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Bechteler J, Schäfer-Verwimp A, Glenny D, Cargill DC, Maul K, Schütz N, von Konrat M, Quandt D, Nebel M. The evolution and biogeographic history of epiphytic thalloid liverworts. Mol Phylogenet Evol 2021; 165:107298. [PMID: 34464738 DOI: 10.1016/j.ympev.2021.107298] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 08/05/2021] [Accepted: 08/26/2021] [Indexed: 11/28/2022]
Abstract
Among liverworts, the epiphytic lifestyle is not only present in leafy forms but also in thalloid liverworts, which so far has received little attention in evolutionary and biogeographical studies. Metzgeria, with about 107 species worldwide, is the only genus of thalloid liverworts that comprises true epiphytes. In the present study, we provide the first comprehensive molecular phylogeny, including estimated divergence times and ancestral ranges of this genus. Analyses are based on a plastid marker dataset representing about half of the Metzgeria species diversity. We show for the first time with molecular data that Austrometzgeria is indeed a member of Metzgeria and that two morpho-species M. furcata and M. leptoneura are not monophyletic, but rather represent geographically well-defined clades. Our analyses indicate that Metzgeria started to diversify in the Cretaceous in an area encompassing today's South America and Australasia. Thus, Metzgeria is one of the few known epiphytic liverwort genera whose biogeographic history was directly shaped by Gondwana vicariance. Subsequent dispersal events in the Cenozoic resulted in the colonization of Asia, Africa, North America, and Europe and led to today's worldwide distribution of its species. We also provide the first reliable stem age estimate for Metzgeria due to the inclusion of its sister taxon Vandiemenia in our dating analyses. Additionally, this stem age estimate of about 240 million years most likely marks the starting point of a transition from a terrestrial to an epiphytic lifestyle in thalloid liverworts of the Metzgeriales. We assume that the Cretaceous Terrestrial Revolution played a key role in the evolution of epiphytic thalloid liverworts similar to that known for leafy liverworts.
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Affiliation(s)
- Julia Bechteler
- Nees Institute for Biodiversity of Plants, University of Bonn, Meckenheimer Allee 170, Bonn D-53115, Germany.
| | | | - David Glenny
- Allan Herbarium, Manaaki Whenua, PO Box 69-040, Lincoln 7640, New Zealand
| | - D Christine Cargill
- Australian National Herbarium, Centre for Australian National Biodiversity Research, (a joint venture between Parks Australia and CSIRO), GPO Box 1700, Canberra, 2601 ACT, Australia
| | - Karola Maul
- Nees Institute for Biodiversity of Plants, University of Bonn, Meckenheimer Allee 170, Bonn D-53115, Germany
| | - Nicole Schütz
- Department of Botany, Natural History Museum Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Matt von Konrat
- Gantz Family Collections Center, Science & Education, Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605-2496, U.S.A
| | - Dietmar Quandt
- Nees Institute for Biodiversity of Plants, University of Bonn, Meckenheimer Allee 170, Bonn D-53115, Germany
| | - Martin Nebel
- Nees Institute for Biodiversity of Plants, University of Bonn, Meckenheimer Allee 170, Bonn D-53115, Germany
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Saługa M. At the crossroads of botanical collections and molecular genetics laboratory: a preliminary study of obtaining amplifiable DNA from moss herbarium material. PeerJ 2020; 8:e9109. [PMID: 32518721 PMCID: PMC7258893 DOI: 10.7717/peerj.9109] [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: 08/14/2019] [Accepted: 04/10/2020] [Indexed: 12/04/2022] Open
Abstract
Background Research focused on extreme environments is often associated with difficulties in obtaining fresh plant material. Herbaria may provide great support as they house large collections of specimens from different parts of the world. Accordingly, there is also a growing interest in methods using herbarium specimens in molecular studies. Much of the literature on herbarium DNA is aimed to improve extraction and PCR amplification and is focused mostly on vascular plants. Here, I provide a brief study of DNA extraction efficiency from moss herbarium specimens, emphasizing the importance of herbaria as an invaluable source of material from hard-to-access geographical areas, such as the Antarctic region. Methods The presented study is based on herbarium collections of 25 moss species collected in the austral polar regions between 1979 and 2013. The majority of samples were obtained using the DNeasy Plant Mini Kit (Qiagen, Hilden, Germany). The remaining, smaller part was extracted using an adapted CTAB-based approach. The performance of DNA extraction methods in terms of PCR amplification success was measured by testing several DNA fragments of various size. Furthermore, in order to estimate of DNA fragmentation level, an automated on-chip electrophoresis system was used. Results Results reveal that DNA purity and the length of the target genetic region are the fundamental agents which drive the successful PCR reaction. Conversely, the DNA yield and specimen age seem to be less relevant. With this study, I present also an optimized CTAB-based approach which may effectively suppress inhibitors in the herbarium DNA. This method can be considered a cheaper alternative to column-based technology, particularly useful for dealing with a large number of samples. Results of this study confirmed previous reports and contribute to filling the existing gap in molecular analyses which involve the use of herbarium collections of mosses.
