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Wu CS, Wang RJ, Chaw SM. Integration of large and diverse angiosperm DNA fragments into Asian Gnetum mitogenomes. BMC Biol 2024; 22:140. [PMID: 38915079 PMCID: PMC11197197 DOI: 10.1186/s12915-024-01924-y] [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: 10/22/2023] [Accepted: 05/21/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND Horizontal gene transfer (HGT) events have rarely been reported in gymnosperms. Gnetum is a gymnosperm genus comprising 25‒35 species sympatric with angiosperms in West African, South American, and Southeast Asian rainforests. Only a single acquisition of an angiosperm mitochondrial intron has been documented to date in Asian Gnetum mitogenomes. We wanted to develop a more comprehensive understanding of frequency and fragment length distribution of such events as well as their evolutionary history in this genus. RESULTS We sequenced and assembled mitogenomes from five Asian Gnetum species. These genomes vary remarkably in size and foreign DNA content. We identified 15 mitochondrion-derived and five plastid-derived (MTPT) foreign genes. Our phylogenetic analyses strongly indicate that these foreign genes were transferred from diverse eudicots-mostly from the Rubiaceae genus Coptosapelta and ten genera of Malpighiales. This indicates that Asian Gnetum has experienced multiple independent HGT events. Patterns of sequence evolution strongly suggest DNA-mediated transfer between mitochondria as the primary mechanism giving rise to these HGT events. Most Asian Gnetum species are lianas and often entwined with sympatric angiosperms. We therefore propose that close apposition of Gnetum and angiosperm stems presents opportunities for interspecific cell-to-cell contact through friction and wounding, leading to HGT. CONCLUSIONS Our study reveals that multiple HGT events have resulted in massive amounts of angiosperm mitochondrial DNA integrated into Asian Gnetum mitogenomes. Gnetum and its neighboring angiosperms are often entwined with each other, possibly accounting for frequent HGT between these two phylogenetically remote lineages.
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Affiliation(s)
- Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Rui-Jiang Wang
- South China Botanical Garden, Chinese Academy of Science, Guangzhou, China
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
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Liu K, Huang X, Ding X, Chen N. The high molecular diversity in Noctiluca scintillans is dominated by intra-genomic variations revealed by single cell high-throughput sequencing of 18S rDNA V4. HARMFUL ALGAE 2024; 132:102568. [PMID: 38331542 DOI: 10.1016/j.hal.2024.102568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/21/2023] [Accepted: 01/03/2024] [Indexed: 02/10/2024]
Abstract
The application of high-throughput sequencing (HTS) technologies has revolutionized research on phytoplankton biodiversity by generating an unprecedented amount of molecular data in marine ecosystem surveys. However, high-level of molecular diversity uncovered in HTS-based metabarcoding analyses may lead to overinterpretation of phytoplankton diversity due to excessive intra-genomic variations (IGVs). The aims in this study are to explore the nature of phytoplankton molecular diversity and to test the hypothesis. We carried out single-cell metabarcoding analysis of 18S rDNA V4 sequences obtained in single Noctiluca scintillans cells isolated from various sites in coastal waters of China. Results showed that each single N. scintillans cell harbored a high level of IGVs with about 100 amplicon sequence variants (ASVs). The large numbers of non-dominant ASVs identified in N. scintillans cells, which might correspond to the larger numbers of ASVs annotated as N. scintillans and showed similar temporal dynamics in metabarcoding analyses, could inflate the inter-species diversity or intra-species genetic diversity. In addition, there were large numbers of additional ASVs that were not annotated as N. scintillans. These non-N. scintillans ASVs might represent diverse preys for N. scintillans, consistent with previous reports that N. scintillans may act as chance predator of a broad-spectrum preys. This single-cell study has unambiguously demonstrated that the existence of high levels of IGVs in N. scintillans and most likely many other phytoplankton species, demonstrating that the majority of the molecular diversity revealed in metabarcoding analysis, which were generally interpreted as the sum of inter-species diversity and intra-species diversity, actually included high levels of IGVs and should be interpreted with caution.
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Affiliation(s)
- Kuiyan Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xianliang Huang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xiangxiang Ding
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada.
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Wang W, Zhang X, Garcia S, Leitch AR, Kovařík A. Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between? Heredity (Edinb) 2023; 131:179-188. [PMID: 37402824 PMCID: PMC10462631 DOI: 10.1038/s41437-023-00634-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
The classical model of concerted evolution states that hundreds to thousands of ribosomal DNA (rDNA) units undergo homogenization, making the multiple copies of the individual units more uniform across the genome than would be expected given mutation frequencies and gene redundancy. While the universality of this over 50-year-old model has been confirmed in a range of organisms, advanced high throughput sequencing techniques have also revealed that rDNA homogenization in many organisms is partial and, in rare cases, even apparently failing. The potential underpinning processes leading to unexpected intragenomic variation have been discussed in a number of studies, but a comprehensive understanding remains to be determined. In this work, we summarize information on variation or polymorphisms in rDNAs across a wide range of taxa amongst animals, fungi, plants, and protists. We discuss the definition and description of concerted evolution and describe whether incomplete concerted evolution of rDNAs predominantly affects coding or non-coding regions of rDNA units and if it leads to the formation of pseudogenes or not. We also discuss the factors contributing to rDNA variation, such as interspecific hybridization, meiotic cycles, rDNA expression status, genome size, and the activity of effector genes involved in genetic recombination, epigenetic modifications, and DNA editing. Finally, we argue that a combination of approaches is needed to target genetic and epigenetic phenomena influencing incomplete concerted evolution, to give a comprehensive understanding of the evolution and functional consequences of intragenomic variation in rDNA.
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Affiliation(s)
- Wencai Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Xianzhi Zhang
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Sònia Garcia
- Institut Botànic de Barcelona, IBB (CSIC - Ajuntament de Barcelona), Barcelona, Spain
| | - Andrew R Leitch
- School of Biological and Behavioral Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Aleš Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ-61200, Czech Republic.
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Lack of ITS sequence homogenization in Erysimum species (Brassicaceae) with different ploidy levels. Sci Rep 2022; 12:16907. [PMID: 36207443 PMCID: PMC9546898 DOI: 10.1038/s41598-022-20194-8] [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] [Received: 05/29/2022] [Accepted: 09/09/2022] [Indexed: 11/29/2022] Open
Abstract
The internal transcribed spacers (ITS) exhibit concerted evolution by the fast homogenization of these sequences at the intragenomic level. However, the rate and extension of this process are unclear and might be conditioned by the number and divergence of the different ITS copies. In some cases, such as hybrid species and polyploids, ITS sequence homogenization appears incomplete, resulting in multiple haplotypes within the same organism. Here, we studied the dynamics of concerted evolution in 85 individuals of seven plant species of the genus Erysimum (Brassicaceae) with multiple ploidy levels. We estimated the rate of concerted evolution and the degree of sequence homogenization separately for ITS1 and ITS2 and whether these varied with ploidy. Our results showed incomplete sequence homogenization, especially for polyploid samples, indicating a lack of concerted evolution in these taxa. Homogenization was usually higher in ITS2 than in ITS1, suggesting that concerted evolution operates more efficiently on the former. Furthermore, the hybrid origin of several species appears to contribute to the maintenance of high haplotype diversity, regardless of the level of ploidy. These findings indicate that sequence homogenization of ITS is a dynamic and complex process that might result in varying intra- and inter-genomic diversity levels.
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Zhang J, Chi X, Zhong J, Fernie A, Alseekh S, Huang L, Qian D. Extensive nrDNA ITS polymorphism in Lycium: Non-concerted evolution and the identification of pseudogenes. FRONTIERS IN PLANT SCIENCE 2022; 13:984579. [PMID: 36092433 PMCID: PMC9453804 DOI: 10.3389/fpls.2022.984579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/01/2022] [Indexed: 06/01/2023]
Abstract
The internal transcribed spacer (ITS) is one of the most extensively sequenced molecular markers in plant systematics due to its generally concerted evolution. While non-concerted evolution has been found in some plant taxa, such information is missing in Lycium. Molecular studies of six species and two variants of the genus Lycium revealed high levels of intra- and inter-individual polymorphism in the ITS, indicating non-concerted evolution. All genomic DNA ITS paralogues were identified as putative pseudogenes or functional paralogues through a series of comparisons of sequence features, including length and substitution variation, GC content, secondary structure stability, and the presence of conserved motifs in the 5.8S gene, and the rate of evolution. Approximately, 60% of ITS pseudogenes could be easily detected. Based on phylogenetic analysis, all pseudogenes were highly distinct from their corresponding functional copies, tended to evolve neutrally, and clustered randomly together in the evolutionary tree. The results probably suggest that this ITS non-concerted evolution is related to the recent divergence between tandem repeats within the Lycium genome and hybridization between species. Our study complements those of pseudogenes in plant taxa and provides a theoretical basis for the phylogeny and genetic origin of the genus Lycium while having important implications for the use of ITS molecular markers for phylogenetic reconstruction.
