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Kim SH, Yang J, Cho MS, Stuessy TF, Crawford DJ, Kim SC. Chloroplast Genome Provides Insights into Molecular Evolution and Species Relationship of Fleabanes ( Erigeron: Tribe Astereae, Asteraceae) in the Juan Fernández Islands, Chile. PLANTS (BASEL, SWITZERLAND) 2024; 13:612. [PMID: 38475459 DOI: 10.3390/plants13050612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
Erigeron represents the third largest genus on the Juan Fernández Islands, with six endemic species, five of which occur exclusively on the younger Alejandro Selkirk Island with one species on both islands. While its continental sister species is unknown, Erigeron on the Juan Fernández Islands appears to be monophyletic and most likely evolved from South American progenitor species. We characterized the complete chloroplast genomes of five Erigeron species, including accessions of E. fernandezia and one each from Alejandro Selkirk and Robinson Crusoe Islands, with the purposes of elucidating molecular evolution and phylogenetic relationships. We found highly conserved chloroplast genomes in size, gene order and contents, and further identified several mutation hotspot regions. In addition, we found two positively selected chloroplast genes (ccsA and ndhF) among species in the islands. The complete plastome sequences confirmed the monophyly of Erigeron in the islands and corroborated previous phylogenetic relationships among species. New findings in the current study include (1) two major lineages, E. turricola-E. luteoviridis and E. fernandezia-E. ingae-E. rupicola, (2) the non-monophyly of E. fernandezia occurring on the two islands, and (3) the non-monophyly of the alpine species E. ingae complex.
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Affiliation(s)
- Seon-Hee Kim
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - JiYoung Yang
- Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Myong-Suk Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Tod F Stuessy
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel J Crawford
- Department of Ecology and Evolutionary Biology and the Biodiversity Institute, The University of Kansas, Lawrence, KS 66045, USA
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
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Kim Y, Kim SH, Yang J, Cho MS, Koldaeva M, Ito T, Maki M, Kim SC. Plastome-based backbone phylogeny of East Asian Phedimus (Subgenus Aizoon: Crassulaceae), with special emphasis on Korean endemics. FRONTIERS IN PLANT SCIENCE 2023; 14:1089165. [PMID: 36998693 PMCID: PMC10043388 DOI: 10.3389/fpls.2023.1089165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/23/2023] [Indexed: 06/19/2023]
Abstract
Although the monophyly of Phedimus has been strongly demonstrated, the species relationships among approximately 20 species of Phedimus have been difficult to determine because of the uniformity of their floral characteristics and extreme variation of their vegetative characters, often accompanied by high polyploid and aneuploid series and diverse habitats. In this study, we assembled 15 complete chloroplast genomes of Phedimus species from East Asia and generated a plastome-based backbone phylogeny of the subgenus Aizoon. As a proxy for nuclear phylogeny, we reconstructed the nuclear ribosomal DNA internal transcribed spacer (nrDNA ITS) phylogeny independently. The 15 plastomes of subg. Aizoon were highly conserved in structure and organization; hence, the complete plastome phylogeny fully resolved the species relationships with strong support. We found that P. aizoon and P. kamtschaticus were polyphyletic and morphologically distinct or ambiguous species, and they most likely evolved from the two species complex. The crown age of subg. Aizoon was estimated to be 27 Ma, suggesting its origin to be in the late Oligocene; however, the major lineages were diversified during the Miocene. The two Korean endemics, P. takesimensis and P. zokuriensis, were inferred to have originated recently during the Pleistocene, whereas the other endemic, P. latiovalifolium, originated in the late Miocene. Several mutation hotspots and seven positively selected chloroplast genes were identified in the subg. Aizoon.
