1
|
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.
Collapse
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
| |
Collapse
|
2
|
Contreras-Díaz R, Carevic FS, van den Brink L, Huanca-Mamani W, Jung P. Structure, gene composition, divergence time and phylogeny analysis of the woody desert species Neltuma alba, Neltuma chilensis and Strombocarpa strombulifera. Sci Rep 2024; 14:13604. [PMID: 38871769 DOI: 10.1038/s41598-024-64287-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 06/06/2024] [Indexed: 06/15/2024] Open
Abstract
Neltuma alba (Algarrobo blanco), Neltuma chilensis (Algarrobo Chileno) and Strombocarpa strombulifera (Fortuna) are some of the few drought resistant trees and shrubs found in small highly fragmented populations, throughout the Atacama Desert. We reconstructed their plastid genomes using de novo assembly of paired-end reads from total genomic DNA. We found that the complete plastid genomes of N. alba and N. chilensis are larger in size compared to species of the Strombocarpa genus. The Strombocarpa species presented slightly more GC content than the Neltuma species. Therefore, we assume that Strombocarpa species have been exposed to stronger natural selection than Neltuma species. We observed high variation values in the number of cpSSRs (chloroplast simple sequence repeats) and repeated elements among Neltuma and Strombocarpa species. The p-distance results showed a low evolutionary divergence within the genus Neltuma, whereas a high evolutionary divergence was observed between Strombocarpa species. The molecular divergence time found in Neltuma and Strombocarpa show that these genera diverged in the late Oligocene. With this study we provide valuable information about tree species that provide important ecosystem services in hostile environments which can be used to determine these species in the geographically isolated communities, and keep the highly fragmented populations genetically healthy.
Collapse
Affiliation(s)
- Roberto Contreras-Díaz
- Centro Regional de Investigación de Desarrollo Sustentable de Atacama (CRIDESAT), Universidad de Atacama, Copayapu 485, Copiapó, Chile.
- Núcleo Milenio de Ecología Histórica Aplicada Para los Bosques Áridos (AFOREST), Santiago, Chile.
| | - Felipe S Carevic
- Laboratorio de Ecología Vegetal, Facultad de Recursos Naturales Renovables, Universidad Arturo Prat, Campus Huayquique, Iquique, Chile
- Núcleo Milenio de Ecología Histórica Aplicada Para los Bosques Áridos (AFOREST), Santiago, Chile
| | - Liesbeth van den Brink
- ECOBIOSIS, Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Wilson Huanca-Mamani
- Laboratorio de Biología Molecular de Plantas, Facultad de Ciencias Agronómicas, Centro de Genética y Genómica UASARA, Universidad de Tarapacá, 1000000, Arica, Chile
| | - Patrick Jung
- Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Carl-Schurz-Str. 10-16, 66953, Pirmasens, Germany
| |
Collapse
|
3
|
Li QQ, Zhang ZP, Aogan, Wen J. Comparative chloroplast genomes of Argentina species: genome evolution and phylogenomic implications. FRONTIERS IN PLANT SCIENCE 2024; 15:1349358. [PMID: 38766467 PMCID: PMC11099909 DOI: 10.3389/fpls.2024.1349358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/25/2024] [Indexed: 05/22/2024]
Abstract
The genus Argentina Hill belongs to the tribe Potentilleae Sweet and contains approximately 75 species predominantly distributed in the Sino-Himalayan region and the Malesian archipelago. So far we have less knowledge on the phylogenetic relationships within Argentina owing to limited sampling of Argentina taxa or gene fragments in previous studies. Moreover, to date there is no phylogenetic study on Argentina from the perspective of comparative chloroplast (cp) genomics. Here we performed comparative genomic analyses on the cp genomes of 39 accessions representing 18 taxa of Argentina. The Argentina cp genomes presented the typical quadripartite structure, with the sizes ranging from 155 096 bp to 157 166 bp. The 39 Argentina cp genomes contained a set of 112 unique genes, comprising four ribosomal RNA (rRNA) genes, 30 transfer RNA (tRNA) genes, as well as 78 protein-coding genes (PCGs). The cp genome organization, gene content and order in Argentina were highly conserved, but some visible divergences were present in IR/SC boundary regions. Ten regions (trnH-GUG-psbA, trnG-GCC-trnfM-CAU, trnD-GUC-trnY-GUA, rpl32-trnL-UAG, atpH-atpI, rps16-trnQ-UUG, trnS-GCU-trnG-UCC, ndhF-rpl32, trnR-UCU-atpA, and accD-psaI) were identified as excellent candidate DNA markers for future studies on species identification, population genetics and phylogeny of Argentina. Our results indicated that Argentina is monophyletic. In the current sampling, the A. smithiana - A. anserina clade was sister to the remainder of Argentina. Our results corroborated the previous taxonomic treatments to transfer A. phanerophlebia and A. micropetala from the genus Sibbaldia L. to Argentina. Our results showed close relationships among A. stenophylla, A. microphylla, A. taliensis, and A. tatsienluensis, congruent with previous studies based on the morphology of these species. Twenty-six genes (rps3, rps15, rps16, rps19, rpl16, rpl20, rpl22, rpoA, rpoB, rpoC1, rpoC2, atpA, atpF, psbB, psbF, ndhA, ndhB, ndhC, ndhD, ndhF, rbcL, accD, ccsA, matK, ycf1, ycf2) were with sites under positive selection, and adaptive evolution of these genes might have played crucial roles in Argentina species adaptation to the harsh mountain environment. This study will facilitate future work on taxonomy, phylogenetics, and adaptive evolution of Argentina.
