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Zhu J, Huang Y, Chai W, Xia P. Decoding the Chloroplast Genome of Tetrastigma (Vitaceae): Variations and Phylogenetic Selection Insights. Int J Mol Sci 2024; 25:8290. [PMID: 39125860 PMCID: PMC11312916 DOI: 10.3390/ijms25158290] [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: 05/25/2024] [Revised: 07/26/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
Tetrastigma (Vitaceae) is known for its ornamental, medicinal, and ecological significance. However, the structural and variational characteristics of the Tetrastigma chloroplast genome and their impact on phylogenetic relationships remain underexplored. This study utilized bioinformatics methods to assemble and annotate the chloroplast genomes of 10 Tetrastigma species and compare them with five previously sequenced species. This study analyzed gene composition, simple sequence repeats, and codon usage patterns, revealing a high A/T content, uniquely identified pentanucleotide repeats in five species and several preferred codons. In addition, comparative analyses were conducted of the chloroplast genomes of 15 Tetrastigma species, examining their structural differences and identifying polymorphic hotspots (rps16, rps16-trnQ, trnS, trnD, psbC-trnS-psbZ, accD-psaI, psbE-petL-petG, etc.) suitable for DNA marker development. Furthermore, phylogenetic and selective pressure analyses were performed based on the chloroplast genomes of these 15 Tetrastigma species, validating and elucidating intra-genus relationships within Tetrastigma. Futhermore, several genes under positive selection, such as atpF and accD, were identified, shedding light on the adaptive evolution of Tetrastigma. Utilizing 40 Vitaceae species, the divergence time of Tetrastigma was estimated, clarifying the evolutionary relationships within Tetrastigma relative to other genera. The analysis revealed diverse divergences of Tetrastigma in the Miocene and Pliocene, with possible ancient divergence events before the Eocene. Furthermore, family-level selective pressure analysis identified key features distinguishing Tetrastigma from other genera, showing a higher degree of purifying selection. This research enriches the chloroplast genome data for Tetrastigma and offers new insights into species identification, phylogenetic analysis, and adaptive evolution, enhancing our understanding of the genetic diversity and evolutionary history of these species.
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Affiliation(s)
- Junqiao Zhu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Yang Huang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Weiguo Chai
- Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China;
| | - Pengguo Xia
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
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Feng Z, Ye W, Feng L. Bioactives and metabolites of Tetrastigma hemsleyanum root extract alleviate DSS-induced ulcerative colitis by targeting the SYK protein in the B cell receptor signaling pathway. JOURNAL OF ETHNOPHARMACOLOGY 2024; 322:117563. [PMID: 38104876 DOI: 10.1016/j.jep.2023.117563] [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: 09/26/2023] [Revised: 11/27/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Tetrastigma hemsleyanum is an endemic Chinese herb with a wide range of pharmacological activities, including anti-inflammatory, antiviral, antioxidant, antitumor, and immunomodulatory activities. However, the effect and mechanisms of the anti-inflammatory activity of T. hemsleyanum root extract against dextran sodium sulfate (DSS)-induced ulcerative colitis (UC) have not yet been fully investigated. AIM OF THE STUDY This study aimed to explore the therapeutic effect and molecular mechanisms of T. hemsleyanum root extract in DSS-induced UC mice and knockdown cells. MATERIALS AND METHODS T. hemsleyanum root extract was obtained and analyzed by high-performance liquid chromatography (HPLC). The therapeutic effects of T. hemsleyanum root extract on DSS-induced UC mice were evaluated by the disease activity index (DAI) score, colon length, serum inflammatory cytokines and oxidant/antioxidant levels, and histopathological features of the ileum and colon. Genome-wide gene expression profiles of ileal and colonic tissues were collected by transcriptomics, and signaling pathways were analyzed by the KEGG database. UC-related pathways were uploaded to the STRING database, then the protein-protein interactions (PPIs) were determined by Cytoscape, and the enriched genes were evaluated by real-time quantitative PCR (qPCR). The protein-ligand complexes were docked by AutoDock, and the genes were knocked down in Caco-2 cells by shRNA. The non-targeted metabolomic profiling of ileal contents was analyzed by ultra-high-performance liquid chromatography (UHPLC), and gut microflora were sequenced by an Illumina MiSeq System. RESULTS Ten components that alleviated UC symptoms in mice by decreasing the DAI and serum inflammatory cytokines and oxidant levels, promoting intestinal development, and increasing serum antioxidant levels were identified in T. hemsleyanum root extract. T. hemsleyanum root extract activated the B cell receptor signaling pathway in the colon tissue of UC mice, in which two components, rutin and astragaline, bound to the spleen tyrosine kinase (SYK) protein but also restored gut microflora diversity and increased the proportion of probiotics. Furthermore, metabolites of T. hemsleyanum root extract were involved in vitamin metabolism, fatty acid metabolism, and ferroptosis. CONCLUSIONS The rutin and astragaline components of T. hemsleyanum root extract, by binding to SYK protein, activated the B cell receptor signaling pathway and restored gut microflora diversity to alleviate UC symptoms in mice.