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Affiliation(s)
- Jiao Zhang
- Beijing Key Laboratory of Research of Chinese Medicine on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiulian Chi
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Juying Zhong
- Beijing Key Laboratory of Research of Chinese Medicine on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, China
| | - Alisdair Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Dan Qian
- Beijing Key Laboratory of Research of Chinese Medicine on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, China
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Phylogenetic Analysis and Molecular Diversity of Capsicum Based on rDNA-ITS Region. HORTICULTURAE 2020. [DOI: 10.3390/horticulturae6040087] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The genus Capsicum is comprised of 5 domesticated and more than 30 wild species. The region of nuclear ribosomal DNA internal transcribed spacers (rDNA-ITS) has widely been used for species identification, but has rarely been used in Capsicum. In this study, the evaluation of genetic diversity and a phylogenetic analysis were conducted using rDNA-ITS of 28 Capsicum accessions, including five domesticated and two wild species. We surveyed six conventional keys of domesticated species and another five traits in Capsicum accessions. Specific morphological characteristics were found in C. annuum, C. baccatum, and C.pubescens. Three subclones of each accession were sequenced, and rDNA-ITS polymorphisms were detected in all accessions excluding C. annuum, suggesting that incomplete concerted evolution occurred in rDNA-ITS of Capsicum. The genetic diversity was evaluated using nucleotide polymorphism and diversity. C. annuum had the lowest genetic diversity of all species in this study. The phylogenetic tree formed a species-specific clade for C. annuum, C. baccatum, and C. pubescens. The C. chinense clade existed in the C. frutescens clade, implying that it was a cultivated variant of C. frutescens. C. chacoense likely belonged to the C. baccatum complex according to its morphologic and genetic features. This study indicated that the rDNA-ITS region can be used for simple identification of domesticated Capsicum species.
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RIP mutated ITS genes in populations of Ophiocordyceps sinensis and their implications for molecular systematics. IMA Fungus 2020; 11:18. [PMID: 32974122 PMCID: PMC7493409 DOI: 10.1186/s43008-020-00040-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 07/01/2020] [Indexed: 11/23/2022] Open
Abstract
Different hypotheses have been proposed to interpret the observed unusual ITS (internal transcribed spacer) sequences in Ophiocordyceps sinensis. The coexistence of diverged ITS paralogs in a single genome was previously shown by amplifying the ITS region from mono-ascospore isolates using specific primers designed for different ITS paralog groups. Among those paralogs, are AT-biased ITS sequences which were hypothesized to result from repeat-induced point mutation (RIP). This is a process that detects and mutates repetitive DNA and frequently leads to epigenetic silencing, and these mutations have been interpreted as pseudogenes. Here we investigate the occurrence and frequency of ITS pseudogenes in populations of O. sinensis using large-scale sampling, and discusses the implications of ITS pseudogenes for fungal phylogenetic and evolutionary studies. Our results demonstrate a wide distribution of ITS pseudogenes amongst different geographic populations, and indicate how ITS pseudogenes can contribute to the reconstruction of the evolutionary history of the species.
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Jin WY, Liu B, Zhang SZ, Wan T, Hou C, Yang Y. Gnetum chinense, a new species of Gnetaceae from southwestern China. PHYTOKEYS 2020; 148:105-117. [PMID: 32523394 PMCID: PMC7266837 DOI: 10.3897/phytokeys.148.48510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/31/2020] [Indexed: 06/11/2023]
Abstract
Gnetum chinense sp. nov., a new lianoid species of Gnetaceae, is described from southwestern China. The new species is morphologically similar to G. montanum Markgr. in its oblong elliptic leaves and the ovoid to ellipsoid chlamydosperm, but differs from the latter by its shorter male spikes having fewer involucral collars (7-10 vs. 13-18 in G. montanum). We also did a new molecular analysis using one nuclear marker (i.e. nrITS) and four chloroplast markers (i.e. matK gene, rpoC1 intron, psbB-rps12 IGS, and trnF-trnV IGS). The result suggests that this specific clade is sister to a large clade consisting of all other known Chinese lianoid species of Gnetum except G. parvifolium (Warb.) W.C. Cheng.
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Affiliation(s)
- Wei-Yin Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, ChinaInstitute of Botany, Chinese Academy of SciencesBeijingChina
- Tonghua Normal University, 950 Yucai Road, Dongchang District, Tonghua City, Jilin Province 134000, ChinaGuangdong Academy of ForestryGuangzhouChina
| | - Bing Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, ChinaInstitute of Botany, Chinese Academy of SciencesBeijingChina
| | - Shou-Zhou Zhang
- Shenzhen Fairy Lake Botanical Garden, Shenzhen, ChinaTonghua Normal UniversityTonghuaChina
| | - Tao Wan
- Shenzhen Fairy Lake Botanical Garden, Shenzhen, ChinaTonghua Normal UniversityTonghuaChina
| | - Chen Hou
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China
- Guangdong Academy of Forestry, Guangzhou, 510520, ChinaShenzhen Fairy Lake Botanical GardenShenzhenChina
| | - Yong Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, ChinaInstitute of Botany, Chinese Academy of SciencesBeijingChina
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Xuan Y, Wu Y, Li P, Liu R, Luo Y, Yuan J, Xiang Z, He N. Molecular phylogeny of mulberries reconstructed from ITS and two cpDNA sequences. PeerJ 2019; 7:e8158. [PMID: 31844573 PMCID: PMC6911693 DOI: 10.7717/peerj.8158] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 11/04/2019] [Indexed: 11/20/2022] Open
Abstract
Background Species in the genus Morus (Moraceae) are deciduous woody plants of great economic importance. The classification and phylogenetic relationships of Morus, especially the abundant mulberry resources in China, is still undetermined. Internal transcribed spacer (ITS) regions are among the most widely used molecular markers in phylogenetic analyses of angiosperms. However, according to the previous phylogenetic analyses of ITS sequences, most of the mulberry accessions collected in China were grouped into the largest clade lacking for phylogenetic resolution. Compared with functional ITS sequences, ITS pseudogenes show higher sequence diversity, so they can provide useful phylogenetic information. Methods We sequenced the ITS regions and the chloroplast DNA regions TrnL-TrnF and TrnT-TrnL from 33 mulberry accessions, and performed phylogenetic analyses to explore the evolution of mulberry. Results We found ITS pseudogenes in 11 mulberry accessions. In the phylogenetic tree constructed from ITS sequences, clade B was separated into short-type sequence clades (clades 1 and 2), and a long-type sequence clade (clade 3). Pseudogene sequences were separately clustered into two pseudogroups, designated as pseudogroup 1 and pseudogroup 2. The phylogenetic tree generated from cpDNA sequences also separated clade B into two clades. Conclusions Two species were separated in clade B. The existence of three connection patterns and incongruent distribution patterns between the phylogenetic trees generated from cpDNA and ITS sequences suggested that the ITS pseudogene sequences connect with genetic information from the female progenitor. Hybridization has played important roles in the evolution of mulberry, resulting in low resolution of the phylogenetic analysis based on ITS sequences. An evolutionary pattern illustrating the evolution history of mulberry is proposed. These findings have significance for the conservation of local mulberry resources. Polyploidy, hybridization, and concerted evolution have all played the roles in the evolution of ITS sequences in mulberry. This study will expand our understanding of mulberry evolution.
