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Guo L, Zhai J, Gu Y. The complete chloroplast genome sequence of Isoetes baodongii (Isoetaceae). Mitochondrial DNA B Resour 2024; 9:667-671. [PMID: 38774187 PMCID: PMC11107852 DOI: 10.1080/23802359.2024.2356128] [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: 01/08/2024] [Accepted: 05/11/2024] [Indexed: 05/24/2024] Open
Abstract
Isoetes baodongii is a diploid species of Isoetaceae distributed in low altitude area, its megaspore ornamentation is similar to tetraploid species I. sinensis. We collected leaf material of I. baodongii and sequenced it for low depth whole genome sequence, then, a complete chloroplast genome of I. baodongii was assembled and annotated. This chloroplast genome has a circular structure of 145,494 bp in length with a GC content of 38.0%, comprising a large single copy (LSC) region of 91,860 bp, a pair of inverted repeat (IR) regions of 13,207 bp each, and a small single copy (SSC) region of 27,220 bp. 136 genes were annotated, including 84 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. A maximum likelihood phylogeny tree was reconstructed after the sequences alignment, the result showed that I. baodongii formed a sister clade to the one clustered by I. sinensis, I. taiwanensis and I. orientalis. Although the chloroplast genome structure of I. baodongii is extremely similar to other species distributed in China, a well-supported phylogenetic relationship was reconstructed here, these results may provide new messages for further studies on phylogeny and evolution of vascular plant on the earth.
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Affiliation(s)
- Lin Guo
- Ecology and Nature Conservation Institue, Chinese Academy of Forestry, Beijing, China
| | - Junwen Zhai
- Fujian Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yufeng Gu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, the National Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
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Sun W, Wei Z, Gu Y, Wang T, Liu B, Yan Y. Chloroplast genome structure analysis of Equisetum unveils phylogenetic relationships to ferns and mutational hotspot region. FRONTIERS IN PLANT SCIENCE 2024; 15:1328080. [PMID: 38665369 PMCID: PMC11044155 DOI: 10.3389/fpls.2024.1328080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/02/2024] [Indexed: 04/28/2024]
Abstract
Equisetum is one of the oldest extant group vascular plants and is considered to be the key to understanding vascular plant evolution. Equisetum is distributed almost all over the world and has a high degree of adaptability to different environments. Despite the fossil record of horsetails (Equisetum, Equisetaceae) dating back to the Carboniferous, the phylogenetic relationship of this genus is not well, and the chloroplast evolution in Equisetum remains poorly understood. In order to fill this gap, we sequenced, assembled, and annotated the chloroplast genomes of 12 species of Equisetum, and compared them to 13 previously published vascular plants chloroplast genomes to deeply examine the plastome evolutionary dynamics of Equisetum. The chloroplast genomes have a highly conserved quadripartite structure across the genus, but these chloroplast genomes have a lower GC content than other ferns. The size of Equisetum plastomes ranges from 130,773 bp to 133,684 bp and they encode 130 genes. Contraction/expansion of IR regions and the number of simple sequences repeat regions underlie large genomic variations in size among them. Comparative analysis revealed we also identified 13 divergence hotspot regions. Additionally, the genes accD and ycf1 can be used as potential DNA barcodes for the identification and phylogeny of the genus Equisetum. Twelve photosynthesis-related genes were specifically selected in Equisetum. Comparative genomic analyses implied divergent evolutionary patterns between Equisetum and other ferns. Phylogenomic analyses and molecular dating revealed a relatively distant phylogenetic relationship between Equisetum and other ferns, supporting the division of pteridophyte into Lycophytes, Equisetaceae and ferns. The results show that the chloroplast genome can be used to solve phylogenetic problems within or between Equisetum species, and also provide genomic resources for the study of Equisetum systematics and evolution.
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Affiliation(s)
- Weiyue Sun
- Key Laboratory of Plant Biology, College of Heilongjiang Province, Harbin Normal University, Harbin, China
- Key Laboratory of National Forestry and Grassland Administration for Orehid Conservation and Utilization, the Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
| | - Zuoying Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Guangzhou, China
| | - Yuefeng Gu
- Key Laboratory of National Forestry and Grassland Administration for Orehid Conservation and Utilization, the Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
| | - Ting Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Guangzhou, China
| | - Baodong Liu
- Key Laboratory of Plant Biology, College of Heilongjiang Province, Harbin Normal University, Harbin, China
- Key Laboratory of National Forestry and Grassland Administration for Orehid Conservation and Utilization, the Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
| | - Yuehong Yan
- Key Laboratory of National Forestry and Grassland Administration for Orehid Conservation and Utilization, the Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
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Hwang Y, Lee YK, Son Y, Lee H. The complete chloroplast genome of an Arctic lycophyte, Huperzia arctica (Tolm.) Sipliv. 1973 (Lycopodiaceae). Mitochondrial DNA B Resour 2023; 8:1391-1395. [PMID: 38130736 PMCID: PMC10732209 DOI: 10.1080/23802359.2023.2292144] [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: 05/04/2023] [Accepted: 12/02/2023] [Indexed: 12/23/2023] Open
Abstract
Huperzia arctica (Tolm.) Sipliv. 1973 is a lycophyte species belonging to the Lycopodiaceae family, which is widely distributed in the Arctic region of Svalbard, Norway. To determine its taxonomic position, we sequenced the chloroplast genome of H. arctica. The complete chloroplast genome of H. arctica is 153,956 bp in length with 122 annotated genes, including 87 protein-coding genes, 31 tRNA genes, and 4 rRNA genes. To evaluate its evolutionary position, we performed phylogenetic analysis using 36 conserved orthologous protein-coding gene sequences from the chloroplast genomes of H. arctica and publicly available data from other Lycopodiaceae. H. arctica formed a monophyletic group with four other Huperzia species: H. lucidula, H. serrata, H. crispata, and H. javanica. However, it appeared as a separate species with a highly supported bootstrap value.
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Affiliation(s)
- Youngsim Hwang
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Yoo Kyung Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
- Polar Science, University of Science and Technology, Incheon, Republic of Korea
| | - Yowhan Son
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Hyoungseok Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
- Polar Science, University of Science and Technology, Incheon, Republic of Korea
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Glass SE, McCourt RM, Gottschalk SD, Lewis LA, Karol KG. Chloroplast genome evolution and phylogeny of the early-diverging charophycean green algae with a focus on the Klebsormidiophyceae and Streptofilum. JOURNAL OF PHYCOLOGY 2023; 59:1133-1146. [PMID: 37548118 DOI: 10.1111/jpy.13359] [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: 02/01/2023] [Revised: 05/10/2023] [Accepted: 05/23/2023] [Indexed: 08/08/2023]
Abstract
The Klebsormidiophyceae are a class of green microalgae observed globally in both freshwater and terrestrial habitats. Morphology-based classification schemes of this class have been shown to be inadequate due to the simple morphology of these algae, the tendency of morphology to vary in culture versus field conditions, and rampant morphological homoplasy. Molecular studies revealing cryptic diversity have renewed interest in this group. We sequenced the complete chloroplast genomes of a broad series of taxa spanning the known taxonomic breadth of this class. We also sequenced the chloroplast genomes of three strains of Streptofilum, a recently discovered green algal lineage with close affinity to the Klebsormidiophyceae. Our results affirm the previously hypothesized polyphyly of the genus Klebsormidium as well as the polyphyly of the nominal species in this genus, K. flaccidum. Furthermore, plastome sequences strongly support the status of Streptofilum as a distinct, early-diverging lineage of charophytic algae sister to a clade comprising Klebsormidiophyceae plus Phragmoplastophyta. We also uncovered major structural alterations in the chloroplast genomes of species in Klebsormidium that have broad implications regarding the underlying mechanisms of chloroplast genome evolution.
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Affiliation(s)
- Sarah E Glass
- Lewis B. and Dorothy Cullman Program for Molecular Systematics, The New York Botanical Garden, Bronx, New York, USA
- Department of Biological Sciences, Lehman College, The City University of New York, New York, New York, USA
| | - Richard M McCourt
- Academy of Natural Sciences of Drexel University, Philadelphia, Pennsylvania, USA
| | - Stephen D Gottschalk
- Lewis B. and Dorothy Cullman Program for Molecular Systematics, The New York Botanical Garden, Bronx, New York, USA
- Department of Biological Sciences, Fordham University, Bronx, New York, USA
| | - Louise A Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Kenneth G Karol
- Lewis B. and Dorothy Cullman Program for Molecular Systematics, The New York Botanical Garden, Bronx, New York, USA
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Gu YF, Shu JP, Lu YJ, Shen H, Shao W, Zhou Y, Sun QM, Chen JB, Liu BD, Yan YH. Insights into cryptic speciation of quillworts in China. PLANT DIVERSITY 2023; 45:284-301. [PMID: 37397601 PMCID: PMC10311115 DOI: 10.1016/j.pld.2022.11.003] [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: 06/27/2022] [Revised: 10/24/2022] [Accepted: 11/08/2022] [Indexed: 07/04/2023]
Abstract
Cryptic species are commonly misidentified because of high morphological similarities to other species. One group of plants that may harbor large numbers of cryptic species is the quillworts (Isoëtes spp.), an ancient aquatic plant lineage. Although over 350 species of Isoëtes have been reported globally, only ten species have been recorded in China. The aim of this study is to better understand Isoëtes species diversity in China. For this purpose, we systematically explored the phylogeny and evolution of Isoëtes using complete chloroplast genome (plastome) data, spore morphology, chromosome number, genetic structure, and haplotypes of almost all Chinese Isoëtes populations. We identified three ploidy levels of Isoëtes in China-diploid (2n = 22), tetraploid (2n = 44), and hexaploid (2n = 66). We also found four megaspore and microspore ornamentation types in diploids, six in tetraploids, and three in hexaploids. Phylogenetic analyses confirmed that I. hypsophila as the ancestral group of the genus and revealed that Isoëtes diploids, tetraploids, and hexaploids do not form monophyletic clades. Most individual species possess a single genetic structure; however, several samples have conflicting positions on the phylogenetic tree based on SNPs and the tree based on plastome data. All 36 samples shared 22 haplotypes. Divergence time analysis showed that I. hypsophila diverged in the early Eocene (∼48.05 Ma), and most other Isoëtes species diverged 3-20 Ma. Additionally, different species of Isoëtes were found to inhabit different water systems and environments along the Yangtze River. These findings provide new insights into the relationships among Isoëtes species in China, where highly similar morphologic populations may harbor many cryptic species.
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Affiliation(s)
- Yu-Feng Gu
- Life Science and Technology College, Harbin Normal University, Key Laboratory of Plant Biology in Colleges of Heilongjiang Province, Harbin, 150025, China
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, and Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Jiang-Ping Shu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, and Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Yi-Jun Lu
- Zhejiang University City College, Hangzhou, 310015, China
| | - Hui Shen
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Wen Shao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yan Zhou
- Jiande Xin'anjiang Forest Farm, Jiande, 311600, China
| | - Qi-Meng Sun
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Jian-Bing Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, and Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Bao-Dong Liu
- Life Science and Technology College, Harbin Normal University, Key Laboratory of Plant Biology in Colleges of Heilongjiang Province, Harbin, 150025, China
| | - Yue-Hong Yan
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, and Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
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Wikström N, Larsén E, Khodabandeh A, Rydin C. No phylogenomic support for a Cenozoic origin of the "living fossil" Isoetes. AMERICAN JOURNAL OF BOTANY 2023; 110:e16108. [PMID: 36401556 PMCID: PMC10108322 DOI: 10.1002/ajb2.16108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 11/11/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
PREMISE The isoetalean lineage has a rich fossil record that extends to the Devonian, but the age of the living clade is unclear. Recent results indicate that it is young, from the Cenozoic, whereas earlier work based on less data from a denser taxon sampling yielded Mesozoic median ages. METHODS We analyzed node ages in Isoetes using two genomic data sets (plastome and nuclear ribosomal cistron), three clock models implemented in MrBayes (ILN, WN, and TK02 models), and a conservative approach to calibration. RESULTS While topological results were consistently resolved in Isoetes estimated crown group ages range from the latest Paleozoic (mid-Permian) to the Mesozoic depending on data type and clock model. The oldest estimates were retrieved using the autocorrelated TK02 clock model. An (early) Cenozoic age was only obtained under one specific condition (plastome data analyzed with the uncorrelated ILN clock model). That same plastome data set also yielded the oldest (mid-Permian) age estimate when analyzed with the autocorrelated TK02 clock model. Adding the highly divergent, recently established sister species Isoetes wormaldii to the data set approximately doubled the average median node depth to the Isoetes crown group. CONCLUSIONS There is no consistent support for a Cenozoic origin of the living clade Isoetes. We obtained seemingly well-founded, yet strongly deviating results depending on data type and clock model. The single most important future improvement is probably to add calibration points, which requires an improved understanding of the isoetalean fossil record or alternative bases for calibration.