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Affiliation(s)
- Yongsung Kim
- Department of Islands and Coast Biodiversity, Division of Botany, Honam National Institute of Biological Resources, Mokpo, Republic of Korea
| | - Seon-Hee Kim
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - JiYoung Yang
- Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, Republic of Korea
| | - Myong-Suk Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
| | - Marina Koldaeva
- Botanical Garden-Institute, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Takuro Ito
- Botanical Gardens, Tohoku University, Sendai, Japan
| | | | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
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Yanfei N, Tai S, Chunhua W, Jia D, Fazhong Y. Complete chloroplast genome sequences of the medicinal plant Aconitum transsectum (Ranunculaceae): comparative analysis and phylogenetic relationships. BMC Genomics 2023; 24:90. [PMID: 36855055 PMCID: PMC9976445 DOI: 10.1186/s12864-023-09180-0] [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] [Received: 06/22/2022] [Accepted: 02/10/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Aconitum transsectum Diels. (Ranunculaceae) is an important medicinal plant that is widely used in traditional Chinese medicine, but its morphological traits make it difficult to recognize from other Aconitum species. No research has sequenced the chloroplast genome of A.transsectum, despite the fact that phylogenetic analysis based on chloroplast genome sequences provides essential evidence for plant classification. RESULTS In this study, the chloroplast (cp) genome of A. transsectum was sequenced, assembled, and annotated. A. transsectum cp genome is a 155,872 bp tetrameric structure including a large single copy (LSC, 87,671 bp) and a small single copy (SSC, 18,891 bp) section, as well as a pair of inverted repeat sequences (IRa and IRb, 25,894 bp each). 131 genes are encoded by the complete cp genome, comprising 86 protein-coding genes, 37 tRNAs, and 8 rRNAs. The most favored codon in the A. transsectum cp genome is AUG, and 46 repeats and 241 SSRs were also identified. The A. transsectum cp genome is similar in size, gene composition, and IR expansion and contraction to the cp genomes of seven Ranunculaceae species. Phylogenetic analysis of cp genomes of 28 plants from the Ranunculaceae family shows that A. transsectum is most closely related to A. vilmorinianum, A. episcopale, and A. forrestii of Subgen. Aconitum. CONCLUSIONS Overall, this study provides complete cp genome resources for A. transsectum that will be beneficial for identifying potential.
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Affiliation(s)
- Niu Yanfei
- grid.412720.20000 0004 1761 2943Key Laboratory for Forest Resources Conservation and Utilization, Southwest Mountains of China, Southwest Forestry University, Kunming, 650224 China ,grid.506261.60000 0001 0706 7839Yunnan Institute of Materia Medica, Kunming, 650111 China ,Yunnan Baiyao Group Chinese Medicinal Resources Division, Kunming, 650500 China
| | - Su Tai
- grid.506261.60000 0001 0706 7839Yunnan Institute of Materia Medica, Kunming, 650111 China
| | - Wu Chunhua
- Key Laboratory of State Forestry and Grassland Administration On Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Kunming, 650224, China. .,College of Chemical Engineering, Southwest Forestry University, Kunming, 650224, China.
| | - Deng Jia
- grid.412720.20000 0004 1761 2943Key Laboratory for Forest Resources Conservation and Utilization, Southwest Mountains of China, Southwest Forestry University, Kunming, 650224 China
| | - Yang Fazhong
- grid.412720.20000 0004 1761 2943Key Laboratory for Forest Resources Conservation and Utilization, Southwest Mountains of China, Southwest Forestry University, Kunming, 650224 China ,Key Laboratory of State Forestry and Grassland Administration On Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Kunming, 650224 China
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Sandoval-Padilla I, Zamora-Tavares MDP, Ruiz-Sánchez E, Pérez-Alquicira J, Vargas-Ponce O. Characterization of the plastome of Physaliscordata and comparative analysis of eight species of Physalis sensu stricto. PHYTOKEYS 2022; 210:109-134. [PMID: 36760406 PMCID: PMC9836641 DOI: 10.3897/phytokeys.210.85668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/07/2022] [Indexed: 06/18/2023]
Abstract
In this study, we sequenced, assembled, and annotated the plastome of Physaliscordata Mill. and compared it with seven species of the genus Physalis sensu stricto. Sequencing, annotating, and comparing plastomes allow us to understand the evolutionary mechanisms associated with physiological functions, select possible molecular markers, and identify the types of selection that have acted in different regions of the genome. The plastome of P.cordata is 157,000 bp long and presents the typical quadripartite structure with a large single-copy (LSC) region of 87,267 bp and a small single-copy (SSC) region of 18,501 bp, which are separated by two inverted repeat (IRs) regions of 25,616 bp each. These values are similar to those found in the other species, except for P.angulata L. and P.pruinosa L., which presented an expansion of the LSC region and a contraction of the IR regions. The plastome in all Physalis species studied shows variation in the boundary of the regions with three distinct types, the percentage of the sequence identity between coding and non-coding regions, and the number of repetitive regions and microsatellites. Four genes and 10 intergenic regions show promise as molecular markers and eight genes were under positive selection. The maximum likelihood analysis showed that the plastome is a good source of information for phylogenetic inference in the genus, given the high support values and absence of polytomies. In the Physalis plastomes analyzed here, the differences found, the positive selection of genes, and the phylogenetic relationships do not show trends that correspond to the biological or ecological characteristics of the species studied.
