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Sebastin R, Kim J, Jo IH, Yu JK, Jang W, Han S, Park HS, AlGarawi AM, Hatamleh AA, So YS, Shim D, Chung JW. Comparative chloroplast genome analyses of cultivated and wild Capsicum species shed light on evolution and phylogeny. BMC PLANT BIOLOGY 2024; 24:797. [PMID: 39179978 PMCID: PMC11344449 DOI: 10.1186/s12870-024-05513-7] [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: 05/16/2024] [Accepted: 08/12/2024] [Indexed: 08/26/2024]
Abstract
The chloroplast (cp.) genome, also known as plastome, plays crucial roles in plant survival, adaptation, and evolution. The stable genetic structure of cp. genomes provides an ideal system for investigating species evolution. We sequenced three complete cp. genome sequences of Capsicum species and analyzed them using sequences of various Capsicum species retrieved from the NCBI database. The cp. genome of Capsicum species maintains a well-preserved quadripartite structure consisting of two inverted repeats (IRs) flanked by a large single copy (LSC) region and a small single copy (SSC) region. The sizes of cp. genome sequences ranged from 156,583 bp (C. lycianthoides) to 157,390 bp (C.pubescens). A total of 127-132 unique genes, including 83-87 protein-coding, 36-37 tRNA, and eight rRNA genes, were predicted. Comparison of cp. genomes of 10 Capsicum species revealed high sequence similarity in genome-wide organization and gene arrangements. Fragments of trnT-UGU/trnL-UAA, ccsA, ndhD, rps12, and ycf1 were identified as variable regions, and nucleotide variability of LSC and SSC was higher than that of IR. Phylogenetic speciation analysis showed that the major domesticated C. annuum species were the most extensively divergent species and closely related to C. tovarii and C. frutescens. Analysis of divergent times suggested that a substantial range of speciation events started occurring ~ 25.79 million years ago (Mya). Overall, comparative analysis of cp. genomes of Capsicum species not only offers new insights into their genetic variation and phylogenetic relationships, but also lays a foundation for evolutionary history, genetic diversity, conservation, and biological breeding of Capsicum species.
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Affiliation(s)
- Raveendar Sebastin
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Jaewook Kim
- Department of Biology Education, Korea National University of Education, Cheongju, 28173, Republic of Korea
| | - Ick-Hyun Jo
- Department of Crop Science and Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Ju-Kyung Yu
- Department of Crop Science, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Woojong Jang
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, 58245, Republic of Korea
| | - Seahee Han
- Honam National Institute of Biological Resources, Mokpo, 58762, Republic of Korea
| | - Hyun-Seung Park
- Department of Integrative Biological Sciences and Industry, Convergence Research Center for Natural Products, Sejong University, Seoul, 05006, Republic of Korea
| | - Amal Mohamed AlGarawi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Ashraf Atef Hatamleh
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Yoon-Sup So
- Department of Crop Science, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Donghwan Shim
- Department of Biological Science, Chungnam National University, Daejeon, 34134, Republic of Korea.
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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Zhou P, Lei WS, Shi YK, Liu YZ, Luo Y, Li JH, Xiang XG. Plastome Evolution, Phylogenomics, and DNA Barcoding Investigation of Gastrochilus (Aeridinae, Orchidaceae), with a Focus on the Systematic Position of Haraella retrocalla. Int J Mol Sci 2024; 25:8500. [PMID: 39126069 PMCID: PMC11312641 DOI: 10.3390/ijms25158500] [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: 06/29/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024] Open
Abstract
Gastrochilus is an orchid genus containing about 70 species in tropical and subtropical Asia with high morphological diversity. The phylogenetic relationships among this genus have not been fully resolved, and the plastome evolution has not been investigated either. In this study, five plastomes of Gastrochilus were newly reported, and sixteen plastomes of Gastrochilus were used to conduct comparative and phylogenetic analyses. Our results showed that the Gastrochilus plastomes ranged from 146,183 to 148,666 bp, with a GC content of 36.7-36.9%. There were 120 genes annotated, consisting of 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. No contraction and expansion of IR borders, gene rearrangements, or inversions were detected. Additionally, the repeat sequences and codon usage bias of Gastrochilus plastomes were highly conserved. Twenty hypervariable regions were selected as potential DNA barcodes. The phylogenetic relationships within Gastrochilus were well resolved based on the whole plastome, especially among main clades. Furthermore, both molecular and morphological data strongly supported Haraella retrocalla as a member of Gastrochilus (G. retrocallus).
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Affiliation(s)
- Peng Zhou
- Key Laboratory of Poyang Lake Environment and Resource Utilization Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China; (P.Z.); (W.-S.L.); (Y.-K.S.); (Y.-Z.L.)
| | - Wan-Shun Lei
- Key Laboratory of Poyang Lake Environment and Resource Utilization Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China; (P.Z.); (W.-S.L.); (Y.-K.S.); (Y.-Z.L.)
| | - Ying-Kang Shi
- Key Laboratory of Poyang Lake Environment and Resource Utilization Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China; (P.Z.); (W.-S.L.); (Y.-K.S.); (Y.-Z.L.)
| | - Yi-Zhen Liu
- Key Laboratory of Poyang Lake Environment and Resource Utilization Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China; (P.Z.); (W.-S.L.); (Y.-K.S.); (Y.-Z.L.)
| | - Yan Luo
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666300, China;
| | - Ji-Hong Li
- Kadoorie Farm and Botanic Garden, Hong Kong Lam Kam Road, Tai Po, New Territories, Hong Kong 999077, China;
| | - Xiao-Guo Xiang
- Key Laboratory of Poyang Lake Environment and Resource Utilization Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China; (P.Z.); (W.-S.L.); (Y.-K.S.); (Y.-Z.L.)
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Lee SR, Oh A, Son DC. Characterization, comparison, and phylogenetic analyses of chloroplast genomes of Euphorbia species. Sci Rep 2024; 14:15352. [PMID: 38961172 PMCID: PMC11222452 DOI: 10.1038/s41598-024-66102-0] [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: 02/27/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024] Open
Abstract
The genus Euphorbia (Euphorbiaceae) has near-cosmopolitan distribution and serves as a significant resource for both ornamental and medicinal purposes. Despite its economic importance, Euphorbia's taxonomy has long been challenged by the intricate nature of morphological traits exhibiting high levels of convergence. While molecular markers are essential for phylogenetic studies, their availability for Euphorbia has been limited. To address this gap, we conducted comparative analyses focusing on the chloroplast (CP) genomes of nine Euphorbia species, incorporating three newly sequenced and annotated accessions. In addition, phylogenetic informativeness and nucleotide diversity were computed to identify candidate markers for phylogenetic analyses among closely related taxa in the genus. Our investigation revealed relatively conserved sizes and structures of CP genomes across the studied species, with notable interspecific variations observed primarily in non-coding regions and IR/SC borders. By leveraging phylogenetic informativeness and nucleotide diversity, we identified rpoB gene as the optimal candidate for species delimitation and shallow-level phylogenetic inference within the genus. Through this comprehensive analysis of CP genomes across multiple taxa, our study sheds light on the evolutionary dynamics and taxonomic intricacies of Euphorbia, offering valuable insights into its CP genome evolution and taxonomy.
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Affiliation(s)
- Soo-Rang Lee
- Department of Biology Education, College of Education, Chosun University, Gwangju, 61452, Republic of Korea.
| | - Ami Oh
- Department of Biology Education, College of Education, Chosun University, Gwangju, 61452, Republic of Korea
| | - Dong Chan Son
- Division of Forest Biodiversity and Herbarium, Korea National Arboretum, Pocheon, 11186, Republic of Korea.
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Hai Y, Qian Y, Yang M, Zhang Y, Xu H, Yang Y, Xia C. The chloroplast genomes of two medicinal species (Veronica anagallis-aquatica L. and Veronica undulata Wall.) and its comparative analysis with related Veronica species. Sci Rep 2024; 14:13945. [PMID: 38886540 PMCID: PMC11183227 DOI: 10.1038/s41598-024-64896-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 06/13/2024] [Indexed: 06/20/2024] Open
Abstract
Veronica anagallis-aquatica L. and Veronica undulata Wall. are widely used ethnomedicinal plants in China. The two species have different clinical efficacies, while their extremely similar morphology and unclear interspecific relationship make it difficult to accurately identify them, leading to increased instances of mixed usage. This article reports on the complete chloroplast genomes sequence of these two species and their related Veronica species to conduct a comparative genomics analysis and phylogenetic construction. The results showed that the chloroplast (cp) genomes of Veronica exhibited typical circular quadripartite structures, with total lengths of 149,386 to 152,319 base pairs (bp), and GC content of 37.9 to 38.1%, and the number of genes was between 129-134. The total number of simple sequence repeats (SSRs) in V. anagallis-aquatica and V. undulata is 37 and 36, while V. arvensis had the highest total number of 56, predominantly characterized by A/T single bases. The vast majority of long repeat sequence types are forward repeats and palindromic repeats. Selective Ka/Ks values showed that three genes were under positive selection. Sequence differences often occur in the non-coding regions of the large single-copy region (LSC) and small single-copy region (SSC), with the lowest sequence variation in the inverted repeat regions (IR). Seven highly variable regions (trnT-GGU-psbD, rps8-rpl16, trnQ-UUG, trnN-GUU-ndhF, petL, ycf3, and ycf1) were detected, which may be potential molecular markers for identifying V. anagallis-aquatica and V. undulata. The phylogenetic tree indicates that there is a close genetic relationship between the genera Veronica and Neopicrorhiza, and V. anagallis-aquatica and V. undulata are sister groups. The molecular clock analysis results indicate that the divergence time of Veronica may occur at ∼ 9.09 Ma, and the divergence time of these two species occurs at ∼ 0.48 Ma. It is speculated that climate change may be the cause of Veronica species diversity and promote the radiation of the genus. The chloroplast genome data of nine Veronica specie provides important insights into the characteristics and evolution of the chloroplast genome of this genus, as well as the phylogenetic relationships of the genus Veronica.
