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Geng LY, Jiang TY, Chen X, Li Q, Ma JH, Hou WX, Tang CQ, Wang Q, Deng YF. Plastome structure, phylogeny and evolution of plastid genes in Reevesia (Helicteroideae, Malvaceae). JOURNAL OF PLANT RESEARCH 2024; 137:589-604. [PMID: 38739241 DOI: 10.1007/s10265-024-01547-y] [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: 12/18/2023] [Accepted: 04/29/2024] [Indexed: 05/14/2024]
Abstract
Reevesia is an eastern Asian-eastern North American disjunction genus in the family Malvaceae s.l. and comprises approximately 25 species. The relationships within the genus are not well understood. Here, 15 plastomes representing 12 Reevesia species were compared, with the aim of better understanding the species circumscription and phylogenetic relationships within the genus and among genera in the family Malvaceae s.l. The 11 newly sequenced plastomes range between 161,532 and 161, 945 bp in length. The genomes contain 114 unique genes, 18 of which are duplicated in the inverted repeats (IRs). Gene content of these plastomes is nearly identical. All the protein-coding genes are under purifying selection in the Reevesia plastomes compared. The top ten hypervariable regions, SSRs, and the long repeats identified are potential molecular markers for future population genetic and phylogenetic studies. Phylogenetic analysis based on the whole plastomes confirmed the monophyly of Reevesia and a close relationship with Durio (traditional Bombacaceae) in subfamily Helicteroideae, but not with the morphologically similar genera Pterospermum and Sterculia (both of traditional Sterculiaceae). Phylogenetic relationships within Reevesia suggested that two species, R. pubescens and R. thyrsoidea, as newly defined, are not monophyletic. Six taxa, R. membranacea, R. xuefengensis, R. botingensis, R. lofouensis, R. longipetiolata and R. pycnantha, are suggested to be recognized.
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Affiliation(s)
- Li-Yang Geng
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Tian-Yi Jiang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Xin Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China.
| | - Qiang Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Jian-Hui Ma
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Wen-Xiang Hou
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Chen-Qian Tang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Qin Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yun-Fei Deng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
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Wang J, Kan J, Wang J, Yan X, Li Y, Soe T, Tembrock LR, Xing G, Li S, Wu Z, Jia M. The pan-plastome of Prunus mume: insights into Prunus diversity, phylogeny, and domestication history. FRONTIERS IN PLANT SCIENCE 2024; 15:1404071. [PMID: 38887455 PMCID: PMC11181306 DOI: 10.3389/fpls.2024.1404071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 04/29/2024] [Indexed: 06/20/2024]
Abstract
Backgrounds Prunus mume in the Rosaceae and commonly referred to as mei or Chinese plum is widely used as a traditional ornamental flowering plant and fruit tree in China. Although some population and genetic analyses have been conducted for this species, no extensive comparisons of genetic variation from plastomes have yet been investigated. Methods We de novo assembled a total of 322 complete P. mume plastomes in this study and did a series of comparative analyses to better resolve pan-plastomic patterns of P. mume. To determine the phylogeny and domestication history of this species, we reconstructed the phylogenetic tree of Prunus genus, and resolved the population structure of P. mume. We also examined the nucleotide variation of P. mume to find potential DNA barcodes. Results The assembled plastomes exhibited a typical quadripartite structure and ranged from 157,871 bp to 158,213 bp in total size with a GC content ranging from 36.73 to 36.75%. A total of 112 unique genes were identified. Single nucleotide variants (SNVs) were the most common variants found among the plastomes, followed by nucleotide insertions/deletions (InDels), and block substitutions with the intergenic spacer (IGS) regions containing the greatest number of variants. From the pan-plastome data six well-supported genetic clusters were resolved using multiple different population structure analyses. The different cultivars were unevenly distributed among multiple clades. We also reconstructed a phylogeny for multiple species of Prunus to better understand genus level diversity and history from which a complex introgressive relationship between mei and other apricots/plums was resolved. Conclusion This study constructed the pan-plastome of P. mume, which indicated the domestication of P. mume involved multiple genetic origins and possible matrilineal introgression from other species. The phylogenetic analysis in Prunus and the population structure of P. mume provide an important maternal history for Prunus and the groundwork for future studies on intergenomic sequence transfers, cytonuclear incompatibility, and conservation genetics.
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Affiliation(s)
- Jie Wang
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Junhu Kan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Xinlin Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yi Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Thida Soe
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Luke R. Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Guoming Xing
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
| | - Sen Li
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
| | - Zhiqiang Wu
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Minlong Jia
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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Gia Huy T, Thi NPA, Do HDK, Khang DT. The complete chloroplast genome of Durio zibethinus L. cultivar Ri6 (Helicteroideae, Malvaceae). Mitochondrial DNA B Resour 2024; 9:625-630. [PMID: 38737395 PMCID: PMC11086024 DOI: 10.1080/23802359.2024.2350619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/28/2024] [Indexed: 05/14/2024] Open
Abstract
Durian, a member of the Malvaceae family, is famous for its delicious fruits, which have strong scents and are rich in nutrients. In this study, we sequenced and characterized the complete chloroplast genome of Durio zibethinus L. 1774 cultivar Ri6, a popular durian cultivar in Vietnam, using the Illumina Hiseq platform. The results showed a circular chloroplast genome composed of a large single copy of 96,115 bp, a small single copy of 20,819 bp, and two inverted repeat regions of 24,185 bp. This genome consisted of 79 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. The overall GC content of this genome was 35.7%. Phylogenetic analysis inferred from 78 protein-coding regions revealed monophyly of Durio species and a close relationship between D. zibethinus cultivar Ri6 and cultivar Mongthong. This study provides essential information for further studies examining genetic population, breedings, and species identification among Durio taxa and cultivars.