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Affiliation(s)
- Yahui Xuan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Yue Wu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Peng Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Ruiling Liu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Yiwei Luo
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Jianglian Yuan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Zhonghuai Xiang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Ningjia He
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
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Renner S, Sousa dos Santos A. The organization of nuclear ribosomal DNA in gnetophytes - physically separate and physically linked arrangements of 35S and 5S genes. A commentary on: 'Remarkable variation of ribosomal DNA organization and copy number in gnetophytes, a distinct lineage of gymnosperms'. ANNALS OF BOTANY 2019; 123:vi-vii. [PMID: 31106810 PMCID: PMC6526311 DOI: 10.1093/aob/mcz056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This article comments on: Wencai Wang, Tao Wan, Hannes Becher, Alena Kuderova, Ilia J. Leitch, Sonia Garcia, Andrew R. Leitch and Aleš Kovařík. 2019. Remarkable variation of ribosomal DNA organization and copy number in gnetophytes, a distinct lineage of gymnosperms. Annals of Botany 123(5): 767–781.
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Affiliation(s)
- Susanne Renner
- University of Munich (LMU), Systematic Botany and Mycology, Munich, Germany
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Wang W, Wan T, Becher H, Kuderova A, Leitch IJ, Garcia S, Leitch AR, Kovařík A. Remarkable variation of ribosomal DNA organization and copy number in gnetophytes, a distinct lineage of gymnosperms. ANNALS OF BOTANY 2019; 123:767-781. [PMID: 30265284 PMCID: PMC6526317 DOI: 10.1093/aob/mcy172] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 09/04/2018] [Indexed: 05/10/2023]
Abstract
INTRODUCTION Gnetophytes, comprising the genera Ephedra, Gnetum and Welwitschia, are an understudied, enigmatic lineage of gymnosperms with a controversial phylogenetic relationship to other seed plants. Here we examined the organization of ribosomal DNA (rDNA) across representative species. METHODS We applied high-throughput sequencing approaches to isolate and reconstruct rDNA units and to determine their intragenomic homogeneity. In addition, fluorescent in situ hybridization and Southern blot hybridization techniques were used to reveal the chromosome and genomic organization of rDNA. KEY RESULTS The 5S and 35S rRNA genes were separate (S-type) in Gnetum montanum, Gnetum gnemon and Welwitschia mirabilis and linked (L-type) in Ephedra altissima. There was considerable variability in 5S rDNA abundance, ranging from as few as ~4000 (W. mirabilis) to >100 000 (G. montanum) copies. A similar large variation was also observed in 5S rDNA locus numbers (two to 16 sites per diploid cell). 5S rRNA pseudogenes were interspersed between functional genes forming a single unit in E. altissima and G. montanum. Their copy number was comparable or even higher than that of functional 5S rRNA genes. In E. altissima internal transcribed spacers of 35S rDNA were long and intrinsically repetitive while in G. montanum and W. mirabilis they were short without the subrepeats. CONCLUSIONS Gnetophytes are distinct from other gymnosperms and angiosperms as they display surprisingly large variability in rDNA organization and rDNA copy and locus numbers between genera, with no relationship between copy numbers and genome sizes apparent. Concerted evolution of 5S rDNA units seems to have led to the amplification of 5S pseudogenes in both G. montanum and E. altissima. Evolutionary patterns of rDNA show both gymnosperm and angiosperm features underlining the diversity of the group.
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Affiliation(s)
- Wencai Wang
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Tao Wan
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzen, PR China
- Sino-Africa Joint Research Center, Chinese Academy of Science, Wuhan, PR China
| | - Hannes Becher
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Alena Kuderova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Ilia J Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Passeig del Migdia s/n, Parc de Montjuïc, Barcelona, Catalonia, Spain
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Aleš Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
- For correspondence. E-mail
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Lücking R, Kirk PM, Hawksworth DL. Sequence-based nomenclature: a reply to Thines et al. and Zamora et al. and provisions for an amended proposal "from the floor" to allow DNA sequences as types of names. IMA Fungus 2018; 9:185-198. [PMID: 30018879 PMCID: PMC6048568 DOI: 10.5598/imafungus.2018.09.01.12] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 06/08/2018] [Indexed: 02/07/2023] Open
Abstract
We reply to two recently published, multi-authored opinion papers by opponents of sequence-based nomenclature, namely Zamora et al. (IMA Fungus9: 167-175,2018) and Thines et al. (IMA Fungus9: 177-183, 2018). While we agree with some of the principal arguments brought forward by these authors, we address misconceptions and demonstrate that some of the presumed evidence presented in these papers has been wrongly interpreted. We disagree that allowing sequences as types would fundamentally alter the nature of types, since a similar nature of abstracted features as type is already allowed in the Code (Art. 40.5), namely an illustration. We also disagree that there is a high risk of introducing artifactual taxa, as this risk can be quantified at well below 5 %, considering the various types of high-throughput sequencing errors. Contrary to apparently widespread misconceptions, sequence-based nomenclature cannot be based on similarity-derived OTUs and their consensus sequences, but must be derived from rigorous, multiple alignment-based phylogenetic methods and quantitative, single-marker species recognition algorithms, using original sequence reads; it is therefore identical in its approach to single-marker studies based on physical types, an approach allowed by the Code. We recognize the limitations of the ITS as a single fungal barcoding marker, but point out that these result in a conservative approach, with "false negatives" surpassing "false positives"; a desirable feature of sequence-based nomenclature. Sequence-based nomenclature does not aim at accurately resolving species, but at naming sequences that represent unknown fungal lineages so that these can serve as a means of communication, so ending the untenable situation of an exponentially growing number of unlabeled fungal sequences that fill online repositories. The risks are outweighed by the gains obtained by a reference library of named sequences spanning the full array of fungal diversity. Finally, we elaborate provisions in addition to our original proposal to amend the Code that would take care of the issues brought forward by opponents to this approach. In particular, taking up the idea of the Candidatus status of invalid, provisional names in prokaryote nomenclature, we propose a compromise that would allow valid publication of voucherless, sequence-based names in a consistent manner, but with the obligate designation as "nom. seq." (nomen sequentiae). Such names would not have priority over specimen- or culture-based names unless either epitypified with a physical type or adopted for protection on the recommendation of a committee of the International Commission on the Taxonomy of Fungi following evaluation based on strict quality control of the underlying studies based on established rules or recommendations.
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Affiliation(s)
- Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6-8, D-14195 Berlin, Germany
| | - Paul M. Kirk
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Biodiversity Informatics & Spatial Analysis, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
| | - David L. Hawksworth
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Jilin Agricultural University, Chanchung, Jilin province, 130118 China
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13
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Thines M, Crous PW, Aime MC, Aoki T, Cai L, Hyde KD, Miller AN, Zhang N, Stadler M. Ten reasons why a sequence-based nomenclature is not useful for fungi anytime soon. IMA Fungus 2018; 9:177-183. [PMID: 30018878 PMCID: PMC6048572 DOI: 10.5598/imafungus.2018.09.01.11] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 05/23/2018] [Indexed: 11/08/2022] Open
Abstract
The large number of species still to be discovered in fungi, together with an exponentially growing number of environmental sequences that cannot be linked to known taxa, has fuelled the idea that it might be necessary to formally name fungi on the basis of sequence data only. Here we object to this idea due to several shortcomings of the approach, ranging from concerns regarding reproducibility and the violation of general scientific principles to ethical issues. We come to the conclusion that sequence-based nomenclature is potentially harmful for mycology as a discipline. Additionally, a classification based on sequences as types is not within reach anytime soon, because there is a lack of consensus regarding common standards due to the fast pace at which sequencing technologies develop.
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Affiliation(s)
- Marco Thines
- Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, D-60483 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Pedro W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - M. Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Takayuki Aoki
- Genetic Resources Center, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Kevin D. Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Andrew N. Miller
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA
| | - Ning Zhang
- Department of Plant Biology, Rutgers University, 59 Dudley Road, Foran Hall 201, New Brunswick, New Jersey 08901, USA
| | - Marc Stadler
- Department of Microbial Drugs, Helmholtz-Zentrum für Infektionsforschung, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
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14
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Grimm GW, Renner SS, Stamatakis A, Hemleben V. A Nuclear Ribosomal DNA Phylogeny of Acer Inferred with Maximum Likelihood, Splits Graphs, and Motif Analysis of 606 Sequences. Evol Bioinform Online 2017. [DOI: 10.1177/117693430600200014] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The multi-copy internal transcribed spacer (ITS) region of nuclear ribosomal DNA is widely used to infer phylogenetic relationships among closely related taxa. Here we use maximum likelihood (ML) and splits graph analyses to extract phylogenetic information from ~ 600 mostly cloned ITS sequences, representing 81 species and subspecies of Acer, and both species of its sister Dipteronia. Additional analyses compared sequence motifs in Acer and several hundred Ana-cardiaceae, Burseraceae, Meliaceae, Rutaceae, and Sapindaceae ITS sequences in GenBank. We also assessed the effects of using smaller data sets of consensus sequences with ambiguity coding (accounting for within-species variation) instead of the full (partly redundant) original sequences. Neighbor-nets and bipartition networks were used to visualize conflict among character state patterns. Species clusters observed in the trees and networks largely agree with morphology-based classifications; of de Jong's (1994) 16 sections, nine are supported in neighbor-net and bipartition networks, and ten by sequence motifs and the ML tree; of his 19 series, 14 are supported in networks, motifs, and the ML tree. Most nodes had higher bootstrap support with matrices of 105 or 40 consensus sequences than with the original matrix. Within-taxon ITS divergence did not differ between diploid and polyploid Acer, and there was little evidence of differentiated parental ITS haplotypes, suggesting that concerted evolution in Acer acts rapidly.
