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Chen L, Song BN, Yang L, Wang Y, Wang YY, Aou X, He XJ, Zhou SD. Phylogeny, adaptive evolution, and taxonomy of Acronema (Apiaceae): evidence from plastid phylogenomics and morphological data. FRONTIERS IN PLANT SCIENCE 2024; 15:1425158. [PMID: 39220016 PMCID: PMC11362068 DOI: 10.3389/fpls.2024.1425158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 07/24/2024] [Indexed: 09/04/2024]
Abstract
Introduction The genus Acronema, belonging to Apiaceae, includes approximately 25 species distributed in the high-altitude Sino-Himalayan region from E Nepal to SW China. This genus is a taxonomically complex genus with often indistinct species boundaries and problematic generic delimitation with Sinocarum and other close genera, largely due to the varied morphological characteristics. Methods To explore the phylogenetic relationships and clarify the limits of the genus Acronema and its related genera, we reconstructed a reliable phylogenetic framework with high support and resolution based on two molecular datasets (plastome data and ITS sequences) and performed morphological analyses. Results Both phylogenetic analyses robustly supported that Acronema was a non-monophyletic group that fell into two clades: Acronema Clade and East-Asia Clade. We also newly sequenced and assembled sixteen Acronema complete plastomes and performed comprehensively comparative analyses for this genus. The comparative results showed that the plastome structure, gene number, GC content, codon bias patterns were high similarity, but varied in borders of SC/IR and we identified six different types of SC/IR border. The SC/IR boundaries of Acronema chienii were significantly different from the other Acronema members which was consistent with the type VI pattern in the genus Tongoloa. We also identified twelve potential DNA barcode regions (ccsA, matK, ndhF, ndhG, psaI, psbI, rpl32, rps15, ycf1, ycf3, psaI-ycf4 and psbM-trnD) for species identification in Acronema. The molecular evolution of Acronema was relatively conservative that only one gene (petG) was found to be under positive selection (ω = 1.02489). Discussion The gene petG is one of the genes involved in the transmission of photosynthetic electron chains during photosynthesis, which plays a crucial role in the process of photosynthesis in plants. This is also a manifestation of the adaptive evolution of plants in high-altitude areas to the environment. In conclusion, our study provides novel insights into the plastome adaptive evolution, phylogeny, and taxonomy of genus Acronema.
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Affiliation(s)
| | | | | | | | | | | | | | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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Kang JS, Yu JG, Xiang QP, Zhang XC. The Possible Earliest Allopolyploidization in Tracheophytes Revealed by Phylotranscriptomics and Morphology of Selaginellaceae. Mol Biol Evol 2024; 41:msae153. [PMID: 39101470 PMCID: PMC11299036 DOI: 10.1093/molbev/msae153] [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: 09/26/2023] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 08/06/2024] Open
Abstract
Selaginellaceae, originated in the Carboniferous and survived the Permian-Triassic mass extinction, is the largest family of lycophyte, which is sister to other tracheophytes. It stands out from tracheophytes by exhibiting extraordinary habitat diversity and lacking polyploidization. The organelle genome-based phylogenies confirmed the monophyly of Selaginella, with six or seven subgenera grouped into two superclades, but the phylogenetic positions of the enigmatic Selaginella sanguinolenta clade remained problematic. Here, we conducted a phylogenomic study on Selaginellaceae utilizing large-scale nuclear gene data from RNA-seq to elucidate the phylogeny and explore the causes of the phylogenetic incongruence of the S. sanguinolenta clade. Our phylogenetic analyses resolved three different positions of the S. sanguinolenta clade, which were supported by the sorted three nuclear gene sets, respectively. The results from the gene flow test, species network inference, and plastome-based phylogeny congruently suggested a probable hybrid origin of the S. sanguinolenta clade involving each common ancestor of the two superclades in Selaginellaceae. The hybrid hypothesis is corroborated by the evidence from rhizophore morphology and spore micromorphology. The chromosome observation and Ks distributions further suggested hybridization accompanied by polyploidization. Divergence time estimation based on independent datasets from nuclear gene sets and plastid genome data congruently inferred that allopolyploidization occurred in the Early Triassic. To our best knowledge, the allopolyploidization in the Mesozoic reported here represents the earliest record of tracheophytes. Our study revealed a unique triad of phylogenetic positions for a hybrid-originated group with comprehensive evidence and proposed a hypothesis for retaining both parental alleles through gene conversion.
