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Yang S, Chen J, Li Z, Huang X, Zhang X, Liu Q, Tojibaev K, Sun H, Deng T. Comparative chloroplast genomes of Dactylicapnos species: insights into phylogenetic relationships. BMC PLANT BIOLOGY 2024; 24:350. [PMID: 38684982 PMCID: PMC11059739 DOI: 10.1186/s12870-024-04989-7] [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: 09/14/2023] [Accepted: 04/04/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND Dactylicapnos is a climbing herbaceous vine, distributed from the Himalayas to southwestern China, and some of the species have important medicinal values. However, the chloroplast genomes of Dactylicapnos have never been investigated. In this study, chloroplast genomes of seven Dactylicapnos species covering all three sections and one informal group of Dactylicapnos were sequenced and assembled, and the detailed comparative analyses of the chloroplast genome structure were provided for the first time. RESULTS The results showed that the chloroplast genomes of Dactylicapnos have a typical quadripartite structure with lengths from 172,344 bp to 176,370 bp, encoding a total of 133-140 genes, containing 88-94 protein-coding genes, 8 rRNAs and 37-39 tRNAs. 31 codons were identified as relative synonymous codon usage values greater than one in the chloroplast genome of Dactylicapnos genus based on 80 protein-coding genes. The results of the phylogenetic analysis showed that seven Dactylicapnos species can be divided into three main categories. Phylogenetic analysis revealed that seven species form three major clades which should be treated as three sections. CONCLUSIONS This study provides the initial report of the chloroplast genomes of Dactylicapnos, their structural variation, comparative genomic and phylogenetic analysis for the first time. The results provide important genetic information for development of medical resources, species identification, infrageneric classification and diversification of Dactylicapnos.
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Affiliation(s)
- Shunquan Yang
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- School of Life Sciences, Yunnan Normal University, Kunming, 650500, China
| | - Juntong Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhimin Li
- School of Life Sciences, Yunnan Normal University, Kunming, 650500, China
| | - Xianhan Huang
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Qun Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Komiljon Tojibaev
- Institute of Botany, Academy Sciences of Uzbekistan, Tashkent, 100125, Uzbekistan
| | - Hang Sun
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Tao Deng
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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He L, Xu S, Cheng X, Huang H, Dai H, Wang X, Ding Z, Xu M, Gu H, Yan N, Wang C. Chloroplast genomes in seven Lagerstroemia species provide new insights into molecular evolution of photosynthesis genes. Front Genet 2024; 15:1378403. [PMID: 38628576 PMCID: PMC11019025 DOI: 10.3389/fgene.2024.1378403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/08/2024] [Indexed: 04/19/2024] Open
Abstract
Lagerstroemia indica is an important commercial tree known for the ornamental value. In this study, the complete chloroplast genome sequence of Lagerstroemia indica "Pink Velour" (Lagerstroemia "Pink Velour") was 152,174 bp in length with a GC content of 39.50%. It contained 85 protein coding genes (PCGs), 37 tRNAs, and 8 rRNA genes. 207 simple sequence repeats (SSRs) and 31 codons with relative synonymous codon (RSCU)value > 1 were detected. Phylogenetic analysis divided 10 Lagerstroemia species into evolutionary branches of clade A and clade B. We conducted a comparative analysis of Lagerstroemia "Pink Velours" complete chloroplast genome with the genomes of six closely related Lagerstroemia species from different origins. The structural features of all seven species were similar, except for the deletion of ycf1 nucleobases at the JSA boundary. The large single-copy (LSC) and the small single-copy (SSC) had a higher sequence divergence than the IR region, and 8 genes that were highly divergent (trnK-UUU, petN, psbF, psbJ, ndhE, ndhD, ndhI, ycf1) had been identified and could be used as molecular markers in future studies. High nucleotide diversity was present in genes belonging to the photosynthesis category. Mutation of single nucleic acid was mainly influenced by codon usage. The value percentage of nonsynonymous substitutions (Ka) and synonymous substitutions (Ks) in 6 Lagerstroemia species revealed that more photosynthesis genes have Ka or Ks only in Lagerstroemia fauriei, Lagerstroemia limii, and Lagerstroemia subcostata. These advances will facilitate the breeding of closely related Lagerstroemia species and deepen understanding on climatic adaptation of Lagerstroemia plants.
