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Liang X, Yang L, Xu X, Chi X. The complete plastome of Saxifraga giraldiana Engler and its phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:1157-1161. [PMID: 39234582 PMCID: PMC11370695 DOI: 10.1080/23802359.2024.2397983] [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: 01/17/2024] [Accepted: 08/24/2024] [Indexed: 09/06/2024] Open
Abstract
Saxifraga giraldiana Engler is a common subalpine and alpine plant belonging to Saxifragaceae. However, the genetic diversity of this species has remained to be explored. In this study, we have assembled and characterized the complete chloroplast genome of S. giraldiana, filling this knowledge gap and uncovering its genetic composition. The chloroplast genome is 147,267 bp long and contains 131 genes, including 85 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Furthermore, we have performed a phylogenetic analysis of 19 representative species within Saxifraga. As a result, we have found that S. giraldiana, together with S. implicans and S. stellariifolia, forms a monophyletic group. These findings have implications for the conservation and utilization of S. giraldiana.
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Affiliation(s)
- Xin Liang
- College of Life Sciences, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan University, Chengdu, China
| | - Luxuan Yang
- College of Life Sciences, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan University, Chengdu, China
| | - Xiaoting Xu
- College of Life Sciences, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan University, Chengdu, China
| | - Xiulian Chi
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, PR China
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Li DM, Pan YG, Wu XY, Zou SP, Wang L, Zhu GF. Comparative chloroplast genomics, phylogenetic relationships and molecular markers development of Aglaonema commutatum and seven green cultivars of Aglaonema. Sci Rep 2024; 14:11820. [PMID: 38783007 PMCID: PMC11116548 DOI: 10.1038/s41598-024-62586-y] [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: 01/02/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024] Open
Abstract
Aglaonema commutatum is a famous species in the Aglaonema genus, which has important ornamental and economic value. However, its chloroplast genome information and phylogenetic relationships among popular green cultivars of Aglaonema in southern China have not been reported. Herein, chloroplast genomes of one variety of A. commutatum and seven green cultivars of Aglaonema, namely, A. commutatum 'San Remo', 'Kai Sa', 'Pattaya Beauty', 'Sapphire', 'Silver Queen', 'Snow White', 'White Gem', and 'White Horse Prince', were sequenced and assembled for comparative analysis and phylogeny. These eight genomes possessed a typical quadripartite structure that consisted of a LSC region (90,799-91,486 bp), an SSC region (20,508-21,137 bp) and a pair of IR regions (26,661-26,750 bp). Each genome contained 112 different genes, comprising 79 protein-coding genes, 29 tRNA genes and 4 rRNA genes. The gene orders, GC contents, codon usage frequency, and IR/SC boundaries were highly conserved among these eight genomes. Long repeats, SSRs, SNPs and indels were analyzed among these eight genomes. Comparative analysis of 15 Aglaonema chloroplast genomes identified 7 highly variable regions, including trnH-GUG-exon1-psbA, trnS-GCU-trnG-UCC-exon1, trnY-GUA-trnE-UUC, psbC-trnS-UGA, trnF-GAA-ndhJ, ccsA-ndhD, and rps15-ycf1-D2. Reconstruction of the phylogenetic trees based on chloroplast genomes, strongly supported that Aglaonema was a sister to Anchomanes, and that the Aglaonema genus was classified into two sister clades including clade I and clade II, which corresponded to two sections, Aglaonema and Chamaecaulon, respectively. One variety and five cultivars, including A. commutatum 'San Remo', 'Kai Sa', 'Pattaya Beauty', 'Silver Queen', 'Snow White', and 'White Horse Prince', were classified into clade I; and the rest of the two cultivars, including 'Sapphire' and 'White Gem', were classified into clade II. Positive selection was observed in 34 protein-coding genes at the level of the amino acid sites among 77 chloroplast genomes of the Araceae family. Based on the highly variable regions and SSRs, 4 DNA markers were developed to differentiate the clade I and clade II in Aglaonema. In conclusion, this study provided chloroplast genomic resources for Aglaonema, which were useful for its classification and phylogeny.
