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Jin Z, Zhou T, Chen J, Lang C, Zhang Q, Qin J, Lan H, Li J, Zeng X. Genome-wide identification and expression analysis of the BZR gene family in Zanthoxylum armatum DC and functional analysis of ZaBZR1 in drought tolerance. PLANTA 2024; 260:41. [PMID: 38954109 DOI: 10.1007/s00425-024-04469-0] [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: 12/20/2023] [Accepted: 06/19/2024] [Indexed: 07/04/2024]
Abstract
MAIN CONCLUSION In this study, six ZaBZRs were identified in Zanthoxylum armatum DC, and all the ZaBZRs were upregulated by abscisic acid (ABA) and drought. Overexpression of ZaBZR1 enhanced the drought tolerance of transgenic Nicotiana benthamian. Brassinosteroids (BRs) are a pivotal class of sterol hormones in plants that play a crucial role in plant growth and development. BZR (brassinazole resistant) is a crucial transcription factor in the signal transduction pathway of BRs. However, the BZR gene family members have not yet been identified in Zanthoxylum armatum DC. In this study, six members of the ZaBZR family were identified by bioinformatic methods. All six ZaBZRs exhibited multiple phosphorylation sites. Phylogenetic and collinearity analyses revealed a closest relationship between ZaBZRs and ZbBZRs located on the B subgenomes. Expression analysis revealed tissue-specific expression patterns of ZaBZRs in Z. armatum, and their promoter regions contained cis-acting elements associated with hormone response and stress induction. Additionally, all six ZaBZRs showed upregulation upon treatment after abscisic acid (ABA) and polyethylene glycol (PEG), indicating their participation in drought response. Subsequently, we conducted an extensive investigation of ZaBZR1. ZaBZR1 showed the highest expression in the root, followed by the stem and terminal bud. Subcellular localization analysis revealed that ZaBZR1 is present in the cytoplasm and nucleus. Overexpression of ZaBZR1 in transgenic Nicotiana benthamiana improved seed germination rate and root growth under drought conditions, reducing water loss rates compared to wild-type plants. Furthermore, ZaBZR1 increased proline content (PRO) and decreased malondialdehyde content (MDA), indicating improved tolerance to drought-induced oxidative stress. The transgenic plants also showed a reduced accumulation of reactive oxygen species. Importantly, ZaBZR1 up-regulated the expression of drought-related genes such as NbP5CS1, NbDREB2A, and NbWRKY44. These findings highlight the potential of ZaBZR1 as a candidate gene for enhancing drought resistance in transgenic N. benthamiana and provide insight into the function of ZaBZRs in Z. armatum.
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Affiliation(s)
- Zhengyu Jin
- Guizhou Key Laboratory of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering/ Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, Guizhou, China
| | - Tao Zhou
- Guizhou Key Laboratory of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering/ Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, Guizhou, China
| | - Jiajia Chen
- Guizhou Key Laboratory of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering/ Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, Guizhou, China
| | - Chaoting Lang
- Guizhou Key Laboratory of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering/ Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, Guizhou, China
| | - Qingqing Zhang
- Guizhou Key Laboratory of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering/ Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, Guizhou, China
| | - Jin Qin
- Guizhou Key Laboratory of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering/ Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, Guizhou, China
| | - Haibo Lan
- Guizhou Key Laboratory of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering/ Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, Guizhou, China
| | - Jianrong Li
- Guizhou Key Laboratory of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering/ Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, Guizhou, China
| | - Xiaofang Zeng
- Guizhou Key Laboratory of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering/ Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, Guizhou, China.
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Zheng X, Duan Y, Zheng H, Tang H, Zheng L, Yu X. Genome-Wide Identification and Characterization of the RWP-RK Proteins in Zanthoxylum armatum. Genes (Basel) 2024; 15:665. [PMID: 38927601 PMCID: PMC11202622 DOI: 10.3390/genes15060665] [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: 04/09/2024] [Revised: 05/13/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
Apomixis is a common reproductive characteristic of Zanthoxylum plants, and RWP-RKs are plant-specific transcription factors known to regulate embryonic development. However, the genome-wide analysis and function prediction of RWP-RK family genes in Z. armatum are unclear. In this study, 36 ZaRWP-RK transcription factors were identified in the genome of Z. armatum, among which 15 genes belonged to the RKD subfamily and 21 belonged to the NLP subfamily. Duplication events of ZaRWP-RK genes were mainly segmental duplication, and synteny analysis revealed a close phylogenetic relationship between Z. armatum and Arabidopsis. The analysis of cis-elements indicated that ZaRWP-RK genes may be involved in the regulation of the embryonic development of Z. armatum by responding to plant hormones such as abscisic acid, auxin, and gibberellin. Results of a real-time PCR showed that the expression levels of most ZaRWP-RK genes were significantly increased from flowers to young fruits. Protein-protein interaction network analysis further revealed the potential roles of the ZaRWP-RK proteins in apomixis. Collectively, this study is expected to improve our understanding of ZaRWP-RK transcription factors and provide a theoretical basis for future investigations into the ZaRWP-RK genes and their regulatory mechanisms in the apomixis process of Z. armatum.
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Affiliation(s)
| | | | | | | | | | - Xiaobo Yu
- Southwest Research Center for Cross Breeding of Special Economic Plants, School of Life Science, Leshan Normal University, Leshan 614000, China; (X.Z.); (Y.D.); (H.Z.); (H.T.); (L.Z.)
