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Zhou C, Tao F, Long R, Yang X, Wu X, Xiang L, Zhou X, Girdthai T. The complete chloroplast genome of Mussaenda pubescens and phylogenetic analysis. Sci Rep 2024; 14:9131. [PMID: 38644374 PMCID: PMC11033256 DOI: 10.1038/s41598-024-55010-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: 01/09/2024] [Accepted: 02/19/2024] [Indexed: 04/23/2024] Open
Abstract
The chloroplast (cp) genome sequence of Mussaenda pubescens, a promising resource that is used as a traditional medicine and drink, is important for understanding the phylogenetic relationships among the Mussaenda family and genetic improvement and reservation. This research represented the first comprehensive description of the morphological characteristics of M. pubescens, as well as an analysis of the complete cp genome and phylogenetic relationship. The results indicated a close relationship between M. pubescens and M. hirsutula based on the morphological characteristics of the flower and leaves. The cp was sequenced using the Illumina NovaSeq 6000 platform. The results indicated the cp genome of M. pubescens spanned a total length of 155,122 bp, including a pair of inverted repeats (IRA and IRB) with a length of 25,871 bp for each region, as well as a large single-copy (LSC) region and a small single-copy (SSC) region with lengths of 85,370 bp and 18,010 bp, respectively. The results of phylogenetic analyses demonstrated that species within the same genus displayed a tendency to group closely together. It was suggested that Antirhea, Cinchona, Mitragyna, Neolamarckia, and Uncaria might have experienced an early divergence. Furthermore, M. hirsutula showed a close genetic connection to M. pubescens, with the two species having partially overlapping distributions in China. This study presents crucial findings regarding the identification, evolution, and phylogenetic research on Mussaenda plants, specifically targeting M. pubescens.
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Affiliation(s)
- Caibi Zhou
- School of Crop Production Technology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun, 558000, China
| | - Fang Tao
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun, 558000, China
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Rupiao Long
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun, 558000, China
| | - Xiaoting Yang
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun, 558000, China
| | - Xingli Wu
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun, 558000, China
| | - Lan Xiang
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun, 558000, China.
| | - Xiaolu Zhou
- School of Crop Production Technology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand.
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun, 558000, China.
| | - Teerayoot Girdthai
- School of Crop Production Technology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand.
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Kim TH, Ha YH, Setoguchi H, Choi K, Kim SC, Kim HJ. First Record of Comparative Plastid Genome Analysis and Phylogenetic Relationships among Corylopsis Siebold & Zucc. (Hamamelidaceae). Genes (Basel) 2024; 15:380. [PMID: 38540439 PMCID: PMC10970243 DOI: 10.3390/genes15030380] [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: 02/29/2024] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 06/14/2024] Open
Abstract
Corylopsis Siebold & Zucc. (Hamamelidaceae) is widely used as a horticultural plant and comprises approximately 25 species in East Asia. Molecular research is essential to distinguish Corylopsis species, which are morphologically similar. Molecular research has been conducted using a small number of genes but not in Corylopsis. Plastid genomes of Corylopsis species (Corylopsis gotoana, Corylopsis pauciflora, and Corylopsis sinensis) were sequenced using next-generation sequencing techniques. Repeats and nucleotide diversity that could be used as DNA markers were also investigated. A phylogenetic investigation was carried out using 79 protein-coding genes to infer the evolutionary relationships within the genus Corylopsis. By including new plastomes, the overall plastid genome structure of Corylopsis was similar. Simple sequence repeats of 73-106 SSRs were identified in the protein-coding genes of the plastid genomes, and 33-40 long repeat sequences were identified in the plastomes. The Pi value of the rpl33_rps18 region, an intergenic spacer, was the highest. Phylogenetic analysis demonstrated that Corylopsis is a monophyletic group and Loropetalum is closely related to Corylopsis. C. pauciflora, C. gotoana, and C. spicata formed a clade distributed in Japan, whereas C. sinensis, C. glandulifera, and C. velutina formed a clade that was distributed in China.
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Affiliation(s)
- Tae-Hee Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon 11186, Republic of Korea; (T.-H.K.)
| | - Young-Ho Ha
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon 11186, Republic of Korea; (T.-H.K.)