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Affiliation(s)
- Guido W. Grimm
- Institute of Geosciences, Department of Biogeology and Applied Paleontology, University of Tübingen, Germany
| | | | - Alexandros Stamatakis
- Swiss Federal Institute of Technology, School of Computer & Communication Sciences, Lausanne, Switzerland
| | - Vera Hemleben
- Center of Plant Molecular Biology, Department of Genetics, University of Tübingen, Germany
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15
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Xu B, Zeng XM, Gao XF, Jin DP, Zhang LB. ITS non-concerted evolution and rampant hybridization in the legume genus Lespedeza (Fabaceae). Sci Rep 2017; 7:40057. [PMID: 28051161 PMCID: PMC5209741 DOI: 10.1038/srep40057] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 11/30/2016] [Indexed: 12/27/2022] Open
Abstract
The internal transcribed spacer (ITS) as one part of nuclear ribosomal DNA is one of the most extensively sequenced molecular markers in plant systematics. The ITS repeats generally exhibit high-level within-individual homogeneity, while relatively small-scale polymorphism of ITS copies within individuals has often been reported in literature. Here, we identified large-scale polymorphism of ITS copies within individuals in the legume genus Lespedeza (Fabaceae). Divergent paralogs of ITS sequences, including putative pseudogenes, recombinants, and multiple functional ITS copies were sometimes detected in the same individual. Thirty-seven ITS pseudogenes could be easily detected according to nucleotide changes in conserved 5.8S motives, the significantly lower GC contents in at least one of three regions, and the lost ability of 5.8S rDNA sequence to fold into a conserved secondary structure. The distribution patterns of the putative functional clones were highly different between the traditionally recognized two subgenera, suggesting different rates of concerted evolution in two subgenera which could be attributable to their different extents/frequencies of hybridization, confirmed by our analysis of the single-copy nuclear gene PGK. These findings have significant implications in using ITS marker for reconstructing phylogeny and studying hybridization.
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MESH Headings
- Base Composition
- Cluster Analysis
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Evolution, Molecular
- Lespedeza/classification
- Lespedeza/genetics
- Nucleic Acid Hybridization
- Phylogeny
- Polymorphism, Genetic
- RNA, Ribosomal, 5.8S/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Bo Xu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan 610041, China
| | - Xiao-Mao Zeng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan 610041, China
| | - Xin-Fen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan 610041, China
| | - Dong-Pil Jin
- Department of Biological Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Li-Bing Zhang
- Missouri Botanical Garden, P.O. Box 299, St. Louis, Missouri 63166, USA
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16
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Non-concerted evolution in ribosomal ITS2 sequence in Cynoglossus zanzibarensis (Pleuronectiformes: Cynoglossidae). BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Wang W, Ma L, Becher H, Garcia S, Kovarikova A, Leitch IJ, Leitch AR, Kovarik A. Astonishing 35S rDNA diversity in the gymnosperm species Cycas revoluta Thunb. Chromosoma 2015; 125:683-99. [PMID: 26637996 PMCID: PMC5023732 DOI: 10.1007/s00412-015-0556-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 11/05/2015] [Indexed: 11/28/2022]
Abstract
In all eukaryotes, the highly repeated 35S ribosomal DNA (rDNA) sequences encoding 18S-5.8S-26S ribosomal RNA (rRNA) typically show high levels of intragenomic uniformity due to homogenisation processes, leading to concerted evolution of 35S rDNA repeats. Here, we compared 35S rDNA divergence in several seed plants using next generation sequencing and a range of molecular and cytogenetic approaches. Most species showed similar 35S rDNA homogeneity indicating concerted evolution. However, Cycas revoluta exhibits an extraordinary diversity of rDNA repeats (nucleotide sequence divergence of different copies averaging 12 %), influencing both the coding and non-coding rDNA regions nearly equally. In contrast, its rRNA transcriptome was highly homogeneous suggesting that only a minority of genes (<20 %) encode functional rRNA. The most common SNPs were C > T substitutions located in symmetrical CG and CHG contexts which were also highly methylated. Both functional genes and pseudogenes appear to cluster on chromosomes. The extraordinary high levels of 35S rDNA diversity in C. revoluta, and probably other species of cycads, indicate that the frequency of repeat homogenisation has been much lower in this lineage, compared with all other land plant lineages studied. This has led to the accumulation of methylation-driven mutations and pseudogenisation. Potentially, the reduced homology between paralogs prevented their elimination by homologous recombination, resulting in long-term retention of rDNA pseudogenes in the genome.
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Affiliation(s)
- Wencai Wang
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Lu Ma
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Hannes Becher
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Sònia Garcia
- Laboratori de Botànica-Unitat associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028, Barcelona, Catalonia, Spain
| | - Alena Kovarikova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ-61265, Czech Republic
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Ales Kovarik
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ-61265, Czech Republic.
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18
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Szczecińska M, Sawicki J. Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae. Int J Mol Sci 2015; 16:22258-79. [PMID: 26389887 PMCID: PMC4613307 DOI: 10.3390/ijms160922258] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/24/2015] [Accepted: 08/25/2015] [Indexed: 11/25/2022] Open
Abstract
Background: The European continent is presently colonized by nine species of the genus Pulsatilla, five of which are encountered only in mountainous regions of southwest and south-central Europe. The remaining four species inhabit lowlands in the north-central and eastern parts of the continent. Most plants of the genus Pulsatilla are rare and endangered, which is why most research efforts focused on their biology, ecology and hybridization. The objective of this study was to develop genomic resources, including complete plastid genomes and nuclear rRNA clusters, for three sympatric Pulsatilla species that are most commonly found in Central Europe. The results will supply valuable information about genetic variation, which can be used in the process of designing primers for population studies and conservation genetics research. The complete plastid genomes together with the nuclear rRNA cluster can serve as a useful tool in hybridization studies. Methodology/principal findings: Six complete plastid genomes and nuclear rRNA clusters were sequenced from three species of Pulsatilla using the Illumina sequencing technology. Four junctions between single copy regions and inverted repeats and junctions between the identified locally-collinear blocks (LCB) were confirmed by Sanger sequencing. Pulsatilla genomes of 120 unique genes had a total length of approximately 161–162 kb, and 21 were duplicated in the inverted repeats (IR) region. Comparative plastid genomes of newly-sequenced Pulsatilla and the previously-identified plastomes of Aconitum and Ranunculus species belonging to the family Ranunculaceae revealed several variations in the structure of the genome, but the gene content remained constant. The nuclear rRNA cluster (18S-ITS1-5.8S-ITS2-26S) of studied Pulsatilla species is 5795 bp long. Among five analyzed regions of the rRNA cluster, only Internal Transcribed Spacer 2 (ITS2) enabled the molecular delimitation of closely-related Pulsatilla patens and Pulsatillavernalis. Conclusions/significance: The determination of complete plastid genome and nuclear rRNA cluster sequences in three species of the genus Pulsatilla is an important contribution to our knowledge of the evolution and phylogeography of those endangered taxa. The resulting data can be used to identify regions that are particularly useful for barcoding, phylogenetic and phylogeographic studies. The investigated taxa can be identified at each stage of development based on their species-specific SNPs. The nuclear and plastid genomic resources enable advanced studies on hybridization, including identification of parent species, including their roles in that process. The identified nonsynonymous mutations could play an important role in adaptations to changing environments. The results of the study will also provide valuable information about the evolution of the plastome structure in the family Ranunculaceae.