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Gong D, Li B, Wu B, Fu D, Li Z, Wei H, Guo S, Ding G, Wang B. The Integration of the Metabolome and Transcriptome for Dendrobium nobile Lindl. in Response to Methyl Jasmonate. Molecules 2023; 28:7892. [PMID: 38067620 PMCID: PMC10707931 DOI: 10.3390/molecules28237892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Dendrobium nobile Lindl., as an endangered medicinal plant within the genus Dendrobium, is widely distributed in southwestern China and has important ecological and economic value. There are a variety of metabolites with pharmacological activity in D. nobile. The alkaloids and polysaccharides contained within D. nobile are very important active components, which mainly have antiviral, anti-tumor, and immunity improvement effects. However, the changes in the compounds and functional genes of D. nobile induced by methyl jasmonate (MeJA) are not clearly understood. In this study, the metabolome and transcriptome of D. nobile were analyzed after exposure to MeJA. A total of 377 differential metabolites were obtained through data analysis, of which 15 were related to polysaccharide pathways and 35 were related to terpenoids and alkaloids pathways. Additionally, the transcriptome sequencing results identified 3256 differentially expressed genes that were discovered in 11 groups. Compared with the control group, 1346 unigenes were differentially expressed in the samples treated with MeJA for 14 days (TF14). Moreover, the expression levels of differentially expressed genes were also significant at different growth and development stages. According to GO and KEGG annotations, 189 and 99 candidate genes were identified as being involved in terpenoid biosynthesis and polysaccharide biosynthesis, respectively. In addition, the co-expression analysis indicated that 238 and 313 transcription factors (TFs) may contribute to the regulation of terpenoid and polysaccharide biosynthesis, respectively. Through a heat map analysis, fourteen terpenoid synthetase genes, twenty-three cytochrome P450 oxidase genes, eight methyltransferase genes, and six aminotransferase genes were identified that may be related to dendrobine biosynthesis. Among them, one sesquiterpene synthase gene was found to be highly expressed after the treatment with MeJA and was positively correlated with the content of dendrobine. This study provides important and valuable metabolomics and transcriptomic information for the further understanding of D. nobile at the metabolic and molecular levels and provides candidate genes and possible intermediate compounds for the dendrobine biosynthesis pathway, which lays a certain foundation for further research on and application of Dendrobium.
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Affiliation(s)
- Daoyong Gong
- College of Bioengineering, Chongqing University, Chongqing 400045, China;
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; (B.W.); (H.W.); (S.G.); (G.D.)
| | - Biao Li
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; (B.W.); (H.W.); (S.G.); (G.D.)
| | - Bin Wu
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; (B.W.); (H.W.); (S.G.); (G.D.)
| | - Deru Fu
- Steinhardt School of Culture, Education, and Human Development, New York University, New York, NY 10003, USA;
| | - Zesheng Li
- Dehong Tropical Agriculture Research Institute of Yunnan, Ruili 678600, China;
| | - Haobo Wei
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; (B.W.); (H.W.); (S.G.); (G.D.)
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Shunxing Guo
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; (B.W.); (H.W.); (S.G.); (G.D.)
| | - Gang Ding
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; (B.W.); (H.W.); (S.G.); (G.D.)
| | - Bochu Wang
- College of Bioengineering, Chongqing University, Chongqing 400045, China;
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Han S, Xu X, Yuan H, Li S, Lin T, Liu Y, Li S, Zhu T. Integrated Transcriptome and Metabolome Analysis Reveals the Molecular Mechanism of Rust Resistance in Resistant (Youkang) and Susceptive (Tengjiao) Zanthoxylum armatum Cultivars. Int J Mol Sci 2023; 24:14761. [PMID: 37834210 PMCID: PMC10573174 DOI: 10.3390/ijms241914761] [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: 08/21/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Chinese pepper rust is a live parasitic fungal disease caused by Coleosporium zanthoxyli, which seriously affects the cultivation and industrial development of Z. armatum. Cultivating and planting resistant cultivars is considered the most economical and environmentally friendly strategy to control this disease. Therefore, the mining of excellent genes for rust resistance and the analysis of the mechanism of rust resistance are the key strategies to achieve the targeted breeding of rust resistance. However, there is no relevant report on pepper rust resistance at present. The aim of the present study was to further explore the resistance mechanism of pepper by screening the rust-resistant germplasm resources in the early stage. Combined with the analysis of plant pathology, transcriptomics, and metabolomics, we found that compared with susceptible cultivar TJ, resistant cultivar YK had 2752 differentially expressed genes (DEGs, 1253 up-, and 1499 downregulated) and 321 differentially accumulated metabolites (DAMs, 133 up- and 188 down-accumulated) after pathogen infection. And the genes and metabolites related to phenylpropanoid metabolism were highly enriched in resistant varieties, which indicated that phenylpropanoid metabolism might mediate the resistance of Z. armatum. This finding was further confirmed by a real-time quantitative polymerase chain reaction analysis, which revealed that the expression levels of core genes involved in phenylpropane metabolism in disease-resistant varieties were high. In addition, the difference in flavonoid and MeJA contents in the leaves between resistant and susceptible varieties further supported the conclusion that the flavonoid pathway and methyl jasmonate may be involved in the formation of Chinese pepper resistance. Our research results not only help to better understand the resistance mechanism of Z. armatum rust but also contribute to the breeding and utilization of resistant varieties.
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Affiliation(s)
- Shan Han
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; (S.H.); (X.X.); (H.Y.); (S.L.); (T.L.); (Y.L.); (S.L.)
- Key Laboratory of Forest Protection of Sichuan Education Department, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiu Xu
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; (S.H.); (X.X.); (H.Y.); (S.L.); (T.L.); (Y.L.); (S.L.)
| | - Huan Yuan
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; (S.H.); (X.X.); (H.Y.); (S.L.); (T.L.); (Y.L.); (S.L.)
| | - Shujiang Li
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; (S.H.); (X.X.); (H.Y.); (S.L.); (T.L.); (Y.L.); (S.L.)
- Key Laboratory of Forest Protection of Sichuan Education Department, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Sichuan Agricultural University, Chengdu 611130, China
| | - Tiantian Lin
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; (S.H.); (X.X.); (H.Y.); (S.L.); (T.L.); (Y.L.); (S.L.)
| | - Yinggao Liu
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; (S.H.); (X.X.); (H.Y.); (S.L.); (T.L.); (Y.L.); (S.L.)
- Key Laboratory of Forest Protection of Sichuan Education Department, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Sichuan Agricultural University, Chengdu 611130, China
| | - Shuying Li
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; (S.H.); (X.X.); (H.Y.); (S.L.); (T.L.); (Y.L.); (S.L.)