Collapse
Affiliation(s)
- Qin-Qin Li
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot, China
- Key Laboratory of Biodiversity Conservation and Sustainable Utilization in Mongolian Plateau for College and University of Inner Mongolia Autonomous Region, Hohhot, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Zhi-Ping Zhang
- College of Computer Science and Technology, Inner Mongolia Normal University, Hohhot, China
| | - Aogan
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| |
Collapse
|
4
|
He S, Xu B, Chen S, Li G, Zhang J, Xu J, Wu H, Li X, Yang Z. Sequence characteristics, genetic diversity and phylogenetic analysis of the Cucurbita ficifolia (Cucurbitaceae) chloroplasts genome. BMC Genomics 2024; 25:384. [PMID: 38637729 PMCID: PMC11027378 DOI: 10.1186/s12864-024-10278-2] [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: 11/28/2023] [Accepted: 04/02/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Curcubita ficifolia Bouché (Cucurbitaceae) has high value as a food crop and medicinal plant, and also has horticultural value as rootstock for other melon species. China is home to many different cultivars, but the genetic diversity of these resources and the evolutionary relationships among them, as well as the differences between C. ficifolia and other Cucurbita species, remain unclear. RESULTS We investigated the chloroplast (cp) genomes of 160 C. ficifolia individuals from 31 populations in Yunnan, a major C. ficifolia production area in China. We found that the cp genome of C. ficifolia is ~151 kb and contains 128 genes, of which 86 are protein coding genes, 34 encode tRNA, and eight encode rRNAs. We also identified 64 SSRs, mainly AT repeats. The cp genome was found to contain a total of 204 SNP and 57 indels, and a total of 21 haplotypes were found in the 160 study individuals. The reverse repeat (IR) region of C. ficifolia contained a few differences compared with this region in the six other Cucurbita species. Sequence difference analysis demonstrated that most of the variable regions were concentrated in the single copy (SC) region. Moreover, the sequences of the coding regions were found to be more similar among species than those of the non-coding regions. The phylogenies reconstructed from the cp genomes of 61 representative species of Cucurbitaceae reflected the currently accepted classification, in which C. ficifolia is sister to the other Cucurbita species, however, different interspecific relationships were found between Cucurbita species. CONCLUSIONS These results will be valuable in the classification of C. ficifolia genetic resources and will contribute to our understanding of evolutionary relationships within the genus Cucurbita.
Collapse
Affiliation(s)
- Shuilian He
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Bin Xu
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Siyun Chen
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
| | - Gengyun Li
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Jie Zhang
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Junqiang Xu
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Hang Wu
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Xuejiao Li
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China.
| | - Zhengan Yang
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China.