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Affiliation(s)
- Tran Gia Huy
- Department of Molecular Biology, Institute of Food and Biotechnology, Can Tho University, Can Tho City, Viet Nam
| | - Nguyen Pham Anh Thi
- Department of Molecular Biology, Institute of Food and Biotechnology, Can Tho University, Can Tho City, Viet Nam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam
| | - Do Tan Khang
- Department of Molecular Biology, Institute of Food and Biotechnology, Can Tho University, Can Tho City, Viet Nam
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Nguyen HD, Vu MT, Do HDK. Characterization of the complete chloroplast genome of Helicteres hirsuta Lour. 1790 (Helicteriodeae: Malvaceae). Mitochondrial DNA B Resour 2024; 9:568-573. [PMID: 38707209 PMCID: PMC11067558 DOI: 10.1080/23802359.2024.2345794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 04/16/2024] [Indexed: 05/07/2024] Open
Abstract
Helicteres hirsuta Lour. 1790 is a precious medicinal plant species, especially for treating chronic liver diseases. Genomic data on H. hirsuta are limited. Therefore, this current study aimed to characterize the chloroplast genome of H. hirsuta and reconstruct the phylogenetic relationship among Helicteroideae taxa. Consequently, the complete chloroplast genome of H. hirsuta was 163,404 bp in length and contained 113 unique genes (79 protein-coding genes, 30 tRNA genes, and four rRNA genes). Notably, two introns of clpP gene of H. hirsuta were lost in comparison to that of other Helicteroideae species. The phylogenetic tree based on chloroplast genomes of eleven Helicteroideae species revealed that H. hirsuta was closely related to Reevesia species. In conclusion, our study described the first complete chloroplast genome of H. hirsuta, which is essential for tracing evolutionary history in the Helicteroideae subfamily.
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Affiliation(s)
- Hoang Danh Nguyen
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Minh Thiet Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
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Wang Y, Zhao X, Chen Q, Yang J, Hu J, Jia D, Ma R. Complete Chloroplast Genome of Alternanthera sessilis and Comparative Analysis with Its Congeneric Invasive Weed Alternanthera philoxeroides. Genes (Basel) 2024; 15:544. [PMID: 38790173 PMCID: PMC11121667 DOI: 10.3390/genes15050544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Alternanthera sessilis is considered the closest relative to the invasive weed Alternanthera philoxeroides in China, making it an important native species for studying the invasive mechanisms and adaptations of A. philoxeroides. Chloroplasts play a crucial role in a plant's environmental adaptation, with their genomes being pivotal in the evolution and adaptation of both invasive and related species. However, the chloroplast genome of A. sessilis has remained unknown until now. In this study, we sequenced and assembled the complete chloroplast genome of A. sessilis using high-throughput sequencing. The A. sessilis chloroplast genome is 151,935 base pairs long, comprising two inverted repeat regions, a large single copy region, and a small single copy region. This chloroplast genome contains 128 genes, including 8 rRNA-coding genes, 37 tRNA-coding genes, 4 pseudogenes, and 83 protein-coding genes. When compared to the chloroplast genome of the invasive weed A. philoxeroides and other Amaranthaceae species, we observed significant variations in the ccsA, ycf1, and ycf2 regions in the A. sessilis chloroplast genome. Moreover, two genes, ccsA and accD, were found to be undergoing rapid evolution due to positive selection pressure. The phylogenetic trees were constructed for the Amaranthaceae family, estimating the time of independent species formation between A. philoxeroides and A. sessilis to be approximately 3.5186-8.8242 million years ago. These findings provide a foundation for understanding the population variation within invasive species among the Alternanthera genus.
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Affiliation(s)
- Yuanxin Wang
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China; (Y.W.); (X.Z.); (Q.C.); (J.Y.); (J.H.)
| | - Xueying Zhao
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China; (Y.W.); (X.Z.); (Q.C.); (J.Y.); (J.H.)
| | - Qianhui Chen
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China; (Y.W.); (X.Z.); (Q.C.); (J.Y.); (J.H.)
| | - Jun Yang
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China; (Y.W.); (X.Z.); (Q.C.); (J.Y.); (J.H.)
| | - Jun Hu
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China; (Y.W.); (X.Z.); (Q.C.); (J.Y.); (J.H.)
| | - Dong Jia
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China; (Y.W.); (X.Z.); (Q.C.); (J.Y.); (J.H.)
- Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production with High-Quality and Effciency in Loess Plateau, Taigu 030801, China
| | - Ruiyan Ma
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China; (Y.W.); (X.Z.); (Q.C.); (J.Y.); (J.H.)
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), Shanxi Agricultural University, Taiyuan 030031, China
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Le HTT, Hioki Y, Nguyen DV, Le TKD, Nguyen VK, Dang TT, Nguyen TAT, Nguyen THT, Vu THD, Pham TKN, Kita M, Chavasiri W. Identification and α-glucosidase inhibitory activity evaluation of two new coumarins derived from Mansonia gagei J. R. Drumm. Nat Prod Res 2024:1-6. [PMID: 38422455 DOI: 10.1080/14786419.2024.2324367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 02/22/2024] [Indexed: 03/02/2024]
Abstract
Five coumarins were isolated from the heartwood of Mansonia gagei, which included two newly discovered compounds, namely 11-hydroxypopulene E (1) and mansorin D (2), along with three previously identified compounds. The structures were determined through the utilisation of comprehensive spectroscopic data, ECD calculations, and a thorough comparison with existing literature data. The α-glucosidase inhibitory activities of all isolated compounds were assessed in yeast. Out of the compounds tested, compound 2 exhibited the most significant activity, displaying a percentage inhibition of 34.33% at a concentration of 200 μM.
