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Xu P, Zhang L, Lu L, Zhu Y, Gao D, Liu S. Patterns in Genome-Wide Codon Usage Bias in Representative Species of Lycophytes and Ferns. Genes (Basel) 2024; 15:887. [PMID: 39062666 PMCID: PMC11276031 DOI: 10.3390/genes15070887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/29/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
The latest research shows that ferns and lycophytes have distinct evolutionary lineages. The codon usage patterns of lycophytes and ferns have not yet been documented. To investigate the gene expression profiles across various plant lineages with respect to codon usage, analyze the disparities and determinants of gene evolution in primitive plant species, and identify appropriate exogenous gene expression platforms, the whole-genome sequences of four distinct species were retrieved from the NCBI database. The findings indicated that Ceratopteris richardii, Adiantum capillus-veneris, and Selaginella moellendorffii exhibited an elevated A/U content in their codon base composition and a tendency to end with A/U. Additionally, S. capillus-veneris had more C/G in its codons and a tendency to end with C/G. The ENC values derived from both ENC-plot and ENC-ratio analyses deviated significantly from the standard curves, suggesting that the codon usage preferences of these four species were primarily influenced by genetic mutations and natural selection, with natural selection exerting a more prominent influence. This finding was further supported by PR2-Plot, neutrality plot analysis, and COA. A combination of RSCU and ENC values was used as a reference criterion to rank the codons and further identify the optimal codons. The study identified 24 high-frequency codons in C. richardii, A. capillus-veneris, and Diphasiastrum complanatum, with no shared optimal codons among the four species. Arabidopsis thaliana and Ginkgo biloba exhibited similar codon preferences to the three species, except for S. moellendorffii. This research offers a theoretical framework at the genomic codon level for investigating the phylogenetic relationships between lycophytes and ferns, shedding light on gene codon optimization and its implications for genetic engineering in breeding.
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Affiliation(s)
- Piaoran Xu
- China-Malaysia National Joint Laboratory, Biomedical Reserch Center, Northwest Minzu University, Lanzhou 730030, China; (P.X.); (L.L.); (Y.Z.)
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China;
| | - Lijuan Zhang
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China;
| | - Liping Lu
- China-Malaysia National Joint Laboratory, Biomedical Reserch Center, Northwest Minzu University, Lanzhou 730030, China; (P.X.); (L.L.); (Y.Z.)
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China;
| | - Yanli Zhu
- China-Malaysia National Joint Laboratory, Biomedical Reserch Center, Northwest Minzu University, Lanzhou 730030, China; (P.X.); (L.L.); (Y.Z.)
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China;
| | - Dandan Gao
- China-Malaysia National Joint Laboratory, Biomedical Reserch Center, Northwest Minzu University, Lanzhou 730030, China; (P.X.); (L.L.); (Y.Z.)
| | - Shanshan Liu
- China-Malaysia National Joint Laboratory, Biomedical Reserch Center, Northwest Minzu University, Lanzhou 730030, China; (P.X.); (L.L.); (Y.Z.)
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China;
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Choi IJ, Joh HJ, Lee WH, Kim DS. The complete chloroplast genome sequence and phylogenetic analysis of Asplenium antiquum Makino 1929, an Endangered species in Korea. Mitochondrial DNA B Resour 2024; 9:663-666. [PMID: 38774189 PMCID: PMC11107858 DOI: 10.1080/23802359.2024.2356139] [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: 01/24/2024] [Accepted: 05/11/2024] [Indexed: 05/24/2024] Open
Abstract
Asplenium antiquum Makino 1929 is one of the Endangered endemic species on the Korean Peninsula. The complete chloroplast of A. antiquum is 150,690 bp in length with typical quadripartite structure comprised of large single-copy region of (83,166 bp), a small single copy region (21,932 bp), and two inverted repeat regions, each 22,796 bp in length. 114 genes were detected in the chloroplast genome of A. antiquum, comprising 84 protein-encoding genes, 26 tRNA genes, and 4 rRNA genes. The phylogenetic analysis revealed a monophyletic relationship, placing A. antiquum as a sister to voth A. Prolongatum and A. nidus, forming a subclade of Asplenium species within the Aspleniaceae family. The genomic data obtained from this study will serve as valuable information for the species' genetic classification of Asplenium.
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Affiliation(s)
- I-Jin Choi
- Plant Management & Research Division, Seoul Botanical Park, Seoul, Republic of Korea
| | - Ho Jun Joh
- Plant Management & Research Division, Seoul Botanical Park, Seoul, Republic of Korea
| | - Wan-Hee Lee
- Plant Management & Research Division, Seoul Botanical Park, Seoul, Republic of Korea
| | - Dae-Sung Kim
- Plant Management & Research Division, Seoul Botanical Park, Seoul, Republic of Korea
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3
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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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Kang JS, Giang VNL, Park HS, Park YS, Cho W, Nguyen VB, Shim H, Waminal NE, Park JY, Kim HH, Yang TJ. Evolution of the Araliaceae family involved rapid diversification of the Asian Palmate group and Hydrocotyle specific mutational pressure. Sci Rep 2023; 13:22325. [PMID: 38102332 PMCID: PMC10724125 DOI: 10.1038/s41598-023-49830-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023] Open
Abstract
The Araliaceae contain many valuable species in medicinal and industrial aspects. We performed intensive phylogenomics using the plastid genome (plastome) and 45S nuclear ribosomal DNA sequences. A total of 66 plastome sequences were used, 13 of which were newly assembled in this study, 12 from new sequences, and one from existing data. While Araliaceae plastomes showed conserved genome structure, phylogenetic reconstructions based on four different plastome datasets revealed phylogenetic discordance within the Asian Palmate group. The divergence time estimation revealed that splits in two Araliaceae subfamilies and the clades exhibiting phylogenetic discordances in the Asian Palmate group occurred at two climatic optima, suggesting that global warming events triggered species divergence, particularly the rapid diversification of the Asian Palmate group during the Middle Miocene. Nucleotide substitution analyses indicated that the Hydrocotyloideae plastomes have undergone accelerated AT-biased mutations (C-to-T transitions) compared with the Aralioideae plastomes, and the acceleration may occur in their mitochondrial and nuclear genomes as well. This implies that members of the genus Hydrocotyle, the only aquatic plants in the Araliaceae, have experienced a distinct evolutionary history from the other species. We also discussed the intercontinental disjunction in the genus Panax and proposed a hypothesis to complement the previously proposed hypothesis. Our results provide the evolutionary trajectory of Araliaceae and advance our current understanding of the evolution of Araliaceae species.
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Affiliation(s)
- Jong-Soo Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Vo Ngoc Linh Giang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 700000, Vietnam
| | - Hyun-Seung Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, South Korea
| | - Young Sang Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Woohyeon Cho
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Van Binh Nguyen
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Faculty of Biology, Dalat University, Dalat, 670000, Vietnam
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Nomar Espinosa Waminal
- Department of Life Science, Chromosome Research Institute, Sahmyook University, Seoul, 01795, South Korea
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Seeland, Gatersleben, Germany
| | - Jee Young Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Hyun Hee Kim
- Department of Life Science, Chromosome Research Institute, Sahmyook University, Seoul, 01795, South Korea.
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.
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Xu XM, Wei Z, Sun JZ, Zhao QF, Lu Y, Wang ZL, Zhu SX. Phylogeny of Leontopodium (Asteraceae) in China-with a reference to plastid genome and nuclear ribosomal DNA. FRONTIERS IN PLANT SCIENCE 2023; 14:1163065. [PMID: 37583593 PMCID: PMC10425225 DOI: 10.3389/fpls.2023.1163065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 07/10/2023] [Indexed: 08/17/2023]
Abstract
The infrageneric taxonomy system, species delimitation, and interspecies systematic relationships of Leontopodium remain controversial and complex. However, only a few studies have focused on the molecular phylogeny of this genus. In this study, the characteristics of 43 chloroplast genomes of Leontopodium and its closely related genera were analyzed. Phylogenetic relationships were inferred based on chloroplast genomes and nuclear ribosomal DNA (nrDNA). Finally, together with the morphological characteristics, the relationships within Leontopodium were identified and discussed. The results showed that the chloroplast genomes of Filago, Gamochaeta, and Leontopodium were well-conserved in terms of gene number, gene order, and GC content. The most remarkable differences among the three genera were the length of the complete chloroplast genome, large single-copy region, small single-copy region, and inverted repeat region. In addition, the chloroplast genome structure of Leontopodium exhibited high consistency and was obviously different from that of Filago and Gamochaeta in some regions, such as matk, trnK (UUU)-rps16, petN-psbM, and trnE (UUC)-rpoB. All the phylogenetic trees indicated that Leontopodium was monophyletic. Except for the subgeneric level, our molecular phylogenetic results were inconsistent with the previous taxonomic system, which was based on morphological characteristics. Nevertheless, we found that the characteristics of the leaf base, stem types, and carpopodium base were phylogenetically correlated and may have potential value in the taxonomic study of Leontopodium. In the phylogenetic trees inferred using complete chloroplast genomes, the subgen. Leontopodium was divided into two clades (Clades 1 and 2), with most species in Clade 1 having herbaceous stems, amplexicaul, or sheathed leaves, and constricted carpopodium; most species in Clade 2 had woody stems, not amplexicaul and sheathed leaves, and not constricted carpopodium.
