie Li
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Lei Zhang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Jianghua Song
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Jinfeng Hou
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Lingyun Yuan
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China
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Liu W, Lyu T, Xu L, Hu Z, Xiong X, Liu T, Cao J. Complex Molecular Evolution and Expression of Expansin Gene Families in Three Basic Diploid Species of Brassica. Int J Mol Sci 2020; 21:ijms21103424. [PMID: 32408673 PMCID: PMC7279145 DOI: 10.3390/ijms21103424] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/07/2020] [Accepted: 05/11/2020] [Indexed: 12/12/2022] Open
Abstract
Expansins are a kind of structural proteins of the plant cell wall, and they enlarge cells by loosening the cell walls. Therefore, expansins are involved in many growth and development processes. The complete genomic sequences of Brassica rapa, Brassica oleracea and Brassica nigra provide effective platforms for researchers to study expansin genes, and can be compared with analogues in Arabidopsis thaliana. This study identified and characterized expansin families in B. rapa, B. oleracea, and B. nigra. Through the comparative analysis of phylogeny, gene structure, and physicochemical properties, the expansin families were divided into four subfamilies, and then their expansion patterns and evolution details were explored accordingly. Results showed that after the three species underwent independent evolution following their separation from A. thaliana, the expansin families in the three species had increased similarities but fewer divergences. By searching divergences of promoters and coding sequences, significant positive correlations were revealed among orthologs in A. thaliana and the three basic species. Subsequently, differential expressions indicated extensive functional divergences in the expansin families of the three species, especially in reproductive development. Hence, these results support the molecular evolution of basic Brassica species, potential functions of these genes, and genetic improvement of related crops.
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Affiliation(s)
- Weimiao Liu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (W.L.); (T.L.); (L.X.); (Z.H.); (X.X.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Tianqi Lyu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (W.L.); (T.L.); (L.X.); (Z.H.); (X.X.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Liai Xu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (W.L.); (T.L.); (L.X.); (Z.H.); (X.X.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Ziwei Hu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (W.L.); (T.L.); (L.X.); (Z.H.); (X.X.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Xingpeng Xiong
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (W.L.); (T.L.); (L.X.); (Z.H.); (X.X.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Tingting Liu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (W.L.); (T.L.); (L.X.); (Z.H.); (X.X.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Jiashu Cao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (W.L.); (T.L.); (L.X.); (Z.H.); (X.X.); (T.L.)
- 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
- Correspondence: ; Tel.: +86-571-8898-2597
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Red Chinese Cabbage Transcriptome Analysis Reveals Structural Genes and Multiple Transcription Factors Regulating Reddish Purple Color. Int J Mol Sci 2020; 21:ijms21082901. [PMID: 32326209 PMCID: PMC7215907 DOI: 10.3390/ijms21082901] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/16/2020] [Accepted: 04/18/2020] [Indexed: 02/06/2023] Open
Abstract
Reddish purple Chinese cabbage (RPCC) is a popular variety of Brassica rapa (AA = 20). It is rich in anthocyanins, which have many health benefits. We detected novel anthocyanins including cyanidin 3-(feruloyl) diglucoside-5-(malonoyl) glucoside and pelargonidin 3-(caffeoyl) diglucoside-5-(malonoyl) glucoside in RPCC. Analyses of transcriptome data revealed 32,395 genes including 3345 differentially expressed genes (DEGs) between 3-week-old RPCC and green Chinese cabbage (GCC). The DEGs included 218 transcription factor (TF) genes and some functionally uncharacterized genes. Sixty DEGs identified from the transcriptome data were analyzed in 3-, 6- and 9-week old seedlings by RT-qPCR, and 35 of them had higher transcript levels in RPCC than in GCC. We detected cis-regulatory motifs of MYB, bHLH, WRKY, bZIP and AP2/ERF TFs in anthocyanin biosynthetic gene promoters. A network analysis revealed that MYB75, MYB90, and MYBL2 strongly interact with anthocyanin biosynthetic genes. Our results show that the late biosynthesis genes BrDFR, BrLDOX, BrUF3GT, BrUGT75c1-1, Br5MAT, BrAT-1,BrAT-2, BrTT19-1, and BrTT19-2 and the regulatory MYB genes BrMYB90, BrMYB75, and BrMYBL2-1 are highly expressed in RPCC, indicative of their important roles in anthocyanin biosynthesis, modification, and accumulation. Finally, we propose a model anthocyanin biosynthesis pathway that includes the unique anthocyanin pigments and genes specific to RPCC.