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Affiliation(s)
- Huong Thi Thu Le
- Department of Chemistry, Ho Chi Minh City University of Education, Ho Chi Minh City, Vietnam
| | - Yusuke Hioki
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Duy Vu Nguyen
- Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Thailand
| | - Thi-Kim-Dung Le
- Laboratory of Biophysics, Institute for Advanced Study in Technology, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Van-Kieu Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City, Vietnam
- Faculty of Natural Sciences, Duy Tan University, Da Nang, Vietnam
| | - Tien T Dang
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, Ho Chi Minh City Vietnam
| | - Thi-Anh-Tuyet Nguyen
- Department of Chemistry, Ho Chi Minh City University of Education, Ho Chi Minh City, Vietnam
| | - Thi-Hoai-Thu Nguyen
- Faculty of Basic Sciences, University of Medicine and Pharmacy at, Ho Chi Minh City, Vietnam
| | - Thi-Hai-Duyen Vu
- Department of Chemistry, Ho Chi Minh City University of Education, Ho Chi Minh City, Vietnam
| | - Thi-Kim-Ngan Pham
- Education and Training Department of Lang Son Province, Lang Son City, Vietnam
| | - Masaki Kita
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Warinthorn Chavasiri
- Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Thailand
- Nanotec-CU Center of Excellence on Food and Agriculture, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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Li YL, Nie LY, Deng SW, Duan L, Wang ZF, Charboneau JLM, Ho BC, Chen HF. Characterization of Firmiana danxiaensis plastomes and comparative analysis of Firmiana: insight into its phylogeny and evolution. BMC Genomics 2024; 25:203. [PMID: 38389079 PMCID: PMC10885454 DOI: 10.1186/s12864-024-10046-2] [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: 08/18/2023] [Accepted: 01/24/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND Firmiana danxiaensis is a critically endangered and ecologically important tree currently only found in four locations in Danxia or Karst habitats in northern Guangdong Province, China. The specialized habitat preference makes it an ideal model species for study of adaptive evolution. Meanwhile, the phylogenetic relationships of F. danxiaensis in four locations under two landforms are unclear. Therefore, we sequenced its complete chloroplast (cp.) genomes and conducted comprehensive interspecific and intrageneric plastome studies. RESULTS The F. danxiaensis plastomes in four locations showed a typical quadripartite and circular structure that ranged from 160,832 to 161,206 bp in size, with 112 unique genes encoded. Comparative genomics showed that the plastomes of F. danxiaensis were relatively conserved with high similarity of genome organization, gene number, GC content and SSRs. While the genomes revealed higher biased codon preferences in Karst habitat than those in Danxia habitats. Eighteen and 11 divergent hotpots were identified at interspecific and intrageneric levels for species identification and further phylogenetic studies. Seven genes (clpP, accD, ccsA, ndhH, rpl20, rpoC2, and rps4) were under positive selection and may be related to adaptation. Phylogenetic analysis revealed that F. danxiaensis is sister to F. major and F. simplex. However, the interspecific relationships are not consistent with the habitat types. CONCLUSIONS The characteristics and interspecific relationship of F. danxiaensis plastomes provide new insights into further integration of geographical factors, environmental factors, and genetic variations on the genomic study of F. danxiaensis. Together, our study will contribute to the study of species identification, population genetics, and conservation biology of F. danxiaensis.
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Affiliation(s)
- Ya-Li Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Yun Nie
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuang-Wen Deng
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Duan
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zheng-Feng Wang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510650, China
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Key Laboratory of Carbon Sequestration in Terrestrial Ecosystem, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Joseph L M Charboneau
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Boon-Chuan Ho
- Singapore Botanic Gardens, National Parks Board, 1 Cluny Road, Singapore, 259569, Republic of Singapore
| | - Hong-Feng Chen
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
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Liu R, Xie L, Wang D. The complete chloroplast genome of Malvaviscus penduliflorus (Malvaceae). Mitochondrial DNA B Resour 2023; 8:886-889. [PMID: 37614528 PMCID: PMC10443977 DOI: 10.1080/23802359.2023.2246670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 08/04/2023] [Indexed: 08/25/2023] Open
Abstract
In this study, we assembled the complete chloroplast (cp) genome of Malvaviscus penduliflorus using high-throughput Illumina sequencing reads. The resulting plastome assembly displayed a typical quadripartite structure with a total length of 160,332 bp, containing a pair of inverted repeat regions (IRs) of 26,313 bp separated by a large single-copy region (LSC) of 88,750 bp and a small single-copy region (SSC) of 18,956 bp. The M. penduliflorus cp genome contained 128 genes, and its overall GC content was 36.96%. Phylogenetic analysis among M. penduliflorus and five other Malvaceae species demonstrated that M. penduliflorus was closely related to Urena procumbens and Hibiscus cannabinus. The M. penduliflorus cp genome presented in this study will lay a good foundation for further genetic and genomic studies of the genus Malvaviscus as well as Malvaceae.
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Affiliation(s)
- Rong Liu
- School of Preclinical Medicine, Chengdu University, Chengdu, China
| | - Li Xie
- School of Preclinical Medicine, Chengdu University, Chengdu, China
| | - Dan Wang
- Department of Pharmacy, Sichuan Nursing Vocational College, Chengdu, China
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Hou WJ, Men WX, Bian C, Song YY, Yang YY, Xu L, Kang TG. The complete chloroplast genome of Grewia biloba var. parviflora (Bunge) Hand.-Mazz. (Malvaceae). Mitochondrial DNA B Resour 2023; 8:804-808. [PMID: 37545553 PMCID: PMC10399491 DOI: 10.1080/23802359.2023.2240057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 07/18/2023] [Indexed: 08/08/2023] Open
Abstract
Grewia biloba var. parviflora (Bunge) Hand.-Mazz. (1933), a shrub or small tree, is native to northern and southern China. It is an excellent relief and medicinal plant. The complete chloroplast genome is 158,043 bp in length, with a large single-copy region of 86,957 bp, a small single-copy region of 20,138 bp, two inverted repeat regions of 25,474 bp each, and a GC content of 37.4%. There were 129 genes annotated, including 84 known protein-coding genes, 37 tRNAs, and eight rRNAs. The phylogenetic trees are constructed using plastome data from 38 species and the maximum-likelihood method. The results of the chloroplast genome-wide analysis and the phylogenetic tree show the taxonomic phylogeny of the G. biloba var. parviflora in relation to other species, increasing the accuracy of the phylogenetic classification of the plant.