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Affiliation(s)
- Niklas Wikström
- Bergius Foundation, The Royal Swedish Academy of Sciences Box 50005SE‐104 05StockholmSweden
- Department of Ecology, Environment, and Plant SciencesStockholm UniversitySE‐106 91StockholmSweden
| | - Eva Larsén
- Department of Ecology, Environment, and Plant SciencesStockholm UniversitySE‐106 91StockholmSweden
| | - Anbar Khodabandeh
- Bergius Foundation, The Royal Swedish Academy of Sciences Box 50005SE‐104 05StockholmSweden
- Department of Ecology, Environment, and Plant SciencesStockholm UniversitySE‐106 91StockholmSweden
| | - Catarina Rydin
- Bergius Foundation, The Royal Swedish Academy of Sciences Box 50005SE‐104 05StockholmSweden
- Department of Ecology, Environment, and Plant SciencesStockholm UniversitySE‐106 91StockholmSweden
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Wang Y, Xie Y, Jin J, Li J, Qiu X, Tong Y, Li Z, Zhang Z, Lai W. Comparison of the chloroplast genomes and phylogenomic analysis of Elaeocarpaceae. PeerJ 2023; 11:e15322. [PMID: 37187516 PMCID: PMC10178313 DOI: 10.7717/peerj.15322] [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: 10/13/2022] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Background Elaeocarpaceae is a vital family in tropical and subtropical forests. Compared with the important position of Elaeocarpaceae species in forest ecosystem and the concern of medicinal value, the most research on Elaeocarpaceae are classification and taxonomy. Molecular systematics has corrected the morphological misjudgment, and it belongs to Oxalidales. Phylogenetic and divergence time estimates of Elaeocarpaceae is mostly constructed by using chloroplast gene fragments. At present, although there are reports on the chloroplast structure of Elaeocarpaceae, a comprehensive analysis of the chloroplast structure of Elaeocarpaceae is lacking. Methods To understand the variation in chloroplast sequence size and structure in Elaeocarpaceae, the chloroplast genomes of nine species were sequenced using the Illumina HiSeq 2500 platform and further assembled and annotated with Elaeocarpus japonicus and Sloanea sinensis (family Elaeocarpaceae) as references. A phylogenomic tree was constructed based on the complete chloroplast genomes of the 11 species representing five genera of Elaeocarpaceae. Chloroplast genome characteristics were examined by using Circoletto and IRscope software. Results The results revealed the following: (a) The 11 sequenced chloroplast genomes ranged in size from 157,546 to 159,400 bp. (b) The chloroplast genomes of Elaeocarpus, Sloanea, Crinodendron and Vallea lacked the rpl32 gene in the small single-copy (SSC) region. The large single-copy (LSC) region of the chloroplast genomes lacked the ndhK gene in Elaeocarpus, Vallea stipularis, and Aristotelia fruticosa. The LSC region of the chloroplast genomes lacked the infA gene in genus Elaeocarpus and Crinodendron patagua. (c) Through inverted repeat (IR) expansion and contraction analysis, a significant difference was found between the LSC/IRB and IRA/LSC boundaries among these species. Rps3 was detected in the neighboring regions of the LSC and IRb regions in Elaeocarpus. (d) Phylogenomic analysis revealed that the genus Elaeocarpus is closely related to Crinodendron patagua on an independent branch and Aristotelia fruticosa is closely related to Vallea stipularis, forming a clade with the genus Sloanea. Structural comparisons showed that Elaeocarpaceae diverged at 60 Mya, the genus Elaeocarpus diverged 53 Mya and that the genus Sloanea diverged 0.44 Mya. These results provide new insight into the evolution of the Elaeocarpaceae.
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Affiliation(s)
- Yihui Wang
- School of Life Sciences, Gannan Normal University, Ganzhou, P.R. China
- School of Landscape Architecture, Beijing Forestry University, Beijing, P.R. China
| | - Yifei Xie
- School of Life Sciences, Gannan Normal University, Ganzhou, P.R. China
- Key Laboratory of Nanling Plant Resources Conservation and Utilization, Ganzhou, P.R. China
| | - Jiayi Jin
- School of Life Sciences, Gannan Normal University, Ganzhou, P.R. China
| | - Jinyue Li
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Xishuangbanna, P.R. China
| | - Xiangdong Qiu
- School of Life Sciences, Gannan Normal University, Ganzhou, P.R. China
| | - Yang Tong
- School of Life Sciences, Gannan Normal University, Ganzhou, P.R. China
| | - Zhongyang Li
- School of Life Sciences, Gannan Normal University, Ganzhou, P.R. China
- Key Laboratory of Nanling Plant Resources Conservation and Utilization, Ganzhou, P.R. China
| | - Zhixiang Zhang
- School of Ecology and Nature conservation, Beijing Forestry University, Beijing, P.R. China
| | - Wenling Lai
- School of Life Sciences, Gannan Normal University, Ganzhou, P.R. China
- Key Laboratory of Nanling Plant Resources Conservation and Utilization, Ganzhou, P.R. China
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Fouracre JP, Harrison CJ. How was apical growth regulated in the ancestral land plant? Insights from the development of non-seed plants. PLANT PHYSIOLOGY 2022; 190:100-112. [PMID: 35771646 PMCID: PMC9434304 DOI: 10.1093/plphys/kiac313] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Land plant life cycles are separated into distinct haploid gametophyte and diploid sporophyte stages. Indeterminate apical growth evolved independently in bryophyte (moss, liverwort, and hornwort) and fern gametophytes, and tracheophyte (vascular plant) sporophytes. The extent to which apical growth in tracheophytes co-opted conserved gametophytic gene networks, or exploited ancestral sporophytic networks, is a long-standing question in plant evolution. The recent phylogenetic confirmation of bryophytes and tracheophytes as sister groups has led to a reassessment of the nature of the ancestral land plant. Here, we review developmental genetic studies of apical regulators and speculate on their likely evolutionary history.
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Affiliation(s)
| | - C Jill Harrison
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
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Du XY, Kuo LY, Zuo ZY, Li DZ, Lu JM. Structural Variation of Plastomes Provides Key Insight Into the Deep Phylogeny of Ferns. FRONTIERS IN PLANT SCIENCE 2022; 13:862772. [PMID: 35645990 PMCID: PMC9134734 DOI: 10.3389/fpls.2022.862772] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/04/2022] [Indexed: 06/02/2023]
Abstract
Structural variation of plastid genomes (plastomes), particularly large inversions and gene losses, can provide key evidence for the deep phylogeny of plants. In this study, we investigated the structural variation of fern plastomes in a phylogenetic context. A total of 127 plastomes representing all 50 recognized families and 11 orders of ferns were sampled, making it the most comprehensive plastomic analysis of fern lineages to date. The samples included 42 novel plastomes of 15 families with a focus on Hymenophyllales and Gleicheniales. We reconstructed a well-supported phylogeny of all extant fern families, detected significant structural synapomorphies, including 9 large inversions, 7 invert repeat region (IR) boundary shifts, 10 protein-coding gene losses, 7 tRNA gene losses or anticodon changes, and 19 codon indels (insertions or deletions) across the deep phylogeny of ferns, particularly on the backbone nodes. The newly identified inversion V5, together with the newly inferred expansion of the IR boundary R5, can be identified as a synapomorphy of a clade composed of Dipteridaceae, Matoniaceae, Schizaeales, and the core leptosporangiates, while a unique inversion V4, together with an expansion of the IR boundary R4, was verified as a synapomorphy of Gleicheniaceae. This structural evidence is in support of our phylogenetic inference, thus providing key insight into the paraphyly of Gleicheniales. The inversions of V5 and V7 together filled the crucial gap regarding how the "reversed" gene orientation in the IR region characterized by most extant ferns (Schizaeales and the core leptosporangiates) evolved from the inferred ancestral type as retained in Equisetales and Osmundales. The tRNA genes trnR-ACG and trnM-CAU were assumed to be relicts of the early-divergent fern lineages but intact in most Polypodiales, particularly in eupolypods; and the loss of the tRNA genes trnR-CCG, trnV-UAC, and trnR-UCU in fern plastomes was much more prevalent than previously thought. We also identified several codon indels in protein-coding genes within the core leptosporangiates, which may be identified as synapomorphies of specific families or higher ranks. This study provides an empirical case of integrating structural and sequence information of plastomes to resolve deep phylogeny of plants.
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Affiliation(s)
- Xin-Yu Du
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Li-Yaung Kuo
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Zheng-Yu Zuo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jin-Mei Lu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
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Plastid Genome of Equisetum xylochaetum from the Atacama Desert, Chile and the Relationships of Equisetum Based on Frequently Used Plastid Genes and Network Analysis. PLANTS 2022; 11:plants11071001. [PMID: 35406981 PMCID: PMC9002811 DOI: 10.3390/plants11071001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/02/2022] [Accepted: 04/04/2022] [Indexed: 11/22/2022]
Abstract
The modern pteridophyte genus Equisetum is the only survivor of Sphenopsida, an ancient clade known from the Devonian. This genus, of nearly worldwide distribution, comprises approximately 15 extant species. However, genomic information is limited. In this study, we assembled the complete chloroplast genome of the giant species Equisetum xylochaetum from a metagenomic sequence and compared the plastid genome structure and protein-coding regions with information available for two other Equisetum species using network analysis. Equisetum chloroplast genomes showed conserved traits of quadripartite structure, gene content, and gene order. Phylogenetic analysis based on plastome protein-coding regions corroborated previous reports that Equisetum is monophyletic, and that E. xylochaetum is more closely related to E. hyemale than to E. arvense. Single-gene phylogenetic estimation and haplotype analysis showed that E. xylochaetum belonged to the subgenus Hippochaete. Single-gene haplotype analysis revealed that E. arvense, E. hyemale, E. myriochaetum, and E. variegatum resolved more than one haplotype per species, suggesting the presence of a high diversity or a high mutation rate of the corresponding nucleotide sequence. Sequences from E. bogotense appeared as a distinct group of haplotypes representing the subgenus Paramochaete that diverged from Hippochaete and Equisetum. In addition, the taxa that were frequently located at the joint region of the map were E. scirpoides and E. pratense, suggesting the presence of some plastome characters among the Equiseum subgenera.
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Hao J, Xu X, Zhang L. Seasonal Dynamics of Photochemical Performance of PS II of Terrestrial Mosses from Different Elevations. PLANTS 2021; 10:plants10122613. [PMID: 34961084 PMCID: PMC8705637 DOI: 10.3390/plants10122613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022]
Abstract
Mosses are critical components of tropical forest ecosystems and have multiple essential ecological functions. The drying and rehydrating and often hot environments in tropical regions present some of the greatest challenges for their photosynthetic activities. There is limited knowledge available on the physiological responses to the changing environments such as temperature and water pattern changes for terrestrial mosses. We examined the seasonal dynamics of photochemical performance of PS II through the measuring of chlorophyll fluorescence of 12 terrestrial mosses in situ from five different elevations by Photosynthesis Yield Analyzer MINI-PAM-II, along with the seasonal changes of climatic factors (air temperature, dew point, relative humidity and rainfall), which were collected by local weather stations and self-deployed mini weather stations. The results showed a great seasonality during observing periods, which, mainly the changes of rainfall and relative humidity pattern, presented significant impacts on the photochemical performance of PS II of terrestrial mosses. All these tested moss species developed a suitable regulated and non-regulated strategy to avoid the detrimental effect of abiotic stresses. We found that only Hypnum plumaeforme, Pterobryopsis crassicaulis and Pogonatum inflexum were well adapted to the changes of habitat temperature and water patterns, even though they still experienced a lower CO2 assimilation efficiency in the drier months. The other nine species were susceptible to seasonality, especially during the months of lower rainfall and relative humidity when moss species were under physiologically reduced PS II efficiency. Anomobryum julaceum, Pogonatum neesii, Sematophyllum subhumile, Pseudotaxiphyllum pohliaecarpum and Leucobryum boninense, and especially Brachythecium buchananii, were sensitive to the changes of water patterns, which enable them as ideal ecological indicators of photosynthetic acclimation to stressed environments as a result of climate change.
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Affiliation(s)
- Jiewei Hao
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Correspondence: (J.H.); (L.Z.); Tel.: +86-199-8987-9261 (J.H.); +86-189-0768-2999 (L.Z.)
| | - Xueyan Xu
- Center for Eco-Environmental Restoration Engineering of Hainan Province, Hainan University, 58 Renmin Road, Haikou 570228, China;
- Center for Terrestrial Biodiversity of the South China Sea, Hainan University, 58 Renmin Road, Haikou 570228, China
| | - Lina Zhang
- Center for Eco-Environmental Restoration Engineering of Hainan Province, Hainan University, 58 Renmin Road, Haikou 570228, China;
- Center for Terrestrial Biodiversity of the South China Sea, Hainan University, 58 Renmin Road, Haikou 570228, China
- Correspondence: (J.H.); (L.Z.); Tel.: +86-199-8987-9261 (J.H.); +86-189-0768-2999 (L.Z.)
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12
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Sadamitsu A, Inoue Y, Sakakibara K, Tsubota H, Yamaguchi T, Deguchi H, Nishiyama T, Shimamura M. The complete plastid genome sequence of the enigmatic moss, Takakia lepidozioides (Takakiopsida, Bryophyta): evolutionary perspectives on the largest collection of genes in mosses and the intensive RNA editing. PLANT MOLECULAR BIOLOGY 2021; 107:431-449. [PMID: 34817767 DOI: 10.1007/s11103-021-01214-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
Complete chloroplast genome sequence of a moss, Takakia lepidozioides (Takakiopsida) is reported. The largest collection of genes in mosses and the intensive RNA editing were discussed from evolutionary perspectives. We assembled the entire plastid genome sequence of Takakia lepidozioides (Takakiopsida), emerging from the first phylogenetic split among extant mosses. The genome sequences were assembled into a circular molecule 149,016 bp in length, with a quadripartite structure comprising a large and a small single-copy region separated by inverted repeats. It contained 88 genes coding for proteins, 32 for tRNA, four for rRNA, two open reading frames, and at least one pseudogene (tufA). This is the largest number of genes of all sequenced plastid genomes in mosses and Takakia is the only moss that retains the seven coding genes ccsA, cysA, cysT, petN rpoA, rps16 and trnPGGG. Parsimonious interpretation of gene loss suggests that the last common ancestor of bryophytes had all seven genes and that mosses lost at least three of them during their diversification. Analyses of the plastid transcriptome identified the extraordinary frequency of RNA editing with more than 1100 sites. We indicated a close correlation between the monoplastidy of vegetative tissue and the intensive RNA editing sites in the plastid genome in land plant lineages. Here, we proposed a hypothesis that the small population size of plastids in each vegetative cell of some early diverging land plants, including Takakia, might cause the frequent fixation of mutations in plastid genome through the intracellular genetic drift and that deleterious mutations might be continuously compensated by RNA editing during or following transcription.