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Affiliation(s)
- Ling He
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Sujuan Xu
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xinnian Cheng
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Hanlin Huang
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Hongyu Dai
- College of Medicine, Southeast University, Nanjing, China
| | - Xin Wang
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Zhiyang Ding
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Ming Xu
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Haoran Gu
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Na Yan
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Chunyan Wang
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
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Lam DT, Kataoka T, Yamagishi H, Sun G, Udatsu T, Tanaka K, Ishikawa R. Origin of domesticated water chestnuts ( Trapa bispinosa Roxb.) and genetic variation in wild water chestnuts. Ecol Evol 2024; 14:e10925. [PMID: 38333092 PMCID: PMC10850921 DOI: 10.1002/ece3.10925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 10/09/2023] [Accepted: 01/24/2024] [Indexed: 02/10/2024] Open
Abstract
The water chestnut Trapa bispinosa Roxb. has been domesticated in China and has been reported as the only domesticated species of this genus. To understand the origin of T. bispinosa and its evolution pathway, we compared the genetic similarity and seed morphology of domesticated water chestnut T. bispinosa with three wild species T. natans, T. incisa, and T. japonica along with archeological seed samples from the Tianluoshan site (approximately 7000-6300 cal BP) in China. The largest seed size was observed only in the domesticated species, whereas other wild species showed smaller size including T. natans L. genetically close to the domesticated type, and T. incisa was the smallest in size. The volumes of the seed capsule and endosperm were measured using X ray CT scans, showing the ratios of total volumes between T. bispinosa and wild species ranged from 4.2 to 4.5. The ratios of endosperm volume ranged from 3.3 to 3.7. Both measurements showed domesticated species have larger seed volume. Genome size was indirectly estimated by flow cytometry. Domesticated species with larger seed size was estimated as diploid, as were the wild species except for tetraploid species T. japonica. Domesticated species clearly showed the largest edible organs, but it was not a result of ploidy level changes. Maternal lineages traced using complete whole chloroplast sequences, suggested that T. natans is the closest to T. bispinosa, both of which are close to T. japonica. The result was confirmed by PCR genotyping with chloroplast insertion/deletion (cpINDEL) markers developed in the study. T. incisa showed distinct plastid types within the species, and T. japonica showed a unique plastid genotype. Our study concludes the largest volumes for the edible endosperm have been accomplished through nearly 6000 years of artificial selection, but the domestication did not involve ploidy level changes.
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Affiliation(s)
- Dinh Thi Lam
- Faculty of Agriculture and Life ScienceHirosaki UniversityHirosakiAomoriJapan
| | - Taro Kataoka
- Faculty of Humanity and Social ScienceHirosaki UniversityHirosakiAomoriJapan
| | - Hiroki Yamagishi
- Faculty of Agriculture and Life ScienceHirosaki UniversityHirosakiAomoriJapan
| | - Guoping Sun
- Zhejiang Provincial Research Institute of Cultural Relics and ArchaeologyHangzhouChina
| | | | - Katsunori Tanaka
- Faculty of Agriculture and Life ScienceHirosaki UniversityHirosakiAomoriJapan
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life ScienceHirosaki UniversityHirosakiAomoriJapan
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Ran Z, Li Z, Xiao X, An M, Yan C. Complete chloroplast genomes of 13 species of sect. Tuberculata Chang (Camellia L.): genomic features, comparative analysis, and phylogenetic relationships. BMC Genomics 2024; 25:108. [PMID: 38267876 PMCID: PMC10809650 DOI: 10.1186/s12864-024-09982-w] [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: 06/16/2023] [Accepted: 01/06/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Sect. Tuberculata belongs to Camellia, and its members are characterized by a wrinkled pericarp and united filaments. All the plants in this group, which are endemic to China, are highly valuable for exploring the evolution of Camellia and have great potential for use as an oil source. However, due to the complex and diverse phenotypes of these species and the difficulty of investigating them in the field, their complex evolutionary history and interspecific definitions have remained largely unelucidated. RESULTS Therefore, we newly sequenced and annotated 12 chloroplast (cp) genomes and retrieved the published cp genome of Camellia anlungensis Chang in sect. Tuberculata. In this study, comparative analysis of the cp genomes of the thirteen sect. Tuberculata species revealed a typical quadripartite structure characterized by a total sequence length ranging from 156,587 bp to 157,068 bp. The cp.genome arrangement is highly conserved and moderately differentiated. A total of 130 to 136 genes specific to the three types were identified by annotation, including protein-coding genes (coding sequences (CDSs)) (87-91), tRNA genes (35-37), and rRNA genes (8). The total observed frequency ranged from 23,045 (C. lipingensis) to 26,557 (C. anlungensis). IR region boundaries were analyzed to show that the ycf1 gene of C. anlungensis is located in the IRb region, while the remaining species are present only in the IRa region. Sequence variation in the SSC region is greater than that in the IR region, and most protein-coding genes have high codon preferences. Comparative analyses revealed six hotspot regions (tRNA-Thr(GGT)-psbD, psbE-petL, ycf15-tRNA-Leu(CAA), ndhF-rpl32, ndhD, and trnL(CAA)-ycf15) in the cp genomes that could serve as potential molecular markers. In addition, the results of phylogenetic tree construction based on the cp genomes showed that the thirteen sect. Tuberculata species formed a monophyletic group and were divided into two evolutionarily independent clades, confirming the independence of the section. CONCLUSIONS In summary, we obtained the cp genomes of thirteen sect. Tuberculata plants and performed the first comparative analysis of this group. These results will help us better characterize the plants in this section, deepen our understanding of their genetic characteristics and phylogenetic relationships, and lay the theoretical foundation for their accurate classification, elucidation of their evolutionary changes, and rational development and utilization of this section in the future.