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48
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Xue Y, Jiang J, Yang X, Jiang H, Du Y, Liu X, Xie R, Chai Y. Genome-wide mining and comparative analysis of fatty acid elongase gene family in Brassica napus and its progenitors. Gene 2020; 747:144674. [PMID: 32304781 DOI: 10.1016/j.gene.2020.144674] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 03/24/2020] [Accepted: 04/14/2020] [Indexed: 12/31/2022]
Abstract
Very long chain fatty acids (VLCFAs) that are structural components of cell membrane lipid, cuticular waxes and seed oil, play crucial roles in plant growth, development and stress response. Fatty acid elongases (FAEs) comprising KCS and ELO, are key enzymes for VLCFA biosynthesis in plants. Although reference genomes of Brassica napus and its parental speices both have been sequenced, whole-genome analysis of FAE gene family in these Brassica speices is not reported. Here, 58, 33 and 30 KCS genes were identified in B. napus, B. rapa and B. oleracea genomes, respectively, whereas 14, 6 and 8 members were obtained for ELO genes. These KCS genes were unevenly located in 37 chromosomes and 3 scaffolds of 3 Brassica species, while these ELO genes were mapped to 19 chromosomes. The KCS and ELO proteins were divided into 8 and 4 subclasses, respectively. Gene structure and protein motifs remained highly conserved in each KCS or ELO subclass. Most promoters of KCS and ELO genes harbored various plant growth-, phytohormone-, and stress response-related cis-acting elements. 20 SSR loci existed in the KCS and ELO genes/promoters. The whole-genome duplication and segmental duplication mainly contributed to expansion of KCS and ELO genes in these genomes. Transcriptome analysis showed that KCS and ELO genes in 3 Brassica species were expressed in various tissues/organs with different levels, whereas 1 BnELO gene and 6 BnKCS genes might be pathogen-responsive genes. The qRT-PCR assay showed that BnKCS22 and BnELO04 responded to various phytohormone treatments and abiotic stresses. This work lays the foundation for further function identification of KCS and ELO genes in B. napus and its progenitors.
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Affiliation(s)
- Yufei Xue
- College of Agronomy and Biotechnology, Chongqing Rapeseed Engineering Research Center, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Jiayi Jiang
- College of Agronomy and Biotechnology, Chongqing Rapeseed Engineering Research Center, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Xia Yang
- College of Agronomy and Biotechnology, Chongqing Rapeseed Engineering Research Center, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Huanhuan Jiang
- College of Agronomy and Biotechnology, Chongqing Rapeseed Engineering Research Center, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Youjie Du
- College of Agronomy and Biotechnology, Chongqing Rapeseed Engineering Research Center, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Xiaodan Liu
- College of Agronomy and Biotechnology, Chongqing Rapeseed Engineering Research Center, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Ruifang Xie
- College of Agronomy and Biotechnology, Chongqing Rapeseed Engineering Research Center, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Yourong Chai
- College of Agronomy and Biotechnology, Chongqing Rapeseed Engineering Research Center, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China.