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Affiliation(s)
- Yonglin Hai
- College of Pharmacy, Dali University, Dali, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China
| | - Yan Qian
- College of Pharmacy, Dali University, Dali, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China
| | - Meihua Yang
- College of Pharmacy, Dali University, Dali, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China
| | - Yue Zhang
- College of Pharmacy, Dali University, Dali, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China
| | - Huimei Xu
- College of Pharmacy, Dali University, Dali, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China
| | - Yongcheng Yang
- College of Pharmacy, Dali University, Dali, 671000, China.
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China.
| | - Conglong Xia
- College of Pharmacy, Dali University, Dali, 671000, China.
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China.
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Yahara T, Hirota SK, Fujii S, Kokami Y, Fuse K, Sato H, Tagane S, Suyama Y. Molecular phylogeny and taxonomy of Hosta (Asparagaceae) on Shikoku Island, Japan, including five new species, one new subspecies, and two new status assignments. PHYTOKEYS 2023; 235:137-187. [PMID: 38020470 PMCID: PMC10680290 DOI: 10.3897/phytokeys.235.99140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 10/04/2023] [Indexed: 12/01/2023]
Abstract
Japan has 16 native species of the genus Hosta Tratt. (Asparagaceae). A recent study on Hosta based on field surveys and molecular phylogenetic analyses resulted in the discovery of six unknown taxa in Kochi Prefecture, Shikoku Island, southwestern Japan. We aimed to identify these unknown taxa. Therefore, we constructed a finely resolved phylogeny for 320 Hosta samples collected from the Honshu, Shikoku, and Kyushu Islands using multiplex inter-simple sequence repeat genotyping by sequencing (MIG-seq). Based on this phylogenetic analysis and related morphological observations, we describe five new species, H.longipedicellatasp. nov., H.minazukiflorasp. nov., H.polyneuronoidessp. nov., H.samukazemontanasp. nov., and H.takiminazukiflorasp. nov. and one new subspecies, H.takiminazukiflorasubsp.grandissubsp. nov. In addition, we propose two new status assignments, H.tardivasubsp.densinerviacomb. and stat. nov. and H.scabrinerviastat. nov. We also propose classifying H.kikutiivar.tosana as a species, H.tosana. Further studies that combine MIG-seq with careful morphological observations are needed for Hosta plants on all Japanese islands, which may result in the discovery of even more undescribed species.
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Affiliation(s)
- Tetsukazu Yahara
- Kyushu Open University, 744 Motooka, Fukuoka, 819-0395, JapanKyushu Open UniversityFukuokaJapan
| | - Shun K. Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, JapanTohoku UniversityOsakiJapan
- Botanical Gardens, Osaka Metropolitan University, 2000 Kisaichi, Katano, Osaki 576-0004, JapanOsaka Metropolitan UniversityOsakiJapan
| | - Seiko Fujii
- The Kochi Prefectural Makino Botanical Garden, Godai-san 4200-6, Kochi 781-8125, JapanThe Kochi Prefectural Makino Botanical GardenKochiJapan
| | - Yasushi Kokami
- The Kochi Prefectural Makino Botanical Garden, Godai-san 4200-6, Kochi 781-8125, JapanThe Kochi Prefectural Makino Botanical GardenKochiJapan
| | - Kengo Fuse
- Kyushu Open University, 744 Motooka, Fukuoka, 819-0395, JapanKyushu Open UniversityFukuokaJapan
| | - Hiroyuki Sato
- Kyushu Open University, 744 Motooka, Fukuoka, 819-0395, JapanKyushu Open UniversityFukuokaJapan
| | - Shuichiro Tagane
- The Kagoshima University Museum, Kagoshima University, 1-21-30 Korimoto, Kagoshima, 890-0065, JapanKagoshima UniversityKagoshimaJapan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, JapanTohoku UniversityOsakiJapan
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Cui YF, Zhou P, Xiang KL, Zhang Q, Yan H, Zhang LG, Pan B, Huang YS, Guo ZY, Li ZY, Xiang XG. Plastome evolution and phylogenomics of Trichosporeae (Gesneriaceae) with its morphological characters appraisal. FRONTIERS IN PLANT SCIENCE 2023; 14:1160535. [PMID: 37229102 PMCID: PMC10203511 DOI: 10.3389/fpls.2023.1160535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/21/2023] [Indexed: 05/27/2023]
Abstract
Trichosporeae is the largest and most taxonomically difficult tribe of Gesneriaceae due to its diverse morphology. Previous studies have not clarified the phylogenetic relationships within this tribe on several DNA markers, including the generic relationships within subtribes. Recently, plastid phylogenomics have been successfully employed to resolve the phylogenetic relationships at different taxonomic levels. In this study, plastid phylogenomics were used to explore the relationships within Trichosporeae. Eleven plastomes of Hemiboea were newly reported. Comparative analyses, phylogeny and morphological character evolution within Trichosporeae were conducted on 79 species representing seven subtribes. The Hemiboea plastomes range from 152,742 bp to 153,695 bp in length. Within Trichosporeae, the sampled plastomes range from 152,196 bp to 156,614 bp and GC content from 37.2% to 37.8%. A total of 121-133 genes were annotated in each species, including 80-91 protein-coding genes, 34-37 tRNA genes, and 8 rRNA genes. The contraction and expansion of IR borders were not detected, and gene rearrangements and inversions did not occur. The 13 hypervariable regions were proposed as the potential molecular markers for species identification. A total of 24,299 SNPs and 3,378 indels were inferred, and most of the SNPs were functionally missense and silent variations. There were 1968 SSRs, 2055 tandem repeats and 2802 dispersed repeats. The RSCU and ENC values indicated that the codon usage pattern was conserved in Trichosporeae. Both the phylogenetic frameworks based on the whole plastome and 80 CDSs were basically concordant. The sister relationships between Loxocarpinae and Didymocarpinae were confirmed, and Oreocharis was a sister group of Hemiboea with high support. The morphological characters showed a complex evolutionary pattern of Trichosporeae. Our findings may contribute to future research on genetic diversity, morphological evolutionary patterns, and conservation of the tribe Trichosporeae.
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Affiliation(s)
- Yan-Fang Cui
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Peng Zhou
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Kun-Li Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Qiang Zhang
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Hua Yan
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Li-Guo Zhang
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Bo Pan
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Yu-Song Huang
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Zhi-You Guo
- Qiannan Normal College for Nationalities, College of Biological Sciences and Agriculture, Duyun, Guizhou, China
| | - Zhen-Yu Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Guo Xiang
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
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Zhang D, Ren J, Jiang H, Wanga VO, Dong X, Hu G. Comparative and phylogenetic analysis of the complete chloroplast genomes of six Polygonatum species (Asparagaceae). Sci Rep 2023; 13:7237. [PMID: 37142659 PMCID: PMC10160070 DOI: 10.1038/s41598-023-34083-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/24/2023] [Indexed: 05/06/2023] Open
Abstract
Polygonatum Miller belongs to the tribe Polygonateae of Asparagaceae. The horizontal creeping fleshy roots of several species in this genus serve as traditional Chinese medicine. Previous studies have mainly reported the size and gene contents of the plastomes, with little information on the comparative analysis of the plastid genomes of this genus. Additionally, there are still some species whose chloroplast genome information has not been reported. In this study, the complete plastomes of six Polygonatum were sequenced and assembled, among them, the chloroplast genome of P. campanulatum was reported for the first time. Comparative and phylogenetic analyses were then conducted with the published plastomes of three related species. Results indicated that the whole plastome length of the Polygonatum species ranged from 154,564 bp (P. multiflorum) to 156,028 bp (P. stenophyllum) having a quadripartite structure of LSC and SSC separated by two IR regions. A total of 113 unique genes were detected in each of the species. Comparative analysis revealed that gene content and total GC content in these species were highly identical. No significant contraction or expansion was observed in the IR boundaries among all the species except P. sibiricum1, in which the rps19 gene was pseudogenized owing to incomplete duplication. Abundant long dispersed repeats and SSRs were detected in each genome. There were five remarkably variable regions and 14 positively selected genes were identified among Polygonatum and Heteropolygonatum. Phylogenetic results based on chloroplast genome strongly supported the placement of P. campanulatum with alternate leaves in sect. Verticillata, a group characterized by whorled leaves. Moreover, P. verticillatum and P. cyrtonema were displayed as paraphyletic. This study revealed that the characters of plastomes in Polygonatum and Heteropolygonatum maintained a high degree of similarity. Five highly variable regions were found to be potential specific DNA barcodes in Polygonatum. Phylogenetic results suggested that leaf arrangement was not suitable as a basis for delimitation of subgeneric groups in Polygonatum and the definitions of P. cyrtonema and P. verticillatum require further study.