- Key Laboratory of Forest Protection of Sichuan Education Department, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Sichuan Agricultural University, Chengdu 611130, China
| | - Tianhui Zhu
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; (S.H.); (X.X.); (H.Y.); (S.L.); (T.L.); (Y.L.); (S.L.)
- Key Laboratory of Forest Protection of Sichuan Education Department, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Sichuan Agricultural University, Chengdu 611130, China
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Wang W, Li X, Fan S, He Y, Wei M, Wang J, Yin Y, Liu Y. Combined genomic and transcriptomic analysis reveals the contribution of tandem duplication genes to low-temperature adaptation in perennial ryegrass. FRONTIERS IN PLANT SCIENCE 2023; 14:1216048. [PMID: 37502702 PMCID: PMC10368995 DOI: 10.3389/fpls.2023.1216048] [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: 05/03/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023]
Abstract
Perennial ryegrass (Lolium perenne L.) is an agronomically important cool-season grass species that is widely used as forage for ruminant animal production and cultivated in temperate regions for the establishment of lawns. However, the underlying genetic mechanism of the response of L. perenne to low temperature is still unclear. In the present study, we performed a comprehensive study and identified 3,770 tandem duplication genes (TDGs) in L. perenne, and evolutionary analysis revealed that L. perenne might have undergone a duplication event approximately 7.69 Mya. GO and KEGG pathway functional analyses revealed that these TDGs were mainly enriched in photosynthesis, hormone-mediated signaling pathways and responses to various stresses, suggesting that TDGs contribute to the environmental adaptability of L. perenne. In addition, the expression profile analysis revealed that the expression levels of TDGs were highly conserved and significantly lower than those of all genes in different tissues, while the frequency of differentially expressed genes (DEGs) from TDGs was much higher than that of DEGs from all genes in response to low-temperature stress. Finally, in-depth analysis of the important and expanded gene family indicated that the members of the ELIP subfamily could rapidly respond to low temperature and persistently maintain higher expression levels during all low temperature stress time points, suggesting that ELIPs most likely mediate low temperature responses and help to facilitate adaptation to low temperature in L. perenne. Our results provide evidence for the genetic underpinning of low-temperature adaptation and valuable resources for practical application and genetic improvement for stress resistance in L. perenne.
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Affiliation(s)
- Wei Wang
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Xiaoning Li
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Shugao Fan
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Yang He
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Meng Wei
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Jiayi Wang
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Yanling Yin
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Yanfeng Liu
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, Yantai, China
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Yang T, Yin X, Kang H, Yang D, Yang X, Yang Y, Yang Y. Chromosome-level genome assembly of Murraya paniculata sheds light on biosynthesis of floral volatiles. BMC Biol 2023; 21:142. [PMID: 37340448 DOI: 10.1186/s12915-023-01639-6] [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: 11/08/2022] [Accepted: 05/31/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND Murraya paniculata (L.) Jack, commonly called orange jessamine in the family Rutaceae, is an important ornamental plant in tropical and subtropical regions which is famous for its strong fragrance. Although genome assemblies have been reported for many Rutaceae species, mainly in the genus Citrus, full genomic information has not been reported for M. paniculata, which is a prerequisite for in-depth genetic studies on Murraya and manipulation using genetic engineering techniques. Here, we report a high-quality chromosome-level genome assembly of M. paniculata and aim to provide insights on the molecular mechanisms of flower volatile biosynthesis. RESULTS The genome assembly with a contig N50 of 18.25 Mb consists of 9 pseudomolecules and has a total length of 216.86 Mb. Phylogenetic analysis revealed that M. paniculata diverged from the common ancestor approximately 25 million years ago and has not undergone any species-specific whole genome duplication events. Genome structural annotation and comparative genomics analysis revealed that there are obvious differences in transposon contents among the genomes of M. paniculata and Citrus species, especially in the upstream regions of genes. Research on the flower volatiles of M. paniculata and C. maxima at three flowering stages revealed significant differences in volatile composition with the flowers of C. maxima lacking benzaldehyde and phenylacetaldehyde. Notably, there are transposons inserted in the upstream region of the phenylacetaldehyde synthase (PAAS) genes Cg1g029630 and Cg1g029640 in C. maxima, but not in the upstream region of three PAAS genes Me2G_2379, Me2G_2381, and Me2G_2382 in M. paniculata. Our results indicated that compared to the low expression levels of PAAS genes in C. maxima, the higher expression levels of the three PAAS genes in M. paniculata are the main factor affecting the phenylacetaldehyde biosynthesis and causing the content difference of phenylacetaldehyde. The phenylacetaldehyde synthetic activities of the enzymes encoded by M. paniculata PAAS genes were validated by in vitro analyses. CONCLUSIONS Our study provides useful genomic resources of M. paniculata for further research on Rutaceae plants, identifies new PAAS genes, and provides insights into how transposons contribute to variations in flower volatiles among Murraya and Citrus plants.
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Affiliation(s)
- Tianyu Yang
- School of Life Science, Yunnan University, Kunming, 650500, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Yin
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haotong Kang
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biological Resources and Environmental Sciences, Jishou University, Jishou, 416000, China
| | - Danni Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xingyu Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunqiang Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201, China.
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Yongping Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201, China.
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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Tang M, Huang J, Ma X, Du J, Bi Y, Guo P, Lu H, Wang L. A near-complete genome assembly of Thalia dealbata Fraser (Marantaceae). FRONTIERS IN PLANT SCIENCE 2023; 14:1183361. [PMID: 37384358 PMCID: PMC10298163 DOI: 10.3389/fpls.2023.1183361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
This study presents a chromosome-level, near-complete genome assembly of Thalia dealbata (Marantaceae), a typical emergent wetland plant with high ornamental and environmental value. Based on 36.99 Gb PacBio HiFi reads and 39.44 Gb Hi-C reads, we obtained a 255.05 Mb assembly, of which 251.92 Mb (98.77%) were anchored into eight pseudo-chromosomes. Five pseudo-chromosomes were completely assembled, and the other three had one to two gaps. The final assembly had a high contig N50 value (29.80 Mb) and benchmarking universal single-copy orthologs (BUSCO) recovery score (97.52%). The T. dealbata genome had 100.35 Mb repeat sequences, 24,780 protein-coding genes, and 13,679 non-coding RNAs. Phylogenetic analysis revealed that T. dealbata was closest to Zingiber officinale, whose divergence time was approximately 55.41 million years ago. In addition, 48 and 52 significantly expanded and contracted gene families were identified within the T. dealbata genome. Moreover, 309 gene families were specific to T. dealbata, and 1,017 genes were positively selected. The T. dealbata genome reported in this study provides a valuable genomic resource for further research on wetland plant adaptation and the genome evolution dynamics. This genome is also beneficial for the comparative genomics of Zingiberales species and flowering plants.