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Affiliation(s)
- Monika Szczecińska
- Department of Botany and Nature Protection, University of Warmia and Mazury, 10-728 Olsztyn, Poland.
| | - Jakub Sawicki
- Department of Botany and Nature Protection, University of Warmia and Mazury, 10-728 Olsztyn, Poland.
- Department of Biology and Ecology, University of Ostrava, 71000 Ostrava, Czech Republic.
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19
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Filyushin MA, Kochieva EZ, Skryabin KG. 5.8S rRNA sequence and secondary structure in Monotropa hypopitys and related Ericaceae species. DOKL BIOCHEM BIOPHYS 2015; 463:264-7. [PMID: 26335827 DOI: 10.1134/s1607672915040183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Indexed: 11/23/2022]
Abstract
This is the first study to investigate the secondary structure of 5.8S rRNA in M. hypopitys and related Ericaceae species. The identified nucleotide substitutions are localized mostly at the 3' and 5' ends of the gene, in the region of the third hairpin, and do not significantly affect the topology of the secondary structure of the 5.8S rRNA molecule.
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Affiliation(s)
- M A Filyushin
- Bioengineering Center, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7/1, Moscow, 117312, Russia,
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20
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Slugina MA, Torres Minho K, Filyushin MA. Analysis of the sequences of internal transcribed spacers ITS1, ITS2 and the 5.8S ribosomal gene of species of the Amaranthus genus. BIOL BULL+ 2014. [DOI: 10.1134/s1062359014060119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Filyushin MA, Kochieva EZ. 5.8S rDNA variability in Allium species belonging to the third evolutionary group. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414090051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Hodač L, Scheben AP, Hojsgaard D, Paun O, Hörandl E. ITS polymorphisms shed light on hybrid evolution in apomictic plants: a case study on the Ranunculus auricomus complex. PLoS One 2014; 9:e103003. [PMID: 25062066 PMCID: PMC4111349 DOI: 10.1371/journal.pone.0103003] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 06/23/2014] [Indexed: 11/18/2022] Open
Abstract
The reconstruction of reticulate evolutionary histories in plants is still a major methodological challenge. Sequences of the ITS nrDNA are a popular marker to analyze hybrid relationships, but variation of this multicopy spacer region is affected by concerted evolution, high intraindividual polymorphism, and shifts in mode of reproduction. The relevance of changes in secondary structure is still under dispute. We aim to shed light on the extent of polymorphism within and between sexual species and their putative natural as well as synthetic hybrid derivatives in the Ranunculus auricomus complex to test morphology-based hypotheses of hybrid origin and parentage of taxa. We employed direct sequencing of ITS nrDNA from 68 individuals representing three sexuals, their synthetic hybrids and one sympatric natural apomict, as well as cloning of ITS copies in four representative individuals, RNA secondary structure analysis, and landmark geometric morphometric analysis on leaves. Phylogenetic network analyses indicate additivity of parental ITS variants in both synthetic and natural hybrids. The triploid synthetic hybrids are genetically much closer to their maternal progenitors, probably due to ploidy dosage effects, although exhibiting a paternal-like leaf morphology. The natural hybrids are genetically and morphologically closer to the putative paternal progenitor species. Secondary structures of ITS1-5.8S-ITS2 were rather conserved in all taxa. The observed similarities in ITS polymorphisms suggest that the natural apomict R. variabilis is an ancient hybrid of the diploid sexual species R. notabilis and the sexual species R. cassubicifolius. The additivity pattern shared by R. variabilis and the synthetic hybrids supports an evolutionary and biogeographical scenario that R. variabilis originated from ancient hybridization. Concerted evolution of ITS copies in R. variabilis is incomplete, probably due to a shift to asexual reproduction. Under the condition of comprehensive inter- and intraspecific sampling, ITS polymorphisms are powerful for elucidating reticulate evolutionary histories.
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Affiliation(s)
- Ladislav Hodač
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg August University Göttingen, Göttingen, Germany
| | - Armin Patrick Scheben
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg August University Göttingen, Göttingen, Germany
| | - Diego Hojsgaard
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg August University Göttingen, Göttingen, Germany
| | - Ovidiu Paun
- Division of Systematic and Evolutionary Botany, University of Vienna, Vienna, Austria
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg August University Göttingen, Göttingen, Germany
- * E-mail:
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23
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GokulRaj K, Sundaresan N, Ganeshan EJ, Rajapriya P, Muthumary J, Sridhar J, Pandi M. Phylogenetic reconstruction of endophytic fungal isolates using internal transcribed spacer 2 (ITS2) region. Bioinformation 2014; 10:320-8. [PMID: 25097373 PMCID: PMC4110421 DOI: 10.6026/97320630010320] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 05/23/2014] [Indexed: 11/30/2022] Open
Abstract
Endophytic fungi are inhabitants of plants, living most part of their lifecycle asymptomatically which mainly confer protection and
ecological advantages to the host plant. In this present study, 48 endophytic fungi were isolated from the leaves of three medicinal
plants and characterized based on ITS2 sequence – secondary structure analysis. ITS2 secondary structures were elucidated with
minimum free energy method (MFOLD version 3.1) and consensus structure of each genus was generated by 4SALE. ProfDistS
was used to generate ITS2 sequence structure based phylogenetic tree respectively. Our elucidated isolates were belonging to
Ascomycetes family, representing 5 orders and 6 genera. Colletotrichum/Glomerella spp., Diaporthae/Phomopsis spp., and Alternaria
spp., were predominantly observed while Cochliobolus sp., Cladosporium sp., and Emericella sp., were represented by singletons. The
constructed phylogenetic tree has well resolved monophyletic groups with >50% bootstrap value support. Secondary structures
based fungal systematics improves not only the stability; it also increases the precision of phylogenetic inference. Above ITS2 based
phylogenetic analysis was performed for our 48 isolates along with sequences of known ex-types taken from GenBank which
confirms the efficiency of the proposed method. Further, we propose it as superlative marker for reconstructing phylogenetic
relationships at different taxonomic levels due to their lesser length.
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Affiliation(s)
- Kathamuthu GokulRaj
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai - 21, Tamil Nadu, India
| | - Natesan Sundaresan
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai - 21, Tamil Nadu, India
| | - Enthai Jagan Ganeshan
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai - 21, Tamil Nadu, India
| | - Pandi Rajapriya
- Department of Microbial Technology, School of Biological Sciences, Madurai Kamaraj University, Madurai - 21, Tamil Nadu,India
| | - Johnpaul Muthumary
- Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai - 25, Tamil Nadu, India
| | - Jayavel Sridhar
- Department of Biotechnology (DDE), Madurai Kamaraj University, Madurai - 21, Tamil Nadu, India
| | - Mohan Pandi
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai - 21, Tamil Nadu, India
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24
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nrDNA ITS sequence based SCAR marker to authenticate Aconitum heterophyllum and Cyperus rotundus in Ayurvedic raw drug source and prepared herbal products. Food Chem 2014; 145:1015-20. [DOI: 10.1016/j.foodchem.2013.09.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 08/31/2013] [Accepted: 09/04/2013] [Indexed: 11/16/2022]
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25
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Multiple ITS Haplotypes in the Genome of the Lichenized Basidiomycete Cora inversa (Hygrophoraceae): Fact or Artifact? J Mol Evol 2013; 78:148-62. [DOI: 10.1007/s00239-013-9603-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 11/20/2013] [Indexed: 11/25/2022]
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26
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Li Y, Jiao L, Yao YJ. Non-concerted ITS evolution in fungi, as revealed from the important medicinal fungus Ophiocordyceps sinensis. Mol Phylogenet Evol 2013; 68:373-9. [PMID: 23618625 DOI: 10.1016/j.ympev.2013.04.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 04/04/2013] [Accepted: 04/12/2013] [Indexed: 11/16/2022]
Abstract
The internal transcribed spacer (ITS) of nuclear ribosomal DNA (nrDNA) has been widely used as a molecular marker in phylogenetic studies and has been selected as a DNA barcode for fungi. It is generally believed that nrDNA conforms to concerted evolution in most eukaryotes; however, intraindividual-intraspecific polymorphisms of this region were reported in various organisms, suggesting a non-concerted evolutionary process. In Ophiocordyceps sinensis, one of the most valuable medicinal fungi, a remarkable variation of the ITS region has been revealed. Some highly divergent sequences were thought to represent cryptic species, different species or genotypes in previous studies. To clarify the unusual ITS polymorphisms observed in O. sinensis, specific primers were designed to amplify ITS paralogs from pure cultures of both single-ascospore and tissue isolates in this study. All of the available ITS sequences, including those generated by this group and those in GenBank, were analyzed. Several AT-biased ITS paralogs were classified as pseudogenes based on their nucleotide compositions, secondary structures and minimum free energies of their 5.8S rRNAs, substitution rates, phylogenetic positions and gene expression analyses. Furthermore, ITS pseudogenes were amplified with specific primers from 10 of the 28 strains tested, including eight single-ascospore and two tissue isolates. Divergent ITS paralogs were proved to coexist in individual genomes, suggesting a non-concerted mechanism of evolution in the ITS region of O. sinensis. The hypotheses that divergent ITS paralogs represent cryptic or other species or different genotypes were thus rejected.