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Affiliation(s)
- Dongjuan Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Ren
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Hui Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Vincent Okelo Wanga
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guangwan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Senapati A, Chetri BK, Mitra S, Shelke RG, Rangan L. Decoding the complete chloroplast genome of Cissus quadrangularis: insights into molecular structure, comparative genome analysis and mining of mutational hotspot regions. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:709-724. [PMID: 37363414 PMCID: PMC10284753 DOI: 10.1007/s12298-023-01312-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/25/2023] [Accepted: 04/24/2023] [Indexed: 06/28/2023]
Abstract
Cissus quadrangularis L., a member of the Vitaceae family, is an important medicinal plant with widespread application in Indian traditional medicines. C. quadrangularis L. whole chloroplast genome of 160,404 bp was assembled using a genome skimming approach from the whole genome library. The assembled chloroplast genome contained a large single-copy region (88,987 bp), a small single-copy region (18,621 bp), and pairs of inverted repeat regions (26,398 bp). It also comprised 133 genes, including 37 tRNAs, eight rRNAs, and 88 protein-coding genes. Aside from that, we annotated three genes atpH, petB, and psbL, as well as one duplicated copy of the ycf1 gene in C. quadrangularis L. that had previously been missing from the annotation of compared Cissus chloroplast genomes. Five divergent hotspot regions such as petA_psbJ (0.1237), rps16_trnQ-UUG (0.0913), psbC_trnS-UGA (0.0847), rps15_ycf1 (0.0788), and rps2_rpoC2 (0.0788) were identified in the investigation that could aid in future species discrimination. Surprisingly, we found the overlapping genes ycf1 and ndhF on the IRb/SSC junction, rarely seen in angiosperms. The results of the phylogenetic study showed that the genomes of the Cissus species under study formed a single distinct clade. The detailed annotations given in this study could be useful in the future for genome annotations of Cissus species. The current findings of the study have the potential to serve as a useful resource for future research in the field of population genetics and the evolutionary relationships in the Cissus genus. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01312-w.
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Affiliation(s)
- Alok Senapati
- Applied Biodiversity Laboratory, O Block, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
| | - Bimal K. Chetri
- School of Agro and Rural Technology, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
| | - Sudip Mitra
- School of Agro and Rural Technology, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
| | - Rahul G. Shelke
- Applied Biodiversity Laboratory, O Block, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
| | - Latha Rangan
- Applied Biodiversity Laboratory, O Block, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
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Li CJ, Xie XT, Liu HX, Wang RN, Li DZ. Plastome evolution in the East Asian lobelias (Lobelioideae) using phylogenomic and comparative analyses. FRONTIERS IN PLANT SCIENCE 2023; 14:1144406. [PMID: 37063184 PMCID: PMC10102522 DOI: 10.3389/fpls.2023.1144406] [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: 01/14/2023] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
Lobelia species, as rich source of the alkaloid lobeline which has been shown to have important biological activity, have been used in folk medicine throughout East Asia to treat various diseases. However, Lobelia is a complex and varied genus in East Asia and is thus difficult to identify. Genomic resources would aid identification, however the availability of such information is poor, preventing a clear understanding of their evolutionary history from being established. To close this gap in the available genomic data, in this study, 17 plastomes of East Asian lobelias were newly sequenced and assembled. Although the plastomes of Lobelia sect. Hypsela, L. sect. Speirema, and L. sect. Rhynchopetalum shared the gene structure, the inverted repeat (IR)/large single copy (LSC) boundaries, genome size, and the number of repeats were variable, indicating the non-conservative nature of plastome evolution within these sections. However, the genomes of the Lobelia sect. Delostemon and L. sect. Stenotium showed rearrangements, revealing that these two sections might have undergone different evolutionary histories. We assessed nine hotspot genes and 27-51 simple sequence repeat motifs, which will also serve as valuable DNA barcode regions in future population genetics studies and for the delineation of plant species. Our phylogenetic analysis resolved the evolutionary positions of the five sections in agreement with previous evolutionary trees based on morphological features. Although phylogenetic reconstruction of Lobelioideae based on the rpoC2 gene has rarely been performed, our results indicated that it contains a considerable amount of phylogenetic information and offers great promise for further phylogenetic analysis of Lobelioideae. Our site-specific model identified 173 sites under highly positive selections. The branch-site model exhibited 11 positive selection sites involving four genes in the East Asian branches. These four genes may play critical roles in the adaptation of East Asian taxa to diverse environments. Our study is the first to detect plastome organization, phylogenetic utility, and signatures of positive selection in the plastomes of East Asian lobelias, which will help to further advance taxonomic and evolutionary studies and the utilization of medicinal plant resources.
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Affiliation(s)
- Chun-Jiao Li
- College of Life Science, Shenyang Normal University, Shenyang, Liaoning, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xin-Tong Xie
- College of Life Science, Shenyang Normal University, Shenyang, Liaoning, China
| | - Hong-Xin Liu
- College of Life Science, Shenyang Normal University, Shenyang, Liaoning, China
| | - Ruo-Nan Wang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
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Complete Chloroplast Genome Sequences of Four Species in the Caladium Genus: Comparative and Phylogenetic Analyses. Genes (Basel) 2022; 13:genes13122180. [PMID: 36553447 PMCID: PMC9777821 DOI: 10.3390/genes13122180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
Caladiums are promising colorful foliage plants due to their dazzling colors of the leaves, veins, stripes, and patches, which are often cultivated in pots or gardens as decorations. Four wild species, including C. bicolor, C. humboldtii, C. praetermissum, and C. lindenii, were employed in this study, where their chloroplast (cp) genomes were sequenced, assembled, and annotated via high-throughput sequencing. The whole cp genome size ranged from 162,776 bp to 168,888 bp, and the GC contents ranged from 35.09% to 35.91%. Compared with the single large copy (LSC) and single small copy (SSC) regions, more conserved sequences were identified in the inverted repeat regions (IR). We further analyzed the different region borders of nine species of Araceae and found the expansion or contraction of IR/SSC regions might account for the cp genome size variation. Totally, 131 genes were annotated in the cp genomes, including 86 protein-coding genes (PCGs), 37 tRNAs, and eight rRNAs. The effective number of codons (ENC) values and neutrality plot analyses provided the foundation that the natural selection pressure could greatly affect the codon preference. The GC3 content was significantly lower than that of GC1 and GC2, and codons ending with A/U had higher usage preferences. Finally, we conducted phylogenetic relationship analysis based on the chloroplast genomes of twelve species of Araceae, in which C. bicolor and C. humboldtii were grouped together, and C. lindenii was furthest from the other three Caladium species occupying a separate branch. These results will provide a basis for the identification, development, and utilization of Caladium germplasm.
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Tang C, Chen X, Deng Y, Geng L, Ma J, Wei X. Complete chloroplast genomes of Sorbus sensu stricto (Rosaceae): comparative analyses and phylogenetic relationships. BMC PLANT BIOLOGY 2022; 22:495. [PMID: 36273120 PMCID: PMC9587547 DOI: 10.1186/s12870-022-03858-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Sorbus sensu stricto (Sorbus s.s.) is a genus with important economical values because of its beautiful leaves, and flowers and especially the colorful fruits. It belongs to the tribe Maleae of the family Rosaceae, and comprises about 90 species mainly distributed in China. There is on-going dispute about its infrageneric classification and species delimitation as the species are morphologically similar. With the aim of shedding light on the circumscription of taxa within the genus, phylogenetic analyses were performed using 29 Sorbus s.s. chloroplast (cp) genomes (16 newly sequenced) representing two subgenera and eight sections. RESULTS The 16 cp genomes newly sequenced range between 159,646 bp and 160,178 bp in length. All the samples examined and 22 taxa re-annotated in Sorbus sensu lato (Sorbus s.l.) contain 113 unique genes with 19 of these duplicated in the inverted repeat (IR). Six hypervariable regions including trnR-atpA, petN-psbM, rpl32-trnL, trnH-psbA, trnT-trnL and ndhC-trnV were screened and 44-53 SSRs and 14-31 dispersed repeats were identified as potential molecular markers. Phylogenetic analyses under ML/BI indicated that Sorbus s.l. is polyphyletic, but Sorbus s.s. and the other five segregate genera, Aria, Chamaemespilus, Cormus, Micromeles and Torminalis are monophyletic. Two major clades and four sub-clades resolved with full-support within Sorbus s.s. are not consistent with the existing infrageneric classification. Two subgenera, subg. Sorbus and subg. Albocarmesinae are supported as monophyletic when S. tianschanica is transferred to subg. Albocarmesinae from subg. Sorbus and S. hupehensis var. paucijuga transferred to subg. Sorbus from subg. Albocarmesinae, respectively. The current classification at sectional level is not supported by analysis of cp genome phylogeny. CONCLUSION Phylogenomic analyses of the cp genomes are useful for inferring phylogenetic relationships in Sorbus s.s. Though genome structure is highly conserved in the genus, hypervariable regions and repeat sequences used are the most promising molecule makers for population genetics, species delimitation and phylogenetic studies.