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Affiliation(s)
- Jong-Soo Kang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ji-Gao Yu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- China National Botanical Garden, Beijing 100093, China
| | - Qiao-Ping Xiang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xian-Chun Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
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Fu PC, Guo QQ, Chang D, Gao QB, Sun SS. Cryptic diversity and rampant hybridization in annual gentians on the Qinghai-Tibet Plateau revealed by population genomic analysis. PLANT DIVERSITY 2024; 46:194-205. [PMID: 38807911 PMCID: PMC11128845 DOI: 10.1016/j.pld.2023.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 05/30/2024]
Abstract
Understanding the evolutionary and ecological processes involved in population differentiation and speciation provides critical insights into biodiversity formation. In this study, we employed 29,865 single nucleotide polymorphisms (SNPs) and complete plastomes to examine genomic divergence and hybridization in Gentiana aristata, which is endemic to the Qinghai-Tibet Plateau (QTP) region. Genetic clustering revealed that G. aristata is characterized by geographic genetic structures with five clusters (West, East, Central, South and North). The West cluster has a specific morphological character (i.e., blue corolla) and higher values of FST compared to the remaining clusters, likely the result of the geological barrier formed by the Yangtze River. The West cluster diverged from the other clusters in the Early Pliocene; these remaining clusters diverged from one another in the Early Quaternary. Phylogenetic reconstructions based on SNPs and plastid data revealed substantial cyto-nuclear conflicts. Genetic clustering and D-statistics demonstrated rampant hybridization between the Central and North clusters, along the Bayankala Mountains, which form the geological barrier between the Central and North clusters. Species distribution modeling demonstrated the range of G. aristata expanded since the Last Interglacial period. Our findings provide genetic and morphological evidence of cryptic diversity in G. aristata, and identified rampant hybridization between genetic clusters along a geological barrier. These findings suggest that geological barriers and climatic fluctuations have an important role in triggering diversification as well as hybridization, indicating that cryptic diversity and hybridization are essential factors in biodiversity formation within the QTP region.
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Affiliation(s)
- Peng-Cheng Fu
- School of Life Science, Luoyang Normal University, Luoyang 471934, PR China
| | - Qiao-Qiao Guo
- School of Life Science, Luoyang Normal University, Luoyang 471934, PR China
| | - Di Chang
- School of Life Science, Luoyang Normal University, Luoyang 471934, PR China
| | - Qing-Bo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, PR China
| | - Shan-Shan Sun
- School of Life Science, Luoyang Normal University, Luoyang 471934, PR China
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Zhang G, Ma H. Nuclear phylogenomics of angiosperms and insights into their relationships and evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:546-578. [PMID: 38289011 DOI: 10.1111/jipb.13609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/06/2024]
Abstract
Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the "abominable mystery," hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.