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Affiliation(s)
- Dong-Mei Li
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
| | - Yan-Gu Pan
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiao-Ye Wu
- Research Institute of Living Environment, Guangdong Bailin Ecology and Technology Co., LTD, Dongguan, China
| | - Shui-Ping Zou
- Research Institute of Living Environment, Guangdong Bailin Ecology and Technology Co., LTD, Dongguan, China
| | - Lan Wang
- Research Institute of Living Environment, Guangdong Bailin Ecology and Technology Co., LTD, Dongguan, China
| | - Gen-Fa Zhu
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
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Feng Z, Zheng Y, Jiang Y, Pei J, Huang L. Phylogenetic relationships, selective pressure and molecular markers development of six species in subfamily Polygonoideae based on complete chloroplast genomes. Sci Rep 2024; 14:9783. [PMID: 38684694 PMCID: PMC11059183 DOI: 10.1038/s41598-024-58934-7] [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: 08/08/2023] [Accepted: 04/04/2024] [Indexed: 05/02/2024] Open
Abstract
The subfamily Polygonoideae encompasses a diverse array of medicinal and horticultural plants that hold significant economic value. However, due to the lack of a robust taxonomy based on phylogenetic relationships, the classification within this family is perplexing, and there is also a scarcity of reports on the chloroplast genomes of many plants falling under this classification. In this study, we conducted a comprehensive analysis by sequencing and characterizing the complete chloroplast genomes of six Polygonoideae plants, namely Pteroxygonum denticulatum, Pleuropterus multiflorus, Pleuropterus ciliinervis, Fallopia aubertii, Fallopia dentatoalata, and Fallopia convolvulus. Our findings revealed that these six plants possess chloroplast genomes with a typical quadripartite structure, averaging 162,931 bp in length. Comparative chloroplast analysis, codon usage analysis, and repetitive sequence analysis demonstrated a high level of conservation within the chloroplast genomes of these plants. Furthermore, phylogenetic analysis unveiled a distinct clade occupied by P. denticulatum, while P. ciliinrvis displayed a closer relationship to the three plants belonging to the Fallopia genus. Selective pressure analysis based on maximum likelihood trees showed that a total of 14 protein-coding genes exhibited positive selection, with psbB and ycf1 having the highest number of positive amino acid sites. Additionally, we identified four molecular markers, namely petN-psbM, psal-ycf4, ycf3-trnS-GGA, and trnL-UAG-ccsA, which exhibit high variability and can be utilized for the identification of these six plants.
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Affiliation(s)
- Zhan Feng
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, Sichuan, China
| | - Yan Zheng
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Yuan Jiang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, Sichuan, China.
| | - Linfang Huang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
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Wang R, Lan Z, Luo Y, Deng Z. The complete Chloroplast genome of Stachys geobombycis and comparative analysis with related Stachys species. Sci Rep 2024; 14:8523. [PMID: 38609472 PMCID: PMC11014926 DOI: 10.1038/s41598-024-59132-1] [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: 10/11/2023] [Accepted: 04/08/2024] [Indexed: 04/14/2024] Open
Abstract
Herb genomics, at the forefront of traditional Chinese medicine research, combines genomics with traditional practices, facilitating the scientific validation of ancient remedies. This integration enhances public understanding of traditional Chinese medicine's efficacy and broadens its scope in modern healthcare. Stachys species encompass annual or perennial herbs or small shrubs, exhibiting simple petiolate or sessile leaves. Despite their wide-ranging applications across various fields, molecular data have been lacking, hindering the precise identification and taxonomic elucidation of Stachys species. To address this gap, we assembled the complete chloroplast (CP) genome of Stachys geobombycis and conducted reannotation and comparative analysis of seven additional species within the Stachys genus. The findings demonstrate that the CP genomes of these species exhibit quadripartite structures, with lengths ranging from 14,523 to 150,599 bp. Overall, the genome structure remains relatively conserved, hosting 131 annotated genes, including 87 protein coding genes, 36 tRNA genes, and 8 rRNA genes. Additionally, 78 to 98 SSRs and long repeat sequences were detected , and notably, 6 highly variable regions were identified as potential molecular markers in the CP genome through sequence alignment. Phylogenetic analysis based on Bayesian inference and maximum likelihood methods strongly supported the phylogenetic position of the genus Stachys as a member of Stachydeae tribe. Overall, this comprehensive bioinformatics study of Stachys CP genomes lays the groundwork for phylogenetic classification, plant identification, genetic engineering, evolutionary studies, and breeding research concerning medicinal plants within the Stachys genus.