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Kyung Choi
- Division of Garden and Plant Resources, Korea National Arboretum, Pocheon 11186, Republic of Korea
| | - Sang-Chul Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon 11186, Republic of Korea; (T.-H.K.)
| | - Hyuk-Jin Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon 11186, Republic of Korea; (T.-H.K.)
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Mao T, Wang X, Gao H, Gong Z, Liu R, Jiang N, Zhang Y, Zhang H, Guo X, Yu C. Ectopic Expression of MADS-Box Transcription Factor VvAGL12 from Grape Promotes Early Flowering, Plant Growth, and Production by Regulating Cell-Wall Architecture in Arabidopsis. Genes (Basel) 2023; 14:2078. [PMID: 38003021 PMCID: PMC10671436 DOI: 10.3390/genes14112078] [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: 10/12/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
The MADS-box family, a substantial group of plant transcription factors, crucially regulates plant growth and development. Although the functions of AGL12-like subgroups have been elucidated in Arabidopsis, rice, and walnut, their roles in grapes remain unexplored. In this study, we isolated VvAGL12, a member of the grape MADS-box group, and investigated its impact on plant growth and biomass production. VvAGL12 was found to localize in the nucleus and exhibit expression in both vegetative and reproductive organs. We introduced VvAGL12 into Arabidopsis thaliana ecotype Columbia-0 and an agl12 mutant. The resulting phenotypes in the agl12 mutant, complementary line, and overexpressed line underscored VvAGL12's ability to promote early flowering, augment plant growth, and enhance production. This was evident from the improved fresh weight, root length, plant height, and seed production, as well as the reduced flowering time. Subsequent transcriptome analysis revealed significant alterations in the expression of genes associated with cell-wall modification and flowering in the transgenic plants. In summary, the findings highlight VvAGL12's pivotal role in the regulation of flowering timing, overall plant growth, and development. This study offers valuable insights, serving as a reference for understanding the influence of the VvAGL12 gene in other plant species and addressing yield-related challenges.
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Affiliation(s)
- Tingting Mao
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- College of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
| | - Xueting Wang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- College of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
| | - Hongsheng Gao
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- College of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
| | - Zijian Gong
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- College of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
| | - Ruichao Liu
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- College of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
| | - Ning Jiang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- College of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
| | - Yaru Zhang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- College of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
| | - Hongxia Zhang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- College of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, 21 Zhichubei Road, Yantai 264001, China
| | - Xiaotong Guo
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- College of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
| | - Chunyan Yu
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- College of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
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Zhu H, Li H. Comprehensive Analysis of the Complete Chloroplast Genome of Cinnamomum daphnoides (Lauraceae), An Endangered Island Endemic Plant. Mol Biotechnol 2023:10.1007/s12033-023-00950-5. [PMID: 37934387 DOI: 10.1007/s12033-023-00950-5] [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: 07/02/2023] [Accepted: 10/13/2023] [Indexed: 11/08/2023]
Abstract
Cinnamomum daphnoides (Siebold & Zucc 1846) is a rare and endangered island species with a unique Sino-Japanese distribution pattern. However, inormation regarding the species' chloroplast (cp) genome, structural features, and the phylogenetic relationship is still lacking. We utilized high-throughput sequencing technology to assemble and annotate the first cp genome of C. daphnoides (GenBank OR654104), followed by genomic characterization and phylogenetic analysis to fill the gaps in this species' cp genome. Our analysis showed that the cp genome has a quadripartite structure spanning 152,765 bp with a GC content of 39.15%. The genome encodes 126 genes, which include 36 tRNA genes, 8 rRNA genes, and 82 mRNA genes. Specifically, 44 genes are related to photosynthesis, 59 are associated with self-replication, six are other genes, and four have unknown functionality. The Codon usage bias in the genome exhibits a preference for A/U bases. We identified 29 interspaced repeat sequences that belonging to three types of repeat sequences. A total of 217 cpSSR loci were detected with single nucleotide repeats (59.91%) being the most frequent loci, mainly composed of A/T repeats. Our selection pressure analysis revealed that the ycf2 gene experienced strong positive selection (Ka/Ks = 1.81, P > 0.844). Further, we identified three highly variable fragments (psbM, psbT, and ycf1) that can be utilized as specific DNA barcoding markers for species definition and population genetic studies. We conducted boundary analysis, which showed that the structure and gene sequence of the two species were highly conserved. Finally, our phylogenetic analysis supports that C. daphnoides is close to C. cassia in the Cinnamomum genes, indicating that the two species share a common ancestry. Overall, providing genomic information on C. daphnoides will be beneficial for the conservation and utilization of endangered plant genetic resources. It will also serve as a reference for the identification of species and the phylogenetic analysis of Cinnamomum. This information will be useful in future research.