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Affiliation(s)
- Min Tang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| | - Jialin Huang
- School of Chemical Biology and Environment, Yuxi Normal University, Yuxi, China
| | - Xiangli Ma
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Juan Du
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| | - Yufen Bi
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Peiwen Guo
- School of Mathematical Sciences, Xiamen University, Xiamen, China
| | - Hao Lu
- Scientific Research Department, Kunming Novo Medical Laboratory Co., Ltd., Kunming, China
| | - Lei Wang
- Scientific Research Department, Kunming Novo Medical Laboratory Co., Ltd., Kunming, China
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Zhang J, Li C, Niu Q, wang P, Wang L, Li H. Characterization of green peppers based on dynamic repose angle. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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Hu L, Xu Z, Fan R, Wang G, Wang F, Qin X, Yan L, Ji X, Meng M, Sim S, Chen W, Hao C, Wang Q, Zhu H, Zhu S, Xu P, Zhao H, Lindsey K, Daniell H, Wendel JF, Jin S. The complex genome and adaptive evolution of polyploid Chinese pepper (Zanthoxylum armatum and Zanthoxylum bungeanum). PLANT BIOTECHNOLOGY JOURNAL 2023; 21:78-96. [PMID: 36117410 PMCID: PMC9829393 DOI: 10.1111/pbi.13926] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/28/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Zanthoxylum armatum and Zanthoxylum bungeanum, known as 'Chinese pepper', are distinguished by their extraordinary complex genomes, phenotypic innovation of adaptive evolution and species-special metabolites. Here, we report reference-grade genomes of Z. armatum and Z. bungeanum. Using high coverage sequence data and comprehensive assembly strategies, we derived 66 pseudochromosomes comprising 33 homologous phased groups of two subgenomes, including autotetraploid Z. armatum. The genomic rearrangements and two whole-genome duplications created large (~4.5 Gb) complex genomes with a high ratio of repetitive sequences (>82%) and high chromosome number (2n = 4x = 132). Further analysis of the high-quality genomes shed lights on the genomic basis of involutional reproduction, allomones biosynthesis and adaptive evolution in Chinese pepper, revealing a high consistent relationship between genomic evolution, environmental factors and phenotypic innovation. Our study provides genomic resources and new insights for investigating diversification and phenotypic innovation in Chinese pepper, with broader implications for the protection of plants under severe environmental changes.
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Affiliation(s)
- Lisong Hu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage CropsWanningChina
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan ProvinceWanningChina
| | - Zhongping Xu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Rui Fan
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage CropsWanningChina
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan ProvinceWanningChina
| | - Guanying Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Fuqiu Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Xiaowei Qin
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage CropsWanningChina
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan ProvinceWanningChina
| | - Lin Yan
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage CropsWanningChina
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan ProvinceWanningChina
| | - Xunzhi Ji
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage CropsWanningChina
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan ProvinceWanningChina
| | - Minghui Meng
- State Key Laboratory of Grassland and Agro‐Ecosystems, School of Life SciencesLanzhou UniversityLanzhouChina
| | | | - Wei Chen
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Chaoyun Hao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage CropsWanningChina
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan ProvinceWanningChina
| | - Qinghuang Wang
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage CropsWanningChina
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan ProvinceWanningChina
| | - Huaguo Zhu
- College of Biology and Agricultural ResourcesHuanggang Normal UniversityHuanggangHubeiChina
| | - Shu Zhu
- Jinjiaohong Spice Research InstituteJinjiaohong Agricultural Technology Group CorporationNanjingChina
| | - Pan Xu
- State Key Laboratory of Grassland and Agro‐Ecosystems, School of Life SciencesLanzhou UniversityLanzhouChina
| | - Hui Zhao
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction RegionsHaikouChina
- Sanya Research Institute of Chinese Academy of Tropical Agricultural SciencesSanyaChina
| | | | - Henry Daniell
- Department of Biochemistry, School of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Jonathan F. Wendel
- Department Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowaUSA
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
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Tang N, Cao Z, Wu P, Zhang X, Lou J, Liu Y, Wang Q, Hu Y, Si S, Sun X, Chen Z. Genome-wide identification, interaction of the MADS-box proteins in Zanthoxylum armatum and functional characterization of ZaMADS80 in floral development. FRONTIERS IN PLANT SCIENCE 2022; 13:1038828. [PMID: 36507394 PMCID: PMC9732391 DOI: 10.3389/fpls.2022.1038828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/01/2022] [Indexed: 06/17/2023]
Abstract
As a typical dioecious species, Zanthoxylum armatum establishes apomictic reproduction, hence only female trees are cultivated. However, male and hermaphrodite flowers have recently appeared in female plants, resulting in a dramatic yield reduction. To date, the genetic basis underlying sex determination and apomixis in Z. armatum has been largely unknown. Here, we observed abortion of the stamen or carpel prior to primordium initiation, thus corroborating the potential regulation of MADS-box in sex determination. In Z. armatum, a total of 105 MADS-box genes were identified, harboring 86 MIKC-type MADSs with lack of FLC orthologues. Transcriptome analysis revealed candidate MADSs involved in floral organ identity, including ten male-biased MADSs, represented by ZaMADS92/81/75(AP3/PI-like), and twenty-six female-specified, represented by ZaMADS80/49 (STK/AGL11-like) and ZaMADS42 (AG-like). Overexpressing ZaMADS92 resulted in earlier flowering, while ZaMADS80 overexpression triggered precocious fruit set and parthenocarpy as well as dramatic modifications in floral organs. To characterize their regulatory mechanisms, a comprehensive protein-protein interaction network of the represented MADSs was constructed based on yeast two-hybrid and bimolecular fluorescence complementation assays. Compared with model plants, the protein interaction patterns in Z. armatum exhibited both conservation and divergence. ZaMADS70 (SEP3-like) interacted with ZaMADS42 and ZaMADS48 (AP3-like) but not ZaMADS40 (AP1-like), facilitating the loss of petals in Z. armatum. The ZaMADS92/ZaMADS40 heterodimer could be responsible for accelerating flowering in ZaMADS92-OX lines. Moreover, the interactions between ZaMADS80 and ZaMADS67(AGL32-like) might contribute to apomixis. This work provides new insight into the molecular mechanisms of MADS-boxes in sex organ identity in Z. armatum.