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Affiliation(s)
- Isaac Sandoval-Padilla
- Doctorado en Ciencias en Biosistemática, Ecología y Manejo de Recursos Naturales y Agrícolas, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoUniversidad de GuadalajaraZapopanMexico
| | - María del Pilar Zamora-Tavares
- Doctorado en Ciencias en Biosistemática, Ecología y Manejo de Recursos Naturales y Agrícolas, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoUniversidad de GuadalajaraZapopanMexico
| | - Eduardo Ruiz-Sánchez
- Doctorado en Ciencias en Biosistemática, Ecología y Manejo de Recursos Naturales y Agrícolas, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoUniversidad de GuadalajaraZapopanMexico
| | - Jessica Pérez-Alquicira
- Doctorado en Ciencias en Biosistemática, Ecología y Manejo de Recursos Naturales y Agrícolas, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoUniversidad de GuadalajaraZapopanMexico
- Laboratorio Nacional de Identificación y Caracterización Vegetal A(LaniVeg), Consejo Nacional de Ciencia y Tecnología (CONACyT), Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoCONACYTMexico CityMexico
| | - Ofelia Vargas-Ponce
- Doctorado en Ciencias en Biosistemática, Ecología y Manejo de Recursos Naturales y Agrícolas, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sánchez 2100, 45200 Las Agujas, Zapopan, Jalisco, MexicoUniversidad de GuadalajaraZapopanMexico
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Giorgashvili E, Reichel K, Caswara C, Kerimov V, Borsch T, Gruenstaeudl M. Software Choice and Sequencing Coverage Can Impact Plastid Genome Assembly-A Case Study in the Narrow Endemic Calligonum bakuense. FRONTIERS IN PLANT SCIENCE 2022; 13:779830. [PMID: 35874012 PMCID: PMC9296850 DOI: 10.3389/fpls.2022.779830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Most plastid genome sequences are assembled from short-read whole-genome sequencing data, yet the impact that sequencing coverage and the choice of assembly software can have on the accuracy of the resulting assemblies is poorly understood. In this study, we test the impact of both factors on plastid genome assembly in the threatened and rare endemic shrub Calligonum bakuense. We aim to characterize the differences across plastid genome assemblies generated by different assembly software tools and levels of sequencing coverage and to determine if these differences are large enough to affect the phylogenetic position inferred for C. bakuense compared to congeners. Four assembly software tools (FastPlast, GetOrganelle, IOGA, and NOVOPlasty) and seven levels of sequencing coverage across the plastid genome (original sequencing depth, 2,000x, 1,000x, 500x, 250x, 100x, and 50x) are compared in our analyses. The resulting assemblies are evaluated with regard to reproducibility, contig number, gene complement, inverted repeat length, and computation time; the impact of sequence differences on phylogenetic reconstruction is assessed. Our results show that software choice can have a considerable impact on the accuracy and reproducibility of plastid genome assembly and that GetOrganelle produces the most consistent assemblies for C. bakuense. Moreover, we demonstrate that a sequencing coverage between 500x and 100x can reduce both the sequence variability across assembly contigs and computation time. When comparing the most reliable plastid genome assemblies of C. bakuense, a sequence difference in only three nucleotide positions is detected, which is less than the difference potentially introduced through software choice.