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Affiliation(s)
- Yi Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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27
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Moncada B, Lücking R, Suárez A. Molecular phylogeny of the genus Sticta (lichenized Ascomycota: Lobariaceae) in Colombia. FUNGAL DIVERS 2013. [DOI: 10.1007/s13225-013-0230-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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28
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Wei XX, Yang ZY, Li Y, Wang XQ. Molecular phylogeny and biogeography of Pseudotsuga (Pinaceae): Insights into the floristic relationship between Taiwan and its adjacent areas. Mol Phylogenet Evol 2010; 55:776-85. [DOI: 10.1016/j.ympev.2010.03.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Revised: 02/25/2010] [Accepted: 03/03/2010] [Indexed: 11/15/2022]
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29
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Xiao LQ, Möller M, Zhu H. High nrDNA ITS polymorphism in the ancient extant seed plant Cycas: Incomplete concerted evolution and the origin of pseudogenes. Mol Phylogenet Evol 2010; 55:168-177. [PMID: 19945537 DOI: 10.1016/j.ympev.2009.11.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 11/19/2009] [Accepted: 11/20/2009] [Indexed: 11/15/2022]
Affiliation(s)
- Long-Qian Xiao
- Xishuangbanna Tropical Botanical Garden, The Chinese Academy of Sciences, Kunming 650223, China; Graduate University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Michael Möller
- Royal Botanical Garden Edinburgh, Edinburg EH3 5LR, Scotland, United Kingdom
| | - Hua Zhu
- Xishuangbanna Tropical Botanical Garden, The Chinese Academy of Sciences, Kunming 650223, China.
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30
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Mullineux T, Hausner G. Evolution of rDNA ITS1 and ITS2 sequences and RNA secondary structures within members of the fungal genera Grosmannia and Leptographium. Fungal Genet Biol 2009; 46:855-67. [PMID: 19665572 DOI: 10.1016/j.fgb.2009.08.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 07/31/2009] [Accepted: 08/03/2009] [Indexed: 11/29/2022]
Abstract
The two internal transcribed spacers (ITS) of the nuclear ribosomal (r) DNA tandem repeat were examined in ophiostomatoid fungi belonging to the genera Grosmannia and Leptographium and closely-related taxa. Although the DNA sequence of the ITS region evolves rapidly, core features of the RNA secondary structure of the ITS1 and ITS2 segments are conserved. The results demonstrate that structural conservation of GC-rich helical regions is facilitated primarily through compensatory base changes (CBCs), hemi-CBCs, and compensating insertions/deletions (indels), although slippage of the RNA strand is potentially an additional mechanism for maintaining basepairing interactions. The major conclusion of the structural analysis of both ITS segments is that two factors appear to be involved in limiting the type of changes observed: a high GC bias for both ITS1 and ITS2 and structural constraints at the RNA level.
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Affiliation(s)
- Taylor Mullineux
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada R3T 2N2
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Soria-Hernanz DF, Fiz-Palacios O, Braverman JM, Hamilton MB. Reconsidering the generation time hypothesis based on nuclear ribosomal ITS sequence comparisons in annual and perennial angiosperms. BMC Evol Biol 2008; 8:344. [PMID: 19113991 PMCID: PMC2637270 DOI: 10.1186/1471-2148-8-344] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Accepted: 12/29/2008] [Indexed: 11/16/2022] Open
Abstract
Background Differences in plant annual/perennial habit are hypothesized to cause a generation time effect on divergence rates. Previous studies that compared rates of divergence for internal transcribed spacer (ITS1 and ITS2) sequences of nuclear ribosomal DNA (nrDNA) in angiosperms have reached contradictory conclusions about whether differences in generation times (or other life history features) are associated with divergence rate heterogeneity. We compared annual/perennial ITS divergence rates using published sequence data, employing sampling criteria to control for possible artifacts that might obscure any actual rate variation caused by annual/perennial differences. Results Relative rate tests employing ITS sequences from 16 phylogenetically-independent annual/perennial species pairs rejected rate homogeneity in only a few comparisons, with annuals more frequently exhibiting faster substitution rates. Treating branch length differences categorically (annual faster or perennial faster regardless of magnitude) with a sign test often indicated an excess of annuals with faster substitution rates. Annuals showed an approximately 1.6-fold rate acceleration in nucleotide substitution models for ITS. Relative rates of three nuclear loci and two chloroplast regions for the annual Arabidopsis thaliana compared with two closely related Arabidopsis perennials indicated that divergence was faster for the annual. In contrast, A. thaliana ITS divergence rates were sometimes faster and sometimes slower than the perennial. In simulations, divergence rate differences of at least 3.5-fold were required to reject rate constancy in > 80 % of replicates using a nucleotide substitution model observed for the combination of ITS1 and ITS2. Simulations also showed that categorical treatment of branch length differences detected rate heterogeneity > 80% of the time with a 1.5-fold or greater rate difference. Conclusion Although rate homogeneity was not rejected in many comparisons, in cases of significant rate heterogeneity annuals frequently exhibited faster substitution rates. Our results suggest that annual taxa may exhibit a less than 2-fold rate acceleration at ITS. Since the rate difference is small and ITS lacks statistical power to reject rate homogeneity, further studies with greater power will be required to adequately test the hypothesis that annual and perennial plants have heterogeneous substitution rates. Arabidopsis sequence data suggest that relative rate tests based on multiple loci may be able to distinguish a weak acceleration in annual plants. The failure to detect rate heterogeneity with ITS in past studies may be largely a product of low statistical power.
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Song ZK, Wang XZ, Liang GQ. Molecular evolution and phylogenetic utility of the internal transcribed spacer 2 (ITS2) in Calyptratae (Diptera: Brachycera). J Mol Evol 2008; 67:448-64. [PMID: 18850061 DOI: 10.1007/s00239-008-9144-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2007] [Revised: 05/15/2008] [Accepted: 06/23/2008] [Indexed: 11/24/2022]
Abstract
The resolution potential of internal transcribed spacer 2 (ITS2) at deeper levels remains controversial. In this study, 105 ITS2 sequences of 55 species in Calyptratae were analyzed to examine the phylogenetic utility of the spacer above the subfamily level and to further understand its evolutionary characteristics. We predicted the secondary structure of each sequence using the minimum-energy algorithm and constructed two data matrixes for phylogenetic analysis. The ITS2 regions of Calyptratae display strong A-T bias and slight variation in length. The tandem and dispersed repeats embedded in the spacers possibly resulted from replication slippage or transposition. Most foldings conformed to the four-domain model. Sequence comparison in combination with the secondary structures revealed six conserved motifs. Covariation analysis from the conserved motifs indicated that the secondary structure restrains the sequence evolution of the spacer. The deep-level phylogeny derived from the ITS2 data largely agreed with the phylogenetic hypotheses from morphologic and other molecular evidence. Our analyses suggest that the accordant resolutions generated from different analyses can be used to infer deep-level phylogenetic relations.
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Affiliation(s)
- Zhong-kui Song
- Southwest Forestry University, Kunming, 650224, People's Republic of China.