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Affiliation(s)
- Zhengquan Feng
- Department of Oncology, Tongde Hospital of Zhejiang Province, Hangzhou, 310012, China
| | - Wei Ye
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Lifang Feng
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China.
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Wang R, Yang Y, Tian H, Yi H, Xu L, Lv Y, Ge J, Zhao Y, Wang L, Zhou S, Wang F. A Scalable and Robust Chloroplast Genotyping Solution: Development and Application of SNP and InDel Markers in the Maize Chloroplast Genome. Genes (Basel) 2024; 15:293. [PMID: 38540352 PMCID: PMC10970264 DOI: 10.3390/genes15030293] [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: 01/23/2024] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 06/14/2024] Open
Abstract
Maize(Zea mays. L) is a globally important crop, and understanding its genetic diversity is crucial for plant breeding phylogenetic analyses and comparative genetics. While nuclear markers have been extensively used for mapping agriculturally important genes, they are limited in recognizing characteristics, such as cytoplasmic male sterility and reciprocal cross hybrids. In this study, we performed next-generation sequencing of 176samples, and the maize cultivars represented five distinct groups. A total of 89 single nucleotide polymorphisms (SNPs) and 11 insertion/deletion polymorphisms (InDels) were identified. To enable high-throughput detection, we successfully amplified and confirmed 49 SNP and InDel markers, which were defined as a Varietal Chloroplast Panel (VCP) using the Kompetitive Allele Specific PCR (KASP). The specific markers provided a valuable tool for identifying chloroplast groups. The verification experiment, focusing on the identification of reciprocal cross hybrids and cytoplasmic male sterility hybrids, demonstrated the significant advantages of VCP markers in maternal inheritance characterization. Furthermore, only a small subset of these markers is needed to provide useful information, showcasing the effectiveness of these markers in elucidating the artificial selection process of elite maize lines.
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Affiliation(s)
- Rui Wang
- Maize Research Institute, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing 100097, China; (R.W.); (Y.Y.); (H.T.); (H.Y.); (L.X.); (J.G.); (Y.Z.); (L.W.)
| | - Yang Yang
- Maize Research Institute, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing 100097, China; (R.W.); (Y.Y.); (H.T.); (H.Y.); (L.X.); (J.G.); (Y.Z.); (L.W.)
| | - Hongli Tian
- Maize Research Institute, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing 100097, China; (R.W.); (Y.Y.); (H.T.); (H.Y.); (L.X.); (J.G.); (Y.Z.); (L.W.)
| | - Hongmei Yi
- Maize Research Institute, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing 100097, China; (R.W.); (Y.Y.); (H.T.); (H.Y.); (L.X.); (J.G.); (Y.Z.); (L.W.)
| | - Liwen Xu
- Maize Research Institute, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing 100097, China; (R.W.); (Y.Y.); (H.T.); (H.Y.); (L.X.); (J.G.); (Y.Z.); (L.W.)
| | - Yuanda Lv
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
| | - Jianrong Ge
- Maize Research Institute, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing 100097, China; (R.W.); (Y.Y.); (H.T.); (H.Y.); (L.X.); (J.G.); (Y.Z.); (L.W.)
| | - Yikun Zhao
- Maize Research Institute, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing 100097, China; (R.W.); (Y.Y.); (H.T.); (H.Y.); (L.X.); (J.G.); (Y.Z.); (L.W.)
| | - Lu Wang
- Maize Research Institute, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing 100097, China; (R.W.); (Y.Y.); (H.T.); (H.Y.); (L.X.); (J.G.); (Y.Z.); (L.W.)