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Affiliation(s)
| | | | | | | | | | | | - Shi-Xin Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
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6
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Zhang ZL, Zhao HY, Tian Y, Li XY, Liu JX, Shi LC. The complete chloroplast genome and phylogenetic analysis of Lemmaphyllum carnosum var. drymoglossoides (baker) X. P. Wei, 2013. Mitochondrial DNA B Resour 2023; 8:635-638. [PMID: 37312970 PMCID: PMC10259309 DOI: 10.1080/23802359.2023.2220426] [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: 10/25/2022] [Accepted: 05/25/2023] [Indexed: 06/15/2023] Open
Abstract
Lemmaphyllum carnosum var. drymoglossoides (Baker) X. P. Wei, 2013 is a valuable medicinal fern in China. Its complete chloroplast genome was determined using Illumina paired-end sequencing. The genome was 157,571 bp in length with 130 genes, including 87 protein-coding genes, eight ribosomal RNA genes, and 35 tRNA genes. It displayed a quadripartite structure consisting of a small single-copy (SSC) of 21,691 bp, a large single-copy (LSC) of 81,106 bp, and two inverted repeats (IRs) of 27,387 bp, respectively. The phylogenetic results indicated that L. carnosum var. drymoglossoides exhibited the closest relationship with L. intermedium, and this study provided new information for the phylogenetic relationship of the Polypodiaceae family.
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Affiliation(s)
- Zhao-lei Zhang
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
- Key Laboratory of Chinese Medicine Resources Conservation, State dministration of Traditional Chinese Medicine of the People’s Republic of China, Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hong-ye Zhao
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Yu Tian
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Xin-yi Li
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Jin-xin Liu
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
- Key Laboratory of Chinese Medicine Resources Conservation, State dministration of Traditional Chinese Medicine of the People’s Republic of China, Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lin-chun Shi
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
- Key Laboratory of Chinese Medicine Resources Conservation, State dministration of Traditional Chinese Medicine of the People’s Republic of China, Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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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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Shang H, Xue ZQ, Liang ZL, Kessler M, Pollawatn R, Lu NT, Gu YF, Fan XP, Tan YH, Zhang L, Zhou XM, Wan X, Zhang LB. Splitting one species into 22: an unusual tripling of molecular, morphological, and geographical differentiation in the fern family Didymochlaenaceae (Polypodiales). Cladistics 2023. [PMID: 37084123 DOI: 10.1111/cla.12539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 03/06/2023] [Accepted: 03/21/2023] [Indexed: 04/22/2023] Open
Abstract
The pantropical fern genus Didymochlaena (Didymochlaenaceae) has long been considered to contain one species only. Recent studies have resolved this genus/family as either sister to the rest of eupolypods I or as the second branching lineage of eupolypods I, and have shown that this genus is not monospecific, but the exact species diversity is unknown. In this study, a new phylogeny is reconstructed based on an expanded taxon sampling and six molecular markers. Our major results include: (i) Didymochlaena is moderately or weakly supported as sister to the rest of eupolypods I, highlighting the difficulty in resolving the relationships of this important fern lineage in the polypods; (ii) species in Didymochlaena are resolved into a New World clade and an Old World clade, and the latter further into an African clade and an Asian-Pacific clade; (iii) an unusual tripling of molecular, morphological and geographical differentiation in Didymochlaena is detected, suggesting single vicariance or dispersal events in individual regions and no evidence for reversals at all, followed by allopatric speciation at more or less homogeneous rates; (iv) evolution of 18 morphological characters is inferred and two morphological synapomorphies defining the family are recognized-the elliptical sori and fewer than 10 sori per pinnule, the latter never having been suggested before; (v) based on morphological and molecular variation, 22 species in the genus are recognized contrasting with earlier estimates of between one and a few; and (vi) our biogeographical analysis suggests an origin for Didymochlaena in the latest Jurassic-earliest Cretaceous and the initial diversification of the extant lineages in the Miocene-all but one species diverged from their sisters within the last 27 Myr, in most cases associated with allopatric speciation owing to geologic and climatic events, or dispersal.
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Affiliation(s)
- Hui Shang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Missouri Botanical Garden, 4344 Shaw Blvd, St Louis, MO, 63110, USA
| | - Zhi-Qing Xue
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| | - Zhen-Long Liang
- Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan, 610041, China
| | - Michael Kessler
- Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Rossarin Pollawatn
- Plants of Thailand Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Ngan Thi Lu
- Department of Biology, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18th Hoang Quoc Viet Road, Ha Noi, Vietnam
| | - Yu-Feng Gu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation & Research Center of Shenzhen, Shenzhen, Guangdong, 518114, China
| | - Xue-Ping Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan, 610041, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Yun-Hong Tan
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Liang Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Xin-Mao Zhou
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650091, China
| | - Xia Wan
- Missouri Botanical Garden, 4344 Shaw Blvd, St Louis, MO, 63110, USA
- Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan, 610041, China
- College of Life Sciences, Sichuan University, Chengdu, 610065, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Bing Zhang
- Missouri Botanical Garden, 4344 Shaw Blvd, St Louis, MO, 63110, USA
- Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan, 610041, China
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Tang JY, Wei R, Zhang XC, Xiang QP. Mitogenome-based phylogenomics provides insights into the positions of the enigmatic sinensis group and the sanguinolenta group in Selaginellaceae (Lycophyte). Mol Phylogenet Evol 2023; 179:107673. [PMID: 36528332 DOI: 10.1016/j.ympev.2022.107673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 10/14/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022]
Abstract
Spikemoss (Selaginellaceae) is one of the basal lineages of vascular plants. This family has a single genus Selaginella which consists of about 750 extant species. The phylogeny of Selaginellaceae has been extensively studied mainly based on plastid DNA and a few nuclear sequences. However, the placement of the enigmatic sinensis group is a long-term controversy because of the long branch in the plastid DNA phylogeny. The sanguinolenta group is also a phylogenetically problematic clade owing to two alternative positions resulted from different datasets. Here, we newly sequenced 34 mitochondrial genomes (mitogenomes) of individuals representing all seven subgenera and major clades in Selaginellaceae. We assembled the draft mitogenomes and annotated the genes and performed phylogenetic analyses based on the shared 17 mitochondrial genes. Our major results include: (1) all the assembled mitogenomes have complicated structures, unparalleled high GC content and a small gene content set, and the positive correlations among GC content, substitution rates and the number of RNA editing sites hold; (2) the sinensis group was well supported as a member of subg. Stachygynandrum; (3) the sanguinolenta group was strongly resolved as sister to all other Selaginella species except for subg. Selaginella. This study demonstrates the potential of mitogenome data in providing novel insights into phylogenetically recalcitrant problems.
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Affiliation(s)
- Jun-Yong Tang
- 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
| | - Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany, 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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10
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Duan Y, Fu S, Ye Z, Bu W. Phylogeny of Urostylididae (Heteroptera: Pentatomoidea) reveals rapid radiation and challenges traditional classification. ZOOL SCR 2023. [DOI: 10.1111/zsc.12582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Yujie Duan
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
| | - Siying Fu
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
| | - Zhen Ye
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
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11
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Vu TTT, Vu LTK, Le LT, Lo TTM, Chu MH. Analysis of the Chloroplast Genome of Ficus simplicissima Lour Collected in Vietnam and Proposed Barcodes for Identifying Ficus Plants. Curr Issues Mol Biol 2023; 45:1024-1036. [PMID: 36826012 PMCID: PMC9955830 DOI: 10.3390/cimb45020067] [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: 12/31/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 02/03/2023] Open
Abstract
Ficus simplicissima Lour. is an Asian species of fig tree in the family Moraceae. The chloroplast (cp) genome of F. simplicissima m3 was sequenced using the Pacbio sequel platform. The F. simplicissima cpDNA has a size of 160,321 bp in length, of which GC content accounts for 36.13%. The cp genome of F. simplicissima consists of a single large copy (LSC) with a size of 91,346 bp, a single small copy (SSC) with a size of 20,131 bp, and a pair of inverted repeats with a size of 24,421 to 24,423 bp. The cp genome of F. simplicissima has 127 genes, including 85 protein-coding genes, eight rRNA genes, and 34 tRNA genes; 92 simple sequence repeats and 39 long repeats were detected in the cpDNA of F. simplicissim. A comparative cp genome analysis among six species in the Ficus genus indicated that the genome structure and gene content were highly conserved. The non-coding regions show more differentiation than the coding regions, and the LSC and SSC regions show more differences than the inverted repeat regions. Phylogenetic analysis supported that F. simplicissima m3 had a close relationship with F. hirta. The complete cp genome of F. simplicissima was proposed as a chloroplast DNA barcoding for genus-level in the Moraceae family and the psbA-trnH gene region for species-level identification.
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Affiliation(s)
- Thuy Thi Thu Vu
- Department of Genetics and Biotechnology, TNU-University of Education, Thainguyen 250000, Vietnam
| | - Lien Thi Kim Vu
- Institute of Theoretical and Applied Research, Duy Tan University, Hanoi 100000, Vietnam
- Faculty of Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
| | - Lam Tung Le
- VAST Institute of Biotechnology, Hanoi 100000, Vietnam
| | - Thu Thi Mai Lo
- Department of Biology, Taybac University, Sonla 360000, Vietnam
| | - Mau Hoang Chu
- Department of Genetics and Biotechnology, TNU-University of Education, Thainguyen 250000, Vietnam
- Correspondence:
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12
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Xu G, Zhang C, Lee SY, Chen Z, Zeng X. The complete chloroplast genome and phylogenetic analysis of Christella dentata (Forssk.) Brownsey & Jermy (Thelypteridaceae). Mitochondrial DNA B Resour 2023; 8:181-185. [PMID: 36713297 PMCID: PMC9879191 DOI: 10.1080/23802359.2023.2168114] [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] [Indexed: 01/27/2023] Open
Abstract
Christella dentata (Forssk.) Brownsey & Jermy (Thelypteridaceae) is endemic to the tropical and subtropical regions of Africa, Asia, and Asia Pacific. In this study, the complete chloroplast genome sequence of C. dentata was assembled using next-generation sequencing data. The complete chloroplast genome was 151,662 bp in length and had a typical quadripartite structure, which consisted of a small single-copy region (21,776 bp) and a large single-copy region (82,624 bp) that were separated by a pair of inverted repeats (23,631 bp each). A total of 131 genes were predicted, including 89 protein coding (CDS), 34 tRNA, and eight rRNA genes. The overall GC content of the chloroplast genome was 42.48%. Based on the concatenated shared unique CDS sequence dataset, phylogenetic analysis using both the maximum-likelihood and the Bayesian inference methods revealed that C. dentata is placed within Thelypteridaceae and is closely related to Christella appendiculata. Such genetic information would be useful for studies on the evolution pattern in ferns. The availability of chloroplast genome sequence for the species also paves the way to resolving the complicated relationship among members of Christella.