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China.
| |
Collapse
|
5
|
Shang M, Wang J, Dai G, Zheng J, Liao B, Wang J, Duan B. Comparative analysis of chloroplast genome and new insights into phylogenetic relationships of Ajuga and common adulterants. FRONTIERS IN PLANT SCIENCE 2023; 14:1251829. [PMID: 37954994 PMCID: PMC10634298 DOI: 10.3389/fpls.2023.1251829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023]
Abstract
Introduction The potential contamination of herbal medicinal products poses a significant concern for consumer health. Given the limited availability of genetic information concerning Ajuga species, it becomes imperative to incorporate supplementary molecular markers to enhance and ensure accurate species identification. Methods In this study, the chloroplast (cp) genomes of seven species of the genus Ajuag were sequenced, de novo assembled and characterized. Results exhibiting lengths ranging from 150,342 bp to 150,472 bp, encompassing 86 - 88 protein-coding genes (PCGs), 35 - 37 transfer RNA, and eight ribosomal RNA. The repetitive sequences, codon uses, and cp genomes of seven species were highly conserved, and PCGs were the reliable molecular markers for investigating the phylogenetic relationship within the Ajuga genus. Moreover, four mutation hotspot regions (accD-psaI, atpH-atpI, ndhC-trnV(UAC), and ndhF-rpl23) were identified within cp genomes of Ajuga, which could help distinguish A. bracteosa and its contaminants. Based on cp genomes and PCGs, the phylogenetic tree preliminary confirmed the position of Ajuga within the Lamiaceae family. It strongly supported a sister relationship between Subsect. Genevense and Subsect. Biflorae, suggesting the merger of Subsect. Biflorae and Subsect. Genevenses into one group rather than maintaining separate categorizations. Additionally, molecular clock analysis estimated the divergence time of Ajuga to be around 7.78 million years ago. Discussion The species authentication, phylogeny, and evolution analyses of the Ajuga species may benefit from the above findings.
Collapse
Affiliation(s)
- Mingyue Shang
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jiale Wang
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Guona Dai
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jiamei Zheng
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Binbin Liao
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jing Wang
- College of Pharmaceutical Science, Dali University, Dali, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, China
| |
Collapse
|
6
|
Wang T, Tang C, Chen J, Cao Z, He H, Li Y, Li X. Phylogenetic relationship and characterization of the complete chloroplast genome of Rhododendron przewalskii subsp. przewalskii Maximowicz 1877, an ornamental and medicinal plant in China. Mitochondrial DNA B Resour 2023; 8:998-1002. [PMID: 37746034 PMCID: PMC10512896 DOI: 10.1080/23802359.2023.2259040] [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: 06/02/2023] [Accepted: 09/09/2023] [Indexed: 09/26/2023] Open
Abstract
As one of the top 10 famous flowers in Chinese tradition, Rhododendron przewalskii subsp. przewalskii known as 'beauty in flowers,' which has high ornamental and medicinal value. The complete chloroplast (cp) genome of R. przewalskii subsp. przewalskii was determined in this study. The complete chloroplast genome of R. przewalskii subsp. przewalskii was 201,233 bp in length and contained a large single-copy region (LSC, 108,077 bp), and a small single-copy region (SSC, 2624 bp) and a pair of inverted repeat regions (IRa and IRb, 45,266 bp). A total of 142 functional genes were observed in this cp genome, including 91 protein-coding genes (PCGs), 43 transfer RNA genes (tRNAs), and eight ribosomal RNA genes (rRNAs). The R. przewalskii subsp. przewalskii cp genome has an A + T content of 64.06% and presents a positive AT-skew (0.53%) and a negative GC-skew (-1.56%). The maximum likelihood phylogenetic analysis based on the concatenated nucleotide sequences of 13 PCGs strongly supported the monophyletic relationship of R. przewalskii subsp. przewalskii the clade of R. henanense subsp. lingbaoense. This study provides genomic evidence for the vegetation classification of Rhododendron.