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Akter A, Takahashi S, Deng W, Shea DJ, Itabashi E, Shimizu M, Miyaji N, Osabe K, Nishida N, Suzuki Y, Helliwell CA, Seki M, Peacock WJ, Dennis ES, Fujimoto R. The histone modification H3 lysine 27 tri-methylation has conserved gene regulatory roles in the triplicated genome of Brassica rapa L. DNA Res 2020; 26:433-443. [PMID: 31622476 PMCID: PMC6796510 DOI: 10.1093/dnares/dsz021] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 08/30/2019] [Indexed: 01/08/2023] Open
Abstract
Brassica rapa L. is an important vegetable and oilseed crop. We investigated the distribution of the histone mark tri-methylation of H3K27 (H3K27me3) in B. rapa and its role in the control of gene expression at two stages of development (2-day cotyledons and 14-day leaves) and among paralogs in the triplicated genome. H3K27me3 has a similar distribution in two inbred lines, while there was variation of H3K27me3 sites between tissues. Sites that are specific to 2-day cotyledons have increased transcriptional activity, and low levels of H3K27me3 in the gene body region. In 14-day leaves, levels of H3K27me3 were associated with decreased gene expression. In the triplicated genome, H3K27me3 is associated with paralogs that have tissue-specific expression. Even though B. rapa and Arabidopsis thaliana are not closely related within the Brassicaceae, there is conservation of H3K27me3-marked sites in the two species. Both B. rapa and A. thaliana require vernalization for floral initiation with FLC being the major controlling locus. In all four BrFLC paralogs, low-temperature treatment increases H3K27me3 at the proximal nucleation site reducing BrFLC expression. Following return to normal temperature growth conditions, H3K27me3 spreads along all four BrFLC paralogs providing stable repression of the gene.
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Affiliation(s)
- Ayasha Akter
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Satoshi Takahashi
- Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, Japan
| | - Weiwei Deng
- Centre for Crop and Disease Management (CCDM), School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Daniel J Shea
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Etsuko Itabashi
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Motoki Shimizu
- Department of Genomics and Breeding, Iwate Biotechnology Research Center, Narita, Kitakami, Iwate, Japan
| | - Naomi Miyaji
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Kenji Osabe
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Namiko Nishida
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | | | - Motoaki Seki
- Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, Japan.,Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, Japan.,Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
| | - William James Peacock
- Agriculture and Food, CSIRO, Canberra, ACT, Australia.,Department of Life Sciences, University of Technology, Sydney, Broadway, NSW, Australia
| | - Elizabeth S Dennis
- Agriculture and Food, CSIRO, Canberra, ACT, Australia.,Department of Life Sciences, University of Technology, Sydney, Broadway, NSW, Australia
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
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50
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Comprehensive analyses of the annexin (ANN) gene family in Brassica rapa, Brassica oleracea and Brassica napus reveals their roles in stress response. Sci Rep 2020; 10:4295. [PMID: 32152363 PMCID: PMC7062692 DOI: 10.1038/s41598-020-59953-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/13/2019] [Indexed: 12/02/2022] Open
Abstract
Annexins (ANN) are a multigene, evolutionarily conserved family of calcium-dependent and phospholipid-binding proteins that play important roles in plant development and stress resistance. However, a systematic comprehensive analysis of ANN genes of Brassicaceae species (Brassica rapa, Brassica oleracea, and Brassica napus) has not yet been reported. In this study, we identified 13, 12, and 26 ANN genes in B. rapa, B. oleracea, and B. napus, respectively. About half of these genes were clustered on various chromosomes. Molecular evolutionary analysis showed that the ANN genes were highly conserved in Brassicaceae species. Transcriptome analysis showed that different group ANN members exhibited varied expression patterns in different tissues and under different (abiotic stress and hormones) treatments. Meanwhile, same group members from Arabidopsis thaliana, B. rapa, B. oleracea, and B. napus demonstrated conserved expression patterns in different tissues. The weighted gene coexpression network analysis (WGCNA) showed that BnaANN genes were induced by methyl jasmonate (MeJA) treatment and played important roles in jasmonate (JA) signaling and multiple stress response in B. napus.
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