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Almeida-Silva MA, Braga-Ferreira RS, Targueta CP, Corvalán LCJ, Silva-Neto CM, Franceschinelli EV, Sobreiro MB, Nunes R, Telles MPC. Chloroplast genomes of Simarouba Aubl., molecular evolution and comparative analyses within Sapindales. Sci Rep 2024; 14:21358. [PMID: 39266625 PMCID: PMC11393331 DOI: 10.1038/s41598-024-71956-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 09/02/2024] [Indexed: 09/14/2024] Open
Abstract
Simarouba, a neotropical genus in the family Simaroubaceae, currently lacks comprehensive genomic data in existing databases. This study aims to fill this gap by providing genomic resources for three Simarouba species, S. amara, S. versicolor, and S. glauca. It also aims to perform comparative molecular evolutionary analyses in relation to other species within the order Sapindales. The analysis of these three Simarouba species revealed the presence of the typical quadripartite structure expected in plastomes. However, some pseudogenization events were identified in the psbC, infA, rpl22, and ycf1 genes. In particular, the CDS of the psbC gene in S. amara was reduced from 1422 bp to 584 bp due to a premature stop codon. Nucleotide diversity data pointed to gene and intergenic regions as promising candidates for species and family discrimination within the group, specifically matK, ycf1, ndhF, rpl32, petA-psbJ, and trnS-trnG. Selection signal analyses showed strong evidence for positive selection on the rpl23 gene. Phylogenetic analyses indicated that S. versicolor and S. glauca have a closer phylogenetic relationship than S. amara. We provide chloroplast genomes of three Simaruba species and use them to elucidate plastome evolution, highlight the presence of pseudogenization, and identify potential DNA barcode regions.
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Affiliation(s)
- Marla A Almeida-Silva
- Laboratório de Genética and Biodiversidade (LGBio), Universidade Federal de Goiás, Goiânia, GO, Brazil
- Universidade Estadual do Piauí, Campus Prof. Ariston Dias Lima, São Raimundo Nonato, PI, Brazil
| | - Ramilla S Braga-Ferreira
- Laboratório de Genética and Biodiversidade (LGBio), Universidade Federal de Goiás, Goiânia, GO, Brazil
- Universidade Federal de Rondonópolis, Rondonópolis, MT, Brazil
| | - Cíntia P Targueta
- Laboratório de Genética and Biodiversidade (LGBio), Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Leonardo C J Corvalán
- Laboratório de Genética and Biodiversidade (LGBio), Universidade Federal de Goiás, Goiânia, GO, Brazil
- Instituto Federal de Goiás-Polo de Inovação, Goiânia, GO, Brazil
| | - Carlos M Silva-Neto
- Instituto Federal de Goiás-Polo de Inovação, Goiânia, GO, Brazil
- Laboratório de Bioinformática e Biodiversidade (LBB), Universidade Estadual de Goiás, Instituto Acadêmico de Ciências da Saúde e Biológicas (IACSB), Campus Oeste, Unidade Universitária de Iporá, Iporá, GO, 76200-000, Brazil
| | | | - Mariane B Sobreiro
- Laboratório de Genética and Biodiversidade (LGBio), Universidade Federal de Goiás, Goiânia, GO, Brazil
- Laboratório Estadual de Saúde Pública Dr. Giovanni Cysneiros - LACEN-GO, Goiânia, GO, Brazil
| | - Rhewter Nunes
- Laboratório de Genética and Biodiversidade (LGBio), Universidade Federal de Goiás, Goiânia, GO, Brazil.
- Laboratório de Bioinformática e Biodiversidade (LBB), Universidade Estadual de Goiás, Instituto Acadêmico de Ciências da Saúde e Biológicas (IACSB), Campus Oeste, Unidade Universitária de Iporá, Iporá, GO, 76200-000, Brazil.
| | - Mariana P C Telles
- Laboratório de Genética and Biodiversidade (LGBio), Universidade Federal de Goiás, Goiânia, GO, Brazil
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Goiânia, GO, Brazil
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Chen C, Luo D, Wang Z, Miao Y, Liu Q, Zhao T, Liu D. Complete chloroplast genomes of eight Artemisia species: Comparative analysis, molecular identification, and phylogenetic analysis. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:257-269. [PMID: 38169134 DOI: 10.1111/plb.13608] [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: 04/03/2023] [Accepted: 11/13/2023] [Indexed: 01/05/2024]
Abstract
Artemisia L. is the largest genus in the Asteraceae, and well known for its high medicinal value. The morphological features of Artemisia species are similar, making taxonomic identification and evolutionary research difficult. We sequenced chloroplast genomes of eight Artemisia species, all of which are common adulterants of A. argyi. We used novel genetic data and compared these data to the published A. argyi chloroplast genome in to develop molecular markers for species identification and reconstructing phylogenetic relationships between Artemisia species. The eight chloroplast sequences were highly similar in gene order, content, and structure, encoding a total of 114 genes (82 protein-coding genes, 28 tRNAs, and four rRNAs). All species harboured similar repeat sequences and simple sequence repeats (SSRs), ranging from 47 to 49 and 38 to 40 repeats, respectively. In addition, we identified five hypervariable regions (rpl32-trnL, rps16-trnQ, petN-psbM, trnE-rpoB, and atpA-trnR) and ten variable coding genes (ycf1, psbG, rpl36, psaC, psaI, accD, psbT, ndhD, ndhE, and psbH), which can be used to develop chloroplast molecular markers. Finally, phylogenetic reconstructions based on six datasets produced similar topologies, revealing A. argyi is closely related to species often found as adulterants, as expected. Our research provides valuable new information on the evolution and phylogenetic relationships between Artemisia chloroplast genomes and identifies valuable molecular makers to distinguish it from closely related species.