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Affiliation(s)
- Guoliang Xu
- Jiangxi Provincial Management Bureau for Jiulian Mountain National Natural Reserve, Longnan, China
| | - Changyou Zhang
- Jiangxi Provincial Management Bureau for Jiulian Mountain National Natural Reserve, Longnan, China
| | - Shiou Yih Lee
- Faculty of Health and Life Sciences, INTI International University, Nilai, Malaysia
| | - Zhihui Chen
- School of Life Science, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-sen University, Guangzhou, China
| | - Xiaohui Zeng
- Jiangxi Provincial Management Bureau for Jinggang Mountain National Nature Reserve, Ji’an, China,CONTACT Xiaohui Zeng Jiangxi Provincial Management Bureau for Jinggang Mountain National Nature Reserve, Ji’an, Jiangxi343600, China
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13
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Li Y, Chen X, Lin X, Gu Y, Liu B, Zhang R. Complete chloroplast genome of Isoetes orientalis (Isoetaceae), an endangered quillwort from China. Mitochondrial DNA B Resour 2023; 8:342-346. [PMID: 36876143 PMCID: PMC9980155 DOI: 10.1080/23802359.2023.2183070] [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] [Indexed: 03/05/2023] Open
Abstract
Isoetes orientalis is an endangered hexaploidy species of Isoetaceae in China and the complete chloroplast genome of this species has not been reported. In the present study, a complete chloroplast genome of Isoetes orientalis (Isoetaceae) was assembled and annotated. This chloroplast genome has a circular structure of 145,504 bp in length, comprising a pair of inverted repeat (IR) regions of 13,207 bp each, a large single-copy (LSC) region of 91,864 bp, and a small single-copy (SSC) region of 27,226 bp. The chloroplast genome contains 136 genes, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis showed that I. orientalis was closely related to I. sinensis. These results provide additional resources for future studies on Isoetes from China and across the globe.
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Affiliation(s)
- Yanqing Li
- College of Life Sciences, South China Agricultural University, Guangzhou, China.,Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
| | - Xi Chen
- Life Science and Technology College, Harbin Normal University, Key Laboratory of Plant Biology in Colleges of Heilongjiang Province, Harbin, China
| | - Xiaoyan Lin
- Life Science and Technology College, Harbin Normal University, Key Laboratory of Plant Biology in Colleges of Heilongjiang Province, Harbin, 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.,Life Science and Technology College, Harbin Normal University, Key Laboratory of Plant Biology in Colleges of Heilongjiang Province, Harbin, China
| | - Baodong Liu
- Life Science and Technology College, Harbin Normal University, Key Laboratory of Plant Biology in Colleges of Heilongjiang Province, Harbin, China
| | - Rongjing Zhang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
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14
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Zhang ZR, Yang X, Li WY, Peng YQ, Gao J. Comparative chloroplast genome analysis of Ficus (Moraceae): Insight into adaptive evolution and mutational hotspot regions. FRONTIERS IN PLANT SCIENCE 2022; 13:965335. [PMID: 36186045 PMCID: PMC9521400 DOI: 10.3389/fpls.2022.965335] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
As the largest genus in Moraceae, Ficus is widely distributed across tropical and subtropical regions and exhibits a high degree of adaptability to different environments. At present, however, the phylogenetic relationships of this genus are not well resolved, and chloroplast evolution in Ficus remains poorly understood. Here, we sequenced, assembled, and annotated the chloroplast genomes of 10 species of Ficus, downloaded and assembled 13 additional species based on next-generation sequencing data, and compared them to 46 previously published chloroplast genomes. We found a highly conserved genomic structure across the genus, with plastid genome sizes ranging from 159,929 bp (Ficus langkokensis) to 160,657 bp (Ficus religiosa). Most chloroplasts encoded 113 unique genes, including a set of 78 protein-coding genes, 30 transfer RNA (tRNA) genes, four ribosomal RNA (rRNA) genes, and one pseudogene (infA). The number of simple sequence repeats (SSRs) ranged from 67 (Ficus sagittata) to 89 (Ficus microdictya) and generally increased linearly with plastid size. Among the plastomes, comparative analysis revealed eight intergenic spacers that were hotspot regions for divergence. Additionally, the clpP, rbcL, and ccsA genes showed evidence of positive selection. Phylogenetic analysis indicated that none of the six traditionally recognized subgenera of Ficus were monophyletic. Divergence time analysis based on the complete chloroplast genome sequences showed that Ficus species diverged rapidly during the early to middle Miocene. This research provides basic resources for further evolutionary studies of Ficus.
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Affiliation(s)
- Zheng-Ren Zhang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xue Yang
- College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Wei-Ying Li
- Southwest Research Center for Landscape Architecture Engineering Technology, State Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Yan-Qiong Peng
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Jie Gao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
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15
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Nitta JH, Schuettpelz E, Ramírez-Barahona S, Iwasaki W. An open and continuously updated fern tree of life. FRONTIERS IN PLANT SCIENCE 2022; 13:909768. [PMID: 36092417 PMCID: PMC9449725 DOI: 10.3389/fpls.2022.909768] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/12/2022] [Indexed: 05/31/2023]
Abstract
Ferns, with about 12,000 species, are the second most diverse lineage of vascular plants after angiosperms. They have been the subject of numerous molecular phylogenetic studies, resulting in the publication of trees for every major clade and DNA sequences from nearly half of all species. Global fern phylogenies have been published periodically, but as molecular systematics research continues at a rapid pace, these become quickly outdated. Here, we develop a mostly automated, reproducible, open pipeline to generate a continuously updated fern tree of life (FTOL) from DNA sequence data available in GenBank. Our tailored sampling strategy combines whole plastomes (few taxa, many loci) with commonly sequenced plastid regions (many taxa, few loci) to obtain a global, species-level fern phylogeny with high resolution along the backbone and maximal sampling across the tips. We use a curated reference taxonomy to resolve synonyms in general compliance with the community-driven Pteridophyte Phylogeny Group I classification. The current FTOL includes 5,582 species, an increase of ca. 40% relative to the most recently published global fern phylogeny. Using an updated and expanded list of 51 fern fossil constraints, we find estimated ages for most families and deeper clades to be considerably older than earlier studies. FTOL and its accompanying datasets, including the fossil list and taxonomic database, will be updated on a regular basis and are available via a web portal (https://fernphy.github.io) and R packages, enabling immediate access to the most up-to-date, comprehensively sampled fern phylogeny. FTOL will be useful for anyone studying this important group of plants over a wide range of taxonomic scales, from smaller clades to the entire tree. We anticipate FTOL will be particularly relevant for macroecological studies at regional to global scales and will inform future taxonomic systems with the most recent hypothesis of fern phylogeny.
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Affiliation(s)
- Joel H. Nitta
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Eric Schuettpelz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Santiago Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
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16
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Xiang QP, Tang JY, Yu JG, Smith DR, Zhu YM, Wang YR, Kang JS, Yang J, Zhang XC. The evolution of extremely diverged plastomes in Selaginellaceae (lycophyte) is driven by repeat patterns and the underlying DNA maintenance machinery. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:768-784. [PMID: 35648423 DOI: 10.1111/tpj.15851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/25/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Two factors are proposed to account for the unusual features of organellar genomes: the disruptions of organelle-targeted DNA replication, repair, and recombination (DNA-RRR) systems in the nuclear genome and repetitive elements in organellar genomes. Little is known about how these factors affect organellar genome evolution. The deep-branching vascular plant family Selaginellaceae is known to have a deficient DNA-RRR system and convergently evolved organellar genomes. However, we found that the plastid genome (plastome) of Selaginella sinensis has extremely accelerated substitution rates, a low GC content, pervasive repeat elements, a dynamic network structure, and it lacks direct or inverted repeats. Unexpectedly, its organelle DNA-RRR system is short of a plastid-targeted Recombinase A1 (RecA1) and a mitochondrion-targeted RecA3, in line with other explored Selaginella species. The plastome contains a large collection of short- and medium-sized repeats. Given the absence of RecA1 surveillance, we propose that these repeats trigger illegitimate recombination, accelerated mutation rates, and structural instability. The correlations between repeat quantity and architectural complexity in the Selaginella plastomes support these conclusions. We, therefore, hypothesize that the interplay of the deficient DNA-RRR system and the high repeat content has led to the extraordinary divergence of the S. sinensis plastome. Our study not only sheds new light on the mechanism of plastome divergence by emphasizing the power of cytonuclear integration, but it also reconciles the longstanding contradiction on the effects of DNA-RRR system disruption on genome structure evolution.