Collapse
Affiliation(s)
- Tao Wang
- Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining, China
| | - Chuyu Tang
- Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining, China
| | - Jianbo Chen
- Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining, China
| | - Zhengfei Cao
- Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining, China
| | - Hui He
- Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining, China
| | - Yuling Li
- Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining, China
| | - Xiuzhang Li
- Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining, China
| |
Collapse
|
7
|
Hu HS, Mao JY, Wang X, Liang YZ, Jiang B, Zhang DQ. Plastid phylogenomics and species discrimination in the "Chinese" clade of Roscoea (Zingiberaceae). PLANT DIVERSITY 2023; 45:523-534. [PMID: 37936815 PMCID: PMC10625918 DOI: 10.1016/j.pld.2023.03.012] [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] [Received: 11/21/2022] [Revised: 03/15/2023] [Accepted: 03/30/2023] [Indexed: 11/09/2023]
Abstract
Roscoea is an alpine or subalpine genus from the pan-tropical family Zingiberaceae, which consists of two disjunct groups in geography, namely the "Chinese" clade and the "Himalayan" clade. Despite extensive research on the genus, Roscoea species remain poorly defined and relationships between these species are not well resolved. In this study, we used plastid genomes of nine species and one variety to resolve phylogenetic relationships within the "Chinese" clade of Roscoea and as DNA super barcodes for species discrimination. We found that Roscoea plastid genomes ranged in length from 163,063 to 163,796 bp, and encoded 113 genes, including 79 protein-coding genes, 30 tRNA genes, four rRNA genes. In addition, expansion and contraction of the IR regions showed obvious infraspecific conservatism and interspecific differentiation. Plastid phylogenomics revealed that species belonging to the "Chinese" clade of Roscoea can be divided into four distinct subclades. Furthermore, our analysis supported the independence of R. cautleoides var. pubescens, the recovery of Roscoea pubescens Z.Y. Zhu, and a close relationship between R. humeana and R. cautloides. When we used the plastid genome as a super barcode, we found that it possessed strong discriminatory power (90%) with high support values. Intergenic regions provided similar resolution, which was much better than that of protein-coding regions, hypervariable regions, and DNA universal barcodes. However, plastid genomes could not completely resolve Roscoea phylogeny or definitively discriminate species. These limitations are likely related to the complex history of Roscoea speciation, poorly defined species within the genus, and the maternal inheritance of plastid genomes.
Collapse
Affiliation(s)
- Hai-Su Hu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China
- College of Pharmacy, Dali University, Dali 671000, Yunnan, China
| | - Jiu-Yang Mao
- College of Pharmacy, Dali University, Dali 671000, Yunnan, China
| | - Xue Wang
- College of Pharmacy, Dali University, Dali 671000, Yunnan, China
| | - Yu-Ze Liang
- College of Pharmacy, Dali University, Dali 671000, Yunnan, China
| | - Bei Jiang
- College of Pharmacy, Dali University, Dali 671000, Yunnan, China
- Yunnan Key Laboratory of Screening and Research on Anti-pathogenic Plant Resources from Western Yunnan (Cultivation), Dali 671000, Yunnan, China
| | - De-Quan Zhang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China
- College of Pharmacy, Dali University, Dali 671000, Yunnan, China
- Yunnan Key Laboratory of Screening and Research on Anti-pathogenic Plant Resources from Western Yunnan (Cultivation), Dali 671000, Yunnan, China
| |
Collapse
|
8
|
Su N, Hodel RG, Wang X, Wang JR, Xie SY, Gui CX, Zhang L, Chang ZY, Zhao L, Potter D, Wen J. Molecular phylogeny and inflorescence evolution of Prunus (Rosaceae) based on RAD-seq and genome skimming analyses. PLANT DIVERSITY 2023; 45:397-408. [PMID: 37601549 PMCID: PMC10435964 DOI: 10.1016/j.pld.2023.03.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 08/22/2023]
Abstract
Prunus is an economically important genus widely distributed in the temperate Northern Hemisphere. Previous studies on the genus using a variety of loci yielded conflicting phylogenetic hypotheses. Here, we generated nuclear reduced representation sequencing data and plastid genomes for 36 Prunus individuals and two outgroups. Both nuclear and plastome data recovered a well-resolved phylogeny. The species were divided into three main clades corresponding to their inflorescence types, - the racemose group, the solitary-flower group and the corymbose group - with the latter two sister to one another. Prunus was inferred to have diversified initially in the Late Cretaceous around 67.32 million years ago. The diversification of the three major clades began between the Paleocene and Miocene, suggesting that paleoclimatic events were an important driving force for Prunus diversification. Ancestral state reconstructions revealed that the most recent common ancestor of Prunus had racemose inflorescences, and the solitary-flower and corymb inflorescence types were derived by reduction of flower number and suppression of the rachis, respectively. We also tested the hybrid origin hypothesis of the racemose group proposed in previous studies. Prunus has undergone extensive hybridization events, although it is difficult to identify conclusively specific instances of hybridization when using SNP data, especially deep in the phylogeny. Our study provides well-resolved nuclear and plastid phylogenies of Prunus, reveals substantial cytonuclear discord at shallow scales, and sheds new light on inflorescence evolution in this economically important lineage.