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Affiliation(s)
- Zhaohui Ran
- College of Forestry, Guizhou University, Guiyang, China
| | - Zhi Li
- College of Forestry, Guizhou University, Guiyang, China.
- Bioaffiliationersity and Nature Conservation Research Center, Guizhou University, Guiyang, China.
| | - Xu Xiao
- College of Forestry, Guizhou University, Guiyang, China
| | - Mingtai An
- College of Forestry, Guizhou University, Guiyang, China
- Bioaffiliationersity and Nature Conservation Research Center, Guizhou University, Guiyang, China
| | - Chao Yan
- College of Forestry, Guizhou University, Guiyang, China
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Inglis PW, Cavalcanti TB, Facco MG, Bakker FT, Graham SA. A comprehensive genus-level phylogeny and biogeographical history of the Lythraceae based on whole plastome sequences. ANNALS OF BOTANY 2023; 132:293-318. [PMID: 37439499 PMCID: PMC10583215 DOI: 10.1093/aob/mcad091] [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: 05/09/2023] [Accepted: 07/05/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND AND AIMS The Lythraceae are a mainly subtropical to tropical family of the order Myrtales with 28 currently accepted genera and approximately 600 species. There is currently no well-supported phylogenetic and biogeographical hypothesis of the Lythraceae incorporating all currently accepted genera, which we sought to provide. METHODS Plastomes of representative species of 18 distinct Lythraceae genera were sequenced and annotated. Together with existing sequences, plastomes of all 28 currently accepted genera in the Lythraceae were brought together for the first time. The plastomes were aligned and a Bayesian phylogenetic hypothesis was produced. We then conducted a time-calibrated Bayesian analysis and a biogeographical analysis. KEY RESULTS Plastome-based Bayesian and maximum-likelihood phylogenetic trees are generally congruent with recent nuclear phylogenomic data and resolve two deeply branching major clades in the Lythraceae. One major clade concentrates shrubby and arboreal South American and African genera that inhabit seasonally dry environments, with larger, often winged seeds, adapted to dispersal by the wind. The second major clade concentrates North American, Asian, African and several near-cosmopolitan herbaceous, shrubby and arboreal genera, often inhabiting humid or aquatic environments, with smaller seeds possessing structures that facilitate dispersal by water. CONCLUSIONS We hypothesize that the Lythraceae dispersed early in the Late Cretaceous from South American to North American continents, with subsequent expansion in the Late Cretaceous of a North American lineage through Laurasia to Africa via a boreotropical route. Two later expansions of South American clades to Africa in the Palaeocene and Eocene, respectively, are also hypothesized. Transoceanic dispersal in the family is possibly facilitated by adaptations to aquatic environments that are common to many extant genera of the Lythraceae, where long-distance dispersal and vicariance may be invoked to explain several remarkable disjunct distributions in Lythraceae clades.