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Affiliation(s)
- Qiao-Ping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Jun-Yong Tang
- 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
| | - Ji-Gao Yu
- 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
| | - David Roy Smith
- Department of Biology, University of Western Ontario, London, N6A 5B7, Ontario, Canada
| | - Yan-Mei Zhu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Ya-Rong Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Jong-Soo Kang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Jie Yang
- 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
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17
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Pelosi JA, Kim EH, Barbazuk WB, Sessa EB. Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns. FRONTIERS IN PLANT SCIENCE 2022; 13:882441. [PMID: 35909764 PMCID: PMC9330400 DOI: 10.3389/fpls.2022.882441] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/16/2022] [Indexed: 05/31/2023]
Abstract
Ferns are the second largest clade of vascular plants with over 10,000 species, yet the generation of genomic resources for the group has lagged behind other major clades of plants. Transcriptomic data have proven to be a powerful tool to assess phylogenetic relationships, using thousands of markers that are largely conserved across the genome, and without the need to sequence entire genomes. We assembled the largest nuclear phylogenetic dataset for ferns to date, including 2884 single-copy nuclear loci from 247 transcriptomes (242 ferns, five outgroups), and investigated phylogenetic relationships across the fern tree, the placement of whole genome duplications (WGDs), and gene retention patterns following WGDs. We generated a well-supported phylogeny of ferns and identified several regions of the fern phylogeny that demonstrate high levels of gene tree-species tree conflict, which largely correspond to areas of the phylogeny that have been difficult to resolve. Using a combination of approaches, we identified 27 WGDs across the phylogeny, including 18 large-scale events (involving more than one sampled taxon) and nine small-scale events (involving only one sampled taxon). Most inferred WGDs occur within single lineages (e.g., orders, families) rather than on the backbone of the phylogeny, although two inferred events are shared by leptosporangiate ferns (excluding Osmundales) and Polypodiales (excluding Lindsaeineae and Saccolomatineae), clades which correspond to the majority of fern diversity. We further examined how retained duplicates following WGDs compared across independent events and found that functions of retained genes were largely convergent, with processes involved in binding, responses to stimuli, and certain organelles over-represented in paralogs while processes involved in transport, organelles derived from endosymbiotic events, and signaling were under-represented. To date, our study is the most comprehensive investigation of the nuclear fern phylogeny, though several avenues for future research remain unexplored.
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Affiliation(s)
- Jessie A. Pelosi
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Emily H. Kim
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - W. Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Emily B. Sessa
- Department of Biology, University of Florida, Gainesville, FL, United States
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18
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Plastid phylogenomic analyses of the Selaginella sanguinolenta group (Selaginellaceae) reveal conflict signatures resulting from sequence types, outlier genes, and pervasive RNA editing. Mol Phylogenet Evol 2022; 173:107507. [PMID: 35589053 DOI: 10.1016/j.ympev.2022.107507] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 04/11/2022] [Accepted: 04/21/2022] [Indexed: 11/23/2022]
Abstract
Different from the generally conserved plastomes (plastid genomes) of most land plants, the Selaginellaceae plastomes exhibit dynamic structure, high GC content and high substitution rates. Previous plastome analyses identified strong conflict on several clades in Selaginella, however the factors causing the conflictions and the impact on the phylogenetic inference have not been sufficiently investigated. Here, we dissect the distribution of phylogenetic signals and conflicts in Selaginella sanguinolenta group, the plastome of which is DR (direct repeats) structure and with genome-wide RNA editing. We analyzed the data sets including 22 plastomes representing all species of the S. sanguinolenta group, covering the entire geographical distribution from the Himalayas to Siberia and the Russian Far East regions. We recovered four different topologies by applying multispecies coalescent (ASTRAL) and concatenation methods (IQ-TREE and RAxML) on four data sets of PC (protein-coding genes), NC (non-coding sequences), PCN (the concatenated PC and NC), and RC (predicted RNA editing sites "C" were corrected by "T"), respectively. Six monophyletic clades, S. nummularifolia clade, S. rossii clade, S. sajanensis clade, S. sanguinolenta I clade, S. sanguinolenta II clade, and S. sanguinolenta III clade, were consistently resolved and supported by the characteristics of GC content, RNA editing frequency, and gene content. However, the relationships among these clades varied across the four topologies. To explore the underlying causes of the uncertainty, we compared the phylogenetic signals of the four topologies. We identified that the sequence types (coding versus non-coding), outlier genes (genes with extremely high |ΔGLS| values), and C-to-U RNA editing frequency in the protein-coding genes were responsible for the unstable phylogenomic relationship. We further revealed a significant positive correlation between the |ΔGLS| values and the variation coefficient of the RNA editing number. Our results demonstrated that the coalescent method performed better than the concatenation method in overcoming the problems caused by outlier genes and extreme RNA editing events. Our study particularly focused on the importance of exploring the plastid phylogenomic conflicts and suggested conducting concatenated analyses cautiously when adopting organelle genome data.
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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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20
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Yu JH, Zhang R, Liu QL, Wang FG, Yu XL, Dai XL, Liu YB, Yan YH. Ceratopteris chunii and Ceratopteris chingii (Pteridaceae), two new diploid species from China, based on morphological, cytological, and molecular data. PLANT DIVERSITY 2022; 44:300-307. [PMID: 35769586 PMCID: PMC9209876 DOI: 10.1016/j.pld.2021.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 10/16/2021] [Accepted: 10/20/2021] [Indexed: 06/15/2023]
Abstract
Understanding how natural hybridization and polyploidizations originate in plants requires identifying potential diploid ancestors. However, cryptic plant species are widespread, particularly in Ceratopteris (Pteridaceae). Identifying Ceratopteris cryptic species with different polyploidy levels is a challenge because Ceratopteris spp. exhibit high degrees of phenotypic plasticity. Here, two new cryptic species of Ceratopteris, Ceratopteris chunii and Ceratopteris chingii, are described and illustrated. Phylogenetic analyses reveal that each of the new species form a well-supported clade. C. chunii and C. chingii are similar to Ceratopteris gaudichaudii var. vulgaris and C. pteridoides, respectively, but distinct from their relatives in the stipe, basal pinna of the sterile leaf or subelliptic shape of the fertile leaf, as well as the spore surface. In addition, chromosome studies indicate that C. chunii and C. chingii are both diploid. These findings will help us further understand the origin of Ceratopteris polyploids in Asia.
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Affiliation(s)
- Jun-Hao Yu
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
- College of Life Science, Shanghai Normal University, Shanghai, 200234, China
| | - Rui Zhang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Qiao-Ling Liu
- College of Life Science, Shanghai Normal University, Shanghai, 200234, China
| | - Fa-Guo Wang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Xun-Lin Yu
- College of Forestry, Central South University of Forestry & Technology, Changsha, Hunan, 410004, China
| | - Xi-Ling Dai
- College of Life Science, Shanghai Normal University, Shanghai, 200234, China
| | - Yong-Bo Liu
- State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Yue-Hong Yan
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
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21
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Wei R, Yang J, He LJ, Liu HM, Hu JY, Liang SQ, Wei XP, Zhao CF, Zhang XC. Plastid phylogenomics provides novel insights into the infrafamilial relationship of Polypodiaceae. Cladistics 2021; 37:717-727. [PMID: 34841589 DOI: 10.1111/cla.12461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2021] [Indexed: 01/01/2023] Open
Abstract
The polygrammoids (Polypodiaceae) are the most species-rich and diversified epiphytic fern lineages, and hold an important role to understand the deep diverging events and rapid adaptation to changing environments in the plant tree of life. Despite progress in the phylogeny of this group of ferns in previous multilocus phylogenetic studies, uncertainty remains especially in backbone relationships among closely related clades, and the phylogenetic placement of recalcitrant species or lineages. Here, we investigated the deep phylogenetic relationships within Polypodiaceae by sampling all major lineages and using 81 plastid genomes (plastomes), of which 70 plastomes were newly sequenced with high-throughput sequencing technology. Based on parsimony, maximum-likelihood, Bayesian and multispecies coalescent analyses of genome skimming data, we achieved a better resolution of the backbone phylogeny of Polypodiaceae. Using simulated data matrices, we detected that potential phylogenetic artefacts, such as long-branch attraction and insufficient taxonomic sampling, may have a confounding impact on the incongruence of phylogenetic inferences. Furthermore, our phylogenetic analyses offer greater resolution than previous multilocus studies, providing a robust framework for future phylogenetic implications on the subfamilial taxonomy of Polypodiaceae. Our phylogenomic study not only demonstrates the advantage of a character-rich plastome dataset for resolving the recalcitrant lineages that have undergone rapid radiation, but also sheds new light on integrative explorations understanding the evolutionary history of large fern groups in the genomic era.
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Affiliation(s)
- Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jie Yang
- 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
| | - Li-Juan He
- Xiamen Overseas Chinese Subtropical Plant Introduction Garden/Plant Introduction & Quarantine and Plant Product Key Laboratory of Xiamen, Xiamen, Fujian, 361002, China
| | - Hong-Mei Liu
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - Jia-Yu Hu
- 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
| | - 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
| | - Xue-Ping Wei
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Cun-Feng Zhao
- 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
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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22
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Ben-Menni Schuler S, Picazo-Aragonés J, Rumsey FJ, Romero-García AT, Suárez-Santiago VN. Macaronesia Acts as a Museum of Genetic Diversity of Relict Ferns: The Case of Diplazium caudatum (Athyriaceae). PLANTS 2021; 10:plants10112425. [PMID: 34834788 PMCID: PMC8623695 DOI: 10.3390/plants10112425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/05/2022]
Abstract
Macaronesia has been considered a refuge region of the formerly widespread subtropical lauroid flora that lived in Southern Europe during the Tertiary. The study of relict angiosperms has shown that Macaronesian relict taxa preserve genetic variation and revealed general patterns of colonization and dispersal. However, information on the conservation of genetic diversity and range dynamics rapidly diminishes when referring to pteridophytes, despite their dominance of the herbaceous stratum in the European tropical palaeoflora. Here we aim to elucidate the pattern of genetic diversity and phylogeography of Diplazium caudatum, a hypothesized species of the Tertiary Palaeotropical flora and currently with its populations restricted across Macaronesia and disjunctly in the Sierras de Algeciras (Andalusia, southern Iberian Peninsula). We analysed 12 populations across the species range using eight microsatellite loci, sequences of a region of plastid DNA, and carry out species-distribution modelling analyses. Our dating results confirm the Tertiary origin of this species. The Macaronesian archipelagos served as a refuge during at least the Quaternary glacial cycles, where populations of D. caudatum preserved higher levels of genetic variation than mainland populations. Our data suggest the disappearance of the species in the continent and the subsequent recolonization from Macaronesia. The results of the AMOVA analysis and the indices of clonal diversity and linkage disequilibrium suggest that D. caudatum is a species in which inter-gametophytic outcrossing predominates, and that in the Andalusian populations there was a shift in mating system toward increased inbreeding and/or clonality. The model that best explains the genetic diversity distribution pattern observed in Macaronesia is, the initial and recurrent colonization between islands and archipelagos and the relatively recent diversification of restricted area lineages, probably due to the decrease of favorable habitats and competition with lineages previously established. This study extends to ferns the concept of Macaronesia archipelagos as refugia for genetic variation.