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33
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Zheng X, Cai D, Yao L, Teng Y. Non-concerted ITS evolution, early origin and phylogenetic utility of ITS pseudogenes in Pyrus. Mol Phylogenet Evol 2008; 48:892-903. [PMID: 18577457 DOI: 10.1016/j.ympev.2008.05.039] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Revised: 05/28/2008] [Accepted: 05/29/2008] [Indexed: 11/17/2022]
Abstract
Molecular studies of 19 species of the genus Pyrus L. revealed different degrees of intra-individual polymorphism of the internal transcribed spacer (ITS 1, 5.8S rDNA and ITS 2) region due to the existence of putative non-functional copies (pseudogenes), putative recombinants and non-concerted evolution among functional copies. Different types of ITS pseudogenes displaying lower GC content and unstable secondary structure were preferentially amplified under normal PCR conditions. Functional ITS copies were successfully obtained in all investigated accessions under the modified PCR conditions. All pseudogenes were highly divergent from their corresponding functional copies and formed a monophyletic group in the phylogenetic tree based on all paralogs, indicating they were of relatively early origin. Functional ITS copies led to confused and poorly resolved phylogeny as a result of low sequence divergence, existence of unidentified ancient recombinants and a high degree of intra-individual functional ITS polymorphism, while certain types of pseudogenes and some relict pseudogenes offered more credible clues for the evolutionary history of Pyrus species.
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Affiliation(s)
- Xiaoyan Zheng
- Department of Horticulture, The State Agriculture Ministry Laboratory of Horticultural Plant Growth Development & Biotechnology, Zhejiang University, 268 Kaixuan Road, Hangzhou 310029, China
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Reticulate evolution in Thuja inferred from multiple gene sequences: Implications for the study of biogeographical disjunction between eastern Asia and North America. Mol Phylogenet Evol 2008; 47:1190-202. [DOI: 10.1016/j.ympev.2008.02.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Revised: 02/02/2008] [Accepted: 02/05/2008] [Indexed: 11/18/2022]
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35
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Harpke D, Peterson A. Extensive 5.8S nrDNA polymorphism in Mammillaria (Cactaceae) with special reference to the identification of pseudogenic internal transcribed spacer regions. JOURNAL OF PLANT RESEARCH 2008; 121:261-270. [PMID: 18373158 DOI: 10.1007/s10265-008-0156-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Accepted: 02/20/2008] [Indexed: 05/26/2023]
Abstract
The internal transcribed spacer (ITS) region (ITS1, 5.8S rDNA, ITS2) represents the most widely applied nuclear marker in eukaryotic phylogenetics. Although this region has been assumed to evolve in concert, the number of investigations revealing high degrees of intra-individual polymorphism connected with the presence of pseudogenes has risen. The 5.8S rDNA is the most important diagnostic marker for functionality of the ITS region. In Mammillaria, intra-individual 5.8S rDNA polymorphisms of up to 36% and up to nine different types have been found. Twenty-eight of 30 cloned genomic Mammillaria sequences were identified as putative pseudogenes. For the identification of pseudogenic ITS regions, in addition to formal tests based on substitution rates, we attempted to focus on functional features of the 5.8S rDNA (5.8S motif, secondary structure). The importance of functional data for the identification of pseudogenes is outlined and discussed. The identification of pseudogenes is essential, because they may cause erroneous phylogenies and taxonomic problems.
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Affiliation(s)
- Doerte Harpke
- Biozentrum, Martin Luther University of Halle-Wittenberg, Weinbergweg 22, 06120, Halle/Saale, Germany
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36
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Bayly MJ, Udovicic F, Gibbs AK, Parra-O. C, Ladiges PY. Ribosomal DNA pseudogenes are widespread in the eucalypt group (Myrtaceae): implications for phylogenetic analysis. Cladistics 2008. [DOI: 10.1111/j.1096-0031.2007.00175.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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37
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Göker M, Grimm GW. General functions to transform associate data to host data, and their use in phylogenetic inference from sequences with intra-individual variability. BMC Evol Biol 2008; 8:86. [PMID: 18366660 PMCID: PMC2291458 DOI: 10.1186/1471-2148-8-86] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Accepted: 03/18/2008] [Indexed: 11/29/2022] Open
Abstract
Background Amongst the most commonly used molecular markers for plant phylogenetic studies are the nuclear ribosomal internal transcribed spacers (ITS). Intra-individual variability of these multicopy regions is a very common phenomenon in plants, the causes of which are debated in literature. Phylogenetic reconstruction under these conditions is inherently difficult. Our approach is to consider this problem as a special case of the general biological question of how to infer the characteristics of hosts (represented here by plant individuals) from features of their associates (represented by cloned sequences here). Results Six general transformation functions are introduced, covering the transformation of associate characters to discrete and continuous host characters, and the transformation of associate distances to host distances. A pure distance-based framework is established in which these transformation functions are applied to ITS sequences collected from the angiosperm genera Acer, Fagus and Zelkova. The formulae are also applied to allelic data of three different loci obtained from Rosa spp. The functions are validated by (1) phylogeny-independent measures of treelikeness; (2) correlation with independent host characters; (3) visualization using splits graphs and comparison with published data on the test organisms. The results agree well with these three measures and the datasets examined as well as with the theoretical predictions and previous results in the literature. High-quality distance matrices are obtained with four of the six transformation formulae. We demonstrate that one of them represents a generalization of the Sørensen coefficient, which is widely applied in ecology. Conclusion Because of their generality, the transformation functions may be applied to a wide range of biological problems that are interpretable in terms of hosts and associates. Regarding cloned sequences, the formulae have a high potential to accurately reflect evolutionary relationships within angiosperm genera, and to identify hybrids and ancestral taxa. These results corroborate earlier ones which showed that treelikeness measures are a valuable tool in comparative studies of biological distance functions.
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Affiliation(s)
- Markus Göker
- Organismic Botany, Eberhard-Karls-University, Auf der Morgenstelle 1, Tübingen, Germany.
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38
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Bridge PD, Schlitt T, Cannon PF, Buddie AG, Baker M, Borman AM. Domain II hairpin structure in ITS1 sequences as an aid in differentiating recently evolved animal and plant pathogenic fungi. Mycopathologia 2008; 166:1-16. [PMID: 18340548 DOI: 10.1007/s11046-008-9094-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Accepted: 02/04/2008] [Indexed: 11/27/2022]
Abstract
The hypothesis that ITS structural features can be used to define fungal groups, where sequence analysis is unsatisfactory, was examined in plant and animal pathogenic fungi. Structural models of ITS1 regions were predicted for presumed closely related species in Colletotrichum and Trichophyton anamorphs of Arthroderma species. Structural alignment of models and comparison with ITS sequence analysis identified a variable region in a conserved hairpin formed from a common inverted repeat. Thirteen different hairpin structure models were obtained for Colletotrichum species and five different models were obtained for Trichophyton species. The different structure types could be matched to individual species and species complexes as defined by ITS sequence analysis.
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MESH Headings
- Animals
- Arthrodermataceae/classification
- Arthrodermataceae/genetics
- Arthrodermataceae/pathogenicity
- Base Sequence
- Colletotrichum/classification
- Colletotrichum/genetics
- Colletotrichum/pathogenicity
- DNA, Fungal/genetics
- DNA, Ribosomal Spacer/genetics
- Evolution, Molecular
- Fungi/classification
- Fungi/genetics
- Fungi/pathogenicity
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phylogeny
- Plant Diseases/microbiology
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- Repetitive Sequences, Nucleic Acid
- Sequence Alignment
- Sequence Homology, Nucleic Acid
- Species Specificity
- Trichophyton/classification
- Trichophyton/genetics
- Trichophyton/pathogenicity
- Virulence/genetics
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Affiliation(s)
- P D Bridge
- Biological Sciences Division, British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK.
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39
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Grimm GW, Denk T. Its evolution in Platanus (Platanaceae): homoeologues, pseudogenes and ancient hybridization. ANNALS OF BOTANY 2008; 101:403-19. [PMID: 18089582 PMCID: PMC2701810 DOI: 10.1093/aob/mcm305] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Platanaceae is an old family of angiosperms extending back to the Early Cretaceous but consisting of a single extant genus, Platanus. Species of Platanus have long been known to hybridize, and the London plane, Platanus x hispanica, is a well-known example of a hybrid species that formed in historical times. In addition, morphological studies have suggested past interspecific or interlineage hybridization and reticulation as possibly important factors in the evolution of the genus. This study aims at unravelling the complex evolutionary information contained in internal transcribed spacer (ITS) sequences. METHODS The ITS of the 35S nuclear ribosomal DNA are biparentally inherited, multi-copy markers with a high potential for resolving intrageneric relationships especially when ancient hybridization (reticulation) is involved. Phylogenetic trees, splits graphs and motif analysis are used to extract phylogenetic information from 223 cloned ITS sequences, representing ten species and varieties of Platanus. Non-pseudogenous and pseudogenous sequence motives are assessed to explain how different evolutionary modes contribute to possibly conflicting character state patterns in the ITS. KEY RESULTS It was found that putative non-functional ITS copies ('pseudogenes') form distinct groups in phylograms and splits graphs, and that pseudogenous lineages reflect ancient hybridization events conserved in the ITS. Specifically, pseudogenous clones of an 'Atlantic' North American clade share sequence motives with non-pseudogenous clones of the western ('Pacific') North American P. racemosa species aggregate. In addition, evidence was found for recent lateral gene flow as a possible factor in the evolution of the central Mexican P. rzedowskii. CONCLUSIONS Broad ITS data sets that cover intra- and interindividual variability reveal past and ongoing speciation processes in Platanus. Evolutionary pathways can be visualized with splits graphs, but not with bifurcating trees.