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Affiliation(s)
- Ning Tang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, China
| | - Zhengyan Cao
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, China
- College of Horticulture and Gardening, Yangtze University, Jingzhou, China
| | - Peiyin Wu
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, China
- College of Horticulture and Gardening, Yangtze University, Jingzhou, China
| | - Xian Zhang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, China
| | - Juan Lou
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, China
| | - Yanni Liu
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, China
- College of Biology and Food Engineering, Chongqing Three Georges University, Chongqing, China
| | - Qiyao Wang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, China
| | - Yang Hu
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, China
| | - Shuo Si
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, China
| | - Xiaofan Sun
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, China
| | - Zexiong Chen
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, China
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Wang M, Huang J, Liu S, Liu X, Li R, Luo J, Fu Z. Improved assembly and annotation of the sesame genome. DNA Res 2022; 29:6821245. [PMID: 36355766 PMCID: PMC9724774 DOI: 10.1093/dnares/dsac041] [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: 09/22/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
Sesame (Sesamum indicum L.) is an important oilseed crop that produces abundant seed oil and has a pleasant flavor and high nutritional value. To date, several Illumina-based genome assemblies corresponding to different sesame genotypes have been published and widely used in genetic and genomic studies of sesame. However, these assemblies consistently showed low continuity with numerous gaps. Here, we reported a high-quality, reference-level sesame genome assembly by integrating PacBio high-fidelity sequencing and Hi-C technology. Our updated sesame assembly was 309.35 Mb in size with a high chromosome anchoring rate (97.54%) and contig N50 size (13.48 Mb), which were better than previously published genomes. We identified 163.38 Mb repetitive elements and 24,345 high-confidence protein-coding genes in the updated sesame assembly. Comparative genomic analysis showed that sesame shared an ancient whole-genome duplication event with two Lamiales species. A total of 2,782 genes were tandemly duplicated. We also identified several genes that were likely involved in fatty acid and triacylglycerol biosynthesis. Our improved sesame assembly and annotation will facilitate future genetic studies and genomics-assisted breeding of sesame.
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Affiliation(s)
- Mingcheng Wang
- Institute for Advanced Study, Chengdu University, No. 2025 Chengluo Road, Chengdu 610106, China,Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, Chengdu 610106, China
| | | | - Song Liu
- Berry Genomics Corporation, Beijing 100015, China
| | - Xiaofeng Liu
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
| | - Rui Li
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, Chengdu 610106, China,School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Junjia Luo
- To whom correspondence should be addressed. (J.L.); (Z.F.)
| | - Zhixi Fu
- To whom correspondence should be addressed. (J.L.); (Z.F.)
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Su X, Liu T, Liu YP, Harris AJ, Chen JY. Adaptive radiation in Orinus, an endemic alpine grass of the Qinghai-Tibet Plateau, based on comparative transcriptomic analysis. JOURNAL OF PLANT PHYSIOLOGY 2022; 277:153786. [PMID: 35963042 DOI: 10.1016/j.jplph.2022.153786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
The species of Orinus (Poaceae) are important alpine plants with a variety of phenotypic traits and potential usages in molecular breeding toward drought-tolerant forage crops. However, the genetic basis of evolutionary adaption and diversification in the genus is still unclear. In the present study, we obtained transcriptomes for the two most divergent species, O. thoroldii and O. kokonoricus, using the Illumina platform and de novo assembly. In total, we generated 23,029 and 24,086 unigenes with N50 values of 1188 and 1203 for O. thoroldii and O. kokonoricus respectively, and identified 19,005 pairs of putative orthologs between the two species of Orinus. For these orthologs, estimations of non-synonymous/synonymous substitution rate ratios indicated that 568 pairs may be under strongly positive selection (Ka/Ks > 1), and Gene Ontogeny (GO) enrichment analysis revealed that significantly enriched pathways were in DNA repair and resistance to abiotic stress. Meanwhile, the divergence times of species between O. thoroldii and O. kokonoricus occurred 3.2 million years ago (Mya), and the recent evolutionary branch is an allotetraploid species, Cleistogenes songorica. We also detected a Ks peak of ∼0.60 for Orinus. Additionally, we identified 188 pairs of differentially expressed genes (DEGs) between the two species of Orinus, which were significantly enrich in stress resistance and lateral root development. Thus, we considered that the species diversification and evolutionary adaption of this genus was initiated by environmental selection, followed by phenotypic differentiation, finally leading to niche separation in the Qinghai-Tibet Plateau.