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Affiliation(s)
- Samira Ben-Menni Schuler
- Department of Botany, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (S.B.-M.S.); (J.P.-A.); (A.T.R.-G.)
| | - Jesús Picazo-Aragonés
- Department of Botany, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (S.B.-M.S.); (J.P.-A.); (A.T.R.-G.)
| | - Fred J. Rumsey
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK;
| | - Ana Teresa Romero-García
- Department of Botany, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (S.B.-M.S.); (J.P.-A.); (A.T.R.-G.)
| | - Víctor N. Suárez-Santiago
- Department of Botany, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (S.B.-M.S.); (J.P.-A.); (A.T.R.-G.)
- Correspondence: ; Tel.: +34-958-248814
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23
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Du XY, Lu JM, Zhang LB, Wen J, Kuo LY, Mynssen CM, Schneider H, Li DZ. Simultaneous diversification of Polypodiales and angiosperms in the Mesozoic. Cladistics 2021; 37:518-539. [PMID: 34570931 DOI: 10.1111/cla.12457] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2021] [Indexed: 01/21/2023] Open
Abstract
Comprising about 82% of the extant fern species diversity, Polypodiales are generally believed to have diversified in the Late Cretaceous. We estimated the divergence times of Polypodiales using both penalized likelihood and Bayesian methods, based on a dataset consisting of 208 plastomes representing all 28 families and 14 fossil constraints reflecting current interpretations of fossil record. Our plastome phylogeny recovered the same six major lineages as a recent nuclear phylogeny, but the position of Dennstaedtiineae was different. The present phylogeny showed high resolution of relationships among the families of Polypodiales, especially among those forming the Aspleniineae. The divergence time estimates supported the most recent common ancestor of Polypodiales and its closest relative dating back to the Triassic, establishment of the major lineages in the Jurassic, and a likely accelerated radiation during the late Jurassic and the Early Cretaceous. The estimated divergence patterns of Polypodiales and angiosperms converge to a scenario in which their main lineages were established simultaneously shortly before the onset of the Cretaceous Terrestrial Revolution, and further suggest a pre-Cretaceous hidden history for both lineages. The pattern of simultaneous diversifications shown here elucidate an important gap in our understanding of the Terrestrial Revolution that shaped today's ecosystems.
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Affiliation(s)
- Xin-Yu Du
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan, 650201, China.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan, 650201, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, 19 Qingsong Road, Kunming, Yunnan, 650201, China
| | - Jin-Mei Lu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan, 650201, China.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan, 650201, China
| | - Li-Bing Zhang
- Missouri Botanical Garden, 4344 Shaw Blvd, St Louis, MO, 63110, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Li-Yaung Kuo
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan, ROC
| | - Claudine M Mynssen
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Pacheco Leão 915, Rio de Janeiro, RJ, 22460-030, Brazil
| | - Harald Schneider
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666000, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan, 650201, China.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan, 650201, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, 19 Qingsong Road, Kunming, Yunnan, 650201, China
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24
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Fan R, Ma W, Liu S, Huang Q. Integrated analysis of three newly sequenced fern chloroplast genomes: Genome structure and comparative analysis. Ecol Evol 2021; 11:4550-4563. [PMID: 33976830 PMCID: PMC8093657 DOI: 10.1002/ece3.7350] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Some ferns have medicinal properties and are used in therapeutic interventions. However, the classification and phylogenetic relationships of ferns remain incompletely reported. Considering that chloroplast genomes provide ideal information for species identification and evolution, in this study, three unpublished and one published ferns were sequenced and compared with other ferns to obtain comprehensive information on their classification and evolution. MATERIALS AND METHODS The complete chloroplast genomes of Dryopteris goeringiana (Kunze) Koidz, D. crassirhizoma Nakai, Athyrium brevifrons Nakai ex Kitagawa, and Polystichum tripteron (Kunze) Presl were sequenced using the Illumina HiSeq 4,000 platform. Simple sequence repeats (SSRs), nucleotide diversity analysis, and RNA editing were investigated in all four species. Genome comparison and inverted repeats (IR) boundary expansion and contraction analyses were also performed. The relationships among the ferns were studied by phylogenetic analysis based on the whole chloroplast genomes. RESULTS The whole chloroplast genomes ranged from 148,539 to 151,341 bp in size and exhibited typical quadripartite structures. Ten highly variable loci with parsimony informative (Pi) values of > 0.02 were identified. A total of 75-108 SSRs were identified, and only six SSRs were present in all four ferns. The SSRs contained a higher number of A + T than G + C bases. C-to-U conversion was the most common type of RNA editing event. Genome comparison analysis revealed that single-copy regions were more highly conserved than IR regions. IR boundary expansion and contraction varied among the four ferns. Phylogenetic analysis showed that species in the same genus tended to cluster together with and had relatively close relationships. CONCLUSION The results provide valuable information on fern chloroplast genomes that will be useful to identify and classify ferns, and study their phylogenetic relationships and evolution.
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Affiliation(s)
- Ruifeng Fan
- School of PharmacyHeilongjiang University of Chinese MedicineHarbinChina
| | - Wei Ma
- School of PharmacyHeilongjiang University of Chinese MedicineHarbinChina
| | - Shilei Liu
- Experimental Teaching & Practical Training CenterHeilongjiang University of Chinese MedicineHarbinChina
| | - Qingyang Huang
- Department of EcologyInstitute of Natural Resources and EcologyHeilongjiang Academy of ScienceHarbinChina
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25
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Pereira JBS, Giulietti AM, Prado J, Vasconcelos S, Watanabe MTC, Pinangé DSB, Oliveira RRM, Pires ES, Caldeira CF, Oliveira G. Plastome-based phylogenomics elucidate relationships in rare Isoëtes species groups from the Neotropics. Mol Phylogenet Evol 2021; 161:107177. [PMID: 33866010 DOI: 10.1016/j.ympev.2021.107177] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/25/2021] [Accepted: 04/06/2021] [Indexed: 10/21/2022]
Abstract
The genus Isoëtes is globally distributed. Within the Neotropics, Isoëtes occurs in various habitats and ecosystems, making it an interesting case study to address phylogenetic and biogeographic questions. We sequenced and assembled plastomes and ribosomal DNA (rDNA) sequences to reconstruct phylogenetic relationships in Isoëtes from tropical regions in the Neotropics. The ploidy level of nine taxa was established to address the potential source of phylogenetic incongruence in the genus. Node ages were estimated using MCMCTree. The ancestral range estimates were conducted in BioGeoBEARS. Plastome-based phylogenies were congruent throughout distinct matrices and partition schemes, exhibiting high support for almost all nodes. Whereas, we found incongruences between the rDNA and plastome datasets. Chromosome counts identified three diploids, five tetraploids and one likely hexaploid among Neotropical species. Plastome-based node age estimates showed that the radiation of the crown Isoëtes group occurred at 20 Ma, with the diversification of the tropical American (TAA) clade taking place in the Pleistocene at 1.7 Ma. Ancestral range estimates showed that the ancestor of the TAA clade may have evolved first in the dry diagonal area in South America before reaching more humid regions. In addition, the colonization of the Brazilian semiarid region occurred three times, while the occupation of the Cerrado and Amazon regions occurred twice and once, respectively. Our study showed a large unobserved diversity within the genus in warm-dry regions in the Neotropics. Plastomes provided sufficient genomic information to establish a robust phylogenetic framework to answer evolutionary questions in Isoëtes from the Neotropics.
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Affiliation(s)
| | - Ana Maria Giulietti
- Universidade Estadual de Feira de Santana, Programa de Pós-Graduação em Botânica, Feira de Santana, Brazil
| | - Jefferson Prado
- Universidade Estadual de São Paulo, Depto de Zoologia e Botânica, São José do Rio Preto, Brazil
| | | | | | - Diego S B Pinangé
- Universidade Federal do Amazonas, Instituto de Ciências Biológicas, Depto de Genética, Manaus, Brazil
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26
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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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27
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Peng Y, Zhang S, Dong S, Peng T. The complete chloroplast genome of the fern Asplenium tenerum (Aspleniaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3761-3763. [PMID: 33367091 PMCID: PMC7671677 DOI: 10.1080/23802359.2020.1831985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Plastid genomes are useful markers in resolving plant phylogenetic relationships for various taxonomic groups. Here, we sequenced and de novo assembled the complete plastid genome sequence of the fern Asplenium tenerum Forst. (Aspleniaceae, Polypodiales) using the genome skimming data. The newly generated plastid genome is conserved in structure and gene content compared with that of closely related species. Plastid phylogenetic analysis of Polypodiales ferns recovered a robust phylogeny, supporting the close relationship of A. tenerum with Asplenium prolongatum.
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Affiliation(s)
- Yang Peng
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen, China
| | - Suzhou Zhang
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen, China
| | - Shanshan Dong
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen, China
| | - Tao Peng
- School of Life Sciences, Guizhou Normal University, Guiyang, China
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28
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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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29
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Yu J, Wang H, Dong H, Fang Y, Xiang J. The complete chloroplast genome sequence of Brainea insignis (Blechnaceae). Mitochondrial DNA B Resour 2020; 5:2034-2035. [PMID: 33457732 PMCID: PMC7782652 DOI: 10.1080/23802359.2020.1756959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Brainea insignis (Hooker) J. Smith, a member of Blechnaceae, is a rare and endangered species in tropical Asia. Here we assembled and annotated the complete chloroplast (cp) genome. It is 149,730 bp in length and encodes 88 protein-coding genes, 36 transfer RNA (tRNA) genes and eight ribosomal RNA (rRNA) genes. This chloroplast genome sequencing offers a useful resource for future conservation genetics and phylogenetic studies.