Collapse
Affiliation(s)
- Na Su
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Richard G.J. Hodel
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Xi Wang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Jun-Ru Wang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Si-Yu Xie
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Chao-Xia Gui
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Ling Zhang
- College of Life Sciences, Tarim University, Alaer 843300, China
| | - Zhao-Yang Chang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Liang Zhao
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Daniel Potter
- Department of Plant Sciences, MS2, University of California, Davis, CA 95616, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA
| |
Collapse
|
9
|
Shi W, Hu S, Song W, Huang Y, Shi C, Wang S. Uncovering the first complete chloroplast genomics, comparative analysis, and phylogenetic relationships of the medicinal plants Rhamnus cathartica and Frangula alnus ( Rhamnaceae). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:855-869. [PMID: 37520808 PMCID: PMC10382440 DOI: 10.1007/s12298-023-01331-7] [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: 04/02/2023] [Revised: 06/04/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023]
Abstract
Rhamnus cathartica and Frangula alnus are economically valuable medicinal plants from the Rhamnaceae family. However, their chloroplast genome structure, phylogenetic position, relationships, and evolution remain poorly understood. Herein, the complete chloroplast genome resources of R. cathartica and F. alnus have been added. The first comparative analysis of the Rhamnus and Frangula species based on complete chloroplast genomes was provided. The chloroplast genomes of R. cathartica and F. alnus exhibited a quadripartite structure, with total lengths of 161,149 bp and 161,255 bp, respectively. The lack of the infA and psbL genes does not negatively impact the normal functioning of Rhamnus and Frangula species. The rpl20 and rpl33 genes are undergoing rapid evolution. Rhamnus and Frangula species prefer amino acids with A/U-terminal codons. There were between 100 and 126 simple sequence repeats and between 38 and 100 long repeats. Several highly divergent intergenic regions (trnK-UUU-trnQ-UUG, atpH-atpI, trnY-GUA-trnE-UUC, trnG-GCC-trnfM-CAU, trnT-UGU-trnF-GAA, rpl20-rps12, and rpl22-rps19) and highly divergent genes (ycf3, ndhA, rpl32, and ycf1) were identified, which could serve as potential phylogenetic markers due to their variability. We reconstructed the phylogenetic relationships among Rhamnus species and F. alnus using complete chloroplast genomes. There is no significant correlation between the medicinal value of the species analyzed and their phylogenetic relationships. These results provide valuable insights for understanding the phylogenetic relationship and evolution of Rhamnus and Frangula species. These findings could serve as a foundation for future studies on the Rhamnaceae. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01331-7.
Collapse
Affiliation(s)
- Wenbo Shi
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Siqi Hu
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Weicai Song
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Yahui Huang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Chao Shi
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650204 China
| | - Shuo Wang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| |
Collapse
|
10
|
Song S, Cameron KM, Wang Y, Wang S, Jin X, Hina F, Yang Z, Li P. Phylogenomics and phylogeography of Menispermum (Menispermaceae). FRONTIERS IN PLANT SCIENCE 2023; 14:1116300. [PMID: 36909420 PMCID: PMC9992823 DOI: 10.3389/fpls.2023.1116300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Phylogenomics have been widely used to resolve ambiguous and controversial evolutionary relationships among plant species and genera, and the identification of unique indels in plastomes may even help to understand the evolution of some plant families. Menispermum L. (Menispermaceae) consists of three species, M. dauricum DC., M. canadense L., and M. mexicanum Rose, which are disjuncly distributed among East Asia, Eastern North America and Mexico. Taxonomists continue to debate whether M. mexicanum is a distinct species, a variety of M. dauricum, or simply a synonym of M. canadense. To date, no molecular systematics studies have included this doubtful species in phylogenetic analyses. METHODS In this study, we examined phylogenomics and phylogeography of Menispermum across its entire range using 29 whole plastomes of Menispermaceae and 18 ITS1&ITS2 sequences of Menispermeae. We reconstructed interspecific relationships of Menispermum and explored plastome evolution in Menispermaceae, revealing several genomic hotspot regions for the family. RESULTS AND DISCUSSION Phylogenetic and network analyses based on whole plastome and ITS1&ITS2 sequences show that Menispermum clusters into two clades with high support values, Clade A (M. dauricum) and Clade B (M. canadense + M. mexicanum). However, M. mexicanum is nested within M. canadense and, as a result, we support that M. mexicanum is a synonym of M. canadense. We also identified important molecular variations in the plastomes of Menispermaceae. Several indels and consequently premature terminations of genes occur in Menispermaceae. A total of 54 regions were identified as the most highly variable plastome regions, with nucleotide diversity (Pi) values > 0.05, including two coding genes (matK, ycf1), four introns (trnK intron, rpl16 intron, rps16 intron, ndhA intron), and 48 intergenic spacer (IGS) regions. Of these, four informative hotspot regions (trnH-psbA, ndhF-rpl32, trnK-rps16, and trnP-psaJ) should be especially useful for future studies of phylogeny, phylogeography and conservation genetics of Menispermaceae.