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Affiliation(s)
- Xu Su
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China; Key Laboratory of Land Surface Processes and Ecological Conservation of the Qinghai-Tibet Plateau, The Ministry of Education, Qinghai Normal University, Xining, 810008, China
| | - Tao Liu
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; School of Geographical Science, Qinghai Normal University, Xining, 810008, China
| | - Yu Ping Liu
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China.
| | - A J Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Jin Yuan Chen
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China
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13
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Hui W, Zheng H, Fan J, Wang J, Saba T, Wang K, Wu J, Wu H, Zhong Y, Chen G, Gong W. Genome-wide characterization of the MBF1 gene family and its expression pattern in different tissues and stresses in Zanthoxylum armatum. BMC Genomics 2022; 23:652. [PMID: 36104767 PMCID: PMC9472409 DOI: 10.1186/s12864-022-08863-4] [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: 03/30/2022] [Accepted: 08/31/2022] [Indexed: 11/18/2022] Open
Abstract
Background Multiprotein bridging factor 1 (MBF1) is a crucial transcriptional coactivator in animals, plants, and some microorganisms, that plays a necessary role in growth development and stress tolerance. Zanthoxylum armatum is an important perennial plant for the condiments and pharmaceutical industries, whereas the potential information in the genes related to stress resistance remains poorly understood in Z. armatum. Results Herein, six representative species were selected for use in a genome-wide investigation of the MBF1 family, including Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Citrus sinensis, Ginkgo biloba, and Z. armatum. The results showed that the MBF1 genes could be divided into two groups: Group I contained the MBF1a and MBF1b subfamilies, and group II was independent of the MBF1c subfamily.. Most species have at least two different MBF1 genes, and MBF1c is usually an essential member. The three ZaMBF1 genes were respectively located on ZaChr26, ZaChr32, and ZaChr4 of Zanthoxylum chromosomes. The collinearity were occurred between three ZaMBF1 genes, and ZaMBF1c showed the collinearity between Z. armatum and both P. trichocarpa and C. sinensis. Moreover, many cis-elements associated with abiotic stress and phytohormone pathways were detected in the promoter regions of MBF1 of six representative species. The ERF binding sites were the most abundant targets in the sequences of the ZaMBF1 family, and some transcription factor sites related to floral differentiation were also identified in ZaMBF1c, such as MADS, LFY, Dof, and AP2. ZaMBF1a was observed to be very highly expressed in 25 different samples except in the seeds, and ZaMBF1c may be associated with the male and female floral initiation processes. In addition, expression in all the ZaMBF1 genes could be significantly induced by water-logging, cold stress, ethephon, methyl jasmonate, and salicylic acid treatments, especially in ZaMBF1c. Conclusion The present study carried out a comprehensive bioinformatic investigation related to the MBF1 family in six representative species, and the responsiveness of ZaMBF1 genes to various abiotic stresses and phytohormone inductions was also revealed. This work not only lays a solid foundation to uncover the biological roles of the ZaMBF1 family in Z. armatum, but also provides some broad references for conducting the MBF1 research in other plants. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08863-4.
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Hui W, Fan J, Liu X, Zhao F, Saba T, Wang J, Wu A, Zhang X, Zhang J, Zhong Y, Chen G, Gong W. Integrated transcriptome and plant growth substance profiles to identify the regulatory factors involved in floral sex differentiation in Zanthoxylum armatum DC. FRONTIERS IN PLANT SCIENCE 2022; 13:976338. [PMID: 36119602 PMCID: PMC9479546 DOI: 10.3389/fpls.2022.976338] [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: 07/13/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Zanthoxylum armatum is a prominent plant for food industries. Its male flowers often occur in gynogenesis plants; however, the potential mechanism remains poorly understood. Herein, a total of 26 floral sex differentiation stages were observed to select four vital phases to reveal key factors by using RNA-seq, phytohormones and carbohydrates investigation. The results showed that a selective abortion of stamen or pistil primordia could result in the floral sex differentiation in Z. armatum. Carbohydrates might collaborate with cytokinin to effect the male floral differentiation, whereas female floral differentiation was involved in SA, GA1, and ABA biosynthesis and signal transduction pathways. Meanwhile, these endogenous regulators associated with reproductive growth might be integrated into ABCDE model to regulate the floral organ differentiation in Z. armatum. Furthermore, the 21 crucial candidates were identified in co-expression network, which would contribute to uncovering their roles in floral sex differentiation of Z. armatum in further studies. To the best of our knowledge, this study was the first comprehensive investigation to link floral sex differentiation with multi-level endogenous regulatory factors in Z. armatum. It also provided new insights to explore the regulatory mechanism of floral sex differentiation, which would be benefited to cultivate high-yield varieties in Z. armatum.
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Affiliation(s)
- Wenkai Hui
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Jiangtao Fan
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Xianzhi Liu
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Feiyan Zhao
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Tasheen Saba
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Jingyan Wang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Aimin Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xuebin Zhang
- State Key Laboratory of Cotton Biology, Department of Biology, Institute of Plant Stress Biology, Henan University, Kaifeng, China
| | - Junli Zhang
- State Key Laboratory of Cotton Biology, Department of Biology, Institute of Plant Stress Biology, Henan University, Kaifeng, China
| | - Yu Zhong
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Gang Chen
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Wei Gong
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
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15
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Genome-Wide Identification and Analysis of the Growth-Regulating Factor Family in Zanthoxylum armatum DC and Functional Analysis of ZaGRF6 in Leaf Size and Longevity Regulation. Int J Mol Sci 2022; 23:ijms23169043. [PMID: 36012309 PMCID: PMC9409285 DOI: 10.3390/ijms23169043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Growth-regulating factors (GRFs) are plant-specific transcription factors that play an important role in plant growth and development. In this study, fifteen GRF gene members containing QLQ and WRC domains were identified in Zanthoxylum armatum. Phylogenetic and collinearity analysis showed that ZaGRFs were closely related to CsGRFs and AtGRFs, and distantly related to OsGRFs. There are a large number of cis-acting elements related to hormone response and stress induction in the GRF gene promoter region of Z. armatum. Tissue-specific expression analysis showed that except for ZaGRF7, all the ZaGRFs were highly expressed in young parts with active growth and development, including terminal buds, seeds, and young flowers, suggesting their key roles in Z. armatum growth and development. Eight ZaGRFs were selected to investigate the transcriptional response to auxin, gibberellin and drought treatments. A total of six ZaGRFs in the NAA treatment, four ZaGRFs in the GA3 treatment, and six ZaGRFs in the PEG treatment were induced and significantly up-regulated. Overexpression of ZaGRF6 increased branching and chlorophyll content and delayed senescence of transgenic Nicotiana benthamiana. ZaGRF6 increased the expression of CRF2 and suppressed the expression of ARR4 and CKX1, indicating that ZaGRF6 is involved in cytokinin metabolism and signal transduction. These research results lay a foundation for further analysis of the GRF gene function of Z. armatum and provide candidate genes for growth, development, and stress resistance breeding of Z. armatum.