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Affiliation(s)
- Wen-Juan Hou
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Wen-Xiao Men
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Che Bian
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Yue-Yue Song
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Yan-yun Yang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Liang Xu
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Ting-Guo Kang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
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10
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Chen Q, Chen L, Teixeira da Silva JA, Yu X. The plastome reveals new insights into the evolutionary and domestication history of peonies in East Asia. BMC PLANT BIOLOGY 2023; 23:243. [PMID: 37150831 PMCID: PMC10165817 DOI: 10.1186/s12870-023-04246-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 04/24/2023] [Indexed: 05/09/2023]
Abstract
BACKGROUD Paeonia holds considerable value in medicinal, ornamental horticultural, and edible oil industries, but the incomplete state of phylogenetic research in this genus poses a challenge to the effective conservation and development of wild germplasm, and also impedes the practical utilization of existing cultivars. Due to its uniparental inheritance and lack of recombination, the plastome (i.e., plastid genome), which is a valuable molecular marker for phylogenetic analyses, is characterized by an appropriate rate of nucleotide evolution. METHODS In this study, 10 newly assembled data and available reported data were combined to perform a comparative genomics and phylogenetics analysis of 63 plastomes of 16 Paeonia species, primarily from East Asia, which is the origin and diversity center of Paeonia. RESULTS Ranging between 152,153 and 154,405 bp, most plastomes displayed a conserved structure and relatively low nucleotide diversity, except for six plastomes, which showed obvious IR construction or expansion. A total of 111 genes were annotated in the Paeonia plastomes. Four genes (rpl22, rps3, rps19 and ycf1) showed different copy numbers among accessions while five genes (rpl36, petN, psbI, rpl33 and psbJ) showed strong codon usage biases (ENC < 35). Additional selection analysis revealed that no genes were under positive selection during the domestication of tree peony cultivars whereas four core photosynthesis-related genes (petA, psaA, psaB and rbcL) were under positive selection in herbaceous peony cultivars. This discovery might contribute to the wide adaption of these cultivars. Two types of molecular markers (SSR and SNP) were generated from the 63 plastomes. Even though SSR was more diverse than SNP, it had a weaker ability to delimit Paeonia species than SNP. The reconstruction of a phylogenetic backbone of Paeonia in East Asia revealed significant genetic divergence within the P. ostii groups. Evidence also indicated that the majority of P. suffruticosa cultivars had a maternal origin, from P. ostii. The results of this research also suggest that P. delavayi var. lutea, which likely resulted from hybridization with P. ludlowii, should be classified as a lineage within the broader P. delavayi group. CONCLUSIONS Overall, this study's research findings suggest that the Paeonia plastome is highly informative for phylogenetic and comparative genomic analyses, and could be useful in future research related to taxonomy, evolution, and domestication.
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Affiliation(s)
- Qihang Chen
- College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, Beijing, 100083, China
- National Engineering Research Center for Floriculture, Beijing, 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 100083, China
| | - Le Chen
- College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, Beijing, 100083, China
- National Engineering Research Center for Floriculture, Beijing, 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 100083, China
| | | | - Xiaonan Yu
- College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, Beijing, 100083, China.
- National Engineering Research Center for Floriculture, Beijing, 100083, China.
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 100083, China.
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11
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Lu Q, Luo W. The complete chloroplast genome of two Firmiana species and comparative analysis with other related species. Genetica 2022; 150:395-405. [DOI: 10.1007/s10709-022-00169-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 09/21/2022] [Indexed: 11/06/2022]
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12
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Yan L, Wang H, Huang X, Li Y, Yue Y, Wang Z, Tang S. Chloroplast Genomes of Genus Tilia: Comparative Genomics and Molecular Evolution. Front Genet 2022; 13:925726. [PMID: 35873491 PMCID: PMC9305825 DOI: 10.3389/fgene.2022.925726] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/17/2022] [Indexed: 11/26/2022] Open
Abstract
Tilia is a complex genus in the family Malvaceae that has high ecological and economical values. Owing to the lack of sufficient distinguishable morphological and molecular characteristics, interspecific relationships in this genus are not clear. Chloroplast (cp) genomes are small, meanwhile most angiosperms usually undergo matrilineal inheritance. Consequently, they can be used in molecular systematics and phylogenetic analyses. Here, we sequenced and assembled cp genomes from T. endochrysea, T. tomentosa, T. miqueliana, T. americana and T. cordata, and compared them with those of seven previously reported Tilia species. Similar gene contents, gene orders and GC contents existed among the 12 cp genomes, which ranged from 162,564 to 162,855 bp and encoded 113 unique genes. Abundant simple sequence repeats (119–127) and dispersed repeats (97–135) were detected in Tilia cp genomes. In total, 11 hypervariable regions were identified that could be suitable for species identification and phylogenetic studies. A phylogenetic analysis of Malvaceae based on 5 hypervariable genes (matK + ndhF + rpoB + rpoC2+ycf1) revealed that all eight subfamilies were monophyletic groups. Additionally, the genus Tilia was divided into three groups on the basis of all 521 molecular variation loci. The current study provides valuable insights into the genomic evolution of the genus Tilia.