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Affiliation(s)
- Ru Wang
- Hubei Key Laboratory of Biologic Resources Protection and Utilization (Hubei Minzu University), Enshi, 445000, China
| | - Zheng Lan
- Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Yongjian Luo
- Hubei Key Laboratory of Biologic Resources Protection and Utilization (Hubei Minzu University), Enshi, 445000, China
- Central South University of Forestry and Technology, Key Laboratory of Forestry Biotechnology of Hunan Province, Changsha, 410000, China
| | - Zhijun Deng
- Hubei Key Laboratory of Biologic Resources Protection and Utilization (Hubei Minzu University), Enshi, 445000, China.
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Li DM, Pan YG, Liu HL, Yu B, Huang D, Zhu GF. Thirteen complete chloroplast genomes of the costaceae family: insights into genome structure, selective pressure and phylogenetic relationships. BMC Genomics 2024; 25:68. [PMID: 38233753 PMCID: PMC10792896 DOI: 10.1186/s12864-024-09996-4] [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: 01/04/2023] [Accepted: 01/09/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Costaceae, commonly known as the spiral ginger family, consists of approximately 120 species distributed in the tropical regions of South America, Africa, and Southeast Asia, of which some species have important ornamental, medicinal and ecological values. Previous studies on the phylogenetic and taxonomic of Costaceae by using nuclear internal transcribed spacer (ITS) and chloroplast genome fragments data had low resolutions. Additionally, the structures, variations and molecular evolution of complete chloroplast genomes in Costaceae still remain unclear. Herein, a total of 13 complete chloroplast genomes of Costaceae including 8 newly sequenced and 5 from the NCBI GenBank database, representing all three distribution regions of this family, were comprehensively analyzed for comparative genomics and phylogenetic relationships. RESULT The 13 complete chloroplast genomes of Costaceae possessed typical quadripartite structures with lengths from 166,360 to 168,966 bp, comprising a large single copy (LSC, 90,802 - 92,189 bp), a small single copy (SSC, 18,363 - 20,124 bp) and a pair of inverted repeats (IRs, 27,982 - 29,203 bp). These genomes coded 111 - 113 different genes, including 79 protein-coding genes, 4 rRNA genes and 28 - 30 tRNAs genes. The gene orders, gene contents, amino acid frequencies and codon usage within Costaceae were highly conservative, but several variations in intron loss, long repeats, simple sequence repeats (SSRs) and gene expansion on the IR/SC boundaries were also found among these 13 genomes. Comparative genomics within Costaceae identified five highly divergent regions including ndhF, ycf1-D2, ccsA-ndhD, rps15-ycf1-D2 and rpl16-exon2-rpl16-exon1. Five combined DNA regions (ycf1-D2 + ndhF, ccsA-ndhD + rps15-ycf1-D2, rps15-ycf1-D2 + rpl16-exon2-rpl16-exon1, ccsA-ndhD + rpl16-exon2-rpl16-exon1, and ccsA-ndhD + rps15-ycf1-D2 + rpl16-exon2-rpl16-exon1) could be used as potential markers for future phylogenetic analyses and species identification in Costaceae. Positive selection was found in eight protein-coding genes, including cemA, clpP, ndhA, ndhF, petB, psbD, rps12 and ycf1. Maximum likelihood and Bayesian phylogenetic trees using chloroplast genome sequences consistently revealed identical tree topologies with high supports between species of Costaceae. Three clades were divided within Costaceae, including the Asian clade, Costus clade and South American clade. Tapeinochilos was a sister of Hellenia, and Parahellenia was a sister to the cluster of Tapeinochilos + Hellenia with strong support in the Asian clade. The results of molecular dating showed that the crown age of Costaceae was about 30.5 Mya (95% HPD: 14.9 - 49.3 Mya), and then started to diverge into the Costus clade and Asian clade around 23.8 Mya (95% HPD: 10.1 - 41.5 Mya). The Asian clade diverged into Hellenia and Parahellenia at approximately 10.7 Mya (95% HPD: 3.5 - 25.1 Mya). CONCLUSION The complete chloroplast genomes can resolve the phylogenetic relationships of Costaceae and provide new insights into genome structures, variations and evolution. The identified DNA divergent regions would be useful for species identification and phylogenetic inference in Costaceae.