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Affiliation(s)
- Eka Giorgashvili
- Systematische Botanik und Pflanzengeographie, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Katja Reichel
- Systematische Botanik und Pflanzengeographie, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Calvinna Caswara
- Systematische Botanik und Pflanzengeographie, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Vuqar Kerimov
- Institute of Botany, Azerbaijan National Academy of Sciences (ANAS), Baku, Azerbaijan
| | - Thomas Borsch
- Systematische Botanik und Pflanzengeographie, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Michael Gruenstaeudl
- Systematische Botanik und Pflanzengeographie, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
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Jiang C, Fan W, Chen L, Gan X. Complete chloroplast genome sequence of Fagus hayatae Palib. (Fagaceae). Mitochondrial DNA B Resour 2022; 7:944-945. [PMID: 35692643 PMCID: PMC9176376 DOI: 10.1080/23802359.2022.2080015] [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: 11/15/2022] Open
Abstract
Complete chloroplast genome (cpDNA) sequence of Fagus hayatae Palib. is yet to be reported, and the phylogenetic position of this species is still under debate. In this study, the complete cpDNA sequence of F. hayatae was determined from Illumina NovaSeq pair-end sequencing data. Results revealed that it has a sequence length of 158,360 bp and contains 131 annotated genes, which consist of 83 protein-coding genes, 40 tRNA genes, and eight rRNA genes. The phylogenetic analysis of the complete cpDNA sequence indicates that Fagus represents a monophyletic clade within Fagaceae. The species relatedness between F. hayatae and F. engleriana is relatively close.
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Affiliation(s)
- Chaoyang Jiang
- College of Life Sciences, China West Normal University, Nanchong, China
| | - Wenqian Fan
- College of Life Sciences, China West Normal University, Nanchong, China
| | - Lijun Chen
- College of Life Sciences, China West Normal University, Nanchong, China
| | - Xiaohong Gan
- College of Life Sciences, China West Normal University, Nanchong, China.,Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
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Cardoni S, Piredda R, Denk T, Grimm GW, Papageorgiou AC, Schulze E, Scoppola A, Salehi Shanjani P, Suyama Y, Tomaru N, Worth JRP, Cosimo Simeone M. 5S-IGS rDNA in wind-pollinated trees (Fagus L.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:909-926. [PMID: 34808015 PMCID: PMC9299691 DOI: 10.1111/tpj.15601] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 11/02/2021] [Accepted: 11/18/2021] [Indexed: 05/31/2023]
Abstract
Standard models of plant speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality in wind-pollinated trees with long evolutionary histories is more complex: species evolve from other species through isolation when genetic drift exceeds gene flow; lineage mixing can give rise to new species (hybrid taxa such as nothospecies and allopolyploids). The multi-copy, potentially multi-locus 5S rDNA is one of few gene regions conserving signal from dichotomous and reticulate evolutionary processes down to the level of intra-genomic recombination. Therefore, it can provide unique insights into the dynamic speciation processes of lineages that diversified tens of millions of years ago. Here, we provide the first high-throughput sequencing (HTS) of the 5S intergenic spacers (5S-IGS) for a lineage of wind-pollinated subtropical to temperate trees, the Fagus crenata - F. sylvatica s.l. lineage, and its distant relative F. japonica. The observed 4963 unique 5S-IGS variants reflect a complex history of hybrid origins, lineage sorting, mixing via secondary gene flow, and intra-genomic competition between two or more paralogous-homoeologous 5S rDNA lineages. We show that modern species are genetic mosaics and represent a striking case of ongoing reticulate evolution during the past 55 million years.