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Affiliation(s)
- Linjun Yan
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
| | - Huanli Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
| | - Xi Huang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
| | - Yingchao Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yuanhao Yue
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
| | - Zhongwei Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
| | - Shijie Tang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
- *Correspondence: Shijie Tang,
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13
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Liu C, Chen HH, Tang LZ, Khine PK, Han LH, Song Y, Tan YH. Plastid genome evolution of a monophyletic group in the subtribe Lauriineae (Laureae, Lauraceae). PLANT DIVERSITY 2022; 44:377-388. [PMID: 35967258 PMCID: PMC9363652 DOI: 10.1016/j.pld.2021.11.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 06/15/2023]
Abstract
Litsea, a non-monophyletic group of the tribe Laureae (Lauraceae), plays important roles in the tropical and subtropical forests of Asia, Australia, Central and North America, and the islands of the Pacific. However, intergeneric relationships between Litsea and Laurus, Lindera, Parasassafras and Sinosassafras of the tribe Laureae remain unresolved. In this study, we present phylogenetic analyses of seven newly sequenced Litsea plastomes, together with 47 Laureae plastomes obtained from public databases, representing six genera of the Laureae. Our results highlight two highly supported monophyletic groups of Litsea taxa. One is composed of 16 Litsea taxa and two Lindera taxa. The 18 plastomes of these taxa were further compared for their gene structure, codon usage, contraction and expansion of inverted repeats, sequence repeats, divergence hotspots, and gene evolution. The complete plastome size of newly sequenced taxa varied between 152,377 bp (Litsea auriculata) and 154,117 bp (Litsea pierrei). Seven of the 16 Litsea plastomes have a pair of insertions in the IRa (trnL-trnH) and IRb (ycf2) regions. The 18 plastomes of Litsea and Lindera taxa exhibit similar gene features, codon usage, oligonucleotide repeats, and inverted repeat dynamics. The codons with the highest frequency among these taxa favored A/T endings and each of these plastomes had nine divergence hotspots, which are located in the same regions. We also identified six protein coding genes (accD, ndhJ, rbcL, rpoC2, ycf1 and ycf2) under positive selection in Litsea; these genes may play important roles in adaptation of Litsea species to various environments.
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Affiliation(s)
- Chao Liu
- College of Biological Resource and Food Engineering, Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, Yunnan, 655011, China
| | - Huan-Huan Chen
- College of Biological Resource and Food Engineering, Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, Yunnan, 655011, China
| | - Li-Zhou Tang
- College of Biological Resource and Food Engineering, Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, Yunnan, 655011, China
| | - Phyo Kay Khine
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Li-Hong Han
- College of Biological Resource and Food Engineering, Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, Yunnan, 655011, China
| | - Yu Song
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education), Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, Guangxi, 541004, China
| | - Yun-Hong Tan
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282, Myanmar
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Hernández-Gutiérrez R, van den Berg C, Granados Mendoza C, Peñafiel Cevallos M, Freire M. E, Lemmon EM, Lemmon AR, Magallón S. Localized Phylogenetic Discordance Among Nuclear Loci Due to Incomplete Lineage Sorting and Introgression in the Family of Cotton and Cacao (Malvaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:850521. [PMID: 35498660 PMCID: PMC9043901 DOI: 10.3389/fpls.2022.850521] [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: 01/07/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
The economically important cotton and cacao family (Malvaceae sensu lato) have long been recognized as a monophyletic group. However, the relationships among some subfamilies are still unclear as discordant phylogenetic hypotheses keep arising when different sources of molecular data are analyzed. Phylogenetic discordance has previously been hypothesized to be the result of both introgression and incomplete lineage sorting (ILS), but the extent and source of discordance have not yet been evaluated in the context of loci derived from massive sequencing strategies and for a wide representation of the family. Furthermore, no formal methods have been applied to evaluate if the detected phylogenetic discordance among phylogenomic datasets influences phylogenetic dating estimates of the concordant relationships. The objective of this research was to generate a phylogenetic hypothesis of Malvaceae from nuclear genes, specifically we aimed to (1) investigate the presence of major discordance among hundreds of nuclear gene histories of Malvaceae; (2) evaluate the potential source of discordance; and (3) examine whether discordance and loci heterogeneity influence on time estimates of the origin and diversification of subfamilies. Our study is based on a comprehensive dataset representing 96 genera of the nine subfamilies and 268 nuclear loci. Both concatenated and coalescence-based approaches were followed for phylogenetic inference. Using branch lengths and topology, we located the placement of introgression events to directly evaluate whether discordance is due to introgression rather than ILS. To estimate divergence times, concordance and molecular rate were considered. We filtered loci based on congruence with the species tree and then obtained the molecular rate of each locus to distribute them into three different sets corresponding to shared molecular rate ranges. Bayesian dating was performed for each of the different sets of loci with the same parameters and calibrations. Phylogenomic discordance was detected between methods, as well as gene histories. At deep coalescent times, we found discordance in the position of five subclades probably due to ILS and a relatively small proportion of introgression. Divergence time estimation with each set of loci generated overlapping clade ages, indicating that, even with different molecular rate and gene histories, calibrations generally provide a strong prior.
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Affiliation(s)
- Rebeca Hernández-Gutiérrez
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Cássio van den Berg
- Departamento de Ciencias Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Carolina Granados Mendoza
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Efraín Freire M.