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Affiliation(s)
- Dong-Mei Li
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Yan-Gu Pan
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Hai-Lin Liu
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Bo Yu
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Dan Huang
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Gen-Fa Zhu
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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Zhu W, Cui H, Xiang X. The complete chloroplast genome of Torenia violacea (Azaola) Pennell 1943 (Linderniaceae). Mitochondrial DNA B Resour 2023; 8:1145-1148. [PMID: 38188442 PMCID: PMC10769558 DOI: 10.1080/23802359.2023.2274619] [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: 05/02/2023] [Accepted: 10/18/2023] [Indexed: 01/09/2024] Open
Abstract
Torenia violacea (Azaola) Pennell 1943 as a traditional Chinese medicine plant, has been used to treat multiple diseases. In this study, we sequenced, assembled, and characterized the complete plastome of T. violacea. The plastome (OQ167784) exhibited a typical quadripartite structure, with a total length of 154,007 bp, comprising a pair of inverted repeats (IRs; 24,809 bp) separated by a large single-copy (LSC) region (85,559 bp) and a small single-copy (SSC) region (18,830 bp). Through genome annotation, we identified 133 genes, including 87 protein-coding genes, eight rRNA genes, and 38 tRNA genes. Phylogenetic analysis revealed a close relationship between T. violacea and T. fournieri. The research results provide basic genetic resources for the development of species identification and investigation of phylogenetic relationships in the Torenia genus.
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Affiliation(s)
- Wanhui Zhu
- Key Laboratory of Biodiversity and Ecology Conservation in Southwest Anhui, Anqing Normal University, Anqing, China
- College of Life Sciences, Anqing Normal University, Anqing, China
| | - Hanqing Cui
- College of Life Sciences, Anqing Normal University, Anqing, China
| | - Xiaoyan Xiang
- Key Laboratory of Biodiversity and Ecology Conservation in Southwest Anhui, Anqing Normal University, Anqing, China
- College of Life Sciences, Anqing Normal University, Anqing, China
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Zhou SM, Wang F, Yan SY, Zhu ZM, Gao XF, Zhao XL. Phylogenomics and plastome evolution of Indigofera (Fabaceae). FRONTIERS IN PLANT SCIENCE 2023; 14:1186598. [PMID: 37346129 PMCID: PMC10280451 DOI: 10.3389/fpls.2023.1186598] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023]
Abstract
Introduction Indigofera L. is the third largest genus in Fabaceae and includes economically important species that are used for indigo dye-producing, medicinal, ornamental, and soil and water conservation. The genus is taxonomically difficult due to the high level of overlap in morphological characters of interspecies, fewer reliability states for classification, and extensive adaptive evolution. Previous characteristic-based taxonomy and nuclear ITS-based phylogenies have contributed to our understanding of Indigofera taxonomy and evolution. However, the lack of chloroplast genomic resources limits our comprehensive understanding of the phylogenetic relationships and evolutionary processes of Indigofera. Methods Here, we newly assembled 18 chloroplast genomes of Indigofera. We performed a series of analyses of genome structure, nucleotide diversity, phylogenetic analysis, species pairwise Ka/Ks ratios, and positive selection analysis by combining with allied species in Papilionoideae. Results and discussion The chloroplast genomes of Indigofera exhibited highly conserved structures and ranged in size from 157,918 to 160,040 bp, containing 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Thirteen highly variable regions were identified, of which trnK-rbcL, ndhF-trnL, and ycf1 were considered as candidate DNA barcodes for species identification of Indigofera. Phylogenetic analysis using maximum likelihood (ML) and Bayesian inference (BI) methods based on complete chloroplast genome and protein-coding genes (PCGs) generated a well-resolved phylogeny of Indigofera and allied species. Indigofera monophyly was strongly supported, and four monophyletic lineages (i.e., the Pantropical, East Asian, Tethyan, and Palaeotropical clades) were resolved within the genus. The