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Affiliation(s)
- Jiaojun Yu
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang Normal University, Huanggang, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang, China
| | - Hongyu Wang
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang Normal University, Huanggang, China
| | - Hongjin Dong
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang Normal University, Huanggang, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang, China
| | - Yuanping Fang
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang Normal University, Huanggang, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang, China
| | - Jun Xiang
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang Normal University, Huanggang, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang, China
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30
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Kao TT, Rothfels CJ, Melgoza-Castillo A, Pryer KM, Windham MD. Infraspecific diversification of the star cloak fern (Notholaena standleyi) in the deserts of the United States and Mexico. AMERICAN JOURNAL OF BOTANY 2020; 107:658-675. [PMID: 32253761 DOI: 10.1002/ajb2.1461] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/04/2020] [Indexed: 06/11/2023]
Abstract
PREMISE Not all ferns grow in moist and shaded habitats. One well-known example is Notholaena standleyi, a species that thrives in deserts of the southwestern United States and Mexico. This species exhibits several "chemotypes" that differ in farina (flavonoid exudates) color and chemistry. By integrating data from molecular phylogenetics, cytology, biochemistry, and biogeography, we circumscribed the major evolutionary lineages within N. standleyi and reconstructed their diversification histories. METHODS Forty-eight samples were selected from across the geographic distribution of N. standleyi. Phylogenetic relationships were inferred using four plastid and five nuclear markers. Ploidy levels were inferred using spore sizes calibrated by chromosome counts, and farina chemistry was compared using thin-layer chromatography. RESULTS Four clades are recognized, three of which roughly correspond to previously recognized chemotypes. The diploid clades G and Y are found in the Sonoran and Chihuahuan deserts, respectively; they are estimated to have diverged in the Pleistocene, congruent with the postulated timing of climatological events separating these two deserts. Clade P/YG is tetraploid and partially overlaps the distribution of clade Y in the eastern Chihuahuan Desert. It is apparently confined to limestone, a geologic substrate rarely occupied by members of the other clades. The cryptic (C) clade, a diploid group known only from southern Mexico and highly disjunct from the other three clades, is newly recognized here. CONCLUSIONS Our results reveal a complex intraspecific diversification history of N. standleyi, traceable to a variety of evolutionary drivers including classic allopatry, parapatry with or without changes in geologic substrate, and sympatric divergence through polyploidization.
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Affiliation(s)
- Tzu-Tong Kao
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California, 94720, USA
| | - Alicia Melgoza-Castillo
- Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Chihuahua, Chihuahua CP, 31000, Mexico
| | - Kathleen M Pryer
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
| | - Michael D Windham
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
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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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Duan L, Harris A, Su C, Zhang ZR, Arslan E, Ertuğrul K, Loc PK, Hayashi H, Wen J, Chen HF. Chloroplast Phylogenomics Reveals the Intercontinental Biogeographic History of the Liquorice Genus (Leguminosae: Glycyrrhiza). FRONTIERS IN PLANT SCIENCE 2020; 11:793. [PMID: 32636856 PMCID: PMC7318913 DOI: 10.3389/fpls.2020.00793] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 05/18/2020] [Indexed: 05/09/2023]
Abstract
The liquorice genus, Glycyrrhiza L. (Leguminosae), is a medicinal herb with great economic importance and an intriguing intercontinental disjunct distribution in Eurasia, North Africa, the Americas, and Australia. Glycyrrhiza, along with Glycyrrhizopsis Boiss. and Meristotropis Fisch. & C.A.Mey., comprise Glycyrrhiza s.l. Here we reconstructed the phylogenetic relationships and biogeographic history in Glycyrrhiza s.l. using sequence data of whole chloroplast genomes. We found that Glycyrrhiza s.l. is sister to the tribe Wisterieae and is divided into four main clades. Clade I, corresponds to Glycyrrhizopsis and is sister to Glycyrrhiza sensu Meng. Meristotropis is embedded within Glycyrrhiza sensu Meng, and these two genera together form Clades II-IV. Based on biogeographic analyses and divergence time dating, Glycyrrhiza s.l. originated during the late Eocene and its most recent common ancestor (MRCA) was distributed in the interior of Eurasia and the circum-Mediterranean region. A vicariance event, which was possibly a response to the uplifting of the Turkish-Iranian Plateau, may have driven the divergence between Glycyrrhiza sensu Meng and Glycyrrhizopsis in the Middle Miocene. The third and fourth main uplift events of the Qinghai-Tibetan Plateau may have led to rapid evolutionary diversification within Glycyrrhiza sensu Meng. Subsequently, the MRCA of Clade II might have migrated to North America (G. lepidota) via the Bering land bridge during the early Pliocene, and reached temperate South America (G. astragalina) by long-distance dispersal (LDD). Within Clade III, the ancestor of G. acanthocarpa arrived at southern Australia through LDD after the late Pliocene, whereas all other species (the SPEY clade) migrated to the interior of Eurasia and the Mediterranean region in the early Pleistocene. The MRCA of Clade IV was restricted in the interior of Eurasia, but its descendants have become widespread in temperate regions of the Old World Northern Hemisphere during the last million years.
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Affiliation(s)
- Lei Duan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, United States
- *Correspondence: Lei Duan,
| | - A.J. Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Chun Su
- College of Life Science, Northwest A&F University, Yangling, China
| | - Zhi-Rong Zhang
- Germplasm Bank of Wild Species in Southwest China, Kunming Institution of Botany, Chinese Academy of Sciences, Kunming, China
| | - Emine Arslan
- Department of Biology, Faculty of Science, Selçuk University, Konya, Turkey
| | - Kuddisi Ertuğrul
- Department of Biology, Faculty of Science, Selçuk University, Konya, Turkey
| | - Phan Ke Loc
- Department of Botany and HNU, Faculty of Biology, VNU Hanoi University of Science (HUS), Hanoi, Vietnam
| | - Hiroaki Hayashi
- Laboratory of Natural Products Chemistry, College of Pharmaceutical Sciences, Ritsumeikan University, Kyoto, Japan
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, United States
- Jun Wen,
| | - Hong-Feng Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Hong-Feng Chen,
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Li Y, Dong Y, Liu Y, Yu X, Yang M, Huang Y. Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae. FRONTIERS IN PLANT SCIENCE 2020; 11:593984. [PMID: 33643327 PMCID: PMC7905392 DOI: 10.3389/fpls.2020.593984] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/28/2020] [Indexed: 05/06/2023]
Abstract
In this study, we assembled and annotated the chloroplast (cp) genome of the Euonymus species Euonymus fortunei, Euonymus phellomanus, and Euonymus maackii, and performed a series of analyses to investigate gene structure, GC content, sequence alignment, and nucleic acid diversity, with the objectives of identifying positive selection genes and understanding evolutionary relationships. The results indicated that the Euonymus cp genome was 156,860-157,611bp in length and exhibited a typical circular tetrad structure. Similar to the majority of angiosperm chloroplast genomes, the results yielded a large single-copy region (LSC) (85,826-86,299bp) and a small single-copy region (SSC) (18,319-18,536bp), separated by a pair of sequences (IRA and IRB; 26,341-26,700bp) with the same encoding but in opposite directions. The chloroplast genome was annotated to 130-131 genes, including 85-86 protein coding genes, 37 tRNA genes, and eight rRNA genes, with GC contents of 37.26-37.31%. The GC content was variable among regions and was highest in the inverted repeat (IR) region. The IR boundary of Euonymus happened expanding resulting that the rps19 entered into IR region and doubled completely. Such fluctuations at the border positions might be helpful in determining evolutionary relationships among Euonymus. The simple-sequence repeats (SSRs) of Euonymus species were composed primarily of single nucleotides (A)n and (T)n, and were mostly 10-12bp in length, with an obvious A/T bias. We identified several loci with suitable polymorphism with the potential use as molecular markers for inferring the phylogeny within the genus Euonymus. Signatures of positive selection were seen in rpoB protein encoding genes. Based on data from the whole chloroplast genome, common single copy genes, and the LSC, SSC, and IR regions, we constructed an evolutionary tree of Euonymus and related species, the results of which were consistent with traditional taxonomic classifications. It showed that E. fortunei sister to the Euonymus japonicus, whereby E. maackii appeared as sister to Euonymus hamiltonianus. Our study provides important genetic information to support further investigations into the phylogenetic development and adaptive evolution of Euonymus species.
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Affiliation(s)
- Yongtan Li
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Yan Dong
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Yichao Liu
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
- Institute of Landscaping, Hebei Academic of Forestry and Grassland, Shijiazhuang, China
| | - Xiaoyue Yu
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Minsheng Yang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
- *Correspondence: Minsheng Yang,
| | - Yinran Huang
- Institute of Landscaping, Hebei Academic of Forestry and Grassland, Shijiazhuang, China
- Yinran Huang,
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Wei R, Zhang XC. Phylogeny of Diplazium (Athyriaceae) revisited: Resolving the backbone relationships based on plastid genomes and phylogenetic tree space analysis. Mol Phylogenet Evol 2019; 143:106699. [PMID: 31809851 DOI: 10.1016/j.ympev.2019.106699] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/01/2019] [Accepted: 12/01/2019] [Indexed: 11/17/2022]
Abstract
Despite progress in resolving the phylogeny of twinsorus ferns (Diplazium) based on multilocus phylogenetic studies, uncertainty remains especially for deep, or backbone relationships among closely related clades, suggesting a classic case of rapid evolutionary radiation. Here, we investigated the deep phylogenetic relationships within Diplazium by sampling all major clades and using 51 plastid genomes (plastomes), of which 38 were newly sequenced with high-throughput sequencing technology, resulting more than 127,000 informative sites. Using parsimony, maximum likelihood and Bayesian analyses of plastome sequences, we largely resolved the backbone of the phylogeny of Diplazium with strong support. However, we also detected phylogenetic incongruence among different datasets and moderately to poorly supported relationships, particularly at several extremely short internal branches. By using phylogenetic tree space and topology-clustering analyses, we provide evidence that conflicting phylogenetic signals can be found across the trees estimated from individual chloroplast protein-coding genes, which may underlie the difficulty of systematics of Diplazium. Furthermore, our phylogenetic estimate offers more resolution over previous multilocus analyses, providing a framework for future taxonomic revisions of sectional classification of Diplazium. Our study demonstrates the advantage of a character-rich plastome dataset, combining the comparison of different phylogenetic methods, for resolving the recalcitrant lineages that have undergone rapid radiation and dramatic changes in evolutionary 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 100093, China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China.