- Herbario Nacional del Ecuador (QCNE), Instituto Nacional de Biodiversidad, Quito, Ecuador
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, United States
| | - Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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15
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Jiang H, Tian J, Yang J, Dong X, Zhong Z, Mwachala G, Zhang C, Hu G, Wang Q. Comparative and phylogenetic analyses of six Kenya Polystachya (Orchidaceae) species based on the complete chloroplast genome sequences. BMC PLANT BIOLOGY 2022; 22:177. [PMID: 35387599 PMCID: PMC8985347 DOI: 10.1186/s12870-022-03529-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/14/2022] [Indexed: 05/22/2023]
Abstract
BACKGROUND Polystachya Hook. is a large pantropical orchid genus (c. 240 species) distributed in Africa, southern Asia and the Americas, with the center of diversity in Africa. Previous studies on species of this genus have not obtained the complete chloroplast genomes, structures and variations. Additionally, the phylogenetic position of the genus in the Orchidaceae is still controversial and uncertain. Therefore, in this study, we sequenced the complete plastomes of six Kenya Polystachya species based on genome skimming, subjected them to comparative genomic analysis, and reconstructed the phylogenetic relationships with other Orchidaceae species. RESULTS The results exhibited that the chloroplast genomes had a typical quadripartite structure with conserved genome arrangement and moderate divergence. The plastomes of the six Polystachya species ranged from 145,484 bp to 149,274 bp in length and had an almost similar GC content of 36.9-37.0%. Gene annotation revealed 106-109 single-copy genes. In addition, 19 genes are duplicated in the inverted regions, and 16 genes each possessd one or more introns. Although no large structural variations were observed among the Polystachya plastomes, about 1 kb inversion was found in Polystachya modesta and all 11 ndh genes in the Polystachya plastomes were lost or pseudogenized. Comparative analysis of the overall sequence identity among six complete chloroplast genomes confirmed that for both coding and non-coding regions in Polystachya, SC regions exhibit higher sequence variation than IRs. Furthermore, there were various amplifications in the IR regions among the six Polystachya species. Most of the protein-coding genes of these species had a high degree of codon preference. We screened out SSRs and found seven relatively highly variable loci. Moreover, 13 genes were discovered with significant positive selection. Phylogenetic analysis showed that the six Polystachya species formed a monophyletic clade and were more closely related to the tribe Vandeae. Phylogenetic relationships of the family Orchidaceae inferred from the 85 chloroplast genome sequences were generally consistent with previous studies and robust. CONCLUSIONS Our study is the initial report of the complete chloroplast genomes of the six Polystachya species, elucidates the structural characteristics of the chloroplast genome of Polystachya, and filters out highly variable sequences that can contribute to the development of DNA markers for use in the study of genetic variability and evolutionary studies in Polystachya. In addition, the phylogenetic results strongly support that the genus of Polystachya is a part of the tribe Vandeae.
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Affiliation(s)
- Hui Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, 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 Tian
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Jiaxin Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, 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
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhixiang Zhong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, 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
| | - Geoffrey Mwachala
- East African Herbarium, National Museums of Kenya, P.O. Box 45166, Nairobi, 00100, Kenya
| | - Caifei Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, 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.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Qingfeng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, 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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16
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Sielemann K, Pucker B, Schmidt N, Viehöver P, Weisshaar B, Heitkam T, Holtgräwe D. Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives. BMC Genomics 2022; 23:113. [PMID: 35139817 PMCID: PMC8830136 DOI: 10.1186/s12864-022-08336-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/20/2022] [Indexed: 12/24/2022] Open
Abstract
Background As the major source of sugar in moderate climates, sugar-producing beets (Beta vulgaris subsp. vulgaris) have a high economic value. However, the low genetic diversity within cultivated beets requires introduction of new traits, for example to increase their tolerance and resistance attributes – traits that often reside in the crop wild relatives. For this, genetic information of wild beet relatives and their phylogenetic placements to each other are crucial. To answer this need, we sequenced and assembled the complete plastome sequences from a broad species spectrum across the beet genera Beta and Patellifolia, both embedded in the Betoideae (order Caryophyllales). This pan-plastome dataset was then used to determine the wild beet phylogeny in high-resolution. Results We sequenced the plastomes of 18 closely related accessions representing 11 species of the Betoideae subfamily and provided high-quality plastome assemblies which represent an important resource for further studies of beet wild relatives and the diverse plant order Caryophyllales. Their assembly sizes range from 149,723 bp (Beta vulgaris subsp. vulgaris) to 152,816 bp (Beta nana), with most variability in the intergenic sequences. Combining plastome-derived phylogenies with read-based treatments based on mitochondrial information, we were able to suggest a unified and highly confident phylogenetic placement of the investigated Betoideae species. Our results show that the genus Beta can be divided into the two clearly separated sections Beta and Corollinae. Our analysis confirms the affiliation of B. nana with the other Corollinae species, and we argue against a separate placement in the Nanae section. Within the Patellifolia genus, the two diploid species Patellifolia procumbens and Patellifolia webbiana are, regarding the plastome sequences, genetically more similar to each other than to the tetraploid Patellifolia patellaris. Nevertheless, all three Patellifolia species are clearly separated. Conclusion In conclusion, our wild beet plastome assemblies represent a new resource to understand the molecular base of the beet germplasm. Despite large differences on the phenotypic level, our pan-plastome dataset is highly conserved. For the first time in beets, our whole plastome sequences overcome the low sequence variation in individual genes and provide the molecular backbone for highly resolved beet phylogenomics. Hence, our plastome sequencing strategy can also guide genomic approaches to unravel other closely related taxa. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08336-8.
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Affiliation(s)
- Katharina Sielemann
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany.,Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, 33615, Bielefeld, Germany
| | - Boas Pucker
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany.,Evolution and Diversity, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.,Institute of Plant Biology, TU Braunschweig, Braunschweig, Germany
| | - Nicola Schmidt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Prisca Viehöver
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Bernd Weisshaar
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Tony Heitkam
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany.
| | - Daniela Holtgräwe
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany.