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany (LSEB), Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Fengge Wang
- Maize Research Institute, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing 100097, China; (R.W.); (Y.Y.); (H.T.); (H.Y.); (L.X.); (J.G.); (Y.Z.); (L.W.)
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Zhao J, Chen H, Li G, Jumaturti MA, Yao X, Hu Y. Phylogenetics Study to Compare Chloroplast Genomes in Four Magnoliaceae Species. Curr Issues Mol Biol 2023; 45:9234-9251. [PMID: 37998755 PMCID: PMC10670740 DOI: 10.3390/cimb45110578] [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: 10/11/2023] [Revised: 11/07/2023] [Accepted: 11/12/2023] [Indexed: 11/25/2023] Open
Abstract
Magnoliaceae, a family of perennial woody plants, contains several endangered species whose taxonomic status remains ambiguous. The study of chloroplast genome information can help in the protection of Magnoliaceae plants and confirmation of their phylogenetic relationships. In this study, the chloroplast genomes were sequenced, assembled, and annotated in Woonyoungia septentrionalis and three Michelia species (Michelia champaca, Michelia figo, and Michelia macclurei). Comparative analyses of genomic characteristics, repetitive sequences, and sequence differences were performed among the four Magnoliaceae plants, and phylogenetic relationships were constructed with twenty different magnolia species. The length of the chloroplast genomes varied among the four studied species ranging from 159,838 bp (Woonyoungia septentrionalis) to 160,127 bp (Michelia macclurei). Four distinct hotspot regions were identified based on nucleotide polymorphism analysis. They were petA-psbJ, psbJ-psbE, ndhD-ndhE, and rps15-ycf1. These gene fragments may be developed and utilized as new molecular marker primers. By using Liriodendron tulipifera and Liriodendron chinense as outgroups reference, a phylogenetic tree of the four Magnoliaceae species and eighteen other Magnoliaceae species was constructed with the method of Shared Coding Sequences (CDS). Results showed that the endangered species, W. septentrionalis, is relatively genetically distinct from the other three species, indicating the different phylogenetic processes among Magnoliaceae plants. Therefore, further genetic information is required to determine the relationships within Magnoliaceae. Overall, complete chloroplast genome sequences for four Magnoliaceae species reported in this paper have shed more light on phylogenetic relationships within the botanical group.
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Affiliation(s)
- Jianyun Zhao
- Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning 530004, China; (J.Z.); (G.L.); (M.A.J.); (X.Y.)
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning 530004, China
| | - Hu Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China;
| | - Gaiping Li
- Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning 530004, China; (J.Z.); (G.L.); (M.A.J.); (X.Y.)
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning 530004, China
| | - Maimaiti Aisha Jumaturti
- Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning 530004, China; (J.Z.); (G.L.); (M.A.J.); (X.Y.)
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning 530004, China
| | - Xiaomin Yao
- Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning 530004, China; (J.Z.); (G.L.); (M.A.J.); (X.Y.)
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning 530004, China
| | - Ying Hu
- Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning 530004, China; (J.Z.); (G.L.); (M.A.J.); (X.Y.)