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Xu K, Zhang L, Rothfels CJ, Smith AR, Viane R, Lorence D, Wood KR, Chen C, Knapp R, Zhou L, Lu NT, Zhou X, Wei H, Fan Q, Chen S, Cicuzza D, Gao X, Liao W, Zhang L. A global plastid phylogeny of the fern genusAsplenium(Aspleniaceae). Cladistics 2019; 36:22-71. [DOI: 10.1111/cla.12384] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2019] [Indexed: 01/20/2023] Open
Affiliation(s)
- Ke‐Wang Xu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources School of Life Sciences Sun Yat‐sen University Guangzhou
- Missouri Botanical Garden 4344 Shaw Blvd St. Louis MO 63110
| | - Liang Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Kunming
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization Chengdu Institute of Biology Chinese Academy of Sciences P.O. Box 416 Chengdu
| | - Carl J. Rothfels
- University Herbarium and Department of Integrative Biology University of California 1001 Valley Life Sciences Building Berkeley CA 94720
| | - Alan R. Smith
- University Herbarium and Department of Integrative Biology University of California 1001 Valley Life Sciences Building Berkeley CA 94720
| | - Ronald Viane
- Department of Biology Ghent University 9000 Gent
| | - David Lorence
- National Tropical Botanical Garden 3530 Papalina Road Kalāheo HI 96741
| | - Kenneth R. Wood
- National Tropical Botanical Garden 3530 Papalina Road Kalāheo HI 96741
| | - Cheng‐Wei Chen
- Division of Silviculture Taiwan Forestry Research Institute Taipei
| | - Ralf Knapp
- Muséum national d'Histoire naturelle (MNHN, Paris, France) Steigestrasse 78 69412 Eberbach
| | - Lin Zhou
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization Chengdu Institute of Biology Chinese Academy of Sciences P.O. Box 416 Chengdu
| | - Ngan Thi Lu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization Chengdu Institute of Biology Chinese Academy of Sciences P.O. Box 416 Chengdu
- University of Chinese Academy of Sciences Beijing
- Department of Biology Vietnam National Museum of Nature Vietnam Academy of Science and Technology 18th Hoang Quoc Viet Road Ha Noi
| | - Xin‐Mao Zhou
- Laboratory of Ecology and Evolutionary Biology State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan Yunnan University Kunming
| | - Hong‐Jin Wei
- Shanghai Chenshan Botanical Garden Shanghai 201602
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources School of Life Sciences Sun Yat‐sen University Guangzhou
| | - Su‐Fang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources School of Life Sciences Sun Yat‐sen University Guangzhou
| | - Daniele Cicuzza
- Faculty of Science Universiti Brunei Darussalam Bandar Seri Begawan
| | - Xin‐Fen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization Chengdu Institute of Biology Chinese Academy of Sciences P.O. Box 416 Chengdu
| | - Wen‐Bo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources School of Life Sciences Sun Yat‐sen University Guangzhou
| | - Li‐Bing Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization Chengdu Institute of Biology Chinese Academy of Sciences P.O. Box 416 Chengdu
- Missouri Botanical Garden 4344 Shaw Blvd St. Louis MO 63110
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36
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Liu Y, Johnson MG, Cox CJ, Medina R, Devos N, Vanderpoorten A, Hedenäs L, Bell NE, Shevock JR, Aguero B, Quandt D, Wickett NJ, Shaw AJ, Goffinet B. Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes. Nat Commun 2019; 10:1485. [PMID: 30940807 PMCID: PMC6445109 DOI: 10.1038/s41467-019-09454-w] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 03/07/2019] [Indexed: 11/21/2022] Open
Abstract
Mosses are a highly diverse lineage of land plants, whose diversification, spanning at least 400 million years, remains phylogenetically ambiguous due to the lack of fossils, massive early extinctions, late radiations, limited morphological variation, and conflicting signal among previously used markers. Here, we present phylogenetic reconstructions based on complete organellar exomes and a comparable set of nuclear genes for this major lineage of land plants. Our analysis of 142 species representing 29 of the 30 moss orders reveals that relative average rates of non-synonymous substitutions in nuclear versus plastid genes are much higher in mosses than in seed plants, consistent with the emerging concept of evolutionary dynamism in mosses. Our results highlight the evolutionary significance of taxa with reduced morphologies, shed light on the relative tempo and mechanisms underlying major cladogenic events, and suggest hypotheses for the relationships and delineation of moss orders.
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Affiliation(s)
- Yang Liu
- Fairy Lake Botanical Garden & Chinese Academy of Sciences, Shenzhen, 518004, China
- BGI-Shenzhen, Shenzhen, 518120, China
| | | | - Cymon J Cox
- Centro de Ciências do Mar, Universidade do Algarve, Gambelas, 8005-319, Faro, Portugal
| | - Rafael Medina
- Department of Biology, Augustana College, Rock Island, IL, 61201, USA
| | - Nicolas Devos
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | | | - Lars Hedenäs
- Department of Botany, Swedish Museum of Natural History, Stockholm, Box 50007, 10405, Sweden
| | - Neil E Bell
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - James R Shevock
- California Academy of Sciences, San Francisco, CA, 94118, USA
| | - Blanka Aguero
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Dietmar Quandt
- Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, 53115, Germany
| | | | - A Jonathan Shaw
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA.
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Xu L, Xing Y, Wang B, Liu C, Wang W, Kang T. Plastid genome and composition analysis of two medical ferns: Dryopteris crassirhizoma Nakai and Osmunda japonica Thunb. Chin Med 2019; 14:9. [PMID: 30911328 PMCID: PMC6417082 DOI: 10.1186/s13020-019-0230-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 03/05/2019] [Indexed: 11/23/2022] Open
Abstract
Background Dryopteris crassirhizoma Nakai and Osmunda japonica Thunb. are ferns that are popularly used for medicine, as recorded by the Chinese pharmacopoeia, and are distributed in different regions of China. However, O. japonica is not record in the Standards of Chinese Herbal Medicines in Hong Kong. Research on identification methods of D. crassirhizoma and O. japonica is necessary and the phylogenetic position of the two species should be identified. The plastid genome is structurally highly conserved, providing valuable sources of genetic markers for phylogenetic analyses and development of molecule makers for identification. Methods The plastid genome DNA was extracted from both fern species and then sequenced on the Illumina Hiseq 4000. Sequences were assembled into contigs by SOAPdenovo2.04, aligned to the reference genome using BLAST, and then manually corrected. Genome annotation was performed by the online DOGMA tool. General characteristics of the plastid genomes of the two species were analyzed and compared with closely related species. Additionally, phylogenetical trees were reconstructed by maximum likelihood methods. The content of dryocrassin of the two species were determined according to the Standards of Chinese Herbal Medicines in Hong Kong. Results The genome structures of D. crassirhizoma and O. japonica have different characteristics including the genome size, the size of each area, gene location, and types. Moreover, the (simple sequence repeats) SSRs of the plastid genomes were more similar to other species in the same genera. Compared with D. fragrans, D. crassirhizoma shows an inversion (approximately 1.6 kb), and O. japonica shows two inversions (1.9 kb and 216 bp). The nucleotide diversity (polymorphism information, Pi) analysis showed that the psbK gene and rpl14-rpl16 region have the highest Pi value in Dryopteris, and the ycf2-CDS3 and rpl14-rpl16 regions show the highest Pi vale in O. japonica. Phylogenetic analyses showed that the two species were grouped in two separate clades from each other, with both individually located with other members of their genus. The marker content of dryocrassin is not found in O. japonica. Conclusions The study is the first to identify plastid genome features of D. crassirhizoma and O. japonica. The results may provide a theoretical basis for the identification and the application of the two medically important fern species. Electronic supplementary material The online version of this article (10.1186/s13020-019-0230-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Liang Xu
- 1School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China.,2School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Yanping Xing
- 2School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Bing Wang
- 2School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Chunsheng Liu
- 1School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Wenquan Wang
- 1School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China.,3Institute of Medicinal Plant Development, Beijing, China
| | - Tingguo Kang
- 2School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
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38
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Wang YR, Zhao CF, Yu XD, Zhang XC. The complete chloroplast genome sequence of a typical alpine fern Lepisorus waltonii (Ching) S. L. Yu in Polypodiaceae. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1574631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Ya-Rong Wang
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany Chinese Academy of Sciences, Beijing, China
| | - Cun-Feng Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xu-Dong Yu
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany Chinese Academy of Sciences, Beijing, China
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Complete chloroplast genome sequence of Dryopteris fragrans (L.) Schott and the repeat structures against the thermal environment. Sci Rep 2018; 8:16635. [PMID: 30413776 PMCID: PMC6226466 DOI: 10.1038/s41598-018-35061-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 10/15/2018] [Indexed: 01/07/2023] Open
Abstract
Dryopteris fragrans (L.) Schott is a fern growing on the surface of hot rocks and lava. It is exposed to sunlight directly and bears local hot environment. We sequenced the complete nucleotide sequence of its chloroplast (cp) genome. The cp genome was 151,978 bp in length, consisting of a large single-copy region (85,332 bp), a small single-copy region (31,947 bp) and a pair of inverted repeats (17,314 bp). The cp genome contained 112 genes and 345 RNA editing sites in protein-coding genes. Simple sequence repeats (SSRs) and long repeat structure pairs (30–55 bp) were identified. The number and percent of repeat structures are extremely high in ferns. Thermal denaturation experiments showed its cp genome to have numerous, dispersed and high GC percent repeat structures, which conferred the strongest thermal stability. This repeat-heavy genome may provide the molecular basis of how D. fragrans cp survives its hot environment.