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Affiliation(s)
- Atsushi Sadamitsu
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-hiroshima, Hiroshima, 739-8526, Japan
| | - Yuya Inoue
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan
- Hattori Botanical Laboratory, 6-1-26 Obi, Nichinan, Miyazaki, 889-2535, Japan
| | - Keiko Sakakibara
- Department of Life Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan
| | - Hiromi Tsubota
- Miyajima Natural Botanical Garden, Graduate School of Integrated Sciences for Life, Hiroshima University, 1156-2, Mitsumaruko-yama, Miyajima-cho, Hatsukaichi, Hiroshima, 739-0543, Japan
| | - Tomio Yamaguchi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-hiroshima, Hiroshima, 739-8526, Japan
| | - Hironori Deguchi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-hiroshima, Hiroshima, 739-8526, Japan
| | - Tomoaki Nishiyama
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, 920-0934, Japan
| | - Masaki Shimamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-hiroshima, Hiroshima, 739-8526, Japan.
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13
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Suissa JS, Kinosian SP, Schafran PW, Bolin JF, Taylor WC, Zimmer EA. Homoploid hybrids, allopolyploids, and high ploidy levels characterize the evolutionary history of a western North American quillwort (Isoëtes) complex. Mol Phylogenet Evol 2021; 166:107332. [PMID: 34687842 DOI: 10.1016/j.ympev.2021.107332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 10/05/2021] [Accepted: 10/18/2021] [Indexed: 12/26/2022]
Abstract
Polyploidy and hybridization are important processes in seed-free plant evolution. However, a major gap lies in our understanding of how these processes affect the evolutionary history of high-ploidy systems. The heterosporous lycophyte genus Isoëtes is a lineage with many putative hybrids and high-level polyploid taxa (ranging from tetraploid to dodecaploid). Here, we use a complex of western North American Isoëtes, to understand the role of hybridization and high-level polyploidy in generating and maintaining novel diversity. To uncover these processes, we use restriction-site associated DNA sequencing (RADseq), multiple alleles of a single low-copy nuclear marker, whole plastomes, cytology (genome size estimates and chromosome counts), and reproductive status (fertile or sterile). With this dataset, we show that hybridization occurs easily between species in this complex and is bidirectional between identical, but not different, cytotypes. Furthermore, we show that fertile allopolyploids appear to have formed repeatedly from sterile homoploid and interploid hybrids. We propose that low prezygotic reproductive barriers and a high frequency of whole-genome duplication allow for high-level polyploid systems to generate novel lineages, and that these mechanisms may be important in shaping extant Isoëtes diversity.
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Affiliation(s)
- Jacob S Suissa
- The Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; The Arnold Arboretum of Harvard University, Boston, MA, USA; Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
| | - Sylvia P Kinosian
- Department of Biology & Ecology Center, Utah State University, Logan, UT, USA
| | - Peter W Schafran
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA; Boyce Thompson Institute, Ithaca, NY, USA
| | - Jay F Bolin
- Department of Biology, Catawba College, Salisbury, NC, USA
| | - W Carl Taylor
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Elizabeth A Zimmer
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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14
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Abstract
There can be no doubt that early land plant evolution transformed the planet but, until recently, how and when this was achieved was unclear. Coincidence in the first appearance of land plant fossils and formative shifts in atmospheric oxygen and CO2 are an artefact of the paucity of earlier terrestrial rocks. Disentangling the timing of land plant bodyplan assembly and its impact on global biogeochemical cycles has been precluded by uncertainty concerning the relationships of bryophytes to one another and to the tracheophytes, as well as the timescale over which these events unfolded. New genome and transcriptome sequencing projects, combined with the application of sophisticated phylogenomic modelling methods, have yielded increasing support for the Setaphyta clade of liverworts and mosses, within monophyletic bryophytes. We consider the evolution of anatomy, genes, genomes and of development within this phylogenetic context, concluding that many vascular plant (tracheophytes) novelties were already present in a comparatively complex last common ancestor of living land plants (embryophytes). Molecular clock analyses indicate that embryophytes emerged in a mid-Cambrian to early Ordovician interval, compatible with hypotheses on their role as geoengineers, precipitating early Palaeozoic glaciations.
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Affiliation(s)
- Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
| | - C Jill Harrison
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Jordi Paps
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Harald Schneider
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK; Center of Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, China
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15
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Su D, Yang L, Shi X, Ma X, Zhou X, Hedges SB, Zhong B. Large-Scale Phylogenomic Analyses Reveal the Monophyly of Bryophytes and Neoproterozoic Origin of Land Plants. Mol Biol Evol 2021; 38:3332-3344. [PMID: 33871608 PMCID: PMC8321542 DOI: 10.1093/molbev/msab106] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The relationships among the four major embryophyte lineages (mosses, liverworts, hornworts, vascular plants) and the timing of the origin of land plants are enigmatic problems in plant evolution. Here, we resolve the monophyly of bryophytes by improving taxon sampling of hornworts and eliminating the effect of synonymous substitutions. We then estimate the divergence time of crown embryophytes based on three fossil calibration strategies, and reveal that maximum calibration constraints have a major effect on estimating the time of origin of land plants. Moreover, comparison of priors and posteriors provides a guide for evaluating the optimal calibration strategy. By considering the reliability of fossil calibrations and the influences of molecular data, we estimate that land plants originated in the Precambrian (980–682 Ma), much older than widely recognized. Our study highlights the important contribution of molecular data when faced with contentious fossil evidence, and that fossil calibrations used in estimating the timescale of plant evolution require critical scrutiny.
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Affiliation(s)
- Danyan Su
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Lingxiao Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xuan Shi
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoya Ma
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaofan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - S Blair Hedges
- Center for Biodiversity, Temple University, Philadelphia, PA, USA
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China
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16
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Christenhusz MJM, Chase MW, Fay MF, Hidalgo O, Leitch IJ, Pellicer J, Viruel J. Biogeography and genome size evolution of the oldest extant vascular plant genus, Equisetum (Equisetaceae). ANNALS OF BOTANY 2021; 127:681-695. [PMID: 33598697 PMCID: PMC8052921 DOI: 10.1093/aob/mcab005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 01/09/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Extant plant groups with a long fossil history are key elements in understanding vascular plant evolution. Horsetails (Equisetum, Equisetaceae) have a nearly continuous fossil record dating back to the Carboniferous, but their phylogenetic and biogeographic patterns are still poorly understood. We use here the most extensive phylogenetic analysis to date as a framework to evaluate their age, biogeography and genome size evolution. METHODS DNA sequences of four plastid loci were used to estimate divergence times and investigate the biogeographic history of all extant species of Equisetum. Flow cytometry was used to study genome size evolution against the framework of phylogenetic relationships in Equisetum. KEY RESULTS On a well-supported phylogenetic tree including all extant Equisetum species, a molecular clock calibrated with multiple fossils places the node at which the outgroup and Equisetum diverged at 343 Mya (Early Carboniferous), with the first major split among extant species occurring 170 Mya (Middle Jurassic). These dates are older than those reported in some other recent molecular clock studies but are largely in agreement with a timeline established by fossil appearance in the geological record. Representatives of evergreen subgenus Hippochaete have much larger genome sizes than those of deciduous subgenus Equisetum, despite their shared conserved chromosome number. Subgenus Paramochaete has an intermediate genome size and maintains the same number of chromosomes. CONCLUSIONS The first divergences among extant members of the genus coincided with the break-up of Pangaea and the resulting more humid, warmer climate. Subsequent tectonic activity most likely involved vicariance events that led to species divergences combined with some more recent, long-distance dispersal events. We hypothesize that differences in genome size between subgenera may be related to the number of sperm flagellae.
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Affiliation(s)
- Maarten J M Christenhusz
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Mark W Chase
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, UK
- School of Biological Sciences, The University of Western Australia, Perth WA, Australia
| | - Oriane Hidalgo
- Royal Botanic Gardens, Kew, Richmond, UK
- Laboratori de Botànica, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Barcelona, Spain
| | | | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Richmond, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
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17
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Kim H, Kim J. Structural Mutations in the Organellar Genomes of Valeriana sambucifolia f. dageletiana (Nakai. ex Maekawa) Hara Show Dynamic Gene Transfer. Int J Mol Sci 2021; 22:ijms22073770. [PMID: 33916499 PMCID: PMC8038606 DOI: 10.3390/ijms22073770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/04/2021] [Accepted: 04/01/2021] [Indexed: 12/18/2022] Open
Abstract
Valeriana sambucifolia f. dageletiana (Nakai. ex Maekawa) Hara is a broad-leaved valerian endemic to Ulleung Island, a noted hot spot of endemism in Korea. However, despite its widespread pharmacological use, this plant remains comparatively understudied. Plant cells generally contain two types of organellar genomes (the plastome and the mitogenome) that have undergone independent evolution, which accordingly can provide valuable information for elucidating the phylogenetic relationships and evolutionary histories of terrestrial plants. Moreover, the extensive mega-data available for plant genomes, particularly those of plastomes, can enable researchers to gain an in-depth understanding of the transfer of genes between different types of genomes. In this study, we analyzed two organellar genomes (the 155,179 bp plastome and the 1,187,459 bp mitogenome) of V. sambucifolia f. dageletiana and detected extensive changes throughout the plastome sequence, including rapid structural mutations associated with inverted repeat (IR) contraction and genetic variation. We also described features characterizing the first reported mitogenome sequence obtained for a plant in the order Dipsacales and confirmed frequent gene transfer in this mitogenome. We identified eight non-plastome-originated regions (NPRs) distributed within the plastome of this endemic plant, for six of which there were no corresponding sequences in the current nucleotide sequence databases. Indeed, one of these unidentified NPRs unexpectedly showed certain similarities to sequences from bony fish. Although this is ostensibly difficult to explain, we suggest that this surprising association may conceivably reflect the occurrence of gene transfer from a bony fish to the plastome of an ancestor of V. sambucifolia f. dageletiana mediated by either fungi or bacteria.
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Affiliation(s)
- Hyoungtae Kim
- Institute of Agriculture Science and Technology, Chungbuk National University, Cheongju, Chungbuk 28644, Korea;
| | - Jungsung Kim
- Department of Forest Science, Chungbuk National University, Cheongju, Chungbuk 28644, Korea
- Correspondence: ; Tel.: +82-43-261-2535
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18
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Plastid Genomes of the Early Vascular Plant Genus Selaginella Have Unusual Direct Repeat Structures and Drastically Reduced Gene Numbers. Int J Mol Sci 2021; 22:ijms22020641. [PMID: 33440692 PMCID: PMC7827865 DOI: 10.3390/ijms22020641] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 01/20/2023] Open
Abstract
The early vascular plants in the genus Selaginella, which is the sole genus of the Selaginellaceae family, have an important place in evolutionary history, along with ferns, as such plants are valuable resources for deciphering plant evolution. In this study, we sequenced and assembled the plastid genome (plastome) sequences of two Selaginella tamariscina individuals, as well as Selaginella stauntoniana and Selaginella involvens. Unlike the inverted repeat (IR) structures typically found in plant plastomes, Selaginella species had direct repeat (DR) structures, which were confirmed by Oxford Nanopore long-read sequence assembly. Comparative analyses of 19 lycophytes, including two Huperzia and one Isoetes species, revealed unique phylogenetic relationships between Selaginella species and related lycophytes, reflected by structural rearrangements involving two rounds of large inversions that resulted in dynamic changes between IR and DR blocks in the plastome sequence. Furthermore, we present other uncommon characteristics, including a small genome size, drastic reductions in gene and intron numbers, a high GC content, and extensive RNA editing. Although the 16 Selaginella species examined may not fully represent the genus, our findings suggest that Selaginella plastomes have undergone unique evolutionary events yielding genomic features unparalleled in other lycophytes, ferns, or seed plants.