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Drummond CP, Renner T. Genomic insights into the evolution of plant chemical defense. CURRENT OPINION IN PLANT BIOLOGY 2022; 68:102254. [PMID: 35777286 DOI: 10.1016/j.pbi.2022.102254] [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: 11/15/2021] [Revised: 04/22/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Plant trait evolution can be impacted by common mechanisms of genome evolution, including whole-genome and small-scale duplication, rearrangement, and selective pressures. With the increasing accessibility of genome sequencing for non-model species, comparative studies of trait evolution among closely related or divergent lineages have supported investigations into plant chemical defense. Plant defensive compounds include major chemical classes, such as terpenoids, alkaloids, and phenolics, and are used in primary and secondary plant functions. These include the promotion of plant health, facilitation of pollination, defense against pathogens, and responses to a rapidly changing climate. We discuss mechanisms of genome evolution and use examples from recent studies to impress a stronger understanding of the link between genotype and phenotype as it relates to the evolution of plant chemical defense. We conclude with considerations for how to leverage genomics, transcriptomics, metabolomics, and functional assays for studying the emergence and evolution of chemical defense systems.
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Affiliation(s)
- Chloe P Drummond
- The Pennsylvania State University, Department of Entomology, 501 ASI Building University Park, PA 16802, USA.
| | - Tanya Renner
- The Pennsylvania State University, Department of Entomology, 501 ASI Building University Park, PA 16802, USA
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17
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Wang W, Shao A, Xu X, Fan S, Fu J. Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses. BMC PLANT BIOLOGY 2022; 22:355. [PMID: 35864464 PMCID: PMC9306052 DOI: 10.1186/s12870-022-03752-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Zoysiagrass (Zoysia spp.) is a warm-season turfgrass. It is widely used as turfgrasses throughout the world, offers good turf qualities, including salt tolerance, resistance to drought and heat. However, the underlying genetic mechanism of zoysiagrass responsive to salt stress remains largely unexplored. RESULTS In present study, we performed a whole-genome comparative analysis for ten plant genomes. Evolutionary analysis revealed that Chloridoideae diverged from Panicoideae approximately 33.7 million years ago (Mya), and the phylogenetic relationship among three zoysiagrasses species suggested that Zoysia matrella may represent an interspecific hybrid between Zoysia japonica and Zoysia pacifica. Genomic synteny indicated that Zoysia underwent a genus-specific whole-genome duplication (WGD) event approximately 20.8 Mya. The expression bais of homologous genes between the two subgenomes suggested that the B subgenome of Z. japonica contributes to salt tolerance. In additon, comparative genomic analyses revealed that the salt adaptation of Zoysia is likely attributable to the expanded cytochrome P450 and ABA biosynthetic gene families. Furthermore, we further found that many duplicated genes from the extra WGD event exhibited distinct functional divergence in response to salt stress using transcriptomic analysis, suggesting that this WGD event contributed to strong resistance to salt stress. CONCLUSIONS Here, our results revealed that expanded cytochrome P450 and ABA biosynthetic gene families, and many of those duplicated genes from recent zoysia-specific WGD event contributed to salt adaptation of zoysiagrass, which provided insight into the genetic underpinning of salt adaptation and valuable information for further studies on salt stress-related traits in Zoysia.
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Affiliation(s)
- Wei Wang
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, China
| | - An Shao
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, China
| | - Xiao Xu
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, China
| | - Shugao Fan
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, China
| | - Jinmin Fu
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, China.
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Zhang J, Zhou H, Luo F, Wan L, Li C, Wang L. Determination of mechanical properties of Zanthoxylum armatum using the discrete element method. FOOD QUALITY AND SAFETY 2022. [DOI: 10.1093/fqsafe/fyac043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Using the discrete element method (DEM) to investigate the behavior of particles is a crucial strategy in the research and development of novel equipment. Green pepper (Zanthoxylum armatum) is a globally renewable plant-derived medicinal and food homologous commodity with a wide range of uses and great demand, but the mechanical properties needed to develop its processing equipment are scare. Thus, this case of study aimed to systematically explore the necessary input parameters to model green pepper, and to provide new insights for the guidance of future industrial applications worldwide. On the basis of the experimental measured physical properties, the contact properties of green pepper on zinc-coated steel were fist calibrated, and then used to determine the contact properties between particles. The differences between the experimental and simulation results were analyzed for selection and verification of the contact properties accurately. Difference analysis confirmed that the coefficient of restitution, coefficient of static friction and coefficient of rolling friction for contact between the particle and zinc-coated steel have values of 0.392, 0.650, and 0.168, and those coefficients for particle-to-particle contact have values of 0.199, 0.710, and 0.184, respectively. Discoveries in this work may contribute to the research and development of production equipment for green pepper.
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Affiliation(s)
- Jian Zhang
- College of Engineering and Technology, Southwest University, Chongqing , 400715, P.R. China
- Key Laboratory of Agricultural Equipment in Hilly and Mountainous Areas, Chongqing , 400715, P.R. China
| | - Hong Zhou
- College of Plant Protection, Southwest University , Chongqing 400715, P.R. China
| | - Fan Luo
- College of Engineering and Technology, Southwest University, Chongqing , 400715, P.R. China
- Key Laboratory of Agricultural Equipment in Hilly and Mountainous Areas, Chongqing , 400715, P.R. China
| | - Long Wan
- College of Engineering and Technology, Southwest University, Chongqing , 400715, P.R. China
- Key Laboratory of Agricultural Equipment in Hilly and Mountainous Areas, Chongqing , 400715, P.R. China
| | - Chengsong Li
- College of Engineering and Technology, Southwest University, Chongqing , 400715, P.R. China
- Key Laboratory of Agricultural Equipment in Hilly and Mountainous Areas, Chongqing , 400715, P.R. China
| | - Lihong Wang
- College of Engineering and Technology, Southwest University, Chongqing , 400715, P.R. China
- Key Laboratory of Agricultural Equipment in Hilly and Mountainous Areas, Chongqing , 400715, P.R. China
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Sun F, Yan C, Lv Y, Pu Z, Liao Z, Guo W, Dai M. Genome Sequencing of Amomum tsao-ko Provides Novel Insight Into Its Volatile Component Biosynthesis. FRONTIERS IN PLANT SCIENCE 2022; 13:904178. [PMID: 35720564 PMCID: PMC9198571 DOI: 10.3389/fpls.2022.904178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
As an important economic and medicinal crop, Amomum tsao-ko is rich in volatile oils and widely used in food additives, essential oils, and traditional Chinese medicine. However, the lack of the genome remains a limiting factor for understanding its medicinal properties at the molecular level. Here, based on 288.72 Gb of PacBio long reads and 105.45 Gb of Illumina paired-end short reads, we assembled a draft genome for A. tsao-ko (2.70 Gb in size, contig N50 of 2.45 Mb). Approximately 90.07% of the predicted genes were annotated in public databases. Based on comparative genomic analysis, genes involved in secondary metabolite biosynthesis, flavonoid metabolism, and terpenoid biosynthesis showed significant expansion. Notably, the DXS, GGPPS, and CYP450 genes, which participate in rate-limiting steps for terpenoid backbone biosynthesis and modification, may form the genetic basis for essential oil formation in A. tsao-ko. The assembled A. tsao-ko draft genome provides a valuable genetic resource for understanding the unique features of this plant and for further evolutionary and agronomic studies of Zingiberaceae species.