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Affiliation(s)
- Simone Cardoni
- Department of Agricultural and Forestry Science (DAFNE)Università degli studi della TusciaViterbo01100Italy
| | - Roberta Piredda
- Department of Veterinary MedicineUniversity of Bari ‘Aldo Moro’Valenzano70010Italy
| | - Thomas Denk
- Swedish Museum of Natural HistoryStockholm10405Sweden
| | | | | | | | - Anna Scoppola
- Department of Agricultural and Forestry Science (DAFNE)Università degli studi della TusciaViterbo01100Italy
| | - Parvin Salehi Shanjani
- Natural Resources Gene Bank, Research Institute of Forests and RangelandsAgricultural Research, Education and Extension OrganizationTehranIran
| | - Yoshihisa Suyama
- Graduate School of Agricultural ScienceTohoku UniversityOsakiMiyagi989‐6711Japan
| | - Nobuhiro Tomaru
- Graduate School of Bioagricultural SciencesNagoya UniversityNagoyaAichi464‐8601Japan
| | - James R. P. Worth
- Ecological Genetics LaboratoryForestry and Forest Products Research Institute (FFPRI)TsukubaIbaraki305‐8687Japan
| | - Marco Cosimo Simeone
- Department of Agricultural and Forestry Science (DAFNE)Università degli studi della TusciaViterbo01100Italy
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Complete Chloroplast Genome Sequence of Fagus longipetiolata Seemen (Fagaceae): Genome Structure, Adaptive Evolution, and Phylogenetic Relationships. LIFE (BASEL, SWITZERLAND) 2022; 12:life12010092. [PMID: 35054485 PMCID: PMC8778281 DOI: 10.3390/life12010092] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/26/2021] [Accepted: 01/05/2022] [Indexed: 01/08/2023]
Abstract
Fagus longipetiolata Seemen is a deciduous tree of the Fagus genus in Fagaceae, which is endemic to China. In this study, we successfully sequenced the cp genome of F. longipetiolata, compared the cp genomes of the Fagus genus, and reconstructed the phylogeny of Fagaceae. The results showed that the cp genome of F. longipetiolata was 158,350 bp, including a pair of inverted repeat (IRA and IRB) regions with a length of 25,894 bp each, a large single-copy (LSC) region of 87,671 bp, and a small single-copy (SSC) region of 18,891 bp. The genome encoded 131 unique genes, including 81 protein-coding genes, 37 transfer RNA genes (tRNAs), 8 ribosomal RNA genes (rRNAs), and 5 pseudogenes. In addition, 33 codons and 258 simple sequence repeats (SSRs) were identified. The cp genomes of Fagus were relatively conserved, especially the IR regions, which showed the best conservation, and no inversions or rearrangements were found. The five regions with the largest variations were the rps12, rpl32, ccsA, trnW-CCA, and rps3 genes, which spread over in LSC and SSC. The comparison of gene selection pressure indicated that purifying selection was the main selective pattern maintaining important biological functions in Fagus cp genomes. However, the ndhD, rpoA, and ndhF genes of F. longipetiolata were affected by positive selection. Phylogenetic analysis revealed that F. longipetiolata and F. engleriana formed a close relationship, which partially overlapped in their distribution in China. Our analysis of the cp genome of F. longipetiolata would provide important genetic information for further research into the classification, phylogeny and evolution of Fagus.