species pairwise Ka/Ks ratios showed values lower than 1, and 13 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis using the branch-site model, eight of which were associated with photosynthesis. Positive selection of accD suggested that Indigofera species have experienced adaptive evolution to selection pressures imposed by their herbivores and pathogens. Our study provided insight into the structural variation of chloroplast genomes, phylogenetic relationships, and adaptive evolution in Indigofera. These results will facilitate future studies on species identification, interspecific and intraspecific delimitation, adaptive evolution, and the phylogenetic relationships of the genus Indigofera.
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Affiliation(s)
- Sheng-Mao Zhou
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, College of Forestry, Southwest Forestry University, Kunming, China
| | - Fang Wang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, College of Forestry, Southwest Forestry University, Kunming, China
| | - Si-Yuan Yan
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, College of Forestry, Southwest Forestry University, Kunming, China
| | - Zhang-Ming Zhu
- School of Ecology and Environmental Science and Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming, China
| | - Xin-Fen Gao
- Chinese Academy of Sciences (CAS) Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xue-Li Zhao
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, College of Forestry, Southwest Forestry University, Kunming, China
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Mao J, Liang Y, Wang X, Zhang D. Comparison of plastid genomes and ITS of two sister species in Gentiana and a discussion on potential threats for the endangered species from hybridization. BMC PLANT BIOLOGY 2023; 23:101. [PMID: 36800941 PMCID: PMC9940437 DOI: 10.1186/s12870-023-04088-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Gentiana rigescens Franchet is an endangered medicinal herb from the family Gentianaceae with medicinal values. Gentiana cephalantha Franchet is a sister species to G. rigescens possessing similar morphology and wider distribution. To explore the phylogeny of the two species and reveal potential hybridization, we adopted next-generation sequencing technology to acquire their complete chloroplast genomes from sympatric and allopatric distributions, as along with Sanger sequencing to produce the nrDNA ITS sequences. RESULTS The plastid genomes were highly similar between G. rigescens and G. cephalantha. The lengths of the genomes ranged from 146,795 to 147,001 bp in G. rigescens and from 146,856 to 147,016 bp in G. cephalantha. All genomes consisted of 116 genes, including 78 protein-coding genes, 30 tRNA genes, four rRNA genes and four pseudogenes. The total length of the ITS sequence was 626 bp, including six informative sites. Heterozygotes occurred intensively in individuals from sympatric distribution. Phylogenetic analysis was performed based on chloroplast genomes, coding sequences (CDS), hypervariable sequences (HVR), and nrDNA ITS. Analysis based on all the datasets showed that G. rigescens and G. cephalantha formed a monophyly. The two species were well separated in phylogenetic trees using ITS, except for potential hybrids, but were mixed based on plastid genomes. This study supports that G. rigescens and G. cephalantha are closely related, but independent species. However, hybridization was confirmed to occur frequently between G. rigescens and G. cephalantha in sympatric distribution owing to the lack of stable reproductive barriers. Asymmetric introgression, along with hybridization and backcrossing, may probably lead to genetic swamping and even extinction of G. rigescens. CONCLUSION G. rigescens and G. cephalantha are recently diverged species which might not have undergone stable post-zygotic isolation. Though plastid genome shows obvious advantage in exploring phylogenetic relationships of some complicated genera, the intrinsic phylogeny was not revealed because of matrilineal inheritance here; nuclear genomes or regions are hence crucial for uncovering the truth. As an endangered species, G. rigescens faces serious threats from both natural hybridization and human activities; therefore, a balance between conservation and utilization of the species is extremely critical in formulating conservation strategies.