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Affiliation(s)
- C Chen
- Hubei Shizhen Laboratory, Hubei University of Chinese Medicine, Wuhan, China
| | - D Luo
- Hubei Shizhen Laboratory, Hubei University of Chinese Medicine, Wuhan, China
| | - Z Wang
- Hubei Shizhen Laboratory, Hubei University of Chinese Medicine, Wuhan, China
| | - Y Miao
- Hubei Shizhen Laboratory, Hubei University of Chinese Medicine, Wuhan, China
| | - Q Liu
- Hubei Shizhen Laboratory, Hubei University of Chinese Medicine, Wuhan, China
| | - T Zhao
- Hubei Shizhen Laboratory, Hubei University of Chinese Medicine, Wuhan, China
| | - D Liu
- Hubei Shizhen Laboratory, Hubei University of Chinese Medicine, Wuhan, China
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Wan T, Qiao BX, Zhou J, Shao KS, Pan LY, An F, He XS, Liu T, Li PK, Cai YL. Evolutionary and phylogenetic analyses of 11 Cerasus species based on the complete chloroplast genome. FRONTIERS IN PLANT SCIENCE 2023; 14:1070600. [PMID: 36938043 PMCID: PMC10022824 DOI: 10.3389/fpls.2023.1070600] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The subgenus Cerasus, one of the most important groups in the genus Prunus sensu lato, comprises over 100 species; however, the taxonomic classification and phylogenetic relationships of Cerasus remain controversial. Therefore, it is necessary to reconstruct the phylogenetic tree for known Cerasus species. Here, we report the chloroplast (cp) genome sequences of 11 Cerasus species to provide insight into evolution of the plastome. The cp genomes of the 11 Cerasus species (157,571-158,830 bp) displayed a typical quadripartite circular structure. The plastomes contain 115 unique genes, including 80 protein-coding genes, four ribosomal RNAs, and 31 transfer RNAs. Twenty genes were found to be duplicated in inverted repeats as well as at the boundary. The conserved non-coding sequences showed significant divergence compared with the coding regions. We found 12 genes and 14 intergenic regions with higher nucleotide diversity and more polymorphic sites, including matK, rps16, rbcL, rps16-trnQ, petN-psbM, and trnL-trnF. During cp plastome evolution, the codon profile has been strongly biased toward the use of A/T at the third base, and leucine and isoleucine codons appear the most frequently. We identified strong purifying selection on the rpoA, cemA, atpA, and petB genes; whereas ccsA, rps19, matK, rpoC2, ycf2 and ndhI showed a signature of possible positive selection during the course of Cerasus evolution. In addition, we further analyzed the phylogenetic relationships of these species with 57 other congenic related species.Through reconstructing the Cerasus phylogeny tree, we found that true cherry is similar to the flora of China forming a distinct group, from which P. mahaleb was separated as an independent subclade. Microcerasus was genetically closer to Amygdalus, Armeniaca, and Prunus (sensu stricto) than to members of true cherry, whereas P. japonica and P. tomentosa were most closely related to P. triloba and P. pedunculata. However, P. tianshanica formed a clade with P. cerasus, P. fruticosa, P. cerasus × P. canescens 'Gisela 6', and P. avium as a true cherry group. These results provide new insights into the plastome evolution of Cerasus, along with potential molecular markers and candidate DNA barcodes for further phylogenetic and phylogeographic analyses of Cerasus species.