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Affiliation(s)
- Chenqian Tang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Xin Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
| | - Yunfei Deng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Liyang Geng
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Jianhui Ma
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Xueyan Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
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Dong S, Zhou M, Zhu J, Wang Q, Ge Y, Cheng R. The complete chloroplast genomes of Tetrastigma hemsleyanum (Vitaceae) from different regions of China: molecular structure, comparative analysis and development of DNA barcodes for its geographical origin discrimination. BMC Genomics 2022; 23:620. [PMID: 36028808 PMCID: PMC9412808 DOI: 10.1186/s12864-022-08755-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tetrastigma hemsleyanum is a valuable traditional Chinese medicinal plant widely distributed in the subtropical areas of China. It belongs to the Cayratieae tribe, family Vitaceae, and exhibited significant anti-tumor and anti-inflammatory activities. However, obvious differences were observed on the quality of T. hemsleyanum root from different regions, requiring the discrimination strategy for the geographical origins. RESULT This study characterized five complete chloroplast (cp) genomes of T. hemsleynum samples from different regions, and conducted a comparative analysis with other representing species from family Vitaceae to reveal the structural variations, informative markers and phylogenetic relationships. The sequenced cp genomes of T. hemsleyanum exhibited a conserved quadripartite structure with full length ranging from 160,124 bp of Jiangxi Province to 160,618 bp of Zhejiang Province. We identified 112 unique genes (80 protein-coding, 28 tRNA and 4 rRNA genes) in the cp genomes of T. hemsleyanum with highly similar gene order, content and structure. The IR contraction/expansion events occurred on the junctions of ycf1, rps19 and rpl2 genes with different degrees, causing the differences of genome sizes in T. hemsleyanum and Vitaceae plants. The number of SSR markers discovered in T. hemsleyanum was 56-57, exhibiting multiple differences among the five geographic groups. Phylogenetic analysis based on conserved cp genome proteins strongly grouped the five T. hemsleyanum species into one clade, showing a sister relationship with T. planicaule. Comparative analysis of the cp genomes from T. hemsleyanum and Vitaceae revealed five highly variable spacers, including 4 intergenic regions and one protein-coding gene (ycf1). Furthermore, five mutational hotspots were observed among T. hemsleyanum cp genomes from different regions, providing data for designing DNA barcodes trnL and trnN. The combination of molecular markers of trnL and trnN clustered the T. hemsleyanum samples from different regions into four groups, thus successfully separating specimens of Sichuan and Zhejiang from other areas. CONCLUSION Our study obtained the chloroplast genomes of T. hemsleyanum from different regions, and provided a potential molecular tracing tool for determining the geographical origins of T. hemsleyanum, as well as important insights into the molecular identification approach and and phylogeny in Tetrastigma genus and Vitaceae family.
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Affiliation(s)
- Shujie Dong
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China.,School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Manjia Zhou
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jinxing Zhu
- Bureau of Agricultural and Rural Affairs of Suichang, Suichang, China
| | - Qirui Wang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yuqing Ge
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China.
| | - Rubin Cheng
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China. .,Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China.
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Liu XF, Sun YB, Zhu GF, Huang LL, Yu B. Complete chloroplast genomes and comparative analyses of Hippeastrum ‘milady’, Hippeastrum albertii and Hippeastrum reticulatum (Amaryllidaceae). PLoS One 2022; 17:e0271335. [PMID: 35930553 PMCID: PMC9355175 DOI: 10.1371/journal.pone.0271335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 06/29/2022] [Indexed: 11/19/2022] Open
Abstract
Hippeastrum is a genus of ornamental plants with large, brightly colored flowers. Due to the very high seed-setting rate of the hybridization of Hippeastrum, the large population of hybrid progeny and the existence of superparent inheritance, it is difficult to trace the origin of the varieties collected from the market during breeding. In this study, we analyzed the chloroplast genomes of Hippeastrum ‘Milady’, H. alberti, and H. reticulatum using the Illumina NovaSeq sequencing platform and generated full-length sequences of 158,067, 158,067, and 158,522 bp, respectively. All three genomes had the typical tetrad structure. The large single copy, small single copy, and inverted repeat regions of H. reticulatum were observed to be respectively 277, 138, and 20 bp longer than the corresponding regions of H. ‘Milady’ and H. alberti. The results of comparative analysis of simple sequence repeats (SSRs), Ka/Ks ratios, codon preferences, and complete sequences of chloroplasts of these three taxa and 14 other plant species were as follows. First, the chloroplast genomes of H. ‘Milady’, H. alberti, and H. reticulatum contain 209, 209, and 211 SSR sites, respectively, most of which (123, 123, and 122, respectively) are single nucleotide repeats. Second, leucine, arginine, and serine are the most frequently used amino acids in the three chloroplast genomes. Third, H. ‘Milady’, H. alberti, and H. reticulatum are more closely related to Lycoris and Narcissus than to Allium and Agapanthus. Our results will provide information on the study of origins or relatedness of native species, and the identification of cultivars.
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Affiliation(s)
- Xiao-fei Liu
- Environmental Horticulture Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Key Laboratory of Urban Agriculture in South China, Ministry of Agriculture, Guangzhou, China
| | - Ying-bo Sun
- Environmental Horticulture Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Key Laboratory of Urban Agriculture in South China, Ministry of Agriculture, Guangzhou, China
| | - Gen-fa Zhu
- Environmental Horticulture Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Key Laboratory of Urban Agriculture in South China, Ministry of Agriculture, Guangzhou, China
| | - Li-li Huang
- Environmental Horticulture Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Key Laboratory of Urban Agriculture in South China, Ministry of Agriculture, Guangzhou, China
| | - Bo Yu
- Environmental Horticulture Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Key Laboratory of Urban Agriculture in South China, Ministry of Agriculture, Guangzhou, China
- * E-mail:
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Li M, Song YF, Sylvester SP, Sylvester SP, Wang XR. Comparative analysis of the complete plastid genomes in Prunus subgenus Cerasus (Rosaceae): Molecular structures and phylogenetic relationships. PLoS One 2022; 17:e0266535. [PMID: 35385520 PMCID: PMC8985974 DOI: 10.1371/journal.pone.0266535] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 03/22/2022] [Indexed: 11/18/2022] Open
Abstract
Prunus subgenus Cerasus (cherry) is an economically important group that distributed in temperate regions of the northern hemisphere. However, shared interspecific morphological traits and variability across taxa of Cerasus are among the impediments to taxonomic efforts to correctly delimit taxa. This is further complicated by a lack of genetic information on these taxa, with no focused genomic or phylogenetic studies being done on Cerasus. In this study, we conducted comparative analysis on the complete plastid genomes (plastomes) of 20 Cerasus species to gain a greater understanding of the attributes of the plastome of these taxa while helping resolve their phylogenetic placement in Prunus sensu lato and interspecific relationships within the subgenus. Our results displayed that (1) the plastomes of the 20 Cerasus species studied exhibited a typical quadripartite structure with conversed genome arrangement, structure, and moderate divergence. (2) The average size of complete plastomes for the Cerasus taxa studied was 157,861 bp, ranging from 157,458 to 158,024 bp. A total of 134 genes were annotated, including 86 protein-coding genes, 40 tRNAs, and 8 rRNAs across all species. In simple sequence repeat analysis, we found Cerasus had a comparable number of dispersed and tandem repeats to those identified in other angiosperm taxa, with only P. pseudocerasus found to contain trinucleotide repeats. Nucleotide diversity analysis revealed that the trnG-GCC gene and rpl32-trnL region had the highest Pi value showing potential as phylogenetic markers. (3) Two phylogenetic trees of the plastomes verified the monophyletic relationship of Cerasus and provided a more resolved species-level phylogeny. Our study provides detailed plastome information for exploring the phylogeny of subg. Cerasus taxa. We identified various types of repeats and nucleotide diversity hotspots, which can be a reference for species identification and reconstruction of phylogenetic relationships.
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Affiliation(s)
- Meng Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yan-Feng Song
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Steven P. Sylvester
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Steven P. Sylvester
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Xian-Rong Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
- * E-mail:
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15
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Li L, Wu Q, Fang L, Wu K, Li M, Zeng S. Comparative Chloroplast Genomics and Phylogenetic Analysis of Thuniopsis and Closely Related Genera within Coelogyninae (Orchidaceae). Front Genet 2022; 13:850201. [PMID: 35401668 PMCID: PMC8987740 DOI: 10.3389/fgene.2022.850201] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/22/2022] [Indexed: 11/17/2022] Open
Abstract
The genus Thuniopsis was recently proposed for a rare orchid species T. cleistogama formerly classified in the genus Thunia. The relationships between Thuniopsis and its related genera have not yet been conclusively resolved. Recognition of the genus provides a new perspective to illustrate the morphological diversity and plastome evolution within Coelogyninae. In this study, we sequenced and assembled complete chloroplast (cp) genomes for three accessions of Thuniopsis cleistogama and two accessions of Thunia alba. A total of 135 genes were annotated for each cp genome, including 89 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The ENC-plot and neutrality plot analyses revealed that natural selection dominated over mutation pressure in their evolutionary process. Specially, we found that selection played a vital role in shaping the codon usage in Thunia alba cp genome. General characteristics of the cp genomes were further analyzed and compared with those published plastomes of four other related species. Despite the conserved organization and structure, the whole individual cp genome size ranged from 158,394 bp to 159,950 bp. In all the examined plastomes, sequences in the inverted repeat (IR) regions were more conserved than those in the small single copy (SSC) and large single copy (LSC) regions. However, close examination identified contraction and expansion of the IR/SSC boundary regions, which might be the main reason for the cp genome size variation. Our comparative analysis of the cp genomes revealed that single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) provided valuable information for identifying genetic variations within and among genera. Furthermore, sequence variations in the protein-coding regions were more conserved than those in the non-coding regions. We selected eight divergence hotspots with nucleotide sequence diversities (Pi values) higher than 0.08. Most of these polymorphisms were located in the intergenic regions. Phylogenomic analyses recovered largely congruent relationships among major clades and strongly supported the monophyly of Thuniopsis. The results obtained in this study can improve our understanding of the classification of this enigmatic genus. The chloroplast genomic data presented here provide valuable insights into the phylogeny and evolutionary patterns of the Coelogyninae as well as the orchids as a whole.