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Affiliation(s)
- Hong Zhu
- Zhejiang Academy of Forestry, Hangzhou, 310023, China.
| | - Hepeng Li
- Zhejiang Academy of Forestry, Hangzhou, 310023, China
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Shang M, Wang J, Dai G, Zheng J, Liao B, Wang J, Duan B. Comparative analysis of chloroplast genome and new insights into phylogenetic relationships of Ajuga and common adulterants. FRONTIERS IN PLANT SCIENCE 2023; 14:1251829. [PMID: 37954994 PMCID: PMC10634298 DOI: 10.3389/fpls.2023.1251829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023]
Abstract
Introduction The potential contamination of herbal medicinal products poses a significant concern for consumer health. Given the limited availability of genetic information concerning Ajuga species, it becomes imperative to incorporate supplementary molecular markers to enhance and ensure accurate species identification. Methods In this study, the chloroplast (cp) genomes of seven species of the genus Ajuag were sequenced, de novo assembled and characterized. Results exhibiting lengths ranging from 150,342 bp to 150,472 bp, encompassing 86 - 88 protein-coding genes (PCGs), 35 - 37 transfer RNA, and eight ribosomal RNA. The repetitive sequences, codon uses, and cp genomes of seven species were highly conserved, and PCGs were the reliable molecular markers for investigating the phylogenetic relationship within the Ajuga genus. Moreover, four mutation hotspot regions (accD-psaI, atpH-atpI, ndhC-trnV(UAC), and ndhF-rpl23) were identified within cp genomes of Ajuga, which could help distinguish A. bracteosa and its contaminants. Based on cp genomes and PCGs, the phylogenetic tree preliminary confirmed the position of Ajuga within the Lamiaceae family. It strongly supported a sister relationship between Subsect. Genevense and Subsect. Biflorae, suggesting the merger of Subsect. Biflorae and Subsect. Genevenses into one group rather than maintaining separate categorizations. Additionally, molecular clock analysis estimated the divergence time of Ajuga to be around 7.78 million years ago. Discussion The species authentication, phylogeny, and evolution analyses of the Ajuga species may benefit from the above findings.
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Affiliation(s)
- Mingyue Shang
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jiale Wang
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Guona Dai
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jiamei Zheng
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Binbin Liao
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jing Wang
- College of Pharmaceutical Science, Dali University, Dali, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, China
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Xu X, Shen Y, Zhang Y, Li Q, Wang W, Chen L, Chen G, Ng WL, Islam MN, Punnarak P, Zheng H, Zhu X. A comparison of 25 complete chloroplast genomes between sister mangrove species Kandelia obovata and Kandelia candel geographically separated by the South China Sea. FRONTIERS IN PLANT SCIENCE 2023; 13:1075353. [PMID: 36684775 PMCID: PMC9845719 DOI: 10.3389/fpls.2022.1075353] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
In 2003, Kandelia obovata was identified as a new mangrove species differentiated from Kandelia candel. However, little is known about their chloroplast (cp) genome differences and their possible ecological significance. In this study, 25 whole cp genomes, with seven samples of K. candel from Malaysia, Thailand, and Bangladesh and 18 samples of K. obovata from China, were sequenced for comparison. The cp genomes of both species encoded 128 genes, namely 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes, but the cp genome size of K. obovata was ~2 kb larger than that of K. candle due to the presence of more and longer repeat sequences. Of these, tandem repeats and simple sequence repeats exhibited great differences. Principal component analysis based on indels, and phylogenetic tree analyses constructed with homologous protein genes from the single-copy genes, as well as 38 homologous pair genes among 13 mangrove species, gave strong support to the separation of the two species within the Kandelia genus. Homologous genes ndhD and atpA showed intraspecific consistency and interspecific differences. Molecular dynamics simulations of their corresponding proteins, NAD(P)H dehydrogenase chain 4 (NDH-D) and ATP synthase subunit alpha (ATP-A), predicted them to be significantly different in the functions of photosynthetic electron transport and ATP generation in the two species. These results suggest that the energy requirement was a pivotal factor in their adaptation to differential environments geographically separated by the South China Sea. Our results also provide clues for future research on their physiological and molecular adaptation mechanisms to light and temperature.