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Affiliation(s)
- Jiuyang Mao
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China
| | - Yuze Liang
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China
| | - Xue Wang
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China
| | - Dequan Zhang
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China.
- Yunnan Key Laboratory of Screening and Research on Anti-pathogenic Plant Resources from Western Yunnan (Cultivation), Dali, 671000, Yunnan, China.
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Li E, Liu K, Deng R, Gao Y, Liu X, Dong W, Zhang Z. Insights into the phylogeny and chloroplast genome evolution of Eriocaulon (Eriocaulaceae). BMC PLANT BIOLOGY 2023; 23:32. [PMID: 36639619 PMCID: PMC9840334 DOI: 10.1186/s12870-023-04034-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 01/02/2023] [Indexed: 05/13/2023]
Abstract
BACKGROUND Eriocaulon is a wetland plant genus with important ecological value, and one of the famous taxonomically challenging groups among angiosperms, mainly due to the high intraspecific diversity and low interspecific variation in the morphological characters of species within this genus. In this study, 22 samples representing 15 Eriocaulon species from China, were sequenced and combined with published samples of Eriocaulon to test the phylogenetic resolution using the complete chloroplast genome. Furthermore, comparative analyses of the chloroplast genomes were performed to investigate the chloroplast genome evolution of Eriocaulon. RESULTS The 22 Eriocaulon chloroplast genomes and the nine published samples were proved highly similar in genome size, gene content, and order. The Eriocaulon chloroplast genomes exhibited typical quadripartite structures with lengths from 150,222 bp to 151,584 bp. Comparative analyses revealed that four mutation hotspot regions (psbK-trnS, trnE-trnT, ndhF-rpl32, and ycf1) could serve as effective molecular markers for further phylogenetic analyses and species identification of Eriocaulon species. Phylogenetic results supported Eriocaulon as a monophyletic group. The identified relationships supported the taxonomic treatment of section Heterochiton and Leucantherae, and the section Heterochiton was the first divergent group. Phylogenetic tree supported Eriocaulon was divided into five clades. The divergence times indicated that all the sections diverged in the later Miocene and most of the extant Eriocaulon species diverged in the Quaternary. The phylogeny and divergence times supported rapid radiation occurred in the evolution history of Eriocaulon. CONCLUSION Our study mostly supported the taxonomic treatment at the section level for Eriocaulon species in China and demonstrated the power of phylogenetic resolution using whole chloroplast genome sequences. Comparative analyses of the Eriocaulon chloroplast genome developed molecular markers that can help us better identify and understand the evolutionary history of Eriocaulon species in the future.
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Affiliation(s)
- Enze Li
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Kangjia Liu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Rongyan Deng
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Yongwei Gao
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Xinyu Liu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
| | - Zhixiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
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Cai L, Pan R, Zeng Q, Zhang X, Zeng R, Zhu Q. The complete plastome sequence of Momordica cochinchinensis (Cucurbitaceae). Mitochondrial DNA B Resour 2023; 8:329-332. [PMID: 36876141 PMCID: PMC9980024 DOI: 10.1080/23802359.2023.2181649] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
Momordica cochinchinensis (Lour.) Spreng. is an important medicinal plant that is used to treat various diseases in South and Southeast Asia. In this study, the complete plastome of M. cochinchinensis was sequenced and found to exhibit a total length of 158,955 bp, with a large single copy (LSC) region of 87,924 bp and a small single copy (SSC) region of 18,479 bp, as well as with two inverted repeats (IRs) that were both 26,726 bp in length. In total, 129 genes were detected, comprising 86 protein-encoding genes, 8 ribosomal RNA (rRNA) genes, and 35 transfer RNA (tRNA) genes. Furthermore, the inferred phylogenetic tree confirmed that M. cochinchinensis belongs to the genus Momordica in the Cucurbitaceae family. The research results will be used for authenticating M. cochinchinensis plant materials and for analyzing the genetic diversity and phylogenetic relationships in Momordica.