Collapse
Affiliation(s)
- Shiqiang Song
- College of Life Sciences and Technologies, Tarim University, Alar, China
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Kenneth M. Cameron
- Department of Botany, University of Wisconsin, Madison, WI, United States
| | - Yuguo Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Shenyi Wang
- Department of Botany, University of Wisconsin, Madison, WI, United States
| | - Xinjie Jin
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Faiza Hina
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhaoping Yang
- College of Life Sciences and Technologies, Tarim University, Alar, China
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| |
Collapse
|
11
|
Qiu H, Zhang ZH, Wang MZ, Jin XJ, Lin JD, Comes HP, Chen JX, Cui RN, Duan RQ, Li P. Plastome evolution and phylogenomics of Impatiens (Balsaminaceae). PLANTA 2023; 257:45. [PMID: 36695892 DOI: 10.1007/s00425-023-04078-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
This study reported seven new plastomes from Impatiens and observed three highly variable regions for phylogeny and DNA barcoding, which resolved the relationships among sections of subgenus Impatiens. Impatiens L. (Balsaminaceae, Ericales) is one of the largest and most diverse genera of angiosperms, widely known for its taxonomic difficulty. In this study, we reevaluated the infrageneric relationships within the genus Impatiens, using complete plastome sequence data. Seven complete plastomes of Impatiens (representing 6 species) were newly sequenced and characterized along with 20 previously published plastomes of other Impatiens species, plus 2 plastomes of outgroups (Hydrocera triflora, Balsaminaceae; Marcgravia coriacea, Marcgraviaceae). The total size of these 29 plastomes ranged from 151,538 bp to 152,917 bp, except 2 samples of Impatiens morsei, which exhibited a shorter length and lost some genes encoding NADH dehydrogenase subunits. Moreover, the number of simple sequence repeats (SSRs) ranged from 51 to 113, and the number of long repeats from 17 to 26. In addition, three highly variable regions were identified (trnG-GCC (The previous one), ndhF-rpl32-trnL-UGA-ccsA, and ycf1). Our phylogenomic analysis based on 80 plastome-derived protein-coding genes strongly supported the monophyly of Impatiens and its two subgenera (Clavicarpa and Impatiens), and fully resolved relationships among the six (out of seven) sampled sections of subgenus Impatiens. Overall, the plastome DNA markers and phylogenetic results reported in this study will facilitate future identification, taxonomic and DNA barcoding studies in Impatiens as well as evolutionary studies in Balsaminaceae.