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Yang J, Choi MJ, Kim SH, Choi HJ, Kim SC. Plastome Characterization and Phylogenomic Analysis Yield New Insights into the Evolutionary Relationships among the Species of the Subgenus Bryocles ( Hosta; Asparagaceae) in East Asia. PLANTS 2021; 10:plants10101980. [PMID: 34685791 PMCID: PMC8538707 DOI: 10.3390/plants10101980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 11/23/2022]
Abstract
The genus Hosta, which has a native distribution in temperate East Asia and a number of species ranging from 23 to 40, represents a taxonomically important and ornamentally popular plant. Despite its taxonomic and horticultural importance, the genus Hosta has remained taxonomically challenging owing to insufficient diagnostic features, continuous morphological variation, and the process of hybridization and introgression, making species circumscription and phylogenetic inference difficult. In this study, we sequenced 11 accessions of Hosta plastomes, including members of three geographically defined subgenera, Hosta, Bryocles, and Giboshi, determined the characteristics of plastomes, and inferred their phylogenetic relationships. We found highly conserved plastomes among the three subgenera, identified several mutation hotspots that can be used as barcodes, and revealed the patterns of codon usage bias and RNA editing sites. Five positively selected plastome genes (rbcL, rpoB, rpoC2, rpl16, and rpl20) were identified. Phylogenetic analysis suggested (1) the earliest divergence of subg. Hosta, (2) non-monophyly of subg. Bryocles and its two sections (Lamellatae and Stoloniferae), (3) a sister relationship between H. sieboldiana (subg. Giboshi) and H. ventricosa (subg. Bryocles), and (4) reciprocally monophyletic and divergent lineages of H. capitata in Korea and Japan, requiring further studies of their taxonomic distinction.
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Affiliation(s)
- JiYoung Yang
- Research Institute for Ulleung-do & Dok-do, College of Natural Sciences, Kyungpook National University, Daegu 41566, Korea;
| | - Mi-Jung Choi
- Department of Biology and Chemistry, Changwon National University, Changwon 51140, Korea;
| | - Seon-Hee Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea;
| | - Hyeok-Jae Choi
- Department of Biology and Chemistry, Changwon National University, Changwon 51140, Korea;
- Correspondence: (H.-J.C.); (S.-C.K.); Tel.: +82-55-213-3457 (H.-J.C.); +82-31-299-4499 (S.-C.K.)
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea;
- Correspondence: (H.-J.C.); (S.-C.K.); Tel.: +82-55-213-3457 (H.-J.C.); +82-31-299-4499 (S.-C.K.)
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10
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Ulaszewski B, Meger J, Mishra B, Thines M, Burczyk J. Complete Chloroplast Genomes of Fagus sylvatica L. Reveal Sequence Conservation in the Inverted Repeat and the Presence of Allelic Variation in NUPTs. Genes (Basel) 2021; 12:1357. [PMID: 34573338 PMCID: PMC8468245 DOI: 10.3390/genes12091357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/21/2021] [Accepted: 08/27/2021] [Indexed: 12/17/2022] Open
Abstract
Growing amounts of genomic data and more efficient assembly tools advance organelle genomics at an unprecedented scale. Genomic resources are increasingly used for phylogenetic analyses of many plant species, but are less frequently used to investigate within-species variability and phylogeography. In this study, we investigated genetic diversity of Fagus sylvatica, an important broadleaved tree species of European forests, based on complete chloroplast genomes of 18 individuals sampled widely across the species distribution. Our results confirm the hypothesis of a low cpDNA diversity in European beech. The chloroplast genome size was remarkably stable (158,428 ± 37 bp). The polymorphic markers, 12 microsatellites (SSR), four SNPs and one indel, were found only in the single copy regions, while inverted repeat regions were monomorphic both in terms of length and sequence, suggesting highly efficient suppression of mutation. The within-individual analysis of polymorphisms showed >9k of markers which were proportionally present in gene and non-gene areas. However, an investigation of the frequency of alternate alleles revealed that the source of this diversity originated likely from nuclear-encoded plastome remnants (NUPTs). Phylogeographic and Mantel correlation analysis based on the complete chloroplast genomes exhibited clustering of individuals according to geographic distance in the first distance class, suggesting that the novel markers and in particular the cpSSRs could provide a more detailed picture of beech population structure in Central Europe.
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Affiliation(s)
- Bartosz Ulaszewski
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064 Bydgoszcz, Poland; (J.M.); (J.B.)
| | - Joanna Meger
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064 Bydgoszcz, Poland; (J.M.); (J.B.)
| | - Bagdevi Mishra
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (B.M.); (M.T.)
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, 60483 Frankfurt am Main, Germany
| | - Marco Thines
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (B.M.); (M.T.)
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, 60483 Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany
| | - Jarosław Burczyk
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064 Bydgoszcz, Poland; (J.M.); (J.B.)
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