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Affiliation(s)
- Xiuming Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yingjia Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yuchen Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qianying Li
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Wenqing Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Luzhen Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Guangcheng Chen
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Wei Lun Ng
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Selangor Darul Ehsan, Malaysia
| | - Md Nazrul Islam
- Forestry and Wood Technology Discipline, Khulna University, Khulna, Bangladesh
| | - Porntep Punnarak
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand
| | - Hailei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Xueyi Zhu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
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Wang X, Cao Q, Wei Y. The complete chloroplast genome sequence of Tamarix arceuthoides Bunge and Tamarix ramosissima Ledeb. (Tamaricaceae). Mitochondrial DNA B Resour 2023; 8:541-545. [PMID: 37187688 PMCID: PMC10177690 DOI: 10.1080/23802359.2023.2209215] [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] [Indexed: 05/17/2023] Open
Abstract
Tamarix L. is of great ecological and economic significance in arid desert ecosystems. This study reports the complete chloroplast (cp) genomic sequences of T. arceuthoides Bunge and T. ramosissima Ledeb., which are currently unknown, by high-throughput sequencing. The cp genomes of T. arceuthoides 1852 and T. ramosissima 1829 were 156,198 and 156,172 bp in length, respectively, and contained a small single-copy region (SSC: 18,247 bp), a large single-copy region (LSC: 84,795 and 84,890 bp, respectively), and a pair of inverted repeat regions (IRs: 26,565 and 26,470 bp, respectively). The two cp genomes possessed 123 genes arranged in the same order, including 79 protein-coding, 36 tRNA, and eight rRNA genes. Of these, 11 protein-coding genes and seven tRNA genes contained at least one intron. The present study found that Tamarix and Myricaria are sister groups with the closest genetic relationship. The obtained knowledge could provide useful information for future phylogenetic, taxonomic, and evolutionary studies on Tamaricaceae.
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Affiliation(s)
- Xiyong Wang
- College of Grassland Sciences, Xinjiang Agricultural University, Urumqi, China
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Chinese Academy of Sciences, Urumqi, China
| | - Qiumei Cao
- College of Grassland Sciences, Xinjiang Agricultural University, Urumqi, China
- The Specimen Museum of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Yan Wei
- College of Grassland Sciences, Xinjiang Agricultural University, Urumqi, China
- CONTACT Yan Wei College of Grassland Sciences, Xinjiang Agricultural University, Urumqi, China
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Han S, Ding H, Bi D, Zhang S, Yi R, Gao J, Yang J, Ye Y, Wu L, Kan X. Structural Diversities and Phylogenetic Signals in Plastomes of the Early-Divergent Angiosperms: A Case Study in Saxifragales. PLANTS (BASEL, SWITZERLAND) 2022; 11:3544. [PMID: 36559654 PMCID: PMC9787361 DOI: 10.3390/plants11243544] [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: 11/15/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
As representative of the early-divergent groups of angiosperms, Saxifragales is extremely divergent in morphology, comprising 15 families. Within this order, our previous case studies observed significant structural diversities among the plastomes of several lineages, suggesting a possible role in elucidating their deep phylogenetic relationships. Here, we collected 208 available plastomes from 11 constituent families to explore the evolutionary patterns among Saxifragales. With thorough comparisons, the losses of two genes and three introns were found in several groups. Notably, 432 indel events have been observed from the introns of all 17 plastomic intron-containing genes, which could well play an important role in family barcoding. Moreover, numerous heterogeneities and strong intrafamilial phylogenetic implications were revealed in pttRNA (plastomic tRNA) structures, and the unique structural patterns were also determined for five families. Most importantly, based on the well-supported phylogenetic trees, evident phylogenetic signals were detected in combinations with the identified pttRNAs features and intron indels, demonstrating abundant lineage-specific characteristics for Saxifragales. Collectively, the results reported here could not only provide a deeper understanding into the evolutionary patterns of Saxifragales, but also provide a case study for exploring the plastome evolution at a high taxonomic level of angiosperms.