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40
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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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Robison TA, Grusz AL, Wolf PG, Mower JP, Fauskee BD, Sosa K, Schuettpelz E. Mobile Elements Shape Plastome Evolution in Ferns. Genome Biol Evol 2018; 10:2558-2571. [PMID: 30165616 PMCID: PMC6166771 DOI: 10.1093/gbe/evy189] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2018] [Indexed: 12/22/2022] Open
Abstract
Plastid genomes display remarkable organizational stability over evolutionary time. From green algae to angiosperms, most plastid genomes are largely collinear, with only a few cases of inversion, gene loss, or, in extremely rare cases, gene addition. These plastome insertions are mostly clade-specific and are typically of nuclear or mitochondrial origin. Here, we expand on these findings and present the first family-level survey of plastome evolution in ferns, revealing a novel suite of dynamic mobile elements. Comparative plastome analyses of the Pteridaceae expose several mobile open reading frames that vary in sequence length, insertion site, and configuration among sampled taxa. Even between close relatives, the presence and location of these elements is widely variable when viewed in a phylogenetic context. We characterize these elements and refer to them collectively as Mobile Open Reading Frames in Fern Organelles (MORFFO). We further note that the presence of MORFFO is not restricted to Pteridaceae, but is found across ferns and other plant clades. MORFFO elements are regularly associated with inversions, intergenic expansions, and changes to the inverted repeats. They likewise appear to be present in mitochondrial and nuclear genomes of ferns, indicating that they can move between genomic compartments with relative ease. The origins and functions of these mobile elements are unknown, but MORFFO appears to be a major driver of structural genome evolution in the plastomes of ferns, and possibly other groups of plants.
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Affiliation(s)
| | - Amanda L Grusz
- Department of Biology, University of Minnesota Duluth
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, District of Colombia
| | - Paul G Wolf
- Department of Biology, Utah State University
| | - Jeffrey P Mower
- Department of Agronomy, Center for Plant Science Innovation, University of Nebraska
| | | | | | - Eric Schuettpelz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, District of Colombia
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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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Wolf PG, Robison TA, Johnson MG, Sundue MA, Testo WL, Rothfels CJ. Target sequence capture of nuclear-encoded genes for phylogenetic analysis in ferns. APPLICATIONS IN PLANT SCIENCES 2018; 6:e01148. [PMID: 30131890 PMCID: PMC5991577 DOI: 10.1002/aps3.1148] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 03/04/2018] [Indexed: 05/07/2023]
Abstract
PREMISE OF THE STUDY Until recently, most phylogenetic studies of ferns were based on chloroplast genes. Evolutionary inferences based on these data can be incomplete because the characters are from a single linkage group and are uniparentally inherited. These limitations are particularly acute in studies of hybridization, which is prevalent in ferns; fern hybrids are common and ferns are able to hybridize across highly diverged lineages, up to 60 million years since divergence in one documented case. However, it not yet clear what effect such hybridization has on fern evolution, in part due to a paucity of available biparentally inherited (nuclear-encoded) markers. METHODS We designed oligonucleotide baits to capture 25 targeted, low-copy nuclear markers from a sample of 24 species spanning extant fern diversity. RESULTS Most loci were successfully sequenced from most accessions. Although the baits were designed from exon (transcript) data, we successfully captured intron sequences that should be useful for more focused phylogenetic studies. We present phylogenetic analyses of the new target sequence capture data and integrate these into a previous transcript-based data set. DISCUSSION We make our bait sequences available to the community as a resource for further studies of fern phylogeny.
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Affiliation(s)
- Paul G. Wolf
- Ecology Center and Department of BiologyUtah State UniversityLoganUtah84322USA
| | - Tanner A. Robison
- Ecology Center and Department of BiologyUtah State UniversityLoganUtah84322USA
| | - Matthew G. Johnson
- Department of Biological SciencesTexas Tech UniversityLubbockTexas79409USA
| | - Michael A. Sundue
- Pringle HerbariumDepartment of Plant BiologyUniversity of VermontBurlingtonVermont05405USA
| | - Weston L. Testo
- Pringle HerbariumDepartment of Plant BiologyUniversity of VermontBurlingtonVermont05405USA
| | - Carl J. Rothfels
- University Herbarium and Department of Integrative BiologyUniversity of CaliforniaBerkeleyCalifornia94720USA
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Complete chloroplast genome of seven Fritillaria species, variable DNA markers identification and phylogenetic relationships within the genus. PLoS One 2018; 13:e0194613. [PMID: 29543905 PMCID: PMC5854438 DOI: 10.1371/journal.pone.0194613] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/06/2018] [Indexed: 02/07/2023] Open
Abstract
Fritillaria spp. constitute important traditional Chinese medicinal plants. Xinjiang is one of two diversity hotspots in China in which eight Fritillaria species occur, two of which are endemic to the region. Furthermore, the phylogenetic relationships of Xinjiang Fritillaria species (including F. yuminensis) within the genus are unclear. In the present study, we sequenced the chloroplast (cp) genomes of seven Fritillaria species in Xinjiang using the Illumina HiSeq platform, with the aim of assessing the global structural patterns of the seven cp genomes and identifying highly variable cp DNA sequences. These were compared to previously sequenced Fritillaria cp genomes. Phylogenetic analysis was then used to evaluate the relationships of the Xinjiang species and assess the evolution of an undivided stigma. The seven cp genomes ranged from 151,764 to 152,112 bp, presenting a traditional quadripartite structure. The gene order and gene content of the seven cp genomes were identical. A comparison of the 13 cp genomes indicated that the structure is highly conserved. Ten highly divergent regions were identified that could be valuable in phylogenetic and population genetic studies. The phylogenetic relationships of the 13 Fritillaria species inferred from the protein-coding genes, large single-copy, small single-copy, and inverted repeat regions were identical and highly resolved. The phylogenetic relationships of the species corresponded with their geographic distribution patterns, in that the north group (consisting of eight species from Xinjiang and Heilongjiang in North China) and the south group (including six species from South China) were basically divided at 40°N. Species with an undivided stigma were not monophyletic, suggesting that this trait might have evolved several times in the genus.
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Wei R, Ebihara A, Zhu YM, Zhao CF, Hennequin S, Zhang XC. A total-evidence phylogeny of the lady fern genus Athyrium Roth (Athyriaceae) with a new infrageneric classification. Mol Phylogenet Evol 2018; 119:25-36. [DOI: 10.1016/j.ympev.2017.10.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/17/2017] [Accepted: 10/26/2017] [Indexed: 10/18/2022]
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Logacheva MD, Krinitsina AA, Belenikin MS, Khafizov K, Konorov EA, Kuptsov SV, Speranskaya AS. Comparative analysis of inverted repeats of polypod fern (Polypodiales) plastomes reveals two hypervariable regions. BMC PLANT BIOLOGY 2017; 17:255. [PMID: 29297348 PMCID: PMC5751766 DOI: 10.1186/s12870-017-1195-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
BACKGROUND Ferns are large and underexplored group of vascular plants (~ 11 thousands species). The genomic data available by now include low coverage nuclear genomes sequences and partial sequences of mitochondrial genomes for six species and several plastid genomes. RESULTS We characterized plastid genomes of three species of Dryopteris, which is one of the largest fern genera, using sequencing of chloroplast DNA enriched samples and performed comparative analysis with available plastomes of Polypodiales, the most species-rich group of ferns. We also sequenced the plastome of Adianthum hispidulum (Pteridaceae). Unexpectedly, we found high variability in the IR region, including duplication of rrn16 in D. blanfordii, complete loss of trnI-GAU in D. filix-mas, its pseudogenization due to the loss of an exon in D. blanfordii. Analysis of previously reported plastomes of Polypodiales demonstrated that Woodwardia unigemmata and Lepisorus clathratus have unusual insertions in the IR region. The sequence of these inserted regions has high similarity to several LSC fragments of ferns outside of Polypodiales and to spacer between tRNA-CGA and tRNA-TTT genes of mitochondrial genome of Asplenium nidus. We suggest that this reflects the ancient DNA transfer from mitochondrial to plastid genome occurred in a common ancestor of ferns. We determined the marked conservation of gene content and relative evolution rate of genes and intergenic spacers in the IRs of Polypodiales. Faster evolution of the four intergenic regions had been demonstrated (trnA- orf42, rrn16-rps12, rps7-psbA and ycf2-trnN). CONCLUSIONS IRs of Polypodiales plastomes are dynamic, driven by such events as gene loss, duplication and putative lateral transfer from mitochondria.
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Affiliation(s)
| | | | - Maxim S Belenikin
- M.V. Lomonosov Moscow State University, 119991, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Moscow Region, Russia
| | - Kamil Khafizov
- Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Moscow Region, Russia
- Federal Budget Institution of Science Central Research Institute of Epidemiology of The Federal Service on Customers, 111123, Moscow, Russia
| | - Evgenii A Konorov
- M.V. Lomonosov Moscow State University, 119991, Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, Moscow, Russia
| | | | - Anna S Speranskaya
- M.V. Lomonosov Moscow State University, 119991, Moscow, Russia.
- Federal Budget Institution of Science Central Research Institute of Epidemiology of The Federal Service on Customers, 111123, Moscow, Russia.
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