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Affiliation(s)
- Lin Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Qiuping Wu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lin Fang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Kunlin Wu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Mingzhi Li
- Guangzhou Bio and Data Biotechnology Co., Ltd., Guangzhou, China
| | - Songjun Zeng
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- *Correspondence: Songjun Zeng,
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16
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Jamshed S, Kim JH. Disjunction and Vicariance Between East and West Asia: A Case Study on Euonymus sect. Uniloculares Based on Plastid Genome Analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:825209. [PMID: 35360330 PMCID: PMC8963480 DOI: 10.3389/fpls.2022.825209] [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: 11/30/2021] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
Scientists have long been captivated by biogeographic disjunctions, and disjunctions between East Asia and North America have been particularly well-studied at the genus and family levels. By contrast, disjunctions between eastern and western Asia have received less attention. Euonymus L. is taxonomically divided into two sections based on the number of cells in anthers as follows: E. sect. Uniloculares has one-celled anthers and occurs mainly in Asia, whereas E. sect. Biloculares has two-celled anthers and is distributed globally. We used Illumina sequencing to investigate the genomes of four species in sect. Uniloculares. The chloroplast (cp) genomes are highly conserved (157,290-158,094 bp). Pseudogenisation of ndhF and intron loss in rps16 was detected. Based on the cp genomes of the four species of E. sect. Uniloculares, we propose a novel hypothesis of disjunction between eastern and western Asia. Biogeographic reconstruction and molecular dating revealed that sect. Uniloculares separated from its sect. Biloculares forebears 4.0 Mya during the Pliocene era. The radial diversification of sect. Uniloculares from East Asia and the establishment of the western Asian clade during the Pleistocene era (1.9 Mya) were the results of both dispersal and vicariance, making the section the youngest diverged clade conforming to age estimation. The centre of origin of sect. Uniloculares was determined to be in East Asia. Disjunctions and diversification between eastern and western Asia in sect. Uniloculares are thought to have been caused by changes in monsoon patterns, temperature variations, and the emergence of the Gobi Desert.
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Dong S, Ying Z, Yu S, Wang Q, Liao G, Ge Y, Cheng R. Complete chloroplast genome of Stephania tetrandra (Menispermaceae) from Zhejiang Province: insights into molecular structures, comparative genome analysis, mutational hotspots and phylogenetic relationships. BMC Genomics 2021; 22:880. [PMID: 34872502 PMCID: PMC8647421 DOI: 10.1186/s12864-021-08193-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 11/16/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The Stephania tetrandra S. Moore (S. tetrandra) is a medicinal plant belonging to the family Menispermaceae that has high medicinal value and is well worth doing further exploration. The wild resources of S. tetrandra were widely distributed in tropical and subtropical regions of China, generating potential genetic diversity and unique population structures. The geographical origin of S. tetrandra is an important factor influencing its quality and price in the market. In addition, the species relationship within Stephania genus still remains uncertain due to high morphological similarity and low support values of molecular analysis approach. The complete chloroplast (cp) genome data has become a promising strategy to determine geographical origin and understand species evolution for closely related plant species. Herein, we sequenced the complete cp genome of S. tetrandra from Zhejiang Province and conducted a comparative analysis within Stephania plants to reveal the structural variations, informative markers and phylogenetic relationship of Stephania species. RESULTS The cp genome of S. tetrandra voucher ZJ was 157,725 bp, consisting of a large single copy region (89,468 bp), a small single copy region (19,685 bp) and a pair of inverted repeat regions (24,286 bp each). A total of 134 genes were identified in the cp genome of S. tetrandra, including 87 protein-coding genes, 8 rRNA genes, 37 tRNA genes and 2 pseudogene copies (ycf1 and rps19). The gene order and GC content were highly consistent in the Stephania species according to the comparative analysis results, with the highest RSCU value in arginine (1.79) and lowest RSCU value in serine of S. tetrandra, respectively. A total of 90 SSRs have been identified in the cp genome of S. tetrandra, where repeats that consisting of A or T bases were much higher than that of G or C bases. In addition, 92 potential RNA editing sites were identified in 25 protein-coding genes, with the most predicted RNA editing sites in ndhB gene. The variations on length and expansion extent to the junction of ycf1 gene were observed between S. tetrandra vouchers from different regions, indicating potential markers for further geographical origin discrimination. Moreover, the values of transition to transversion ratio (Ts/Tv) in the Stephania species were significantly higher than 1 using Pericampylus glaucus as reference. Comparative analysis of the Stephania cp genomes revealed 5 highly variable regions, including 3 intergenic regions (trnH-psbA, trnD-trnY, trnP) and two protein coding genes (rps16 and ndhA). The identified mutational hotspots of Stephania plants exhibited multiple SNP sites and Gaps, as well as different Ka/Ks ratio values. In addition, five pairs of specific primers targeting the divergence regions were accordingly designed, which could be utilized as potential molecular markers for species identification, population genetic and phylogenetic analysis in Stephania species. Phylogenetic tree analysis based on the conserved chloroplast protein coding genes indicated a sister relationship between S. tetrandra and the monophyletic group of S. japonica and S. kwangsiensis with high support values, suggesting a close genetic relationship within Stephania plants. However, two S. tetrandra vouches from different regions failed to cluster into one clade, confirming the occurrences of genetic diversities and requiring further investigation for geographical tracing strategy. CONCLUSIONS Overall, we provided comprehensive and detailed information on the complete chloroplast genome and identified nucleotide diversity hotspots of Stephania species. The obtained genetic resource of S. tetrandra from Zhejiang Province would facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of Stephania plants.
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Affiliation(s)
- Shujie Dong
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Zhiqi Ying
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Shuisheng Yu
- The Administration Bureau of Zhejiang Jiulongshan National Nature Reserve, Suichang, Zhejiang Province, People's Republic of China
| | - Qirui Wang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Guanghui Liao
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Yuqing Ge
- The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, Zhejiang Province, People's Republic of China.
| | - Rubin Cheng
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China.
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Qin X, Yang X, Huang X, Jin G, Yang X, Wu M, Chen T, Yi K. The complete chloroplast genome of Agave angustifolia. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:3236-3237. [PMID: 34712803 PMCID: PMC8547807 DOI: 10.1080/23802359.2021.1941360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Agave angustifolia is commonly used for the production of bacanora, a kind of fermented and distilled beverage in Mexico. In the present study, we have successfully assembled its chloroplast genome. The full length of the genome is 157,274 bp with the GC content of 37.84%. There is a large single copy region (LSC) of 85,895 bp, a pair of inverted repeat regions (IR) of 26,575 bp and a small single copy region (SSC) of 18,229 bp in the genome. A total of 132 genes are annotated in the cp genome. Among these, there are 86 protein-coding genes, 38 tRNAs and 8 rRNAs. Phylogenetic analysis reveals that A. angustifolia is closely related with A. H11648.
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Affiliation(s)
- Xu Qin
- Guangxi Subtropical Crops Research Institute, Nanning, P. R. China
| | - Xinli Yang
- College of Tropical Crops, Hainan University, Haikou, P. R. China
| | - Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, P. R. China
| | - Gan Jin
- Guangxi Subtropical Crops Research Institute, Nanning, P. R. China
| | - Xiangyan Yang
- Guangxi Subtropical Crops Research Institute, Nanning, P. R. China
| | - Mi Wu
- Guangxi Subtropical Crops Research Institute, Nanning, P. R. China
| | - Tao Chen
- Guangxi Subtropical Crops Research Institute, Nanning, P. R. China
| | - Kexian Yi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, P. R. China
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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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20
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Yahara T, Hirota SK, Fuse K, Sato H, Tagane S, Suyama Y. Validation of Hostaalata (Asparagaceae) as a new species and its phylogenetic affinity. PHYTOKEYS 2021; 181:79-93. [PMID: 34566449 PMCID: PMC8433123 DOI: 10.3897/phytokeys.181.64245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Molecular phylogenetic studies of Hostapulchella (Asparagaceae) and its relatives, which are native to Japan, have been conducted and resulted in a highly resolved phylogeny. Specifically, the relationship of H.pulchella to H.alata Hatusima, nom. nud. is investigated. These data include genome-wide SNPs obtained through conducting multiplexed ISSR genotyping by sequencing (MIG-seq). Based on these phylogenetic results, morphological observations, distribution, and differences in flowering periods of H.alata collections sympatric with H.pulchella, we find the two species closely related, but distinct. As such, we formally describe Hostaalata sp. nov. from the Oita Prefecture of Kyushu island, southwestern Japan.