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Affiliation(s)
- Fenghui Sun
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Chaochao Yan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yunyun Lv
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Science, Neijiang Normal University, Neijiang, China
| | - Zhonghui Pu
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-Origin Food, Chengdu Medical College, Chengdu, China
| | - Zedong Liao
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Wei Guo
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-Origin Food, Chengdu Medical College, Chengdu, China
| | - Min Dai
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-Origin Food, Chengdu Medical College, Chengdu, China
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Zhang J, Xie C, Cao L, Zhou H, Li C, Wang L. Determination of physical and interaction parameters of green pepper (Zanthoxylum armatum): Investigation of the mechanism of significant factors against the repose angle. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113409] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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21
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Wang M, Zhang L, Tong S, Jiang D, Fu Z. Chromosome-level genome assembly of a xerophytic plant, Haloxylon ammodendron. DNA Res 2022; 29:dsac006. [PMID: 35266513 PMCID: PMC8946665 DOI: 10.1093/dnares/dsac006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/09/2022] [Indexed: 01/30/2023] Open
Abstract
Haloxylon ammodendron is a xerophytic perennial shrub or small tree that has a high ecological value in anti-desertification due to its high tolerance to drought and salt stress. Here, we report a high-quality, chromosome-level genome assembly of H. ammodendron by integrating PacBio's high-fidelity sequencing and Hi-C technology. The assembled genome size was 685.4 Mb, of which 99.6% was assigned to nine pseudochromosomes with a contig N50 value of 23.6 Mb. Evolutionary analysis showed that both the recent substantial amplification of long terminal repeat retrotransposons and tandem gene duplication may have contributed to its genome size expansion and arid adaptation. An ample amount of low-GC genes was closely related to functions that may contribute to the desert adaptation of H. ammodendron. Gene family clustering together with gene expression analysis identified differentially expressed genes that may play important roles in the direct response of H. ammodendron to water-deficit stress. We also identified several genes possibly related to the degraded scaly leaves and well-developed root system of H. ammodendron. The reference-level genome assembly presented here will provide a valuable genomic resource for studying the genome evolution of xerophytic plants, as well as for further genetic breeding studies of H. ammodendron.
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Affiliation(s)
- Mingcheng Wang
- Institute for Advanced Study, Chengdu University, Chengdu 610106, China
| | - Lei Zhang
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, College of Biological Science & Engineering, North Minzu University, Yinchuan 750001, China
| | - Shaofei Tong
- MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu 610105, China
| | - Dechun Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Zhixi Fu
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
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Ren G, Jiang Y, Li A, Yin M, Li M, Mu W, Wu Y, Liu J. The genome sequence provides insights into salt tolerance of Achnatherum splendens (Gramineae), a constructive species of alkaline grassland. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:116-128. [PMID: 34487631 PMCID: PMC8710827 DOI: 10.1111/pbi.13699] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 08/18/2021] [Accepted: 09/01/2021] [Indexed: 05/02/2023]
Abstract
Achnatherum splendens Trin. (Gramineae) is a constructive species of the arid grassland ecosystem in Northwest China and is a major forage grass. It has good tolerance of salt and drought stress in alkaline habitats. Here, we report its chromosome-level genome, determined through a combination of Illumina HiSeq sequencing, PacBio sequencing and Hi-C technology. The final assembly of the ~1.17 Gb genome sequence had a super-scaffold N50 of 40.3 Mb. A total of 57 374 protein-coding genes were annotated, of which 54 426 (94.5%) genes have functional protein annotations. Approximately 735 Mb (62.37%) of the assembly were identified as repetitive elements, and among these, LTRs (40.53%) constitute the highest proportion, having made a major contribution to the expansion of genome size in A. splendens. Phylogenetic analysis revealed that A. splendens diverged from the Brachypodium distachyon-Hordeum vulgare-Aegilops tauschii subclade around 37 million years ago (Ma) and that a clade comprising these four species diverged from the Phyllostachys edulis clade ~47 Ma. Genomic synteny indicates that A. splendens underwent an additional species-specific whole-genome duplication (WGD) 18-20 Ma, which further promoted an increase in copies of numerous saline-alkali-related gene families in the A. splendens genome. By transcriptomic analysis, we further found that many of these duplicated genes from this extra WGD exhibited distinct functional divergence in response to salt stress. This WGD, therefore, contributed to the strong resistance to salt stress and widespread arid adaptation of A. splendens.
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Affiliation(s)
- Guangpeng Ren
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Yanyou Jiang
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Ao Li
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Mou Yin
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Minjie Li
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Wenjie Mu
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Ying Wu
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
- Key Laboratory of Bio‐Resources and Eco‐Environment of the Ministry of Education & State Key Lab of Hydraulics & Mountain River EngineeringCollege of Life SciencesSichuan UniversityChengduChina
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