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Affiliation(s)
- Tian Wan
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
| | - Bai-xue Qiao
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
| | - Jing Zhou
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
| | - Ke-sen Shao
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
| | - Liu-yi Pan
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
| | - Feng An
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
| | - Xu-sheng He
- College of Natural Resources and Environment, Northwest Agriculture & Forestry University, Yangling, China
| | - Tao Liu
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
| | - Ping-ke Li
- Center of Experimental Station, Northwest Agriculture & Forestry University, Yangling, China
| | - Yu-liang Cai
- College of Horticulture, Northwest Agriculture & Forestry University, Yangling, China
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Feng JL, Wu LW, Wang Q, Pan YJ, Li BL, Lin YL, Yao H. Comparison Analysis Based on Complete Chloroplast Genomes and Insights into Plastid Phylogenomic of Four Iris Species. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2194021. [PMID: 35937412 PMCID: PMC9348943 DOI: 10.1155/2022/2194021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/06/2022] [Accepted: 07/05/2022] [Indexed: 11/17/2022]
Abstract
Iris species, commonly known as rainbow flowers because of their attractive flowers, are extensively grown in landscape gardens. A few species, including Belamcanda chinensis, the synonym of I. domestica and I. tectorum, are known for their medicinal properties. However, research on the genomes and evolutionary relationships of Iris species is scarce. In the current study, the complete chloroplast (CP) genomes of I. tectorum, I. dichotoma, I. japonica, and I. domestica were sequenced and compared for their identification and relationship. The CP genomes of the four Iris species were circular quadripartite with similar lengths, GC contents, and codon usages. A total of 113 specific genes were annotated, including the ycf1 pseudogene in all species and rps19 in I. japonica alone. All the species had mononucleotide (A/T) simple sequence repeats (SSRs) and long forward and palindromic repeats in their genomes. A comparison of the CP genomes based on mVISTA and nucleotide diversity (Pi) identified three highly variable regions (ndhF-rpl32, rps15-ycf1, and rpl16). Phylogenetic analysis based on the complete CP genomes concluded that I. tectorum is a sister of I. japonica, and the subgenus Pardanthopsis with several I. domestica clustered into one branch is a sister of I. dichotoma. These findings confirm the feasibility of superbarcodes (complete CP genomes) for Iris species authentication and could serve as a resource for further research on Iris phylogeny.
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Affiliation(s)
- Jing-lu Feng
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Li-wei Wu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Qing Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Yun-jia Pan
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Bao-li Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Yu-lin Lin
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Hui Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
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Wang T, Chen LL, Shu HJ, You F, Liang XL, Li J, Ren J, Wanga VO, Mutie FM, Cai XZ, Liu KM, Hu GW. Fortunella venosa (Champ. ex Benth.) C. C. Huang and F. hindsii (Champ. ex Benth.) Swingle as Independent Species: Evidence From Morphology and Molecular Systematics and Taxonomic Revision of Fortunella (Rutaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:867659. [PMID: 35646034 PMCID: PMC9133918 DOI: 10.3389/fpls.2022.867659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
Recently, the systematic status of Fortunella Swingle and its taxonomy has attracted much attention. Flora of China incorporates Fortunella into Citrus Linn. and treats all species of the traditional Fortunella as one species, namely Citrus japonica (Thunb.) Swingle. Furthermore, F. venosa (Champ. ex Benth.) C. C. Huang and F. hindsii (Champ. ex Benth.) Swingle are currently considered as synonyms of C. japonica. In this paper, morphological, palynological, and phylogenetic analyses were used to systematically explore the taxonomic status of traditional Fortunella. The key morphological features that differed among the Fortunella species were the leaf and the petiole hence could be key in its taxonomic classification of the species. Additionally, pollen morphological analysis based on the pollen size, germination grooves, polar, and equatorial axes also supported the separation of the species. The results of the phylogenetic analysis showed that each of the three species clustered separately, hence strongly supporting the conclusion of independent species. In addition, the phylogenetic analysis showed that the two genera clustered closely together hence our results support the incorporation of Fortunella into Citrus. Based on the above, this article has revised the classification of the traditional Fortunella and determined that this genus has three species, namely; F. venosa, F. hindsii, and F. japonica. F. venosa and F. hindsii are placed in the Citrus as separate species, and their species names still use the previous specific epithet. The revised scientific names of the new combinations of F. venosa and F. hindsii are as follows: Citrus venosa (Champ. ex Benth.) K. M. Liu, X. Z. Cai, and G. W. Hu, comb. nov. and Citrus hindsii (Champ. ex Benth.) K. M. Liu, G. W. Hu, and X. Z. Cai, comb. nov. F. venosa is the original species of Fortunella, F. venosa and F. hindsii are both listed as the second-class key protected wild plants in China. Therefore, the establishment of the taxonomic status of F. venosa and F. hindsii not only deepens our understanding, importance, and the complexity of the systematic classification of Fortunella, but is also significant for global biodiversity conservation, genetic resources for breeding purposes, and population genetics.
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Affiliation(s)
- Ting Wang
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Ling-Ling Chen
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Hui-Juan Shu
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Fang You
- Department of Ecological Environment of Hunan Province, Changsha, China
| | - Xiao-Li Liang
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Jun Li
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Jing Ren
- College of Life Sciences, Hunan Normal University, Changsha, China
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Vincent Okelo Wanga
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- UCAS, University of Chinese Academy of Sciences, Beijing, China
| | - Fredrick Munyao Mutie
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- UCAS, University of Chinese Academy of Sciences, Beijing, China
| | - Xiu-Zhen Cai
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Ke-Ming Liu
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Guang-Wan Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- UCAS, University of Chinese Academy of Sciences, Beijing, China
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