Collapse
Affiliation(s)
- He Qiu
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhi-Hui Zhang
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Mei-Zhen Wang
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xin-Jie Jin
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Jie-Dong Lin
- Zhangzhou Huaqiao Middle School, Zhangzhou, 363030, China
| | - Hans Peter Comes
- Department of Environment and Biodiversity, Salzburg University, 5020, Salzburg, Austria
| | - Jing-Xuan Chen
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Rui-Ning Cui
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ru-Qing Duan
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Pan Li
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| |
Collapse
|
12
|
Qin HH, Cai J, Liu CK, Zhou RX, Price M, Zhou SD, He XJ. The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution. BMC PLANT BIOLOGY 2023; 23:9. [PMID: 36604614 PMCID: PMC9814190 DOI: 10.1186/s12870-022-04027-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The Ferula genus encompasses 180-185 species and is one of the largest genera in Apiaceae, with many of Ferula species possessing important medical value. The previous studies provided more information for Ferula, but its infrageneric relationships are still confusing. In addition, its genetic basis of its adaptive evolution remains poorly understood. Plastid genomes with more variable sites have the potential to reconstruct robust phylogeny in plants and investigate the adaptive evolution of plants. Although chloroplast genomes have been reported within the Ferula genus, few studies have been conducted using chloroplast genomes, especially for endemic species in China. RESULTS Comprehensively comparative analyses of 22 newly sequenced and assembled plastomes indicated that these plastomes had highly conserved genome structure, gene number, codon usage, and repeats type and distribution, but varied in plastomes size, GC content, and the SC/IR boundaries. Thirteen mutation hotspot regions were detected and they would serve as the promising DNA barcodes candidates for species identification in Ferula and related genera. Phylogenomic analyses with high supports and resolutions showed that Talassia transiliensis and Soranthus meyeri were nested in the Ferula genus, and thus they should be transferred into the Ferula genus. Our phylogenies also indicated the monophyly of subgenera Sinoferula and subgenera Narthex in Ferula genus. Twelve genes with significant posterior probabilities for codon sites were identified in the positively selective analysis, and their function may relate to the photosystem II, ATP subunit, and NADH dehydrogenase. Most of them might play an important role to help Ferula species adapt to high-temperatures, strong-light, and drought habitats. CONCLUSION Plastome data is powerful and efficient to improve the support and resolution of the complicated Ferula phylogeny. Twelve genes with significant posterior probabilities for codon sites were helpful for Ferula to adapt to the harsh environment. Overall, our study supplies a new perspective for comprehending the phylogeny and evolution of Ferula.
Collapse
Affiliation(s)
- Huan-Huan Qin
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jing Cai
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Chang-Kun Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Ren-Xiu Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Megan Price
- Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| |
Collapse
|
13
|
Li H, Guo Q, Xu L, Gao H, Liu L, Zhou X. CPJSdraw: analysis and visualization of junction sites of chloroplast genomes. PeerJ 2023; 11:e15326. [PMID: 37193025 PMCID: PMC10182761 DOI: 10.7717/peerj.15326] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/10/2023] [Indexed: 05/18/2023] Open
Abstract
Background Chloroplast genomes are usually circular molecules, and most of them are tetrad structures with two inverted repeat (IR) regions, a large single-copy region, and a small single-copy region. IR contraction and expansion are among the genetic diversities during the evolution of plant chloroplast genomes. The only previously released tool for the visualization of junction sites of the regions does not consider the diversity of the starting point of genomes, which leads to incorrect results or even no results for the examination of IR contraction and expansion. Results In this work, a new tool named CPJSdraw was developed for visualizing the junction sites of chloroplast genomes. CPJSdraw can format the starting point of the irregular linearized genome, correct the junction sites of IR and single-copy regions, display the tetrad structure, visualize the junction sites of any number (≥1) of chloroplast genomes, show the transcription direction of genes adjacent to junction sites, and indicate the IR expansion or contraction of chloroplast genomes. Conclusions CPJSdraw is a software that is universal and reliable in analysis and visualization of IR expansion or contraction of chloroplast genomes. CPJSdraw has more accurate analysis and more complete functions when compared with previously released tool. CPJSdraw as a perl package and tested data are available at http://dx.doi.org/10.5281/zenodo.7669480 for English users. In addition, an online version with a Chinese interface is available at http://cloud.genepioneer.com:9929/#/tool/alltool/detail/335.