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Affiliation(s)
- Tetsukazu Yahara
- Kyushu Open University, 744 Motooka, Fukuoka, 819-0395, JapanKyushu Open UniversityFukuokaJapan
| | - Shun K. Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, JapanTohoku UniversityOsakiJapan
| | - Kengo Fuse
- Kyushu Open University, 744 Motooka, Fukuoka, 819-0395, JapanKyushu Open UniversityFukuokaJapan
| | - Hiroyuki Sato
- Kyushu Open University, 744 Motooka, Fukuoka, 819-0395, JapanKyushu Open UniversityFukuokaJapan
| | - Shuichiro Tagane
- The Kagoshima University Museum, Kagoshima University, 1-21-30 Korimoto, Kagoshima, 890-0065, JapanKagoshima UniversityKagoshimaJapan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, JapanTohoku UniversityOsakiJapan
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21
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Luo C, Huang W, Sun H, Yer H, Li X, Li Y, Yan B, Wang Q, Wen Y, Huang M, Huang H. Comparative chloroplast genome analysis of Impatiens species (Balsaminaceae) in the karst area of China: insights into genome evolution and phylogenomic implications. BMC Genomics 2021; 22:571. [PMID: 34303345 PMCID: PMC8310579 DOI: 10.1186/s12864-021-07807-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/14/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Impatiens L. is a genus of complex taxonomy that belongs to the family Balsaminaceae (Ericales) and contains approximately 1000 species. The genus is well known for its economic, medicinal, ornamental, and horticultural value. However, knowledge about its germplasm identification, molecular phylogeny, and chloroplast genomics is limited, and taxonomic uncertainties still exist due to overlapping morphological features and insufficient genomic resources. RESULTS We sequenced the chloroplast genomes of six different species (Impatiens chlorosepala, Impatiens fanjingshanica, Impatiens guizhouensis, Impatiens linearisepala, Impatiens loulanensis, and Impatiens stenosepala) in the karst area of China and compared them with those of six previously published Balsaminaceae species. We contrasted genomic features and repeat sequences, assessed sequence divergence and constructed phylogenetic relationships. Except for those of I. alpicola, I. pritzelii and I. glandulifera, the complete chloroplast genomes ranging in size from 151,366 bp (I. alpicola) to 154,189 bp (Hydrocera triflora) encoded 115 distinct genes [81 protein-coding, 30 transfer RNA (tRNA), and 4 ribosomal RNA (rRNA) genes]. Moreover, the characteristics of the long repeat sequences and simple sequence repeats (SSRs) were determined. psbK-psbI, trnT-GGU-psbD, rpl36-rps8, rpoB-trnC-GCA, trnK-UUU-rps16, trnQ-UUG, trnP-UGG-psaJ, trnT-UGU-trnL-UAA, and ycf4-cemA were identified as divergence hotspot regions and thus might be suitable for species identification and phylogenetic studies. Additionally, the phylogenetic relationships based on Maximum likelihood (ML) and Bayesian inference (BI) of the whole chloroplast genomes showed that the chloroplast genome structure of I. guizhouensis represents the ancestral state of the Balsaminaceae family. CONCLUSION Our study provided detailed information about nucleotide diversity hotspots and the types of repeats, which can be used to develop molecular markers applicable to Balsaminaceae species. We also reconstructed and analyzed the relationships of some Impatiens species and assessed their taxonomic statuses based on the complete chloroplast genomes. Together, the findings of the current study might provide valuable genomic resources for systematic evolution of the Balsaminaceae species.
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Affiliation(s)
- Chao Luo
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture(State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, 650224, China
- Department of Landscape Architecture and Plant Science, University of Connecticut, Storrs, CT, 06269, USA
| | - Wulue Huang
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture(State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Huayu Sun
- Department of Landscape Architecture and Plant Science, University of Connecticut, Storrs, CT, 06269, USA
| | - Huseyin Yer
- Department of Landscape Architecture and Plant Science, University of Connecticut, Storrs, CT, 06269, USA
| | - Xinyi Li
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture(State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Yang Li
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture(State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Bo Yan
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture(State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Qiong Wang
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture(State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Yonghui Wen
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture(State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Meijuan Huang
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture(State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, 650224, China.
| | - Haiquan Huang
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture(State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, 650224, China.
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22
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Qin X, Yang X, Huang X, Huang X, Peng X, Liu M, Chen T, Yi K. The complete chloroplast genome of Agave fourcroydes. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2326-2327. [PMID: 34350343 PMCID: PMC8291057 DOI: 10.1080/23802359.2021.1950065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Agave fourcroydes (henequen) is the only cultivated Agave species in the Yucatan Peninsula, which is mainly used for fiber production. In the present study, we have successfully assembled the chloroplast (cp) genome of A. fourcroydes. The full length of the cp genome is 157,291 bp with a GC content at 37.8%. The cp genome is constructed with an inverted repeat region a (IRa) of 26,573 bp, a small single copy region (SSC) of 18,230 bp, an inverted repeat region b (IRb) of 26,573 bp and a large single copy region (LSC) of 85,915 bp. The annotation result reveals 132 genes on the cp genome, including 86 protein-coding genes, 38 tRNAs and 8 rRNAs. Phylogenetic tree reveals that A. fourcroydes is closely related with A. sisalana.
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Affiliation(s)
- Xu Qin
- Guangxi Subtropical Crops Research Institute, Nanning, PR China
| | - Xinli Yang
- College of Tropical Crops, Hainan University, Haikou, PR China
| | - Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
| | - Xianya Huang
- Guangxi Subtropical Crops Research Institute, Nanning, PR China
| | - Xinyi Peng
- Guangxi Subtropical Crops Research Institute, Nanning, PR China
| | - Ming Liu
- Guangxi Subtropical Crops Research Institute, Nanning, PR China
| | - Tao Chen
- Guangxi Subtropical Crops Research Institute, Nanning, PR China
| | - Kexian Yi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
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23
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Yang X, Huang X, Tan S, Chen T, Qin X, Chen H, Xi J, Yi K. The complete chloroplast genome of Agave sisalana. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1855-1856. [PMID: 34124368 PMCID: PMC8183535 DOI: 10.1080/23802359.2021.1935345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Agave sisalana is one of the Agave cultivars for sisal fiber production around the tropical areas of the world. In the present study, we successfully sequenced and assembled its chloroplast genome. The full size of the genome is 157,268 bp with a GC content at 37.85%. The genome is constructed with a large single copy region (LSC, 85,894 bp), a pair of inverted repeat regions (IR, 26,573 bp) and a small single copy region (SSC, 18,228 bp). Besides, 86 protein-coding genes, 38 tRNAs and 8 rRNAs are annotated on the chloroplast genome. Phylogenetic result reveals that A. sisalana is closely related with A. americana and A. H11648.
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Affiliation(s)
- Xinli Yang
- College of Tropical Crops, Hainan University, Haikou, PR China
| | - Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China.,Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, PR China.,Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou, PR China
| | - Shibei Tan
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China.,Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, PR China.,Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou, PR China
| | - Tao Chen
- Guangxi Subtropical Crops Research Institute, Nanning, PR China
| | - Xu Qin
- Guangxi Subtropical Crops Research Institute, Nanning, PR China
| | - Helong Chen
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China.,Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, PR China.,Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou, PR China
| | - Jingen Xi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China.,Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, PR China.,Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou, PR China
| | - Kexian Yi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China.,Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, PR China.,Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou, PR China
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24
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Jung J, Kim C, Kim JH. Insights into phylogenetic relationships and genome evolution of subfamily Commelinoideae (Commelinaceae Mirb.) inferred from complete chloroplast genomes. BMC Genomics 2021; 22:231. [PMID: 33794772 PMCID: PMC8017861 DOI: 10.1186/s12864-021-07541-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/16/2021] [Indexed: 12/04/2022] Open
Abstract
Background Commelinaceae (Commelinales) comprise 41 genera and are widely distributed in both the Old and New Worlds, except in Europe. The relationships among genera in this family have been suggested in several morphological and molecular studies. However, it is difficult to explain their relationships due to high morphological variations and low support values. Currently, many researchers have been using complete chloroplast genome data for inferring the evolution of land plants. In this study, we completed 15 new plastid genome sequences of subfamily Commelinoideae using the Mi-seq platform. We utilized genome data to reveal the structural variations and reconstruct the problematic positions of genera for the first time. Results All examined species of Commelinoideae have three pseudogenes (accD, rpoA, and ycf15), and the former two might be a synapomorphy within Commelinales. Only four species in tribe Commelineae presented IR expansion, which affected duplication of the rpl22 gene. We identified inversions that range from approximately 3 to 15 kb in four taxa (Amischotolype, Belosynapsis, Murdannia, and Streptolirion). The phylogenetic analysis using 77 chloroplast protein-coding genes with maximum parsimony, maximum likelihood, and Bayesian inference suggests that Palisota is most closely related to tribe Commelineae, supported by high support values. This result differs significantly from the current classification of Commelinaceae. Also, we resolved the unclear position of Streptoliriinae and the monophyly of Dichorisandrinae. Among the ten CDS (ndhH, rpoC2, ndhA, rps3, ndhG, ndhD, ccsA, ndhF, matK, and ycf1), which have high nucleotide diversity values (Pi > 0.045) and over 500 bp length, four CDS (ndhH, rpoC2, matK, and ycf1) show that they are congruent with the topology derived from 77 chloroplast protein-coding genes. Conclusions In this study, we provide detailed information on the 15 complete plastid genomes of Commelinoideae taxa. We identified characteristic pseudogenes and nucleotide diversity, which can be used to infer the family evolutionary history. Also, further research is needed to revise the position of Palisota in the current classification of Commelinaceae. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07541-1.