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19
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Kang JS, Zhang HR, Wang YR, Liang SQ, Mao ZY, Zhang XC, Xiang QP. Distinctive evolutionary pattern of organelle genomes linked to the nuclear genome in Selaginellaceae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1657-1672. [PMID: 33073395 DOI: 10.1111/tpj.15028] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/21/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
Plastids and mitochondria are endosymbiotic organelles that store genetic information. The genomes of these organelles generally exhibit contrasting patterns regarding genome architecture and genetic content. However, they have similar genetic features in Selaginellaceae, and little is known about what causes parallel evolution. Here, we document the multipartite plastid genomes (plastomes) and the highly divergent mitochondrial genomes (mitogenomes) from spikemoss obtained by combining short- and long-reads. The 188-kb multipartite plastome has three ribosomal operon copies in the master genomic conformation, creating the alternative subgenomic conformation composed of 110- and 78-kb subgenomes. The long-read data indicated that the two different genomic conformations were present in almost equal proportions in the plastomes of Selaginella nipponica. The mitogenome of S. nipponica was assembled into 27 contigs with a total size of 110 kb. All contigs contained directly arranged repeats at both ends, which introduced multiple conformations. Our results showed that plastomes and mitogenomes share high tRNA losses, GC-biased nucleotides, elevated substitution rates and complicated organization. The exploration of nuclear-encoded organelle DNA replication, recombination and repair proteins indicated that, several single-targeted proteins, particularly plastid-targeted recombinase A1, have been lost in Selaginellaceae; conversely, the dual-targeted proteins remain intact. According to the reported function of recombinase A1, we propose that the plastomes of spikemoss often fail to pair homologous sequences during recombination, and the dual-targeted proteins play a key role in the convergent genetic features of plastomes and mitogenomes. Our results provide a distinctive evolutionary pattern of the organelle genomes in Selaginellaceae and evidence of their convergent evolution.
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Affiliation(s)
- Jong-Soo Kang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Rui Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ya-Rong Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Si-Qi Liang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi-Yuan Mao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Qiao-Ping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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20
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Rogozhin EA, Vasilchenko AS, Barashkova AS, Smirnov AN, Zavriev SK, Demushkin VP. Peptide Extracts from Seven Medicinal Plants Discovered to Inhibit Oomycete Phytophthora infestans, a Causative Agent of Potato Late Blight Disease. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1294. [PMID: 33007947 PMCID: PMC7599828 DOI: 10.3390/plants9101294] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 11/16/2022]
Abstract
We report the inhibitory effect of peptide extracts obtained from seven medicinal plants against a causative agent of late blight disease Phytophthora infestans. We find that all the extracts possess inhibitory activity toward the zoospores output, zoosporangium germination, and the development of P. infestans on potato disc tubers at different quantitative levels. Based on the biological effects detected, an extract of common horsetail (Equisetum arvense) biomass is recognized as the most effective and is selected for further structural analysis. We perform a combination of amino acid analysis and MALDI-TOF mass spectrometry, which reveal the presence of Asn/Asp- and Gln/Glu-rich short peptides with molecular masses in the range of 500-900 Da and not exceeding 1500 Da as the maximum. Analytical anion-exchange HPLC is successfully applied for separation of the peptide extract from common horsetail (E. arvense). We collect nine dominant components that are combined in two groups with differences in retention times. The N-terminal amino acid sequence of the prevalent compounds after analytical ion-exchange HPLC allows us to identify them as peptide fragments of functionally active proteins associated with photosynthesis, aquatic transport, and chitin binding. The anti-oomycete effects may be associated with the conversion of ribulose-1,5-bisphosphate carboxylase/oxygenase to produce a number of biologically active anionic peptides with possible regulatory functions. These data inform our knowledge regarding biologically active peptide fragments; they are the components of programmed or induced proteolysis of plant proteins and can realize secondary antimicrobial functions.
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Affiliation(s)
- Eugene A. Rogozhin
- Shemyakin and Ovchinnikov Institite of Bioorganic Chemistry Russian Academy of Sciences, 117997 Moscow, Russia; (A.S.B.); (S.K.Z.); (V.P.D.)
- Gause Institute of New Antibiotics, 119021 Moscow, Russia
- All-Russian Institute of Plant Protection, 196608 St.-Petersburg-Pushkin, Russia
| | - Alexey S. Vasilchenko
- Institute of Biological and Agricultural Biology (X-Bio) Tyumen State University, Russian Federation, 625003 Tyumen, Russia;
| | - Anna S. Barashkova
- Shemyakin and Ovchinnikov Institite of Bioorganic Chemistry Russian Academy of Sciences, 117997 Moscow, Russia; (A.S.B.); (S.K.Z.); (V.P.D.)
- Institute of Biological and Agricultural Biology (X-Bio) Tyumen State University, Russian Federation, 625003 Tyumen, Russia;
| | - Alexey N. Smirnov
- Timiryazev Russian State Agrarian University, 127550 Moscow, Russia;
| | - Sergey K. Zavriev
- Shemyakin and Ovchinnikov Institite of Bioorganic Chemistry Russian Academy of Sciences, 117997 Moscow, Russia; (A.S.B.); (S.K.Z.); (V.P.D.)
| | - Vladimir P. Demushkin
- Shemyakin and Ovchinnikov Institite of Bioorganic Chemistry Russian Academy of Sciences, 117997 Moscow, Russia; (A.S.B.); (S.K.Z.); (V.P.D.)
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21
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Dai X, Li X, Huang Y, Liu X. The speciation and adaptation of the polyploids: a case study of the Chinese Isoetes L. diploid-polyploid complex. BMC Evol Biol 2020; 20:118. [PMID: 32928096 PMCID: PMC7490897 DOI: 10.1186/s12862-020-01687-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 09/09/2020] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The Chinese Isoetes L. are distributed in a stairway pattern: diploids in the high altitude and polyploids in the low altitude. The allopolyploid I. sinensis and its diploid parents I. yunguiensis and I. taiwanensis is an ideal system with which to investigate the relationships between polyploid speciation and the ecological niches preferences. RESULTS There were two major clades in the nuclear phylogenetic tree, all of the populations of polyploid were simultaneously located in both clades. The chloroplast phylogenetic tree included two clades with different populations of the polyploid clustered with the diploids separately: I. yunguiensis with partial populations of the I. sinensis and I. taiwanensis with the rest populations of the I. sinensis. The crow node of the I. sinensis allopolyploid system was 4.43 Ma (95% HPD: 2.77-6.97 Ma). The divergence time between I. sinensis and I. taiwanensis was estimated to 0.65 Ma (95% HPD: 0.26-1.91 Ma). The narrower niche breadth in I.sinensis than those of its diploid progenitors and less niche overlap in the pairwise comparisons between the polyploid and its progenitors. CONCLUSIONS Our results elucidate that I. yunguinensis and I. taiwanensis contribute to the speciation of I. sinensis, the diploid parents are the female parents of different populations. The change of altitude might have played an important role in allopolyploid speciation and the pattern of distribution of I. sinensis. Additionally, niche novelty of the allopolyploid population of I. sinensis has been detected, in accordance with the hypothesis that niche shift between the polyploids and its diploid progenitors is important for the establishment and persistence of the polyploids.
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Affiliation(s)
- Xiaokang Dai
- Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072 Hubei People’s Republic of China
| | - Xiang Li
- Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072 Hubei People’s Republic of China
| | - Yuqian Huang
- Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072 Hubei People’s Republic of China
| | - Xing Liu
- Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072 Hubei People’s Republic of China
- College of Sciences, Tibet University, Lhasa, 850012 Tibet People’s Republic of China
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Sousa F, Civáň P, Foster PG, Cox CJ. The Chloroplast Land Plant Phylogeny: Analyses Employing Better-Fitting Tree- and Site-Heterogeneous Composition Models. FRONTIERS IN PLANT SCIENCE 2020; 11:1062. [PMID: 32760416 PMCID: PMC7373204 DOI: 10.3389/fpls.2020.01062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/26/2020] [Indexed: 05/02/2023]
Abstract
The colonization of land by descendants of charophyte green algae marked a turning point in Earth history that enabled the development of the diverse terrestrial ecosystems we see today. Early land plants diversified into three gametophyte-dominant lineages, namely the hornworts, liverworts, and mosses, collectively known as bryophytes, and a sporophyte-dominant lineage, the vascular plants, or tracheophytes. In recent decades, the prevailing view of evolutionary relationships among these four lineages has been that the tracheophytes were derived from a bryophyte ancestor. However, recent phylogenetic evidence has suggested that bryophytes are monophyletic, and thus that the first split among land plants gave rise to the lineages that today we recognize as the bryophytes and tracheophytes. We present a phylogenetic analysis of chloroplast protein-coding data that also supports the monophyly of bryophytes. This newly compiled data set consists of 83 chloroplast genes sampled across 30 taxa that include chlorophytes and charophytes, including four members of the Zygnematophyceae, and land plants, that were sampled following a balanced representation of the main bryophyte and tracheophyte lineages. Analyses of non-synonymous site nucleotide data and amino acid translation data result in congruent phylogenetic trees showing the monophyly of bryophytes, with the Zygnematophyceae as the charophyte group most closely related to land plants. Analyses showing that bryophytes and tracheophytes evolved separately from a common terrestrial ancestor have profound implications for the way we understand the evolution of plant life cycles on land and how we interpret the early land plant fossil record.
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Affiliation(s)
- Filipe Sousa
- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Peter Civáň
- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
- INRA, Université Clermont-Auvergne, Clermont-Ferrand, France
| | - Peter G. Foster
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Cymon J. Cox
- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
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23
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The dynamic evolution of mobile open reading frames in plastomes of Hymenophyllum Sm. and new insight on Hymenophyllum coreanum Nakai. Sci Rep 2020; 10:11059. [PMID: 32632087 PMCID: PMC7338519 DOI: 10.1038/s41598-020-68000-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 06/12/2020] [Indexed: 11/08/2022] Open
Abstract
In this study, four plastomes of Hymenophyllum, distributed in the Korean peninsula, were newly sequenced and phylogenomic analysis was conducted to reveal (1) the evolutionary history of plastomes of early-diverging fern species at the species level, (2) the importance of mobile open reading frames in the genus, and (3) plastome sequence divergence providing support for H. coreanum to be recognized as an independent species distinct from H. polyanthos. In addition, 1C-values of H. polyanthos and H. coreanum were measured to compare the genome size of both species and to confirm the diversification between them. The rrn16-trnV intergenic regions in the genus varied in length caused by Mobile Open Reading Frames in Fern Organelles (MORFFO). We investigated enlarged noncoding regions containing MORFFO throughout the fern plastomes and found that they were strongly associated with tRNA genes or palindromic elements. Sequence identity between plastomes of H. polyanthos and H. coreanum is quite low at 93.35% in the whole sequence and 98.13% even if the variation in trnV-rrn16 intergenic spacer was ignored. In addition, different genome sizes were found for these species based on the 1C-value. Consequently, there is no reason to consider them as a conspecies.
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24
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Wood D, Besnard G, Beerling DJ, Osborne CP, Christin PA. Phylogenomics indicates the "living fossil" Isoetes diversified in the Cenozoic. PLoS One 2020; 15:e0227525. [PMID: 32555586 PMCID: PMC7302493 DOI: 10.1371/journal.pone.0227525] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 05/14/2020] [Indexed: 11/19/2022] Open
Abstract
The fossil record provides an invaluable insight into the temporal origins of extant lineages of organisms. However, establishing the relationships between fossils and extant lineages can be difficult in groups with low rates of morphological change over time. Molecular dating can potentially circumvent this issue by allowing distant fossils to act as calibration points, but rate variation across large evolutionary scales can bias such analyses. In this study, we apply multiple dating methods to genome-wide datasets to infer the origin of extant species of Isoetes, a group of mostly aquatic and semi-aquatic isoetalean lycopsids, which closely resemble fossil forms dating back to the Triassic. Rate variation observed in chloroplast genomes hampers accurate dating, but genome-wide nuclear markers place the origin of extant diversity within this group in the mid-Paleogene, 45-60 million years ago. Our genomic analyses coupled with a careful evaluation of the fossil record indicate that despite resembling forms from the Triassic, extant Isoetes species do not represent the remnants of an ancient and widespread group, but instead have spread around the globe in the relatively recent past.
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Affiliation(s)
- Daniel Wood
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Guillaume Besnard
- CNRS, Université de Toulouse, IRD, UMR 5174, EDB (Laboratoire Évolution & Diversité Biologique), Toulouse, France
| | - David J. Beerling
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Colin P. Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Pascal-Antoine Christin
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, United Kingdom
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25
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Liu S, Wang Z, Wang H, Su Y, Wang T. Patterns and Rates of Plastid rps12 Gene Evolution Inferred in a Phylogenetic Context using Plastomic Data of Ferns. Sci Rep 2020; 10:9394. [PMID: 32523061 PMCID: PMC7287138 DOI: 10.1038/s41598-020-66219-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 05/14/2020] [Indexed: 12/14/2022] Open
Abstract
The trans-splicing rps12 gene of fern plastomes (plastid genomes) exhibits a unique structure owing to its variations in intragenic exon location and intron content, and thus, it provides an excellent model system for examining the effect of plastid gene structure on rates and patterns of molecular evolution. In this study, 16 complete fern plastome sequences were newly generated via the Illumina HiSeq sequencing platform. We reconstructed the phylogeny of ferns and inferred the patterns and rates of plastid rps12 gene evolution in a phylogenetic context by combining these plastome data with those of previously published fern species. We uncovered the diversity of fern plastome evolution by characterizing the structures of these genomes and obtained a highly supported phylogenetic framework for ferns. Furthermore, our results revealed molecular evolutionary patterns that were completely different from the patterns revealed in previous studies. There were significant differences in the patterns and rates of nucleotide substitutions in both intron-containing and intron-less rps12 alleles. Rate heterogeneity between single-copy (SC) and inverted repeat (IR) exons was evident. Unexpectedly, however, IR exons exhibited significantly higher synonymous substitution rates (dS) than SC exons, a pattern that contrasts the regional effect responsible for decreased rates of nucleotide substitutions in IRs. Our results reveal that structural changes in plastid genes have important effects on evolutionary rates, and we propose possible mechanisms to explain the variations in the nucleotide substitution rates of this unusual gene.