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Affiliation(s)
- Lijuan Cai
- Nanchang Business College, Jiangxi Agricultural University, Gongqing, P. R. China
| | - Rao Pan
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, P. R. China
| | - Qun Zeng
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, P. R. China
| | - Xiaoyan Zhang
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, P. R. China
| | - Rongbin Zeng
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, P. R. China
| | - Qianglong Zhu
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, P. R. China
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Li DM, Zhu GF, Yu B, Huang D. Comparative chloroplast genomes and phylogenetic relationships of Aglaonema modestum and five variegated cultivars of Aglaonema. PLoS One 2022; 17:e0274067. [PMID: 36054201 PMCID: PMC9439221 DOI: 10.1371/journal.pone.0274067] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/19/2022] [Indexed: 11/30/2022] Open
Abstract
Aglaonema, commonly called Chinese evergreens, are widely used for ornamental purposes. However, attempts to identify Aglaonema species and cultivars based on leaf morphology have been challenging. In the present study, chloroplast sequences were used to elucidate the phylogenetic relationships of cultivated Aglaonema in South China. The chloroplast genomes of one green species and five variegated cultivars of Aglaonema, Aglaonema modestum, ‘Red Valentine’, ‘Lady Valentine’, ‘Hong Yan’, ‘Hong Jian’, and ‘Red Vein’, were sequenced for comparative and phylogenetic analyses. The six chloroplast genomes of Aglaonema had typical quadripartite structures, comprising a large single copy (LSC) region (91,092–91,769 bp), a small single copy (SSC) region (20,816–26,501 bp), and a pair of inverted repeat (IR) regions (21,703–26,732 bp). The genomes contained 112 different genes, including 79–80 protein coding genes, 28–29 tRNAs and 4 rRNAs. The molecular structure, gene order, content, codon usage, long repeats, and simple sequence repeats (SSRs) were generally conserved among the six sequenced genomes, but the IR-SSC boundary regions were significantly different, and ‘Red Vein’ had a distinct long repeat number and type frequency. For comparative and phylogenetic analyses, Aglaonema costatum was included; it was obtained from the GenBank database. Single-nucleotide polymorphisms (SNPs) and insertions/deletions (indels) were determined among the seven Aglaonema genomes studied. Nine divergent hotspots were identified: trnH-GUG-CDS1_psbA, trnS-GCU_trnS-CGA-CDS1, rps4-trnT-UGU, trnF-GAA-ndhJ, petD-CDS2-rpoA, ycf1-ndhF, rps15-ycf1-D2, ccsA-ndhD, and trnY-GUA-trnE-UUC. Additionally, positive selection was found for rpl2, rps2, rps3, ycf1 and ycf2 based on the analyses of Ka/Ks ratios among 16 Araceae chloroplast genomes. The phylogenetic tree based on whole chloroplast genomes strongly supported monophyletic Aglaonema and clear relationships among Aroideae, Lasioideae, Lemnoideae, Monsteroideae, Orontioideae, Pothoideae and Zamioculcadoideae in the family Araceae. By contrast, protein coding gene phylogenies were poorly to strongly supported and incongruent with the whole chloroplast genome phylogenetic tree. This study provided valuable genome resources and helped identify Aglaonema species and cultivars.
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Affiliation(s)
- Dong-Mei Li
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- * E-mail: (D-ML); (G-FZ)
| | - Gen-Fa Zhu
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- * E-mail: (D-ML); (G-FZ)
| | - Bo Yu
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Dan Huang
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
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