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Affiliation(s)
- Joonhyung Jung
- Department of Life Sciences, Gachon University, 1342 Seongnamdaero, Seongnam-si, Gyeonggi-do, 13120, Republic of Korea
| | - Changkyun Kim
- Plant Research Division, Honam National Institute of Biological Resources, 99 Gohadoan-gil, Mokpo-si, Jeollanam-do, 58762, Republic of Korea
| | - Joo-Hwan Kim
- Department of Life Sciences, Gachon University, 1342 Seongnamdaero, Seongnam-si, Gyeonggi-do, 13120, Republic of Korea.
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Choi KS, Ha YH, Gil HY, Choi K, Kim DK, Oh SH. Two Korean Endemic Clematis Chloroplast Genomes: Inversion, Reposition, Expansion of the Inverted Repeat Region, Phylogenetic Analysis, and Nucleotide Substitution Rates. PLANTS (BASEL, SWITZERLAND) 2021; 10:397. [PMID: 33669616 PMCID: PMC7922562 DOI: 10.3390/plants10020397] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 12/12/2022]
Abstract
Previous studies on the chloroplast genome in Clematis focused on the chloroplast structure within Anemoneae. The chloroplast genomes of Cleamtis were sequenced to provide information for studies on phylogeny and evolution. Two Korean endemic Clematis chloroplast genomes (Clematis brachyura and C. trichotoma) range from 159,170 to 159,532 bp, containing 134 identical genes. Comparing the coding and non-coding regions among 12 Clematis species revealed divergent sites, with carination occurring in the petD-rpoA region. Comparing other Clematis chloroplast genomes suggested that Clematis has two inversions (trnH-rps16 and rps4), reposition (trnL-ndhC), and inverted repeat (IR) region expansion. For phylogenetic analysis, 71 protein-coding genes were aligned from 36 Ranunculaceae chloroplast genomes. Anemoneae (Anemoclema, Pulsatilla, Anemone, and Clematis) clades were monophyletic and well-supported by the bootstrap value (100%). Based on 70 chloroplast protein-coding genes, we compared nonsynonymous (dN) and synonymous (dS) substitution rates among Clematis, Anemoneae (excluding Clematis), and other Ranunculaceae species. The average synonymoussubstitution rates (dS)of large single copy (LSC), small single copy (SSC), and IR genes in Anemoneae and Clematis were significantly higher than those of other Ranunculaceae species, but not the nonsynonymous substitution rates (dN). This study provides fundamental information on plastid genome evolution in the Ranunculaceae.
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Affiliation(s)
- Kyoung Su Choi
- Institute of Natural Science, Yeungnam University, Gyeongsan-si, Gyeongbuk-do 38541, Korea;
- Department of Life Sciences, Yeungnam University, Gyeongsan-si, Gyeongbuk-do 38541, Korea
| | - Young-Ho Ha
- Forest Biodiversity Division, Korea National Arboretum, 415 Gwangneungsumogwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-do 11186, Korea; (Y.-H.H.); (D.-K.K.)
- Department of Life Science, Gachon University, Seongnam-si, Gyeonggi-do 13120, Korea
| | - Hee-Young Gil
- DMZ Botanic Garden, Korea National Arboretum, 916-70, Punchbowl-ro, Haean-myeon, Yanggu, Gangwon-do 24564, Korea;
| | - Kyung Choi
- Research Planning and Coordination Division, Korea National Arboretum, 415 Gwangneungsumogwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-do 11186, Korea;
| | - Dong-Kap Kim
- Forest Biodiversity Division, Korea National Arboretum, 415 Gwangneungsumogwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-do 11186, Korea; (Y.-H.H.); (D.-K.K.)
| | - Seung-Hwan Oh
- Forest Biodiversity Division, Korea National Arboretum, 415 Gwangneungsumogwon-ro, Soheul-eup, Pocheon-si, Gyeonggi-do 11186, Korea; (Y.-H.H.); (D.-K.K.)
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Zhang J, Sui C, Liu H, Chen J, Han Z, Yan Q, Liu S, Liu H. Effect of chlorophyll biosynthesis-related genes on the leaf color in Hosta (Hosta plantaginea Aschers) and tobacco (Nicotiana tabacum L.). BMC PLANT BIOLOGY 2021; 21:45. [PMID: 33451287 PMCID: PMC7811250 DOI: 10.1186/s12870-020-02805-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 12/20/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND 'Regal Splendour' (Hosta variety) is famous for its multi-color leaves, which are useful resources for exploring chloroplast development and color changes. The expressions of chlorophyll biosynthesis-related genes (HrHEMA, HrPOR and HrCAO) in Hosta have been demonstrated to be associated with leaf color. Herein, we isolated, sequenced, and analyzed HrHEMA, HrPOR and HrCAO genes. Subcellular localization was also performed to determine the location of the corresponding enzymes. After plasmid construction, virus-induced gene silencing (VIGS) was carried out to reduce the expressions of those genes. In addition, HrHEMA-, HrPOR- and HrCAO-overexpressing tobacco plants were made to verify the genes function. Changes of transgenic tobacco were recorded under 2000 lx, 6000 lx and 10,000 lx light intensity. Additionally, the contents of enzyme 5-aminolevulinic acid (5-ALA), porphobilinogen (PBG), chlorophyll a and b (Chla and Chlb), carotenoid (Cxc), superoxide dismutase (SOD), peroxidase (POD), malondialdehyde (MDA), proline (Pro) and catalase (CAT) under different light intensities were evaluated. RESULTS The silencing of HrHEMA, HrPOR and HrCAO genes can induce leaf yellowing and chloroplast structure changes in Hosta. Specifically, leaves of Hosta with HrCAO silencing were the most affected, while those with HrPOR silencing were the least affected. Moreover, all three genes in tobacco were highly expressed, whereas no expression was detected in wild-type (WT). However, the sensitivities of the three genes to different light intensities were different. The highest expression level of HrHEMA and HrPOR was detected under 10,000 lx of illumination, while HrCAO showed the highest expression level under 6000 lx. Lastly, the 5-ALA, Chla, Cxc, SOD, POD, MDA, Pro and CAT contents in different transgenic tobaccos changed significantly under different light intensities. CONCLUSION The overexpression of these three genes in tobacco enhanced photosynthesis by accumulating chlorophyll content, but the influential level varied under different light intensities. Furthermore, HrHEMA-, HrPOR- and HrCAO- overexpressing in tobacco can enhance the antioxidant capacity of plants to cope with stress under higher light intensity. However, under lower light intensity, the antioxidant capacity was declined in HrHEMA-, HrPOR- and HrCAO- overexpressing tobaccos.
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Affiliation(s)
- Jingying Zhang
- College of Life sciences, Jilin Agricultural University, 2888 Xincheng Street, Changchun City, 130000, People's Republic of China
| | - Changhai Sui
- College of Life sciences, Jilin Agricultural University, 2888 Xincheng Street, Changchun City, 130000, People's Republic of China
- Jilin Engineering Vocational College, Siping City, Jilin, 136000, People's Republic of China
| | - Huimin Liu
- College of Life sciences, Jilin Agricultural University, 2888 Xincheng Street, Changchun City, 130000, People's Republic of China
| | - Jinjiao Chen
- College of Life sciences, Jilin Agricultural University, 2888 Xincheng Street, Changchun City, 130000, People's Republic of China
| | - Zhilin Han
- College of Life sciences, Jilin Agricultural University, 2888 Xincheng Street, Changchun City, 130000, People's Republic of China
| | - Qian Yan
- College of Life sciences, Jilin Agricultural University, 2888 Xincheng Street, Changchun City, 130000, People's Republic of China
| | - Shuying Liu
- College of Life sciences, Jilin Agricultural University, 2888 Xincheng Street, Changchun City, 130000, People's Republic of China.
| | - Hongzhang Liu
- College of Life sciences, Jilin Agricultural University, 2888 Xincheng Street, Changchun City, 130000, People's Republic of China.
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Yoo MJ, Lee BY, Kim S, Lim CE. Phylogenomics With Hyb-Seq Unravels Korean Hosta Evolution. FRONTIERS IN PLANT SCIENCE 2021; 12:645735. [PMID: 34305959 PMCID: PMC8296909 DOI: 10.3389/fpls.2021.645735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 06/16/2021] [Indexed: 05/14/2023]
Abstract
The genus Hosta (Agavoideae and Asparagaceae) is one of the most popular landscaping and ornamental plants native to temperate East Asia. Their popularity has led to extensive hybridization to develop various cultivars. However, their long history of hybridization, cultivation, and selection has brought about taxonomic confusion in the Hosta species delimitation along with their indistinguishable morphology. Here, we conducted the first broad phylogenetic analyses of Hosta species based on the most comprehensive genomic data set to date. To do so, we captured 246 nuclear gene sequences and plastomes from 55 accessions of Korean Hosta species using the Hyb-Seq method. As a result, this study provides the following novel and significant findings: (1) phylogenetic analyses of the captured sequences retrieved six species of Hosta in South Korea compared to five to eleven species based on the previous studies, (2) their phylogenetic relationships suggested that the large genome size was ancestral and the diversification of Korean Hosta species was accompanied by decreases in genome sizes, (3) comparison between nuclear genes and plastome revealed several introgressive hybridization events between Hosta species, and (4) divergence times estimated here showed that Hosta diverged 35.59 million years ago, while Korean Hosta species rapidly diversified during the late Miocene. Last, we explored whether these genomic data could be used to infer the origin of cultivars. In summary, this study provides the most comprehensive genomic resources to be used in phylogenetic, population, and conservation studies of Hosta, as well as for unraveling the origin of many cultivars.