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Affiliation(s)
- Marta Saługa
- Władysław Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
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Biersma EM, Jackson JA, Hyvönen J, Koskinen S, Linse K, Griffiths H, Convey P. Global biogeographic patterns in bipolar moss species. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170147. [PMID: 28791139 PMCID: PMC5541534 DOI: 10.1098/rsos.170147] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/08/2017] [Indexed: 05/20/2023]
Abstract
A bipolar disjunction is an extreme, yet common, biogeographic pattern in non-vascular plants, yet its underlying mechanisms (vicariance or long-distance dispersal), origin and timing remain poorly understood. Here, combining a large-scale population dataset and multiple dating analyses, we examine the biogeography of four bipolar Polytrichales mosses, common to the Holarctic (temperate and polar Northern Hemisphere regions) and the Antarctic region (Antarctic, sub-Antarctic, southern South America) and other Southern Hemisphere (SH) regions. Our data reveal contrasting patterns, for three species were of Holarctic origin, with subsequent dispersal to the SH, while one, currently a particularly common species in the Holarctic (Polytrichum juniperinum), diversified in the Antarctic region and from here colonized both the Holarctic and other SH regions. Our findings suggest long-distance dispersal as the driver of bipolar disjunctions. We find such inter-hemispheric dispersals are rare, occurring on multi-million-year timescales. High-altitude tropical populations did not act as trans-equatorial 'stepping-stones', but rather were derived from later dispersal events. All arrivals to the Antarctic region occurred well before the Last Glacial Maximum and previous glaciations, suggesting that, despite the harsh climate during these past glacial maxima, plants have had a much longer presence in this southern region than previously thought.
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Affiliation(s)
- E. M. Biersma
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - J. A. Jackson
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - J. Hyvönen
- Finnish Museum of Natural History (Botany) and Viikki Plant Science Centre, Department of Biosciences, University of Helsinki, PO Box 7, Helsinki FIN-00014, Finland
| | - S. Koskinen
- Department of Biochemistry, University of Turku, Turku, 20014, Finland
| | - K. Linse
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - H. Griffiths
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - P. Convey
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK
- National Antarctic Research Center, Institute of Graduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia
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Dong W, Xu C, Li D, Jin X, Li R, Lu Q, Suo Z. Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae). PeerJ 2016; 4:e2699. [PMID: 27867769 PMCID: PMC5111891 DOI: 10.7717/peerj.2699] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/18/2016] [Indexed: 12/11/2022] Open
Abstract
The Haloxylon genus belongs to the Amaranthaceae (formerly Chenopodiaceae) family. The small trees or shrubs in this genus are referred to as the King of psammophytic plants, and perform important functions in environmental protection, including wind control and sand fixation in deserts. To better understand these beneficial plants, we sequenced the chloroplast (cp) genomes of Haloxylon ammodendron (HA) and Haloxylon persicum (HP) and conducted comparative genomic analyses on these and two other representative Amaranthaceae species. Similar to other higher plants, we found that the Haloxylon cp genome is a quadripartite, double-stranded, circular DNA molecule of 151,570 bp in HA and 151,586 bp in HP. It contains a pair of inverted repeats (24,171 bp in HA and 24,177 bp in HP) that separate the genome into a large single copy region of 84,214 bp in HA and 84,217 bp in HP, and a small single copy region of 19,014 bp in HA and 19,015 bp in HP. Each Haloxylon cp genome contains 112 genes, including 78 coding, 30 tRNA, and four ribosomal RNA genes. We detected 59 different simple sequence repeat loci, including 44 mono-nucleotide, three di-nucleotide, one tri-nucleotide, and 11 tetra-nucleotide repeats. Comparative analysis revealed only 67 mutations between the two species, including 44 substitutions, 23 insertions/deletions, and two micro-inversions. The two inversions, with lengths of 14 and 3 bp, occur in the petA-psbJ intergenic region and rpl16 intron, respectively, and are predicted to form hairpin structures with repeat sequences of 27 and 19 bp, respectively, at the two ends. The ratio of transitions to transversions was 0.76. These results are valuable for future studies on Haloxylon genetic diversity and will enhance our understanding of the phylogenetic evolution of Amaranthaceae.