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Affiliation(s)
- Shanshan Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Hui Wang
- Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China. .,Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, 518057, China.
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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26
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Lehtonen S, Poczai P, Sablok G, Hyvönen J, Karger DN, Flores J. Exploring the phylogeny of the marattialean ferns. Cladistics 2020; 36:569-593. [DOI: 10.1111/cla.12419] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2020] [Indexed: 01/21/2023] Open
Affiliation(s)
- Samuli Lehtonen
- Biodiversity Unit University of Turku FI‐20014 Turku Finland
| | - Péter Poczai
- Finnish Museum of Natural History (Botany) University of Helsinki PO Box 7 FI‐00014 Helsinki Finland
| | - Gaurav Sablok
- Finnish Museum of Natural History (Botany) University of Helsinki PO Box 7 FI‐00014 Helsinki Finland
- OEB and ViPS University of Helsinki PO Box 65 FI‐00014 Helsinki Finland
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany) University of Helsinki PO Box 7 FI‐00014 Helsinki Finland
- OEB and ViPS University of Helsinki PO Box 65 FI‐00014 Helsinki Finland
| | - Dirk N. Karger
- Biodiversity Unit University of Turku FI‐20014 Turku Finland
- Swiss Federal Research Institute WSL 8903 Birmensdorf Switzerland
| | - Jorge Flores
- Finnish Museum of Natural History (Botany) University of Helsinki PO Box 7 FI‐00014 Helsinki Finland
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27
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Sousa F, Civáň P, Brazão J, Foster PG, Cox CJ. The mitochondrial phylogeny of land plants shows support for Setaphyta under composition-heterogeneous substitution models. PeerJ 2020; 8:e8995. [PMID: 32377448 PMCID: PMC7194085 DOI: 10.7717/peerj.8995] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/26/2020] [Indexed: 01/04/2023] Open
Abstract
Congruence among analyses of plant genomic data partitions (nuclear, chloroplast and mitochondrial) is a strong indicator of accuracy in plant molecular phylogenetics. Recent analyses of both nuclear and chloroplast genome data of land plants (embryophytes) have, controversially, been shown to support monophyly of both bryophytes (mosses, liverworts, and hornworts) and tracheophytes (lycopods, ferns, and seed plants), with mosses and liverworts forming the clade Setaphyta. However, relationships inferred from mitochondria are incongruent with these results, and typically indicate paraphyly of bryophytes with liverworts alone resolved as the earliest-branching land plant group. Here, we reconstruct the mitochondrial land plant phylogeny from a newly compiled data set. When among-lineage composition heterogeneity is accounted for in analyses of codon-degenerate nucleotide and amino acid data, the clade Setaphyta is recovered with high support, and hornworts are supported as the earliest-branching lineage of land plants. These new mitochondrial analyses demonstrate partial congruence with current hypotheses based on nuclear and chloroplast genome data, and provide further incentive for revision of how plants arose on land.
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Affiliation(s)
- Filipe Sousa
- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Peter Civáň
- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
- INRAE-Université Clermont-Auvergne, Clermont-Ferrand, France
| | - João Brazão
- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Peter G. Foster
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Cymon J. Cox
- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
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28
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Plastome-based phylogenomics resolves the placement of the sanguinolenta group in the spikemoss of lycophyte (Selaginellaceae). Mol Phylogenet Evol 2020; 147:106788. [PMID: 32173413 DOI: 10.1016/j.ympev.2020.106788] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 02/10/2020] [Accepted: 03/09/2020] [Indexed: 11/27/2022]
Abstract
Selaginellaceae have been shown to be monophyletic in previous studies, and include only the single genus Selaginella. However, the two most recent classifications of the genus disagree in terms of the number of subgenera recognized, and the position of problematic clades such as the "sanguinolenta" group, which has been resolved in quite different positions in different studies. Here, we performed a plastid-genome based phylogenomic analysis of Selaginellaceae to address this problem. The sanguinolenta group, represented here by three species, was resolved as sister to the remaining members of subg. Stachygynandrum. Additionally, subg. Exaltatae, subg. Ericetorum, and subg. Gymnogynum in clade A clustered into a well supported monophyletic clade but with conflicting topology between subgenera inside, which is possibly attributed to the early divergence among them. We uncovered substantial variation in both synonymous (dS) and nonsynonymous (dN) substitution rate, and GC content in plastomes of Selaginellaceae. The values of dS, dN, and GC content were significantly higher than those of other lycophytes (Isoetaceae and Lycopodiaceae). We observed a significant positive correlation between the high GC content, and the elevated dS and dN rates. In addition, the dS and dN values inferred among branches of Selaginellaceae were extremely variable. Our data indicate that this unevenly distributed substitution rate likely reflected relaxed or intensified selection among different lineages, which is possibly related to the inconsistency of the subgeneric phylogenetic topologies of Selaginellaceae.
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29
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Henriquez CL, Ahmed I, Carlsen MM, Zuluaga A, Croat TB, McKain MR. Molecular evolution of chloroplast genomes in Monsteroideae (Araceae). PLANTA 2020; 251:72. [PMID: 32112137 DOI: 10.1007/s00425-020-03365-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/14/2020] [Indexed: 05/02/2023]
Abstract
This study provides broad insight into the chloroplast genomes of the subfamily Monsteroideae. The identified polymorphic regions may be suitable for designing unique and robust molecular markers for phylogenetic inference. Monsteroideae is the third largest subfamily (comprises 369 species) and one of the early diverging lineages of the monocot plant family Araceae. The phylogeny of this important subfamily is not well resolved at the species level due to scarcity of genomic resources and suitable molecular markers. Here, we report annotated chloroplast genome sequences of four Monsteroideae species: Spathiphyllum patulinervum, Stenospermation multiovulatum, Monstera adansonii, and Rhaphidophora amplissima. The quadripartite chloroplast genomes (size range 163,335-164,751 bp) consist of a pair of inverted repeats (25,270-25,931 bp), separating a small single copy region (21,448-22,346 bp) from a large single copy region (89,714-91,841 bp). The genomes contain 114 unique genes, including four rRNA genes, 80 protein-coding genes, and 30 tRNA genes. Gene features, amino acid frequencies, codon usage, GC contents, oligonucleotide repeats, and inverted repeats dynamics exhibit similarities among the four genomes. Higher rate of synonymous substitutions was observed as compared to non-synonymous substitutions in 76 protein-coding genes. Positive selection was observed in seven protein-coding genes, including psbK, ndhK, ndhD, rbcL, accD, rps8, and ycf2. Our included species of Araceae showed the monophyly in Monsteroideae and other subfamilies. We report 30 suitable polymorphic regions. The polymorphic regions identified here might be suitable for designing unique and robust markers for inferring the phylogeny and phylogeography among closely related species within the genus Spathiphyllum and among distantly related species within the subfamily Monsteroideae. The chloroplast genomes presented here are a valuable contribution towards understanding the molecular evolutionary dynamics in the family Araceae.
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Affiliation(s)
- Claudia L Henriquez
- University of California, Department of Ecology and Evolutionary Biology, Los Angeles, USA.
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, 45710, Pakistan
| | | | - Alejandro Zuluaga
- Departamento de Biología, Universidad del Valle, Calle 13, 100-00, Cali, Colombia
| | | | - Michael R McKain
- The University of Alabama, Department of Biological Sciences, Tuscaloosa, AL, USA
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30
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Bell D, Lin Q, Gerelle WK, Joya S, Chang Y, Taylor ZN, Rothfels CJ, Larsson A, Villarreal JC, Li FW, Pokorny L, Szövényi P, Crandall-Stotler B, DeGironimo L, Floyd SK, Beerling DJ, Deyholos MK, von Konrat M, Ellis S, Shaw AJ, Chen T, Wong GKS, Stevenson DW, Palmer JD, Graham SW. Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution. AMERICAN JOURNAL OF BOTANY 2020; 107:91-115. [PMID: 31814117 DOI: 10.1002/ajb2.1397] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 11/04/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Phylogenetic trees of bryophytes provide important evolutionary context for land plants. However, published inferences of overall embryophyte relationships vary considerably. We performed phylogenomic analyses of bryophytes and relatives using both mitochondrial and plastid gene sets, and investigated bryophyte plastome evolution. METHODS We employed diverse likelihood-based analyses to infer large-scale bryophyte phylogeny for mitochondrial and plastid data sets. We tested for changes in purifying selection in plastid genes of a mycoheterotrophic liverwort (Aneura mirabilis) and a putatively mycoheterotrophic moss (Buxbaumia), and compared 15 bryophyte plastomes for major structural rearrangements. RESULTS Overall land-plant relationships conflict across analyses, generally weakly. However, an underlying (unrooted) four-taxon tree is consistent across most analyses and published studies. Despite gene coverage patchiness, relationships within mosses, liverworts, and hornworts are largely congruent with previous studies, with plastid results generally better supported. Exclusion of RNA edit sites restores cases of unexpected non-monophyly to monophyly for Takakia and two hornwort genera. Relaxed purifying selection affects multiple plastid genes in mycoheterotrophic Aneura but not Buxbaumia. Plastid genome structure is nearly invariant across bryophytes, but the tufA locus, presumed lost in embryophytes, is unexpectedly retained in several mosses. CONCLUSIONS A common unrooted tree underlies embryophyte phylogeny, [(liverworts, mosses), (hornworts, vascular plants)]; rooting inconsistency across studies likely reflects substantial distance to algal outgroups. Analyses combining genomic and transcriptomic data may be misled locally for heavily RNA-edited taxa. The Buxbaumia plastome lacks hallmarks of relaxed selection found in mycoheterotrophic Aneura. Autotrophic bryophyte plastomes, including Buxbaumia, hardly vary in overall structure.
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Affiliation(s)
- David Bell
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
- UBC Botanical Garden and Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, British Columbia, V6T 1Z4, Canada
- Royal Botanic Garden, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Qianshi Lin
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
- UBC Botanical Garden and Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Wesley K Gerelle
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
- UBC Botanical Garden and Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Steve Joya
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Ying Chang
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Z Nathan Taylor
- Department of Biology, Indiana University, Bloomington, Indiana, 47405, USA
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California Berkeley, Berkeley, California, 94702, USA
| | - Anders Larsson
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Juan Carlos Villarreal
- Department of Biology, Université Laval, Québec, G1V 0A6, Canada
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Plant Biology Section, Cornell University, Ithaca, New York, 14853, USA
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, TW9 3DS, Surrey, UK
- Centre for Plant Biotechnology and Genomics (CBGP, UPM-INIA), 28223, Pozuelo de Alarcón (Madrid), Spain
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | | | - Lisa DeGironimo
- Department of Biology, College of Arts and Science, New York University, New York, New York, 10003, USA
| | - Sandra K Floyd
- School of Biological Sciences, Monash University, Melbourne, Victoria, 3800, Australia
| | - David J Beerling
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Michael K Deyholos
- Department of Biology, University of British Columbia, Kelowna, British Columbia, V1V 1V7, Canada
| | - Matt von Konrat
- Field Museum of Natural History, Chicago, Illinois, 60605, USA
| | - Shona Ellis
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
| | - A Jonathan Shaw
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
| | - Tao Chen
- Shenzhen Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, China
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | | | - Jeffrey D Palmer
- Department of Biology, Indiana University, Bloomington, Indiana, 47405, USA
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
- UBC Botanical Garden and Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, British Columbia, V6T 1Z4, Canada
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31
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Smith SA, Walker-Hale N, Walker JF, Brown JW. Phylogenetic Conflicts, Combinability, and Deep Phylogenomics in Plants. Syst Biol 2019; 69:579-592. [DOI: 10.1093/sysbio/syz078] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 10/16/2019] [Accepted: 11/18/2019] [Indexed: 11/13/2022] Open
Abstract
Abstract
Studies have demonstrated that pervasive gene tree conflict underlies several important phylogenetic relationships where different species tree methods produce conflicting results. Here, we present a means of dissecting the phylogenetic signal for alternative resolutions within a data set in order to resolve recalcitrant relationships and, importantly, identify what the data set is unable to resolve. These procedures extend upon methods for isolating conflict and concordance involving specific candidate relationships and can be used to identify systematic error and disambiguate sources of conflict among species tree inference methods. We demonstrate these on a large phylogenomic plant data set. Our results support the placement of Amborella as sister to the remaining extant angiosperms, Gnetales as sister to pines, and the monophyly of extant gymnosperms. Several other contentious relationships, including the resolution of relationships within the bryophytes and the eudicots, remain uncertain given the low number of supporting gene trees. To address whether concatenation of filtered genes amplified phylogenetic signal for relationships, we implemented a combinatorial heuristic to test combinability of genes. We found that nested conflicts limited the ability of data filtering methods to fully ameliorate conflicting signal amongst gene trees. These analyses confirmed that the underlying conflicting signal does not support broad concatenation of genes. Our approach provides a means of dissecting a specific data set to address deep phylogenetic relationships while also identifying the inferential boundaries of the data set. [Angiosperms; coalescent; gene-tree conflict; genomics; phylogenetics; phylogenomics.]