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Affiliation(s)
- Shiyun Han
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Hengwu Ding
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - De Bi
- College of Landscape Engineering, Suzhou Polytechnic Institute of Agriculture, Suzhou 215000, China
| | - Sijia Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ran Yi
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jinming Gao
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jianke Yang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Yuanxin Ye
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Longhua Wu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xianzhao Kan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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Lu Q, Luo W. The complete chloroplast genome of two Firmiana species and comparative analysis with other related species. Genetica 2022; 150:395-405. [DOI: 10.1007/s10709-022-00169-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 09/21/2022] [Indexed: 11/06/2022]
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10
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Yang L, Abduraimov O, Tojibaev K, Shomurodov K, Zhang YM, Li WJ. Analysis of complete chloroplast genome sequences and insight into the phylogenetic relationships of Ferula L. BMC Genomics 2022; 23:643. [PMID: 36076164 PMCID: PMC9461113 DOI: 10.1186/s12864-022-08868-z] [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: 05/30/2022] [Accepted: 08/30/2022] [Indexed: 11/11/2022] Open
Abstract
Background Ferula L. is one of the largest and most taxonomically complicated genera as well as being an important medicinal plant resource in the family Apiaceae. To investigate the plastome features and phylogenetic relationships of Ferula and its neighboring genera Soranthus Ledeb., Schumannia Kuntze., and Talassia Korovin, we sequenced 14 complete plastomes of 12 species. Results The size of the 14 complete chloroplast genomes ranged from 165,607 to 167,013 base pairs (bp) encoding 132 distinct genes (87 protein-coding, 37 tRNA, and 8 rRNA genes), and showed a typical quadripartite structure with a pair of inverted repeats (IR) regions. Based on comparative analysis, we found that the 14 plastomes were similar in codon usage, repeat sequence, simple sequence repeats (SSRs), and IR borders, and had significant collinearity. Based on our phylogenetic analyses, Soranthus, Schumannia, and Talassia should be considered synonymous with Ferula. Six highly divergent regions (rps16/trnQ-UUG, trnS-UGA/psbZ, psbH/petB, ycf1/ndhF, rpl32, and ycf1) were also detected, which may represent potential molecular markers, and combined with selective pressure analysis, the weak positive selection gene ccsA may be a discriminating DNA barcode for Ferula species. Conclusion Plastids contain abundant informative sites for resolving phylogenetic relationships. Combined with previous studies, we suggest that there is still much room for improvement in the classification of Ferula. Overall, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of this genus. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08868-z.
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Affiliation(s)
- Lei Yang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, No.818 South Beijing Road, Urumqi, 830011, China.,Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, No.818 South Beijing Road, Urumqi, 830011, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Shijingshan District, No.19(A) Yuquan Road, Beijing, 100049, China
| | - Ozodbek Abduraimov
- Institute of Botany, Uzbekistan Academy of Sciences, No.32 Durmon Yuli Street, Tashkent, Uzbekistan, 100125
| | - Komiljon Tojibaev
- Institute of Botany, Uzbekistan Academy of Sciences, No.32 Durmon Yuli Street, Tashkent, Uzbekistan, 100125
| | - Khabibullo Shomurodov
- Institute of Botany, Uzbekistan Academy of Sciences, No.32 Durmon Yuli Street, Tashkent, Uzbekistan, 100125
| | - Yuan-Ming Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, No.818 South Beijing Road, Urumqi, 830011, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Shijingshan District, No.19(A) Yuquan Road, Beijing, 100049, China.,Sino-Tajikistan Joint Laboratory for Conservation and Utilization of Biological Resources, No.818 South Beijing Road, Urumqi, 830011, China
| | - Wen-Jun Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, No.818 South Beijing Road, Urumqi, 830011, China. .,College of Resources and Environment, University of Chinese Academy of Sciences, Shijingshan District, No.19(A) Yuquan Road, Beijing, 100049, China. .,Sino-Tajikistan Joint Laboratory for Conservation and Utilization of Biological Resources, No.818 South Beijing Road, Urumqi, 830011, China. .,The Specimen Museum of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
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