Collapse
Affiliation(s)
- Huie Li
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Qiqiang Guo
- Institute for Forest Resources & Environment of Guizhou, Guizhou University, Guiyang, Guizhou, China
| | - Lei Xu
- Nanjing Genepioneer Biotechnologies Co., Ltd, Nanjing, Jiangsu, China
| | - Haidong Gao
- Nanjing Genepioneer Biotechnologies Co., Ltd, Nanjing, Jiangsu, China
| | - Lei Liu
- Nanjing Genepioneer Biotechnologies Co., Ltd, Nanjing, Jiangsu, China
| | - Xiangyang Zhou
- Nanjing Genepioneer Biotechnologies Co., Ltd, Nanjing, Jiangsu, China
| |
Collapse
|
14
|
Yan K, Ran J, Bao S, Li Y, Islam R, Zhang N, Zhao W, Ma Y, Sun C. The Complete Chloroplast Genome Sequence of Eupatorium fortunei: Genome Organization and Comparison with Related Species. Genes (Basel) 2022; 14:64. [PMID: 36672805 PMCID: PMC9859021 DOI: 10.3390/genes14010064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/17/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
Eupatorium fortunei Turcz, a perennial herb of the Asteraceae family, is one of the horticultural and medicinal plants used for curing various diseases and is widely distributed in China and other Asian countries. It possesses antibacterial, antimetastatic, antiangiogenic, and antioxidant properties along with anticancer potential. However, the intrageneric classification and phylogenetic relationships within Eupatorium have long been controversial due to the lack of high-resolution molecular markers, and the complete chloroplast (cp) genome sequencing has not been reported with new evolutionary insights. In the present study, E. fortunei was used as an experimental material, and its genome was sequenced using high-throughput sequencing technology. We assembled the complete cp genome, and a systematic analysis was conducted for E. fortunei, acquiring the correspondence of its NCBI accession number (OK545755). The results showed that the cp genome of E. fortunei is a typical tetrad structure with a total length of 152,401 bp, and the genome encodes 133 genes. Analysis of the complete cp genomes of 20 Eupatorieae shows that the number of simple sequence repeats (SSRs) ranged from 19 to 36 while the number of long sequence repeats was 50 in all cases. Eleven highly divergent regions were identified and are potentially useful for the DNA barcoding of Eupatorieae. Phylogenetic analysis among 22 species based on protein-coding genes strongly supported that E. fortunei is more closely related to Praxelis clematidea and belongs to the same branch. The genome assembly and analysis of the cp genome of E. fortunei will facilitate the identification, taxonomy, and utilization of E. fortunei as well as provide more accurate evidence for the taxonomic identification and localization of Asteraceae plants.
Collapse
Affiliation(s)
- Kan Yan
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730030, China
| | - Juan Ran
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730030, China
| | - Songming Bao
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730030, China
| | - Yimeng Li
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Rehmat Islam
- Key Laboratory of Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | - Nai Zhang
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730030, China
| | - Wei Zhao
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Yanni Ma
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730030, China
| | - Chao Sun
- College of Agronomy, Gansu Agricultural University, Lanzhou 730101, China
| |
Collapse
|
15
|
Xu K, Lin C, Lee SY, Mao L, Meng K. Comparative analysis of complete Ilex (Aquifoliaceae) chloroplast genomes: insights into evolutionary dynamics and phylogenetic relationships. BMC Genomics 2022; 23:203. [PMID: 35287585 PMCID: PMC8922745 DOI: 10.1186/s12864-022-08397-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 02/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ilex (Aquifoliaceae) are of great horticultural importance throughout the world for their foliage and decorative berries, yet a dearth of genetic information has hampered our understanding of phylogenetic relationships and evolutionary history. Here, we compare chloroplast genomes from across Ilex and estimate phylogenetic relationships. RESULTS We sequenced the chloroplast genomes of seven Ilex species and compared them with 34 previously published Ilex plastomes. The length of the seven newly sequenced Ilex chloroplast genomes ranged from 157,182 bp to 158,009 bp, and contained a total of 118 genes, including 83 protein-coding, 31 rRNA, and four tRNA genes. GC content ranged from 37.6 to 37.69%. Comparative analysis showed shared genomic structures and gene rearrangements. Expansion and contraction of the inverted repeat regions at the LSC/IRa and IRa/SSC junctions were observed in 22 and 26 taxa, respectively; in contrast, the IRb boundary was largely invariant. A total of 2146 simple sequence repeats and 2843 large repeats were detected in the 41 Ilex plastomes. Additionally, six genes (psaC, rbcL, trnQ, trnR, trnT, and ycf1) and two intergenic spacer regions (ndhC-trnV and petN-psbM) were identified as hypervariable, and thus potentially useful for future phylogenetic studies and DNA barcoding. We recovered consistent phylogenetic relationships regardless of inference methodology or choice of loci. We recovered five distinct, major clades, which were inconsistent with traditional taxonomic systems. CONCLUSION Our findings challenge traditional circumscriptions of the genus Ilex and provide new insights into the evolutionary history of this important clade. Furthermore, we detail hypervariable and repetitive regions that will be useful for future phylogenetic and population genetic studies.
Collapse
Affiliation(s)
- Kewang Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 510275, China
| | - Chenxue Lin
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 510275, China
| | - Shiou Yih Lee
- Faculty of Health and Life Sciences, INTI International University, 71800, Nilai, Malaysia
| | - Lingfeng Mao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 510275, China.
| | - Kaikai Meng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
| |
Collapse
|