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Affiliation(s)
- Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Biological Sciences Building, Ann Arbor, MI 48109-1085, USA
| | - Nathanael Walker-Hale
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Biological Sciences Building, Ann Arbor, MI 48109-1085, USA
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, Cambridge, UK
| | - Joseph F Walker
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Biological Sciences Building, Ann Arbor, MI 48109-1085, USA
- Sainsbury Laboratory (SLCU), University of Cambrige, Bateman St, Cambridge CB2 1LR, Cambridge, UK
| | - Joseph W Brown
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, Sheffield, UK
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Zhang HR, Zhang XC, Xiang QP. Directed Repeats Co-occur with Few Short-Dispersed Repeats in Plastid Genome of a Spikemoss, Selaginella vardei (Selaginellaceae, Lycopodiopsida). BMC Genomics 2019; 20:484. [PMID: 31185895 PMCID: PMC6560725 DOI: 10.1186/s12864-019-5843-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 05/24/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND It is hypothesized that the highly conserved inverted repeats (IR) structure of land plant plastid genomes (plastomes) is beneficial for stabilizing plastome organization, whereas the mechanism of the occurrence and stability maintenance of the recently reported direct repeats (DR) structure is yet awaiting further exploration. Here we describe the DR structure of the Selaginella vardei (Selaginellaceae) plastome, to elucidate the mechanism of DR occurrence and stability maintenance. RESULTS The plastome of S. vardei is 121,254 bp in length and encodes 76 genes, of which 62 encode proteins, 10 encode tRNAs, and four encode rRNAs. Unexpectedly, the two identical rRNA gene regions (13,893 bp) are arranged in a direct orientation (DR), rather than inverted. Comparing to the IR organization in Isoetes flaccida (Isoetaceae, Lycopodiopsida) plastome, a ca. 50-kb trnN-trnF inversion that spans one DR copy was found in the plastome of S. vardei, which might cause the orientation change. In addition, we find extremely rare short dispersed repeats (SDRs) in the plastomes of S. vardei and its closely related species S. indica. CONCLUSIONS We suggest that the ca. 50-kb inversion resulted in the DR structure, and the reduction in SDRs plays a key role in maintaining the stability of plastomes with DR structure by avoiding potential secondary recombination. We further confirmed the presence of homologous recombination between DR regions, which are able to generate subgenomes and form diverse multimers. Our study deepens the understanding of Selaginella plastomes and provides new insights into the diverse plastome structures in land plants.
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Affiliation(s)
- Hong-Rui Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
| | - Qiao-Ping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
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de Sousa F, Foster PG, Donoghue PCJ, Schneider H, Cox CJ. Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta Schimp.). THE NEW PHYTOLOGIST 2019; 222:565-575. [PMID: 30411803 DOI: 10.1111/nph.15587] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 10/31/2018] [Indexed: 05/05/2023]
Abstract
Unraveling the phylogenetic relationships between the four major lineages of terrestrial plants (mosses, liverworts, hornworts, and vascular plants) is essential for an understanding of the evolution of traits specific to land plants, such as their complex life cycles, and the evolutionary development of stomata and vascular tissue. Well supported phylogenetic hypotheses resulting from different data and methods are often incongruent due to processes of nucleotide evolution that are difficult to model, for example substitutional saturation and composition heterogeneity. We reanalysed a large published dataset of nuclear data and modelled these processes using degenerate-codon recoding and tree-heterogeneous composition substitution models. Our analyses resolved bryophytes as a monophyletic group and showed that the nonnonmonophyly of the clade that is supported by the analysis of nuclear nucleotide data is due solely to fast-evolving synonymous substitutions. The current congruence among phylogenies of both nuclear and chloroplast analyses lent considerable support to the conclusion that the bryophytes are a monophyletic group. An initial split between bryophytes and vascular plants implies that the bryophyte life cycle (with a dominant gametophyte nurturing an unbranched sporophyte) may not be ancestral to all land plants and that stomata are likely to be a symplesiomorphy among embryophytes.
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Affiliation(s)
- Filipe de Sousa
- Centro de Ciências do Mar, Universidade do Algarve, Gambelas, Faro, 8005-319, Portugal
| | - Peter G Foster
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
| | | | - Harald Schneider
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
- School of Earth Sciences, University of Bristol, Bristol, BS8 1TQ, UK
- Center of Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, 666303, China
| | - Cymon J Cox
- Centro de Ciências do Mar, Universidade do Algarve, Gambelas, Faro, 8005-319, Portugal
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Zhang HR, Xiang QP, Zhang XC. The Unique Evolutionary Trajectory and Dynamic Conformations of DR and IR/DR-Coexisting Plastomes of the Early Vascular Plant Selaginellaceae (Lycophyte). Genome Biol Evol 2019; 11:1258-1274. [PMID: 30937434 PMCID: PMC6486807 DOI: 10.1093/gbe/evz073] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2019] [Indexed: 12/23/2022] Open
Abstract
Both direct repeats (DR) and inverted repeats (IR) are documented in the published plastomes of Selaginella species indicating the unusual and diverse plastome structure in the family Selaginellaceae. In this study, we newly sequenced complete plastomes of seven species from five main lineages of Selaginellaceae and also resequenced three species (Selaginella tamariscina, Selaginella uncinata, and Selaginella moellendorffii) to explore the evolutionary trajectory of Selaginellaceae plastomes. Our results showed that the plastomes of Selaginellaceae vary remarkably in size, gene contents, gene order, and GC contents. Notably, both DR and IR structures existed in the plastomes of Selaginellaceae with DR structure being an ancestral state. The occurrence of DR structure was at ∼257 Ma and remained in most subgenera of Selaginellaceae, whereas IR structure only reoccurred in Selaginella sect. Lepidophyllae (∼143 Ma) and Selaginella subg. Heterostachys (∼19 Ma). The presence of a pair of large repeats psbK-trnQ, together with DR/IR region in Selaginella bisulcata, Selaginella pennata, S. uncinata, and Selaginella hainanensis, could frequently mediate diverse homologous recombination and create approximately equal stoichiometric isomers (IR/DR-coexisting) and subgenomes. High proportion of repeats is presumably responsible for the dynamic IR/DR-coexisting plastomes, which possess a lower synonymous substitution rate (dS) compared with DR-possessing and IR-possessing plastomes. We propose that the occurrence of DR structure, together with few repeats, is possibly selected to keep the stability of plastomes and the IR/DR-coexisting plastomes also reached an equilibrium in plastome organization through highly efficient homologous recombination to maintain stability.
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Affiliation(s)
- Hong-Rui Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiao-Ping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
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Mower JP, Ma P, Grewe F, Taylor A, Michael TP, VanBuren R, Qiu Y. Lycophyte plastid genomics: extreme variation in GC, gene and intron content and multiple inversions between a direct and inverted orientation of the rRNA repeat. THE NEW PHYTOLOGIST 2019; 222:1061-1075. [PMID: 30556907 PMCID: PMC6590440 DOI: 10.1111/nph.15650] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/10/2018] [Indexed: 05/02/2023]
Abstract
Lycophytes are a key group for understanding vascular plant evolution. Lycophyte plastomes are highly distinct, indicating a dynamic evolutionary history, but detailed evaluation is hindered by the limited availability of sequences. Eight diverse plastomes were sequenced to assess variation in structure and functional content across lycophytes. Lycopodiaceae plastomes have remained largely unchanged compared with the common ancestor of land plants, whereas plastome evolution in Isoetes and especially Selaginella is highly dynamic. Selaginella plastomes have the highest GC content and fewest genes and introns of any photosynthetic land plant. Uniquely, the canonical inverted repeat was converted into a direct repeat (DR) via large-scale inversion in some Selaginella species. Ancestral reconstruction identified additional putative transitions between an inverted and DR orientation in Selaginella and Isoetes plastomes. A DR orientation does not disrupt the activity of copy-dependent repair to suppress substitution rates within repeats. Lycophyte plastomes include the most archaic examples among vascular plants and the most reconfigured among land plants. These evolutionary trends correlate with the mitochondrial genome, suggesting shared underlying mechanisms. Copy-dependent repair for DR-localized genes indicates that recombination and gene conversion are not inhibited by the DR orientation. Gene relocation in lycophyte plastomes occurs via overlapping inversions rather than transposase/recombinase-mediated processes.
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Affiliation(s)
- Jeffrey P. Mower
- Center for Plant Science InnovationUniversity of NebraskaLincolnNE68588USA
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNE68583USA
| | - Peng‐Fei Ma
- Center for Plant Science InnovationUniversity of NebraskaLincolnNE68588USA
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingYunnan650201China
| | - Felix Grewe
- Grainger Bioinformatics Center, Science and EducationField Museum of Natural HistoryChicagoIL60605USA
| | - Alex Taylor
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMI48109USA
| | | | - Robert VanBuren
- Department of HorticultureMichigan State UniversityEast LansingMI48824USA
| | - Yin‐Long Qiu
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMI48109USA
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36
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Feng T, Xiao QY, Liang Q, Li WJ, Yu Y. The complete chloroplast genome of Isoetes yunguiensis (Isoetaceae), a rare and endangered fern endemic to China. MITOCHONDRIAL DNA PART B-RESOURCES 2019. [DOI: 10.1080/23802359.2018.1555015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Tu Feng
- School of Ecological Engineering, Guizhou University of Engineering Science, Bijie, PR China
| | - Qun-Ying Xiao
- School of Ecological Engineering, Guizhou University of Engineering Science, Bijie, PR China
| | - Qin Liang
- School of Ecological Engineering, Guizhou University of Engineering Science, Bijie, PR China
| | - Wang Jun Li
- School of Ecological Engineering, Guizhou University of Engineering Science, Bijie, PR China
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China
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Ruiz-Ruano FJ, Navarro-Domínguez B, Camacho JPM, Garrido-Ramos MA. Full plastome sequence of the fern Vandenboschia speciosa (Hymenophyllales): structural singularities and evolutionary insights. JOURNAL OF PLANT RESEARCH 2019; 132:3-17. [PMID: 30552526 DOI: 10.1007/s10265-018-1077-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/26/2018] [Indexed: 05/14/2023]
Abstract
We provide here the first full chloroplast genome sequence, i.e., the plastome, for a species belonging to the fern order Hymenophyllales. The phylogenetic position of this order within leptosporangiate ferns, together with the general scarcity of information about fern plastomes, places this research as a valuable study on the analysis of the diversity of plastomes throughout fern evolution. Gene content of V. speciosa plastome was similar to that in most ferns, although there were some characteristic gene losses and lineage-specific differences. In addition, an important number of genes required U to C RNA editing for proper protein translation and two genes showed start codons alternative to the canonical AUG (AUA). Concerning gene order, V. speciosa shared the specific 30-kb inversion of euphyllophytes plastomes and the 3.3-kb inversion of fern plastomes, keeping the ancestral gene order shared by eusporangiate and early leptosporangiate ferns. Conversely, V. speciosa has expanded IR regions comprising the rps7, rps12, ndhB and trnL genes in addition to rRNA and other tRNA genes, a condition shared with several eusporangiate ferns, lycophytes and hornworts, as well as most seed plants.
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Affiliation(s)
- F J Ruiz-Ruano
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - B Navarro-Domínguez
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - J P M Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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38
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Kim HT, Kim KJ. Evolution of six novel ORFs in the plastome of Mankyua chejuense and phylogeny of eusporangiate ferns. Sci Rep 2018; 8:16466. [PMID: 30405200 PMCID: PMC6220310 DOI: 10.1038/s41598-018-34825-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/26/2018] [Indexed: 11/17/2022] Open
Abstract
In this paper, three plastomes of Mankyua chejuense, Helminthostachys zeylanica, and Botrychium ternatum in Ophioglossaceae were completely sequenced in order to investigate the plastome evolution and phylogeny of eusporangiate ferns. They were similar to each other in terms of length and the gene orders; however, six unknown open reading frames (ORFs) were found between rps4 and trnL-UAA genes in M. chejuense. Similar sequence regions of six ORFs of M. chejuense were found at the plastomes of Ophioglossum californicum and H. zeylanica, as well as the mitochondrial genome (mitogenome) of H. zeylanica, but not in B. ternatum. Interestingly, the translated amino acid sequences of three ORFs were more similar to the proteins of distantly related taxa such as algae and bacteria than they were to proteins in land plants. It is likely that the six ORFs region arose from endosymbiotic gene transfer (EGT) or horizontal gene transfer (HGT), but further study is needed to verify this. Phylogenetic analyses suggested that Mankyua was resolved as the earliest diverging lineage and that Ophioglossum was subsequently diverged in Ophioglossaceae. This result supports why the plastome of M. chejuense have contained the most ancestral six ORFs in the family.
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Affiliation(s)
- Hyoung Tae Kim
- Division of Life Sciences, School of Life Sciences, Korea University, Seoul, 02841, Korea
- Institute of Agricultural Science and Technology, Chungbuk National University, Chengju, 41566, Korea
| | - Ki-Joong Kim
- Division of Life Sciences, School of Life Sciences, Korea University, Seoul, 02841, Korea.