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Affiliation(s)
- Peter W Inglis
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Av. W5 Norte (final), Caixa Postal 02372 – Brasília, DF – CEP 70770-917, Brazil
| | - Taciana B Cavalcanti
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Av. W5 Norte (final), Caixa Postal 02372 – Brasília, DF – CEP 70770-917, Brazil
| | - Marlon G Facco
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Brazil
| | - Freek T Bakker
- Biosystematics Group, Wageningen University & Research, Postbus 647, NL-6700 AP, Wageningen, The Netherlands
| | - Shirley A Graham
- Missouri Botanical Garden, 4344 Shaw Boulevard, Saint Louis, MO 63110, USA
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Qu M, Fan X, Hao C, Zheng Y, Guo S, Wang S, Li W, Xu Y, Gao L, Chen Y. Chromosome-level assemblies of cultivated water chestnut Trapa bicornis and its wild relative Trapa incisa. Sci Data 2023; 10:407. [PMID: 37355767 PMCID: PMC10290653 DOI: 10.1038/s41597-023-02270-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 05/26/2023] [Indexed: 06/26/2023] Open
Abstract
Water chestnut (Trapa L.) is a floating-leaved aquatic plant with high edible and medicinal value. In this study, we presented chromosome-level genome assemblies of cultivated large-seed species Trapa bicornis and its wild small-seed relative Trapa incisa by using PacBio HiFi long reads and Hi-C technology. The T. bicornis and T. incisa assemblies consisted of 479.90 Mb and 463.97 Mb contigs with N50 values of 13.52 Mb and 13.77 Mb, respectively, and repeat contents of 62.88% and 62.49%, respectively. A total of 33,306 and 33,315 protein-coding genes were predicted in T. bicornis and T. incisa assemblies, respectively. There were 159,232 structural variants affecting more than 11 thousand genes detected between the two genomes. The phylogenetic analysis indicated that the lineage leading to Trapa was diverged from the lineage to Sonneratia approximately 23 million years ago. These two assemblies provide valuable resources for future evolutionary and functional genomic research and molecular breeding of water chestnut.
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Affiliation(s)
- Minghao Qu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Plant Germplasm Research Center, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangrong Fan
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Hubei Key laboratory of Wetland evolution & ecological restoration, Wuhan Botanical Garden, Chinese academy of sciences, Wuhan, Hubei, 430074, China
- Research Center for Ecology, College of Science, Tibet University, Lhasa, Tibet, 850000, China
| | - Chenlu Hao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Plant Germplasm Research Center, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Zheng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Sumin Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Plant Germplasm Research Center, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Sen Wang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Wei Li
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Hubei Key laboratory of Wetland evolution & ecological restoration, Wuhan Botanical Garden, Chinese academy of sciences, Wuhan, Hubei, 430074, China
- Research Center for Ecology, College of Science, Tibet University, Lhasa, Tibet, 850000, China
| | - Yanqin Xu
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, Jiangxi, 330004, China.
| | - Lei Gao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Plant Germplasm Research Center, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China.
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China.
| | - Yuanyuan Chen
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China.
- Hubei Key laboratory of Wetland evolution & ecological restoration, Wuhan Botanical Garden, Chinese academy of sciences, Wuhan, Hubei, 430074, China.
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Qin HH, Cai J, Liu CK, Zhou RX, Price M, Zhou SD, He XJ. The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution. BMC PLANT BIOLOGY 2023; 23:9. [PMID: 36604614 PMCID: PMC9814190 DOI: 10.1186/s12870-022-04027-4] [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: 09/06/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The Ferula genus encompasses 180-185 species and is one of the largest genera in Apiaceae, with many of Ferula species possessing important medical value. The previous studies provided more information for Ferula, but its infrageneric relationships are still confusing. In addition, its genetic basis of its adaptive evolution remains poorly understood. Plastid genomes with more variable sites have the potential to reconstruct robust phylogeny in plants and investigate the adaptive evolution of plants. Although chloroplast genomes have been reported within the Ferula genus, few studies have been conducted using chloroplast genomes, especially for endemic species in China. RESULTS Comprehensively comparative analyses of 22 newly sequenced and assembled plastomes indicated that these plastomes had highly conserved genome structure, gene number, codon usage, and repeats type and distribution, but varied in plastomes size, GC content, and the SC/IR boundaries. Thirteen mutation hotspot regions were detected and they would serve as the promising DNA barcodes candidates for species identification in Ferula and related genera. Phylogenomic analyses with high supports and resolutions showed that Talassia transiliensis and Soranthus meyeri were nested in the Ferula genus, and thus they should be transferred into the Ferula genus. Our phylogenies also indicated the monophyly of subgenera Sinoferula and subgenera Narthex in Ferula genus. Twelve genes with significant posterior probabilities for codon sites were identified in the positively selective analysis, and their function may relate to the photosystem II, ATP subunit, and NADH dehydrogenase. Most of them might play an important role to help Ferula species adapt to high-temperatures, strong-light, and drought habitats. CONCLUSION Plastome data is powerful and efficient to improve the support and resolution of the complicated Ferula phylogeny. Twelve genes with significant posterior probabilities for codon sites were helpful for Ferula to adapt to the harsh environment. Overall, our study supplies a new perspective for comprehending the phylogeny and evolution of Ferula.