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Affiliation(s)
- Mi-Jeong Yoo
- Department of Biology, Clarkson University, Potsdam, NY, United States
| | - Byoung-Yoon Lee
- National Institute of Biological Resources, Incheon, South Korea
| | - Sangtae Kim
- Department of Biotechnology, Sungshin Women’s University, Seoul, South Korea
| | - Chae Eun Lim
- National Institute of Biological Resources, Incheon, South Korea
- *Correspondence: Chae Eun Lim,
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28
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Bautista MAC, Zheng Y, Hu Z, Deng Y, Chen T. Comparative Analysis of Complete Chloroplast Genome Sequences of Wild and Cultivated Bougainvillea (Nyctaginaceae). PLANTS (BASEL, SWITZERLAND) 2020; 9:E1671. [PMID: 33260641 PMCID: PMC7760935 DOI: 10.3390/plants9121671] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/26/2020] [Accepted: 11/26/2020] [Indexed: 12/30/2022]
Abstract
Bougainvillea (Nyctaginaceae) is a popular ornamental plant group primarily grown for its striking colorful bracts. However, despite its established horticultural value, limited genomic resources and molecular studies have been reported for this genus. Thus, to address this existing gap, complete chloroplast genomes of four species (Bougainvillea glabra, Bougainvillea peruviana, Bougainvillea pachyphylla, Bougainvillea praecox) and one Bougainvillea cultivar were sequenced and characterized. The Bougainvillea cp genomes range from 153,966 bp to 154,541 bp in length, comprising a large single-copy region (85,159 bp-85,708 bp) and a small single-copy region (18,014 bp-18,078 bp) separated by a pair of inverted repeats (25,377-25,427 bp). All sequenced plastomes have 131 annotated genes, including 86 protein-coding, eight rRNA, and 37 tRNA genes. These five newly sequenced Bougainvillea cp genomes were compared to the Bougainvillea spectabilis cp genome deposited in GeBank. The results showed that all cp genomes have highly similar structures, contents, and organization. They all exhibit quadripartite structures and all have the same numbers of genes and introns. Codon usage, RNA editing sites, and repeat analyses also revealed highly similar results for the six cp genomes. The amino acid leucine has the highest proportion and almost all favored synonymous codons have either an A or U ending. Likewise, out of the 42 predicted RNA sites, most conversions were from serine (S) to leucine (L). The majority of the simple sequence repeats detected were A/T mononucleotides, making the cp genomes A/T-rich. The contractions and expansions of the IR boundaries were very minimal as well, hence contributing very little to the differences in genome size. In addition, sequence variation analyses showed that Bougainvillea cp genomes share nearly identical genomic profiles though several potential barcodes, such as ycf1, ndhF, and rpoA were identified. Higher variation was observed in both B. peruviana and B. pachyphylla cp sequences based on SNPs and indels analysis. Phylogenetic reconstructions further showed that these two species appear to be the basal taxa of Bougainvillea. The rarely cultivated and wild species of Bougainvillea (B. pachyphylla, B. peruviana, B. praecox) diverged earlier than the commonly cultivated species and cultivar (B. spectabilis, B. glabra, B. cv.). Overall, the results of this study provide additional genetic resources that can aid in further phylogenetic and evolutionary studies in Bougainvillea. Moreover, genetic information from this study is potentially useful in identifying Bougainvillea species and cultivars, which is essential for both taxonomic and plant breeding studies.
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Affiliation(s)
- Mary Ann C. Bautista
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
- Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen 518004, China;
- Graduate School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Zheng
- Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen 518004, China;
| | - Zhangli Hu
- School of Life Sciences and Oceanology, Shenzhen University, Shenzhen 518060, China;
| | - Yunfei Deng
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
- Graduate School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Chen
- Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen 518004, China;
- Graduate School, University of Chinese Academy of Sciences, Beijing 100049, China
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29
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Jin G, Huang X, Chen T, Qin X, Xi J, Yi K. The complete chloroplast genome of agave hybrid 11648. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2345-2346. [PMID: 33457785 PMCID: PMC7781945 DOI: 10.1080/23802359.2020.1775145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Agave hybrid 11648 is the most widely cultivated agave variety for sisal fiber production around the world. In the present study, we have successfully sequenced the chloroplast genome of A. H11648. The complete chloroplast genome size is 157,274 bp in length with a GC content of 37.8%. The genome contains a large single copy region (LSC) of 85,896 bp, a small single copy region (SSC) of 18,230 bp, and a pair of inverted repeat regions (IR) of 26,574 bp. 121 genes are annotated in the chloroplast genome. The numbers of protein-coding, tRNA and rRNA genes are 99, 40 and 8, respectively. Phylogenetic tree reveals that A. H11648 is closely related to A. americana.
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Affiliation(s)
- Gang Jin
- Guangxi Subtropical Crops Research Institute, Nanning, PR China
| | - Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China.,Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, PR China.,Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou, PR China
| | - Tao Chen
- Guangxi Subtropical Crops Research Institute, Nanning, PR China
| | - Xu Qin
- Guangxi Subtropical Crops Research Institute, Nanning, PR China
| | - Jingen Xi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China.,Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, PR China.,Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou, PR China
| | - Kexian Yi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China.,Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, PR China.,Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou, PR China
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30
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Li CJ, Wang RN, Li DZ. Comparative analysis of plastid genomes within the Campanulaceae and phylogenetic implications. PLoS One 2020; 15:e0233167. [PMID: 32407424 PMCID: PMC7224561 DOI: 10.1371/journal.pone.0233167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/29/2020] [Indexed: 12/13/2022] Open
Abstract
The conflicts exist between the phylogeny of Campanulaceae based on nuclear ITS sequence and plastid markers, particularly in the subdivision of Cyanantheae (Campanulaceae). Besides, various and complicated plastid genome structures can be found in species of the Campanulaceae. However, limited availability of genomic information largely hinders the studies of molecular evolution and phylogeny of Campanulaceae. We reported the complete plastid genomes of three Cyanantheae species, compared them to eight published Campanulaceae plastomes, and shed light on a deeper understanding of the applicability of plastomes. We found that there were obvious differences among gene order, GC content, gene compositions and IR junctions of LSC/IRa. Almost all protein-coding genes and amino acid sequences showed obvious codon preferences. We identified 14 genes with highly positively selected sites and branch-site model displayed 96 sites under potentially positive selection on the three lineages of phylogenetic tree. Phylogenetic analyses showed that Cyananthus was more closely related to Codonopsis compared with Cyclocodon and also clearly illustrated the relationship among the Cyanantheae species. We also found six coding regions having high nucleotide divergence value. Hotpot regions were considered to be useful molecular markers for resolving phylogenetic relationships and species authentication of Campanulaceae.
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Affiliation(s)
- Chun-Jiao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ruo-Nan Wang
- College of Life Sciences, Northwest University, Xi'an, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
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31
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Kyalo CM, Li ZZ, Mkala EM, Malombe I, Hu GW, Wang QF. The First Glimpse of Streptocarpus ionanthus (Gesneriaceae) Phylogenomics: Analysis of Five Subspecies' Chloroplast Genomes. PLANTS (BASEL, SWITZERLAND) 2020; 9:E456. [PMID: 32260377 PMCID: PMC7238178 DOI: 10.3390/plants9040456] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/29/2020] [Accepted: 04/02/2020] [Indexed: 02/05/2023]
Abstract
Streptocarpus ionanthus (Gesneriaceae) comprise nine herbaceous subspecies, endemic to Kenya and Tanzania. The evolution of Str. ionanthus is perceived as complex due to morphological heterogeneity and unresolved phylogenetic relationships. Our study seeks to understand the molecular variation within Str. ionanthus using a phylogenomic approach. We sequence the chloroplast genomes of five subspecies of Str. ionanthus, compare their structural features and identify divergent regions. The five genomes are identical, with a conserved structure, a narrow size range (170 base pairs (bp)) and 115 unique genes (80 protein-coding, 31 tRNAs and 4 rRNAs). Genome alignment exhibits high synteny while the number of Simple Sequence Repeats (SSRs) are observed to be low (varying from 37 to 41), indicating high similarity. We identify ten divergent regions, including five variable regions (psbM, rps3, atpF-atpH, psbC-psbZ and psaA-ycf3) and five genes with a high number of polymorphic sites (rps16, rpoC2, rpoB, ycf1 and ndhA) which could be investigated further for phylogenetic utility in Str. ionanthus. Phylogenomic analyses here exhibit low polymorphism within Str. ionanthus and poor phylogenetic separation, which might be attributed to recent divergence. The complete chloroplast genome sequence data concerning the five subspecies provides genomic resources which can be expanded for future elucidation of Str. ionanthus phylogenetic relationships.
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Affiliation(s)
- Cornelius M. Kyalo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (C.M.K.); (E.M.M.); (Q.-F.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China;
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Zhi-Zhong Li
- University of Chinese Academy of Sciences, Beijing 100049, China;
| | - Elijah M. Mkala
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (C.M.K.); (E.M.M.); (Q.-F.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China;
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Itambo Malombe
- East African Herbarium, National Museums of Kenya, P.O. Box 45166-00100 Nairobi, Kenya;
| | - Guang-Wan Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (C.M.K.); (E.M.M.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (C.M.K.); (E.M.M.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
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