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Yang J, Hu G, Hu G. Comparative genomics and phylogenetic relationships of two endemic and endangered species (Handeliodendron bodinieri and Eurycorymbus cavaleriei) of two monotypic genera within Sapindales. BMC Genomics 2022; 23:27. [PMID: 34991482 PMCID: PMC8734052 DOI: 10.1186/s12864-021-08259-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/13/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Handeliodendron Rehder and Eurycorymbus Hand.-Mazz. are the monotypic genera in the Sapindaceae family. The phylogenetic relationship of these endangered species Handeliodendron bodinieri (Lévl.) Rehd. and Eurycorymbus cavaleriei (Lévl.) Rehd. et Hand.-Mazz. with other members of Sapindaceae s.l. is not well resolved. A previous study concluded that the genus Aesculus might be paraphyletic because Handeliodendron was nested within it based on small DNA fragments. Thus, their chloroplast genomic information and comparative genomic analysis with other Sapindaceae species are necessary and crucial to understand the circumscription and plastome evolution of this family. RESULTS The chloroplast genome sizes of Handeliodendron bodinieri and Eurycorymbus cavaleriei are 151,271 and 158,690 bp, respectively. Results showed that a total of 114 unique genes were annotated in H. bodinieri and E. cavaleriei, and the ycf1 gene contained abundant SSRs in both genomes. Comparative analysis revealed that gene content, PCGs, and total GC content were remarkably similar or identical within 13 genera from Sapindaceae, and the chloroplast genome size of four genera was generally smaller within the family, including Acer, Dipteronia, Aesculus, and Handeliodendron. IR boundaries of the H. bodinieri showed a significant contraction, whereas it presented a notable expansion in E. cavaleriei cp genome. Ycf1, ndhC-trnV-UAC, and rpl32-trnL-UAG-ccsA were remarkably divergent regions in the Sapindaceae species. Analysis of selection pressure showed that there are a few positively selected genes. Phylogenetic analysis based on different datasets, including whole chloroplast genome sequences, coding sequences, large single-copy, small single-copy, and inverted repeat regions, consistently demonstrated that H. bodinieri was sister to the clade consisting of Aesculus chinensis and A. wangii and strongly support Eurycorymbus cavaleriei as sister to Dodonaea viscosa. CONCLUSION This study revealed that the cp genome size of the Hippocastanoideae was generally smaller compared to the other subfamilies within Sapindaceae, and three highly divergent regions could be used as the specific DNA barcodes within Sapindaceae. Phylogenetic results strongly support that the subdivision of four subfamilies within Sapindaceae, and Handeliodendron is not nested within the genus Aesculus.
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Affiliation(s)
- Jiaxin Yang
- Core Botanical Gardens/Wuhan Botanical Garden, 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.,College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Guoxiong Hu
- College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou, China.
| | - Guangwan Hu
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
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18
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Ogoma CA, Liu J, Stull GW, Wambulwa MC, Oyebanji O, Milne RI, Monro AK, Zhao Y, Li DZ, Wu ZY. Deep Insights Into the Plastome Evolution and Phylogenetic Relationships of the Tribe Urticeae (Family Urticaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:870949. [PMID: 35668809 PMCID: PMC9164014 DOI: 10.3389/fpls.2022.870949] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/15/2022] [Indexed: 05/09/2023]
Abstract
Urticeae s.l., a tribe of Urticaceae well-known for their stinging trichomes, consists of more than 10 genera and approximately 220 species. Relationships within this tribe remain poorly known due to the limited molecular and taxonomic sampling in previous studies, and chloroplast genome (CP genome/plastome) evolution is still largely unaddressed. To address these concerns, we used genome skimming data-CP genome and nuclear ribosomal DNA (18S-ITS1-5.8S-ITS2-26S); 106 accessions-for the very first time to attempt resolving the recalcitrant relationships and to explore chloroplast structural evolution across the group. Furthermore, we assembled a taxon rich two-locus dataset of trnL-F spacer and ITS sequences across 291 accessions to complement our genome skimming dataset. We found that Urticeae plastomes exhibit the tetrad structure typical of angiosperms, with sizes ranging from 145 to 161 kb and encoding a set of 110-112 unique genes. The studied plastomes have also undergone several structural variations, including inverted repeat (IR) expansions and contractions, inversion of the trnN-GUU gene, losses of the rps19 gene, and the rpl2 intron, and the proliferation of multiple repeat types; 11 hypervariable regions were also identified. Our phylogenomic analyses largely resolved major relationships across tribe Urticeae, supporting the monophyly of the tribe and most of its genera except for Laportea, Urera, and Urtica, which were recovered as polyphyletic with strong support. Our analyses also resolved with strong support several previously contentious branches: (1) Girardinia as a sister to the Dendrocnide-Discocnide-Laportea-Nanocnide-Zhengyia-Urtica-Hesperocnide clade and (2) Poikilospermum as sister to the recently transcribed Urera sensu stricto. Analyses of the taxon-rich, two-locus dataset showed lower support but was largely congruent with results from the CP genome and nuclear ribosomal DNA dataset. Collectively, our study highlights the power of genome skimming data to ameliorate phylogenetic resolution and provides new insights into phylogenetic relationships and chloroplast structural evolution in Urticeae.
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Affiliation(s)
- Catherine A. Ogoma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Gregory W. Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Moses C. Wambulwa
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Department of Life Sciences, School of Science and Computing, South Eastern Kenya University, Kitui, Kenya
| | - Oyetola Oyebanji
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Richard I. Milne
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Ying Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- *Correspondence: De-Zhu Li,
| | - Zeng-Yuan Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Zeng-Yuan Wu,
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Ping J, Hao J, Li J, Yang Y, Su Y, Wang T. Loss of the IR region in conifer plastomes: Changes in the selection pressure and substitution rate of protein-coding genes. Ecol Evol 2022; 12:e8499. [PMID: 35136556 PMCID: PMC8809450 DOI: 10.1002/ece3.8499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 12/08/2021] [Accepted: 12/14/2021] [Indexed: 11/10/2022] Open
Abstract
Plastid genomes (plastomes) have a quadripartite structure, but some species have drastically reduced or lost inverted repeat (IR) regions. IR regions are important for genome stability and the evolution rate. In the evolutionary process of gymnosperms, the typical IRs of conifers were lost, possibly affecting the evolutionary rate and selection pressure of genomic protein-coding genes. In this study, we selected 78 gymnosperm species (51 genera, 13 families) for evolutionary analysis. The selection pressure analysis results showed that negative selection effects were detected in all 50 common genes. Among them, six genes in conifers had higher ω values than non-conifers, and 12 genes had lower ω values. The evolutionary rate analysis results showed that 9 of 50 common genes differed between conifers and non-conifers. It is more obvious that in non-conifers, the rates of psbA (trst, trsv, ratio, dN, dS, and ω) were 2.6- to 3.1-fold of conifers. In conifers, trsv, ratio, dN, dS, and ω of ycf2 were 1.2- to 3.6-fold of non-conifers. In addition, the evolution rate of ycf2 in the IR was significantly reduced. psbA is undergoing dynamic change, with an abnormally high evolution rate as a small portion of it enters the IR region. Although conifers have lost the typical IR regions, we detected no change in the substitution rate or selection pressure of most protein-coding genes due to gene function, plant habitat, or newly acquired IRs.