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Affiliation(s)
- Huan-Huan Qin
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jing Cai
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Chang-Kun Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Ren-Xiu Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Megan Price
- Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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Gu C, Ye Y, Zhang G, Yu M, Bai M, Ma Q, Shao W, Zhao Y, Hong S. The chloroplast genome of Cuphea hookeriana Walp. (Lythraceae), a Mexico ornamental plant. Mitochondrial DNA B Resour 2023; 8:522-526. [PMID: 37124996 PMCID: PMC10132219 DOI: 10.1080/23802359.2023.2203783] [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] [Indexed: 05/02/2023] Open
Abstract
Cuphea hookeriana Walp. is an ornamental plant belonging to the Lythraceae. In this study, we reported the complete chloroplast (cp) genome sequence here and analyzed the phylogenetic relationship among Lythraceae plants. The length of the cp genome was 158,999 bp, including a large single-copy (LSC, 89,311 bp) region and a small single-copy (SSC, 18,436 bp) region separated by a pair of inverted repeats (IRs, 25,626 bp). There were 72 unique protein-coding genes (PCGs), 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes in the cp genome of C. hookeriana. A total of 223 simple sequence repeats (SSRs) and 34 long repeat sequences were identified. Phylogenetic analyses using maximum-likelihood (ML) revealed that C. hookeriana was close to C. hyssopifolia. In addition, the two Cuphea species were the sister group of Woodfordia fruticosa.
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Affiliation(s)
- Cuihua Gu
- College of Landscape and Architecture, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A&F University, Hangzhou, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A&F University, Hangzhou, China
| | - Yacheng Ye
- College of Landscape and Architecture, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A&F University, Hangzhou, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A&F University, Hangzhou, China
| | - Guozhe Zhang
- College of Landscape and Architecture, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A&F University, Hangzhou, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A&F University, Hangzhou, China
| | - Mengxin Yu
- College of Landscape and Architecture, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A&F University, Hangzhou, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A&F University, Hangzhou, China
| | - Mingzhu Bai
- College of Landscape and Architecture, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A&F University, Hangzhou, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A&F University, Hangzhou, China
| | - Qingqing Ma
- College of Landscape and Architecture, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A&F University, Hangzhou, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A&F University, Hangzhou, China
| | - Weili Shao
- College of Landscape and Architecture, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A&F University, Hangzhou, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A&F University, Hangzhou, China
- Weili Shao School of Landscape and Architecture, Zhejiang A&F University, Hangzhou311300, China
| | - Yu Zhao
- College of Landscape and Architecture, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A&F University, Hangzhou, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A&F University, Hangzhou, China
- Yu Zhao
| | - Sidan Hong
- College of Landscape and Architecture, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A&F University, Hangzhou, China
- Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A&F University, Hangzhou, China
- CONTACT Sidan Hong
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Sangsrakru D, Sonthirod C, Nawae W, Yundaeng C, Promchoo W, Pootakham W, Tangphatsornruang S. The complete chloroplast genome of Sonneratia griffithii Kurz (Lythraceae). Mitochondrial DNA B Resour 2022; 7:1761-1763. [PMID: 36237205 PMCID: PMC9553166 DOI: 10.1080/23802359.2022.2119818] [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] [Indexed: 10/30/2022] Open
Abstract
Sonneratia griffithii Kurz is a critically endangered mangrove species that can be found along the western coast of Thailand. In this study, we reported the complete chloroplast genome of S. griffithii. The chloroplast genome is 152,730 bp, consisting of one large single-copy (LSC) region, one small single-copy (SSC) region and a pair of inverted repeats (IRs). The LSC, SSC, and IR lengths are 87,226, 17,764, and 23,870 bp, respectively. The genome contains 113 unique genes, including 79 protein-coding, 30 tRNA, and 4 rRNA genes. The GC content of the chloroplast genome is 37.31%. The phylogenetic analysis based on 76 protein-coding genes showed a monophyletic group of S. griffithii and other Sonneratia species.
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Affiliation(s)
- Duangjai Sangsrakru
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wanapinun Nawae
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chutintorn Yundaeng
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Waratthaya Promchoo
- Department of Marine and Coastal Resources, Royal Thai Government Ministry of Natural Resources and Environment, Bangkok, Thailand
| | - Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sithichoke Tangphatsornruang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand,CONTACT Sithichoke Tangphatsornruang National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
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