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning 530004, China
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Niu Z, Lin Z, Tong Y, Chen X, Deng Y. Complete plastid genome structure of 13 Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses. BMC PLANT BIOLOGY 2023; 23:564. [PMID: 37964203 PMCID: PMC10647099 DOI: 10.1186/s12870-023-04532-0] [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: 04/30/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND Justicia L. is the largest genus in Acanthaceae Juss. and widely distributed in tropical and subtropical regions of the world. Previous phylogenetic studies have proposed a general phylogenetic framework for Justicia based on several molecular markers. However, their studies were mainly focused on resolution of phylogenetic issues of Justicia in Africa, Australia and South America due to limited sampling from Asia. Additionally, although Justicia plants are of high medical and ornamental values, little research on its genetics was reported. Therefore, to improve the understanding of its genomic structure and relationships among Asian Justicia plants, we sequenced complete chloroplast (cp.) genomes of 12 Asian plants and combined with the previously published cp. genome of Justicia leptostachya Hemsl. for further comparative genomics and phylogenetic analyses. RESULTS All the cp. genomes exhibit a typical quadripartite structure without genomic rearrangement and gene loss. Their sizes range from 148,374 to 151,739 bp, including a large single copy (LSC, 81,434-83,676 bp), a small single copy (SSC, 16,833-17,507 bp) and two inverted repeats (IR, 24,947-25,549 bp). GC contents range from 38.1 to 38.4%. All the plastomes contain 114 genes, including 80 protein-coding genes, 30 tRNAs and 4 rRNAs. IR variation and repetitive sequences analyses both indicated that Justicia grossa C. B. Clarke is different from other Justicia species because its lengths of ndhF and ycf1 in IRs are shorter than others and it is richest in SSRs and dispersed repeats. The ycf1 gene was identified as the candidate DNA barcode for the genus Justicia. Our phylogenetic results showed that Justicia is a polyphyletic group, which is consistent with previous studies. Among them, J. grossa belongs to subtribe Tetramerinae of tribe Justicieae while the other Justicia members belong to subtribe Justiciinae. Therefore, based on morphological and molecular evidence, J. grossa should be undoubtedly recognized as a new genus. Interestingly, the evolutionary history of Justicia was discovered to be congruent with the morphology evolution. CONCLUSION Our study not only elucidates basic features of Justicia whole plastomes, but also sheds light on interspecific relationships of Asian Justicia plants for the first time.
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Affiliation(s)
- Zhengyang Niu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zheli Lin
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- School of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, 512005, China
| | - Yi Tong
- School of Chinese Materia Medica Medical, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Xin Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Yunfei Deng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
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Yan M, Dong S, Gong Q, Xu Q, Ge Y. Comparative chloroplast genome analysis of four Polygonatum species insights into DNA barcoding, evolution, and phylogeny. Sci Rep 2023; 13:16495. [PMID: 37779129 PMCID: PMC10543443 DOI: 10.1038/s41598-023-43638-1] [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: 02/28/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023] Open
Abstract
The Polygonatum genus represents a perennial herb with the Liliaceae family, boasting substantial economic and medicinal significance. The majority of Polygonatum plants exhibit notable similarity while lacking distinctive identifying characteristics, thus resulting in the proliferation of adulterated medicinal materials within the market. Within this study, we conducted an in-depth analysis of the complete chloroplast (cp) genomes of four Polygonatum plants and compared them with four closely akin species. The primary objectives were to unveil structural variations, species divergence, and the phylogenetic interrelations among taxa. The cp genomes of the four Polygonatum species were typified by a conventional quadripartite structure, incorporating a large single copy region (LSC), a small single copy region (SSC), and a pair of inverted repeat regions. In total, we annotated a range of 131 to 133 genes, encompassing 84 to 86 protein-coding genes, 38 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes, and 0 to 2 pseudogenes (ycf1, infA). Our comparative analyses unequivocally revealed a remarkable consistency in gene order and GC content within the Polygonatum genus. Furthermore, we predicted a potential 59 to 64 RNA editing sites distributed across 22 protein-coding genes, with the ndhB gene exhibiting the most prominent propensity for RNA editing sites, boasting a tally of 15 sites. Notably, six regions of substantial potential variability were ascertained, characterized by elevated Pi values. Noteworthy, molecular markers for species identification, population genetic scrutiny, and phylogenetic investigations within the genus were identified in the form of the psaJ-rpl33 and trnS + trnT-psaD barcodes. The resultant phylogenetic tree unequivocally depicted the formation of a monophyletic clade comprising species within the evolutionary framework of Liliaceae, demonstrating closer evolutionary affinities with Maianthemum, Dracaeneae, and Asparageae. This comprehensive compendium of findings collectively contributes to the advancement of molecular species identification, elucidation of phylogenetic interrelationships, and the establishment of DNA barcodes tailored to the Polygonatum species.
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Affiliation(s)
- Meixiu Yan
- The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, Zhejiang Province, People's Republic of China
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Shujie Dong
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Qiuyi Gong
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Qin Xu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Yuqing Ge
- The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, Zhejiang Province, People's Republic of China.
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