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Affiliation(s)
- Guido W. Grimm
- Institute of Geosciences, Eberhard-Karls-University, Sigwart Strasse 10, 72076 Tübingen, Germany
| | - Thomas Denk
- Department of Palaeobotany, Natural History Museum, Box 50007, 10405 Stockholm, Sweden
- For correspondence. E-mail
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40
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Song Z, Wang X, Liang G. Species identification of some common necrophagous flies in Guangdong province, southern China based on the rDNA internal transcribed spacer 2 (ITS2). Forensic Sci Int 2008; 175:17-22. [PMID: 17582716 DOI: 10.1016/j.forsciint.2007.04.227] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Revised: 03/21/2007] [Accepted: 04/27/2007] [Indexed: 11/19/2022]
Abstract
Recent studies suggest that sequence analysis technique displays a tempting foreground in identifying unknown specimens of necrophagous flies. In this study, we analyzed 63 complete ITS2 sequences concerning 29 fly species to evaluate the identification potential of the ITS2 region, among of which 41 sequence entries were obtained by sequencing and 22 sequence entries were available on the line. Additionally, phenetic method was recommended to substitute for phylogenetic method because it is very difficult to align the ITS2 sequences. The neighbor-joining tree generated by clustalx1.81 allowed us to differentiate each species. Meanwhile the tree topology also suggested that the ITS2 region showed no resolution for the distinction of geographical populations of some species. The overlapping between intra- and interspecific variation revealed by sequence analyses did not affect species identification. High sequence homology between some congeneric species required further sequencing for forensic practice.
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Affiliation(s)
- ZhongKui Song
- State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, People's Republic of China
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41
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Bayly MJ, Ladiges PY. Divergent paralogues of ribosomal DNA in eucalypts (Myrtaceae). Mol Phylogenet Evol 2007; 44:346-56. [DOI: 10.1016/j.ympev.2006.10.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Revised: 10/09/2006] [Accepted: 10/23/2006] [Indexed: 10/23/2022]
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Won H, Renner SS. Dating dispersal and radiation in the gymnosperm Gnetum (Gnetales)--clock calibration when outgroup relationships are uncertain. Syst Biol 2006; 55:610-22. [PMID: 16969937 DOI: 10.1080/10635150600812619] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Most implementations of molecular clocks require resolved topologies. However, one of the Bayesian relaxed clock approaches accepts input topologies that include polytomies. We explored the effects of resolved and polytomous input topologies in a rate-heterogeneous sequence data set for Gnetum, a member of the seed plant lineage Gnetales. Gnetum has 10 species in South America, 1 in tropical West Africa, and 20 to 25 in tropical Asia, and explanations for the ages of these disjunctions involve long-distance dispersal and/or the breakup of Gondwana. To resolve relationships within Gnetum, we sequenced most of its species for six loci from the chloroplast (rbcL, matK, and the trnT-trnF region), the nucleus (rITS/5.8S and the LEAFY gene second intron), and the mitochondrion (nad1 gene second intron). Because Gnetum has no fossil record, we relied on fossils from other Gnetales and from the seed plant lineages conifers, Ginkgo, cycads, and angiosperms to constrain a molecular clock and obtain absolute times for within-Gnetum divergence events. Relationships among Gnetales and the other seed plant lineages are still unresolved, and we therefore used differently resolved topologies, including one that contained a basal polytomy among gymnosperms. For a small set of Gnetales exemplars (n = 13) in which rbcL and matK satisfied the clock assumption, we also obtained time estimates from a strict clock, calibrated with one outgroup fossil. The changing hierarchical relationships among seed plants (and accordingly changing placements of distant fossils) resulted in small changes of within-Gnetum estimates because topologically closest constraints overrode more distant constraints. Regardless of the seed plant topology assumed, relaxed clock estimates suggest that the extant clades of Gnetum began diverging from each other during the Upper Oligocene. Strict clock estimates imply a mid-Miocene divergence. These estimates, together with the phylogeny for Gnetum from the six combined data sets, imply that the single African species of Gnetum is not a remnant of a once Gondwanan distribution. Miocene and Pliocene range expansions are inferred for the Asian subclades of Gnetum, which stem from an ancestor that arrived from Africa. These findings fit with seed dispersal by water in several species of Gnetum, morphological similarities among apparently young species, and incomplete concerted evolution in the nuclear ITS region.
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Affiliation(s)
- Hyosig Won
- Department of Biology, University of Missouri-St. Louis, 8001 Natural Bridge Road, St. Louis, Missouri 63121, USA.
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Wanntorp L, Kocyan A, Renner SS. Wax plants disentangled: a phylogeny of Hoya (Marsdenieae, Apocynaceae) inferred from nuclear and chloroplast DNA sequences. Mol Phylogenet Evol 2006; 39:722-33. [PMID: 16515867 DOI: 10.1016/j.ympev.2006.01.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Revised: 12/29/2005] [Accepted: 01/09/2006] [Indexed: 10/24/2022]
Abstract
Hoya (Marsdenieae, Apocynaceae) includes at least 200 species distributed from India to the Pacific Islands. We here infer major species groups in the genus based on combined sequences from the chloroplast atpB-rbcL spacer, the trnL region, and nuclear ribosomal DNA ITS region for 42 taxa of Hoya and close relatives. To assess levels of ITS polymorphism, ITS sequences for a third of the accessions were obtained by cloning. Most ITS clones grouped by species, indicating that speciation in Hoya usually predates ITS duplication. One ITS sequence of H. carnosa, however, grouped with a sequence of the morphologically similar H. pubicalyx, pointing to recent hybridization or the persistence of paralogous copies through a speciation event. The topology resulting from the combined chloroplast and nuclear data recovers some morphology-based sections, such as Acanthostemma and Eriostemma, as well as a well-supported Australian/New Guinean clade. The combined data also suggest that morphological adaptations for ant-symbiosis evolved at least three times within Hoya.
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Affiliation(s)
- Livia Wanntorp
- Systematic Botany, Ludwig Maximilians University Munich, Menzinger Strasse 67, D-80638 Munich, Germany.
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44
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Won H, Renner SS. The chloroplast trnT-trnF region in the seed plant lineage Gnetales. J Mol Evol 2005; 61:425-36. [PMID: 16155750 DOI: 10.1007/s00239-004-0240-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2004] [Accepted: 05/26/2005] [Indexed: 11/29/2022]
Abstract
The trnT-trnF region is located in the large single-copy region of the chloroplast genome. It consists of the trnL intron, a group I intron, and the trnT-trnL and trnL-trnF intergenic spacers. We analyzed the evolution of the region in the three genera of the gymnosperm lineage Gnetales (Gnetum, Welwitschia, and Ephedra), with especially dense sampling in Gnetum for which we sequenced 41 accessions, representing most of the 25-35 species. The trnL intron has a conserved secondary structure and contains elements that are homologous across land plants, while the spacers are so variable in length and composition that homology cannot be found even among the three genera. Palindromic sequences that form hairpin structures were detected in the trnL-trnF spacer, but neither spacer contained promoter elements for the tRNA genes. The absence of promoters, presence of hairpin structures in the trnL-trnF spacer, and high sequence variation in both spacers together suggest that trnT and trnF are independently transcribed. Our model for the expression and processing of the genes tRNA(Thr)(UGU), tRNA(Leu)(UAA), and tRNA(Phe) (GAA) therefore attributes the seemingly neutral evolution of the two spacers to their escape from functional constraints.
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Affiliation(s)
- Hyosig Won
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA
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