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Affiliation(s)
- Jingyao Ping
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Jing Hao
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Jinye Li
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yiqing Yang
- College of Life Science and TechnologyCentral South University of Forestry and TechnologyChangshaChina
| | - Yingjuan Su
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
- Research Institute of Sun Yat‐sen UniversityShenzhenChina
| | - Ting Wang
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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Li X, Zhao Y, Tu X, Li C, Zhu Y, Zhong H, Liu ZJ, Wu S, Zhai J. Comparative analysis of plastomes in Oxalidaceae: Phylogenetic relationships and potential molecular markers. PLANT DIVERSITY 2021; 43:281-291. [PMID: 34485770 PMCID: PMC8390927 DOI: 10.1016/j.pld.2021.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 04/14/2021] [Accepted: 04/17/2021] [Indexed: 06/13/2023]
Abstract
The wood sorrel family, Oxalidaceae, is mainly composed of annual or perennial herbs, a few shrubs, and trees distributed from temperate to tropical zones. Members of Oxalidaceae are of high medicinal, ornamental, and economic value. Despite the rich diversity and value of Oxalidaceae, few molecular markers or plastomes are available for phylogenetic analysis of the family. Here, we reported four new whole plastomes of Oxalidaceae and compared them with plastomes of three species in the family, as well as the plastome of Rourea microphylla in the closely related family Connaraceae. The eight plastomes ranged in length from 150,673 bp (Biophytum sensitivum) to 156,609 bp (R. microphylla). Genome annotations revealed a total of 129-131 genes, including 83-84 protein-coding genes, eight rRNA genes, 37 tRNA genes, and two to three pseudogenes. Comparative analyses showed that the plastomes of these species have minor variations at the gene level. The smaller plastomes of herbs B. sensitivum and three Oxalis species are associated with variations in IR region sizes, intergenic region variation, and gene or intron loss. We identified sequences with high variation that may serve as molecular markers in taxonomic studies of Oxalidaceae. The phylogenetic trees of selected superrosid representatives based on 76 protein-coding genes corroborated the Oxalidaceae position in Oxalidales and supported it as a sister to Connaraceae. Our research also supported the monophyly of the COM (Celastrales, Oxalidales, and Malpighiales) clade.
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Affiliation(s)
- Xiaoping Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yamei Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiongde Tu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chengru Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yating Zhu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hui Zhong
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shasha Wu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Junwen Zhai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Xu D, Liu M, Ren H, Zhang B, Liu Z, Wang H. Chloroplast genome and phylogenetic analysis of Grewia biloba. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1775-1776. [PMID: 34104770 PMCID: PMC8168777 DOI: 10.1080/23802359.2021.1932626] [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: 11/23/2022]
Abstract
Grewia biloba is a potential medicinal and ornamental resource, and this study is the first to assemble the chloroplast genome of this species using high-throughput sequencing data. The chloroplast genome of G. biloba has a typical composition for higher plant chloroplasts, containing one large single-copy region of 86,978 bp and one small single-copy region of 20,140 bp, which are separated by a pair of inverted-repeat regions of 25,473 bp. The chloroplast genome of this species encodes 130 genes, including 84 protein-coding genes, 38 tRNA genes and 8 rRNA genes. A maximum-likelihood phylogenetic tree was constructed based on sequence information of the chloroplast genomes. The chloroplast genome of G. biloba will provide valuable genetic information for evolutionary research and utilization of this species.
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Affiliation(s)
- Dongya Xu
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Meng Liu
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Haozhan Ren
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Bin Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Zongcai Liu
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Hongwei Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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Zhang B, Wu R, Liu M, Cai X, Cheng Y. Chloroplast genome of Gaura parviflora Douglas and its comparative analysis. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:760-761. [PMID: 33763571 PMCID: PMC7954412 DOI: 10.1080/23802359.2021.1878960] [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: 11/30/2022]
Abstract
Gaura parviflora Douglas (Onagraceae) is an annual or perennial herbaceous plant from the prairie of North America. It has become a harmful exotic invading plant in China due to its strong adaptability, fast growth, massive propagation and reproduction. The complete chloroplast (cp) genome of G. parviflora was reported in this study. The size of the complete cp genome of G. parviflora is 161,318 bp in length, including a pair of inverted repeat (IR) regions of 27,402 bp, a large single-copy (LSC) region of 89,132 bp, and a small single-copy (SSC) region of 17,382 bp. A total of 130 genes were annotated, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Comparison of cp genomes of four species from Onagraceae indicated that Onagraceae cp genomes had high nucleotide diversity. In addition, a few highly variable regions of these cp genomes were also detected. The phylogenetic tree showed that G. parviflora is closely related to Oenothera. Thus, the chloroplast genome of G. parviflora can provide valuable genetic information for species identification and phylogenetic analysis.
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Affiliation(s)
- Bin Zhang
- College of plant protection, Henan Agricultural University, Zhengzhou, China
| | - Ruige Wu
- Nanyang Grain and Oil Quality Inspection Center, Nanyang, China
| | - Meng Liu
- College of plant protection, Henan Agricultural University, Zhengzhou, China
| | - Xiaoran Cai
- College of plant protection, Henan Agricultural University, Zhengzhou, China
| | - Yueqin Cheng
- College of plant protection, Henan Agricultural University, Zhengzhou, China
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