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Kuo LY, Qi X, Ma H, Li FW. Order-level fern plastome phylogenomics: new insights from Hymenophyllales. AMERICAN JOURNAL OF BOTANY 2018; 105:1545-1555. [PMID: 30168575 DOI: 10.1002/ajb2.1152] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 06/18/2018] [Indexed: 05/14/2023]
Abstract
PREMISE OF THE STUDY Filmy ferns (Hymenophyllales) are a highly specialized lineage, having mesophyll one-cell layer thick and inhabiting particularly shaded and humid environments. The phylogenetic placement of Hymenophyllales has been inconclusive, and while over 87 whole fern plastomes have been published, none was from Hymenophyllales. To better understand the evolutionary history of filmy ferns, we sequenced the first complete plastome for this order. METHODS We compiled a phylogenomic plastome data set encompassing all 11 fern orders, and reconstructed phylogenies using different data types (nucleotides, codons, and amino acids) and partition schemes (codon positions and loci). To infer the evolution of fern plastome organization, we coded plastome features, including inversions, inverted repeat boundary shifts, gene losses, and tRNA anticodon sequences as characters, and reconstructed the ancestral states for these characters. KEY RESULTS We discovered a suite of novel, Hymenophyllales-specific plastome structures that likely resulted from repeated expansions and contractions of the inverted repeat regions. Our phylogenetic analyses reveal that Hymenophyllales is highly supported as either sister to Gleicheniales or to Gleicheniales + the remaining non-Osmundales leptosporangiates, depending on the data type and partition scheme. CONCLUSIONS Although our analyses could not confidently resolve the phylogenetic position of Hymenophyalles, the results here highlight the danger of drawing conclusions from "all-in" phylogenomic data set without exploring potential inconsistencies in the data. Finally, our first order-level reconstruction of fern plastome structural evolution provides a useful framework for future plastome research.
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Affiliation(s)
- Li-Yaung Kuo
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Xinping Qi
- Ministry of Education Key Laboratory of Biodiversity, Sciences and Ecological Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong Ma
- Ministry of Education Key Laboratory of Biodiversity, Sciences and Ecological Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
- Department of Biology and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, PA, USA
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
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Nunes GL, Oliveira RRM, Guimarães JTF, Giulietti AM, Caldeira C, Vasconcelos S, Pires E, Dias M, Watanabe M, Pereira J, Jaffé R, Bandeira CHMM, Carvalho-Filho N, da Silva EF, Rodrigues TM, dos Santos FMG, Fernandes T, Castilho A, Souza-Filho PWM, Imperatriz-Fonseca V, Siqueira JO, Alves R, Oliveira G. Quillworts from the Amazon: A multidisciplinary populational study on Isoetes serracarajensis and Isoetes cangae. PLoS One 2018; 13:e0201417. [PMID: 30089144 PMCID: PMC6082551 DOI: 10.1371/journal.pone.0201417] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/13/2018] [Indexed: 01/20/2023] Open
Abstract
Isoetes are ancient quillworts members of the only genus of the order Isoetales. The genus is slow evolving but is resilient, and widespread worldwide. Two recently described species occur in the Eastern Brazilian Amazon, Isoetes serracarajensis and Isoetes cangae. They are found in the ironstone grasslands known as Canga. While I. serracarajensis is present mostly in seasonal water bodies, I. cangae is known to occur in a single permanent lake at the South mountain range. In this work, we undertake an extensive morphological, physiological and genetic characterization of both species to establish species boundaries and better understand the morphological and genetic features of these two species. Our results indicate that the morphological differentiation of the species is subtle and requires a quantitative assessment of morphological elements of the megaspore for diagnosis. We did not detect differences in microspore output, but morphological peculiarities may establish a reproductive barrier. Additionally, genetic analysis using DNA barcodes and whole chloroplast genomes indicate that although the plants are genetically very similar both approaches provide diagnostic characters. There was no indication of population structuring I. serracarajensis. These results set the basis for a deeper understanding of the evolution of the Isoetes genus.
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Affiliation(s)
- Gisele Lopes Nunes
- Environmental Genomics Group, Instituto Tecnológico Vale, Belém, PA, Brazil
| | | | | | - Ana Maria Giulietti
- Biodiversity and Ecosystems Services Group, Instituto Tecnológico Vale, Belém, PA, Brazil
| | - Cecílio Caldeira
- Environmental Technology Group, Instituto Tecnológico Vale, Belém, PA, Brazil
| | | | - Eder Pires
- Environmental Genomics Group, Instituto Tecnológico Vale, Belém, PA, Brazil
| | - Mariana Dias
- Environmental Genomics Group, Instituto Tecnológico Vale, Belém, PA, Brazil
| | - Maurício Watanabe
- Biodiversity and Ecosystems Services Group, Instituto Tecnológico Vale, Belém, PA, Brazil
| | - Jovani Pereira
- Biodiversity and Ecosystems Services Group, Instituto Tecnológico Vale, Belém, PA, Brazil
| | - Rodolfo Jaffé
- Biodiversity and Ecosystems Services Group, Instituto Tecnológico Vale, Belém, PA, Brazil
| | | | | | | | | | | | - Taís Fernandes
- Environmental Studies Office, Vale, Belo Horizonte, MG, Brazil
| | | | | | | | | | - Ronnie Alves
- Environmental Genomics Group, Instituto Tecnológico Vale, Belém, PA, Brazil
| | - Guilherme Oliveira
- Environmental Genomics Group, Instituto Tecnológico Vale, Belém, PA, Brazil
- * E-mail:
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Elgorriaga A, Escapa IH, Rothwell GW, Tomescu AMF, Rubén Cúneo N. Origin of Equisetum: Evolution of horsetails (Equisetales) within the major euphyllophyte clade Sphenopsida. AMERICAN JOURNAL OF BOTANY 2018; 105:1286-1303. [PMID: 30025163 DOI: 10.1002/ajb2.1125] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 06/05/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Equisetum is the sole living representative of Sphenopsida, a clade with impressive species richness, a long fossil history dating back to the Devonian, and obscure relationships with other living pteridophytes. Based on molecular data, the crown group age of Equisetum is mid-Paleogene, although fossils with possible crown synapomorphies appear in the Triassic. The most widely circulated hypothesis states that the lineage of Equisetum derives from calamitaceans, but no comprehensive phylogenetic studies support the claim. Using a combined approach, we provide a comprehensive phylogenetic analysis of Equisetales, with special emphasis on the origin of genus Equisetum. METHODS We performed parsimony phylogenetic analyses to address relationships of 43 equisetalean species (15 extant, 28 extinct) using a combination of morphological and molecular characters. KEY RESULTS We recovered Equisetaceae + Neocalamites as sister to Calamitaceae + a clade of Angaran and Gondwanan horsetails, with the four groups forming a clade that is sister to Archaeocalamitaceae. The estimated age for the Equisetum crown group is mid-Mesozoic. CONCLUSIONS Modern horsetails are not nested within calamitaceans; instead, both groups have explored independent evolutionary trajectories since the Carboniferous. Diverse fossil taxon sampling helps to shed light on the position and relationships of equisetalean lineages, of which only a tiny remnant is present within the extant flora. Understanding these relationships and early character configurations of ancient plant clades as Equisetales provide useful tests of hypotheses about overall phylogenetic relationships of euphyllophytes and foundations for future tests of molecular dates with paleontological data.
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Affiliation(s)
- Andrés Elgorriaga
- CONICET, Museo Paleontológico Egidio Feruglio, Trelew, Chubut, 9100, Argentina
| | - Ignacio H Escapa
- CONICET, Museo Paleontológico Egidio Feruglio, Trelew, Chubut, 9100, Argentina
| | - Gar W Rothwell
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
| | - Alexandru M F Tomescu
- Department of Biological Sciences, Humboldt State University, Arcata, CA, 95521, USA
| | - N Rubén Cúneo
- CONICET, Museo Paleontológico Egidio Feruglio, Trelew, Chubut, 9100, Argentina
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Qi X, Kuo LY, Guo C, Li H, Li Z, Qi J, Wang L, Hu Y, Xiang J, Zhang C, Guo J, Huang CH, Ma H. A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families. Mol Phylogenet Evol 2018; 127:961-977. [PMID: 29981932 DOI: 10.1016/j.ympev.2018.06.043] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/27/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
Abstract
Ferns account for 80% of nonflowering vascular plant species and are the sister lineage of seed plants. Recent molecular phylogenetics have greatly advanced understanding of fern tree of life, but relationships among some major lineages remain unclear. To better resolve the phylogenetic relationships of ferns, we generated transcriptomes from 125 ferns and two lycophytes, with three additional public datasets, to represent all 11 orders and 85% of families of ferns. Our nuclear phylogeny provides strong supports for the monophyly of all four subclasses and nearly all orders and families, and for relationships among these lineages. The only exception is Gleicheniales, which was highly supported as being paraphyletic with Dipteridaceae sister to a clade with Gleicheniaceae + Hymenophyllales. In addition, new and strongly supported phylogenetic relationships are found for suborders and families in Polypodiales. We provide the first dated fern phylogenomic tree using many nuclear genes from a large majority of families, with an estimate for separation of the ancestors of ferns and seed plants in early Devonian at ∼400 Mya and subsequent gradual divergences of fern orders from ∼380 to 200 Mya. Moreover, the newly obtained fern phylogeny provides a framework for gene family analyses, which indicate that the vast majority of transcription factor families found in seed plants were already present in the common ancestor of extant vascular plants. In addition, fern transcription factor genes show similar duplication patterns to those in seed plants, with some showing stable copy number and others displaying independent expansions in both ferns and seed plants. This study provides a robust phylogenetic and gene family evolution framework, as well as rich molecular resources for understanding the morphological and functional evolution in ferns.
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Affiliation(s)
- Xinping Qi
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | | | - Chunce Guo
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Hao Li
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Zhongyang Li
- College of Life and Environmental Sciences, Gannan Normal University, Ganzhou, Jiangxi 341000, China
| | - Ji Qi
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Linbo Wang
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Yi Hu
- Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jianying Xiang
- College of Biodiversity Conservation and Utilization, Southwest Forestry University, 300 Bailong Road, Kunming 650224, China
| | - Caifei Zhang
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Jing Guo
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Chien-Hsun Huang
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China.
| | - Hong Ma
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China; Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
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43
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Song Y, Yu WB, Tan Y, Liu B, Yao X, Jin J, Padmanaba M, Yang JB, Corlett RT. Evolutionary Comparisons of the Chloroplast Genome in Lauraceae and Insights into Loss Events in the Magnoliids. Genome Biol Evol 2018; 9:2354-2364. [PMID: 28957463 PMCID: PMC5610729 DOI: 10.1093/gbe/evx180] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/01/2017] [Indexed: 12/15/2022] Open
Abstract
Available plastomes of the Lauraceae show similar structure and varied size, but there has been no systematic comparison across the family. In order to understand the variation in plastome size and structure in the Lauraceae and related families of magnoliids, we here compare 47 plastomes, 15 newly sequenced, from 27 representative genera. We reveal that the two shortest plastomes are in the parasitic Lauraceae genus Cassytha, with lengths of 114,623 (C. filiformis) and 114,963 bp (C. capillaris), and that they have lost NADH dehydrogenase (ndh) genes in the large single-copy region and one entire copy of the inverted repeat (IR) region. The plastomes of the core Lauraceae group, with lengths from 150,749 bp (Nectandra angustifolia) to 152,739 bp (Actinodaphne trichocarpa), have lost trnI-CAU, rpl23, rpl2, a fragment of ycf2, and their intergenic regions in IRb region, whereas the plastomes of the basal Lauraceae group, with lengths from 157,577 bp (Eusideroxylon zwageri) to 158,530 bp (Beilschmiedia tungfangensis), have lost rpl2 in IRa region. The plastomes of Calycanthus (Calycanthaceae, Laurales) have lost rpl2 in IRb region, but the plastome of Caryodaphnopsis henryi (Lauraceae) remain intact, as do those of the nonLaurales magnoliid genera Piper, Liriodendron, and Magnolia. On the basis of our phylogenetic analysis and structural comparisons, different loss events occurred in different lineages of the Laurales, and fragment loss events in the IR regions have largely driven the contraction of the plastome in the Lauraceae. These results provide new insights into the evolution of the Lauraceae as well as the magnoliids as a whole.
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Affiliation(s)
- Yu Song
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, Myanmar
| | - Wen-Bin Yu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, Myanmar
| | - Yunhong Tan
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, Myanmar
| | - Bing Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xin Yao
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Jianjun Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Michael Padmanaba
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Richard T Corlett
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, Myanmar
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44
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Wei R, Yan YH, Harris AJ, Kang JS, Shen H, Xiang QP, Zhang XC. Plastid Phylogenomics Resolve Deep Relationships among Eupolypod II Ferns with Rapid Radiation and Rate Heterogeneity. Genome Biol Evol 2018; 9:1646-1657. [PMID: 28854625 PMCID: PMC5534337 DOI: 10.1093/gbe/evx107] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2017] [Indexed: 01/21/2023] Open
Abstract
The eupolypods II ferns represent a classic case of evolutionary radiation and, simultaneously, exhibit high substitution rate heterogeneity. These factors have been proposed to contribute to the contentious resolutions among clades within this fern group in multilocus phylogenetic studies. We investigated the deep phylogenetic relationships of eupolypod II ferns by sampling all major families and using 40 plastid genomes, or plastomes, of which 33 were newly sequenced with next-generation sequencing technology. We performed model-based analyses to evaluate the diversity of molecular evolutionary rates for these ferns. Our plastome data, with more than 26,000 informative characters, yielded good resolution for deep relationships within eupolypods II and unambiguously clarified the position of Rhachidosoraceae and the monophyly of Athyriaceae. Results of rate heterogeneity analysis revealed approximately 33 significant rate shifts in eupolypod II ferns, with the most heterogeneous rates (both accelerations and decelerations) occurring in two phylogenetically difficult lineages, that is, the Rhachidosoraceae–Aspleniaceae and Athyriaceae clades. These observations support the hypothesis that rate heterogeneity has previously constrained the deep phylogenetic resolution in eupolypods II. According to the plastome data, we propose that 14 chloroplast markers are particularly phylogenetically informative for eupolypods II both at the familial and generic levels. Our study demonstrates the power of a character-rich plastome data set and high-throughput sequencing for resolving the recalcitrant lineages, which have undergone rapid evolutionary radiation and dramatic changes in substitution rates.