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Affiliation(s)
- Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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Fu PC, Twyford AD, Hao YT, Zhang Y, Chen SL, Sun SS. Hybridization and divergent climatic preferences drive divergence of two allopatric Gentiana species on the Qinghai-Tibet Plateau. ANNALS OF BOTANY 2023; 132:1271-1288. [PMID: 37963010 PMCID: PMC10902892 DOI: 10.1093/aob/mcad179] [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: 06/21/2023] [Revised: 10/19/2023] [Accepted: 11/13/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND AND AIMS Exploring how species diverge is vital for understanding the drivers of speciation. Factors such as geographical separation and ecological selection, hybridization, polyploidization and shifts in mating system are all major mechanisms of plant speciation, but their contributions to divergence are rarely well understood. Here we test these mechanisms in two plant species, Gentiana lhassica and G. hoae, with the goal of understanding recent allopatric species divergence on the Qinghai-Tibet Plateau (QTP). METHODS We performed Bayesian clustering, phylogenetic analysis and estimates of hybridization using 561 302 nuclear genomic single nucleotide polymorphisms (SNPs). We performed redundancy analysis, and identified and annotated species-specific SNPs (ssSNPs) to explore the association between climatic preference and genetic divergence. We also estimated genome sizes using flow cytometry to test for overlooked polyploidy. KEY RESULTS Genomic evidence confirms that G. lhassica and G. hoae are closely related but distinct species, while genome size estimates show divergence occurred without polyploidy. Gentiana hoae has significantly higher average FIS values than G. lhassica. Population clustering based on genomic SNPs shows no signature of recent hybridization, but each species is characterized by a distinct history of hybridization with congeners that has shaped genome-wide variation. Gentiana lhassica has captured the chloroplast and experienced introgression with a divergent gentian species, while G. hoae has experienced recurrent hybridization with related taxa. Species distribution modelling suggested range overlap in the Last Interglacial Period, while redundancy analysis showed that precipitation and temperature are the major climatic differences explaining the separation of the species. The species differ by 2993 ssSNPs, with genome annotation showing missense variants in genes involved in stress resistance. CONCLUSIONS This study suggests that the distinctiveness of these species on the QTP is driven by a combination of hybridization, geographical isolation, mating system differences and evolution of divergent climatic preferences.
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Affiliation(s)
- Peng-Cheng Fu
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, Luoyang 471934, P. R. China
| | - Alex D Twyford
- Institute of Ecology and Evolution, The University of Edinburgh, Edinburgh, EH9 3FL, UK
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Yu-Tong Hao
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, Luoyang 471934, P. R. China
| | - Yue Zhang
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, Luoyang 471934, P. R. China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810001 Xining, P. R. China
| | - Shan-Shan Sun
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, Luoyang 471934, P. R. China
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Hou Y, Zhang Y, Yu J, Wang X. Characteristics of the complete chloroplast genome of Swertia divaricata Harry Sm. (Gentianaceae) and its phylogenetic inference. Mitochondrial DNA B Resour 2023; 8:1132-1136. [PMID: 37928401 PMCID: PMC10621253 DOI: 10.1080/23802359.2023.2270211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 10/07/2023] [Indexed: 11/07/2023] Open
Abstract
Swertia divaricata Harry Sm., 1965, (Gentianaceae) is a perennial herb endemic to Northwest Yunnan, China, belonging to the species-rich genus Swertia. It possesses unique morphological features but its systematic position remains uncertain. To determine its phylogenetic placement, the complete plastid genome of S. divaricata was assembled utilizing high-throughput sequencing data. The genome is circular, spanning 152,073 bp, and comprises a large single-copy (LSC) region of 82,470 bp, a small single-copy (SSC) region of 18,153 bp, and two inverted repeats (IR) regions, each 25,725 bp. A total of 130 genes were annotated, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The plastome of S. divaricata exhibits a structure and gene composition highly similar to those of other Swertia plastomes. Phylogenetic analysis indicated that S. divaricata is closely related to S. erythrosticta, sister to a subclade comprising species from sections Swertia and Apterae. The plastome sequence described herein constitutes a valuable contribution to phylogenetic and evolutionary research on Swertia.
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Affiliation(s)
- Yingying Hou
- Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Integrated Traditional Chinese and Western Medicine, The Academy of Medical Sciences of Zhengzhou University, Zhengzhou, China
| | - Yulong Zhang
- Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Integrated Traditional Chinese and Western Medicine, The Academy of Medical Sciences of Zhengzhou University, Zhengzhou, China
| | - Jing Yu
- Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinjie Wang
- Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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