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Affiliation(s)
- Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, P.R. China
| | - Yue-Hong Yan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, P.R. China
| | - A J Harris
- Department of Botany, Smithsonian Institution, National Museum of Natural History, Washington, District of Columbia
| | - Jong-Soo Kang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, P.R. China.,University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Hui Shen
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, P.R. China
| | - Qiao-Ping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, P.R. China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, P.R. China
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45
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Amiryousefi A, Hyvönen J, Poczai P. The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae. PLoS One 2018; 13:e0196069. [PMID: 29694416 PMCID: PMC5919006 DOI: 10.1371/journal.pone.0196069] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 04/05/2018] [Indexed: 11/18/2022] Open
Abstract
Bittersweet (Solanum dulcamara) is a native Old World member of the nightshade family. This European diploid species can be found from marshlands to high mountainous regions and it is a common weed that serves as an alternative host and source of resistance genes against plant pathogens such as late blight (Phytophthora infestans). We sequenced the complete chloroplast genome of bittersweet, which is 155,580 bp in length and it is characterized by a typical quadripartite structure composed of a large (85,901 bp) and small (18,449 bp) single-copy region interspersed by two identical inverted repeats (25,615 bp). It consists of 112 unique genes from which 81 are protein-coding, 27 tRNA and four rRNA genes. All bittersweet plastid genes including non-functional ones and even intergenic spacer regions are transcribed in primary plastid transcripts covering 95.22% of the genome. These are later substantially edited in a post-transcriptional phase to activate gene functions. By comparing the bittersweet plastid genome with all available Solanaceae sequences we found that gene content and synteny are highly conserved across the family. During genome comparison we have identified several annotation errors, which we have corrected in a manual curation process then we have identified the major plastid genome structural changes in Solanaceae. Interpreted in a phylogenetic context they seem to provide additional support for larger clades. The plastid genome sequence of bittersweet could help to benchmark Solanaceae plastid genome annotations and could be used as a reference for further studies. Such reliable annotations are important for gene diversity calculations, synteny map constructions and assigning partitions for phylogenetic analysis with de novo sequenced plastomes of Solanaceae.
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Affiliation(s)
- Ali Amiryousefi
- Organismal Evolutionary Biology Research Program, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Jaakko Hyvönen
- Organismal Evolutionary Biology Research Program, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland
| | - Péter Poczai
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland
- * E-mail:
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46
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Manzanilla V, Kool A, Nguyen Nhat L, Nong Van H, Le Thi Thu H, de Boer HJ. Phylogenomics and barcoding of Panax: toward the identification of ginseng species. BMC Evol Biol 2018; 18:44. [PMID: 29614961 PMCID: PMC5883351 DOI: 10.1186/s12862-018-1160-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 03/21/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The economic value of ginseng in the global medicinal plant trade is estimated to be in excess of US$2.1 billion. At the same time, the evolutionary placement of ginseng (Panax ginseng) and the complex evolutionary history of the genus is poorly understood despite several molecular phylogenetic studies. In this study, we use a full plastome phylogenomic framework to resolve relationships in Panax and to identify molecular markers for species discrimination. RESULTS We used high-throughput sequencing of MBD2-Fc fractionated Panax DNA to supplement publicly available plastid genomes to create a phylogeny based on fully assembled and annotated plastid genomes from 60 accessions of 8 species. The plastome phylogeny based on a 163 kbp matrix resolves the sister relationship of Panax ginseng with P. quinquefolius. The closely related species P. vietnamensis is supported as sister of P. japonicus. The plastome matrix also shows that the markers trnC-rps16, trnS-trnG, and trnE-trnM could be used for unambiguous molecular identification of all the represented species in the genus. CONCLUSIONS MBD2 depletion reduces the cost of plastome sequencing, which makes it a cost-effective alternative to Sanger sequencing based DNA barcoding for molecular identification. The plastome phylogeny provides a robust framework that can be used to study the evolution of morphological characters and biosynthesis pathways of ginsengosides for phylogenetic bioprospecting. Molecular identification of ginseng species is essential for authenticating ginseng in international trade and it provides an incentive for manufacturers to create authentic products with verified ingredients.
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Affiliation(s)
- V Manzanilla
- The Natural History Museum, University of Oslo, Oslo, Norway.
| | - A Kool
- The Natural History Museum, University of Oslo, Oslo, Norway
| | - L Nguyen Nhat
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - H Nong Van
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - H Le Thi Thu
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - H J de Boer
- The Natural History Museum, University of Oslo, Oslo, Norway
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47
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Park M, Park H, Lee H, Lee BH, Lee J. The Complete Plastome Sequence of an Antarctic Bryophyte Sanionia uncinata (Hedw.) Loeske. Int J Mol Sci 2018; 19:ijms19030709. [PMID: 29494552 PMCID: PMC5877570 DOI: 10.3390/ijms19030709] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/26/2018] [Accepted: 02/27/2018] [Indexed: 11/16/2022] Open
Abstract
Organellar genomes of bryophytes are poorly represented with chloroplast genomes of only four mosses, four liverworts and two hornworts having been sequenced and annotated. Moreover, while Antarctic vegetation is dominated by the bryophytes, there are few reports on the plastid genomes for the Antarctic bryophytes. Sanionia uncinata (Hedw.) Loeske is one of the most dominant moss species in the maritime Antarctic. It has been researched as an important marker for ecological studies and as an extremophile plant for studies on stress tolerance. Here, we report the complete plastome sequence of S. uncinata, which can be exploited in comparative studies to identify the lineage-specific divergence across different species. The complete plastome of S. uncinata is 124,374 bp in length with a typical quadripartite structure of 114 unique genes including 82 unique protein-coding genes, 37 tRNA genes and four rRNA genes. However, two genes encoding the α subunit of RNA polymerase (rpoA) and encoding the cytochrome b6/f complex subunit VIII (petN) were absent. We could identify nuclear genes homologous to those genes, which suggests that rpoA and petN might have been relocated from the chloroplast genome to the nuclear genome.
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Affiliation(s)
- Mira Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Korea.
- Department of Life Science, Sogang University, Seoul 04107, Korea.
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Korea.
- Polar Science, University of Science & Technology, Daejeon 34113, Korea.
| | - Hyoungseok Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Korea.
- Polar Science, University of Science & Technology, Daejeon 34113, Korea.
| | - Byeong-Ha Lee
- Department of Life Science, Sogang University, Seoul 04107, Korea.
| | - Jungeun Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Korea.
- Polar Science, University of Science & Technology, Daejeon 34113, Korea.
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48
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Puttick MN, Morris JL, Williams TA, Cox CJ, Edwards D, Kenrick P, Pressel S, Wellman CH, Schneider H, Pisani D, Donoghue PCJ. The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte. Curr Biol 2018; 28:733-745.e2. [PMID: 29456145 DOI: 10.1016/j.cub.2018.01.063] [Citation(s) in RCA: 242] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/15/2018] [Accepted: 01/22/2018] [Indexed: 11/28/2022]
Abstract
The evolutionary emergence of land plant body plans transformed the planet. However, our understanding of this formative episode is mired in the uncertainty associated with the phylogenetic relationships among bryophytes (hornworts, liverworts, and mosses) and tracheophytes (vascular plants). Here we attempt to clarify this problem by analyzing a large transcriptomic dataset with models that allow for compositional heterogeneity between sites. Zygnematophyceae is resolved as sister to land plants, but we obtain several distinct relationships between bryophytes and tracheophytes. Concatenated sequence analyses that can explicitly accommodate site-specific compositional heterogeneity give more support for a mosses-liverworts clade, "Setaphyta," as the sister to all other land plants, and weak support for hornworts as the sister to all other land plants. Bryophyte monophyly is supported by gene concatenation analyses using models explicitly accommodating lineage-specific compositional heterogeneity and analyses of gene trees. Both maximum-likelihood analyses that compare the fit of each gene tree to proposed species trees and Bayesian supertree estimation based on gene trees support bryophyte monophyly. Of the 15 distinct rooted relationships for embryophytes, we reject all but three hypotheses, which differ only in the position of hornworts. Our results imply that the ancestral embryophyte was more complex than has been envisaged based on topologies recognizing liverworts as the sister lineage to all other embryophytes. This requires many phenotypic character losses and transformations in the liverwort lineage, diminishes inconsistency between phylogeny and the fossil record, and prompts re-evaluation of the phylogenetic affinity of early land plant fossils, the majority of which are considered stem tracheophytes.
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Affiliation(s)
- Mark N Puttick
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK; School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Jennifer L Morris
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK; School of Earth and Ocean Sciences, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Cymon J Cox
- Centro de Ciências do Mar, Universidade do Algarve, Gambelas, 8005-319 Faro, Portugal
| | - Dianne Edwards
- School of Earth and Ocean Sciences, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK
| | - Paul Kenrick
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Silvia Pressel
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Charles H Wellman
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - Harald Schneider
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Center of Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, China.
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
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49
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Wei R, Yan YH, Harris AJ, Kang JS, Shen H, Xiang QP, Zhang XC. Plastid Phylogenomics Resolve Deep Relationships among Eupolypod II Ferns with Rapid Radiation and Rate Heterogeneity. Genome Biol Evol 2017. [PMID: 28854625 DOI: 10.1093/gbe/evx1075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
The eupolypods II ferns represent a classic case of evolutionary radiation and, simultaneously, exhibit high substitution rate heterogeneity. These factors have been proposed to contribute to the contentious resolutions among clades within this fern group in multilocus phylogenetic studies. We investigated the deep phylogenetic relationships of eupolypod II ferns by sampling all major families and using 40 plastid genomes, or plastomes, of which 33 were newly sequenced with next-generation sequencing technology. We performed model-based analyses to evaluate the diversity of molecular evolutionary rates for these ferns. Our plastome data, with more than 26,000 informative characters, yielded good resolution for deep relationships within eupolypods II and unambiguously clarified the position of Rhachidosoraceae and the monophyly of Athyriaceae. Results of rate heterogeneity analysis revealed approximately 33 significant rate shifts in eupolypod II ferns, with the most heterogeneous rates (both accelerations and decelerations) occurring in two phylogenetically difficult lineages, that is, the Rhachidosoraceae-Aspleniaceae and Athyriaceae clades. These observations support the hypothesis that rate heterogeneity has previously constrained the deep phylogenetic resolution in eupolypods II. According to the plastome data, we propose that 14 chloroplast markers are particularly phylogenetically informative for eupolypods II both at the familial and generic levels. Our study demonstrates the power of a character-rich plastome data set and high-throughput sequencing for resolving the recalcitrant lineages, which have undergone rapid evolutionary radiation and dramatic changes in substitution rates.
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Affiliation(s)
- Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, P.R. China
| | - Yue-Hong Yan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, P.R. China
| | - A J Harris
- Department of Botany, Smithsonian Institution, National Museum of Natural History, Washington, District of Columbia
| | - Jong-Soo Kang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, P.R. China
- University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Hui Shen
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, P.R. China
| | - Qiao-Ping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, P.R. China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, P.R. China
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50
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Vasco A, Smalls TL, Graham SW, Cooper ED, Wong GKS, Stevenson DW, Moran RC, Ambrose BA. Challenging the paradigms of leaf evolution: Class III HD-Zips in ferns and lycophytes. THE NEW PHYTOLOGIST 2016; 212:745-758. [PMID: 27385116 DOI: 10.1111/nph.14075] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 05/23/2016] [Indexed: 05/06/2023]
Abstract
Despite the extraordinary significance leaves have for life on Earth, their origin and development remain vigorously debated. More than a century of paleobotanical, morphological, and phylogenetic research has still not resolved fundamental questions about leaves. Developmental genetic data are sparse in ferns, and comparative studies of lycophytes and seed plants have reached opposing conclusions on the conservation of a leaf developmental program. We performed phylogenetic and expression analyses of a leaf developmental regulator (Class III HD-Zip genes; C3HDZs) spanning lycophytes and ferns. We show that a duplication and neofunctionalization of C3HDZs probably occurred in the ancestor of euphyllophytes, and that there is a common leaf developmental mechanism conserved between ferns and seed plants. We show C3HDZ expression in lycophyte and fern sporangia and show that C3HDZs have conserved expression patterns during initiation of lateral primordia (leaves or sporangia). This expression is maintained throughout sporangium development in lycophytes and ferns and indicates an ancestral role of C3HDZs in sporangium development. We hypothesize that there is a deep homology of all leaves and that a sporangium-specific developmental program was coopted independently for the development of lycophyte and euphyllophyte leaves. This provides molecular genetic support for a paradigm shift in theories of lycophyte leaf evolution.
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Affiliation(s)
- Alejandra Vasco
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY, 10458-5126, USA
- Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Mexico DF, 04510, Mexico
| | - Tynisha L Smalls
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY, 10458-5126, USA
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, BC, V6T 1Z4, Canada
| | - Endymion D Cooper
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Dennis W Stevenson
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY, 10458-5126, USA
| | - Robbin C Moran
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY, 10458-5126, USA
| | - Barbara A Ambrose
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY, 10458-5126, USA.
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