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Affiliation(s)
- Wenpan Dong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Delu Li
- Gansu Desert Control Research Institute , Gansu , China
| | - Xiaobai Jin
- Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences , Beijing , China
| | - Ruili Li
- Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences , Beijing , China
| | - Qi Lu
- Institute of Desertification Studies, Chinese Academy of Forestry , Beijing , China
| | - Zhili Suo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences , Beijing , China
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Lang AS, Bocksberger G, Stech M. Phylogeny and species delimitations in European Dicranum (Dicranaceae, Bryophyta) inferred from nuclear and plastid DNA. Mol Phylogenet Evol 2015; 92:217-25. [PMID: 26149758 DOI: 10.1016/j.ympev.2015.06.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 06/24/2015] [Accepted: 06/29/2015] [Indexed: 11/26/2022]
Abstract
DNA sequences have been widely used for taxonomy, inferring phylogenetic relationships and identifying species boundaries. Several specific methods to define species delimitations based on molecular phylogenies have appeared recently, with the generalized mixed Yule coalescent (GMYC) method being most popular. However, only few studies on land plants have been published so far and GMYC analyses of bryophytes are missing. Dicranum is a large genus of mosses whose (morpho-)species are partly ill-defined and frequently confused. To infer molecular species delimitations, we reconstructed phylogenetic trees based on five chloroplast markers and nuclear ribosomal ITS sequences from 27 out of 30 species occurring in Europe. We applied the species delimitation methods GMYC and Poisson tree processes (PTP) in order to compare their discriminatory power with species boundaries inferred from the molecular phylogenetic reconstructions and with the morphological species concept. Phylogenetic circumscriptions were congruent with the morphological concept for 19 species, while eight species were molecularly not well delimited, mostly forming closely related species pairs. The automated species delimitation methods achieved similar results but tended to overestimate the number of potential species and exposed several incongruences between the morphological concept and inference from molecular phylogenetic reconstructions. It is concluded that GMYC and PTP methods potentially provide a useful and objective way of delimiting bryophyte species, but studies on further bryophyte data sets are necessary to infer whether incongruences might ensue from evolutionary processes and to test the suitability of these approaches.
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Affiliation(s)
- Annick S Lang
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Leiden University, Leiden, The Netherlands.
| | - Gaëlle Bocksberger
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Michael Stech
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Leiden University, Leiden, The Netherlands
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Wynns JT, Lange CBA. A comparison of 16 DNA regions for use as phylogenetic markers in the pleurocarpous moss genus Plagiothecium (Hypnales). AMERICAN JOURNAL OF BOTANY 2014; 101:652-669. [PMID: 24699540 DOI: 10.3732/ajb.1300269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY Within the Hypnales-the most derived and species-rich order of pleurocarpous mosses - phylogenies at or below the family level often show poor resolution. In preparation for a phylogeny of the genus Plagiothecium, we wished to identify the DNA markers best suited for evolutionary reconstruction in this group of hypnalean pleurocarps. METHODS For each of 25 collections of Plagiothecium and associated taxa, 16 DNA regions were sequenced: nuclear ITS and 26S, and plastid rps4, rps4-trnL, trnL-F, trnK (matK)-psbA, psbA-trnH, trnM-V, trnD-T, rbcL, atpB-rbcL, psbT-H, rpoC1 exon 2 (partial), the trnG intron, the rpl16 intron and the plastid ribosomal spacer DNA (cpITS). Each region was evaluated on the basis of its ability to resolve clades, the amount of homoplasy present in the data set, and the relative ease of obtaining the data. Descriptive statistics for each region are given. KEY RESULTS Under-utilized plastid markers for bryophytes such as trnK-psbA, rps4-trnL, and trnD-T outperformed more traditional markers such as trnL-F and rps4. Individual plastid topologies were similar, suggesting that only a limited amount of plastid data are needed to recover a backbone phylogeny. Adding a small amount of nuclear ribosomal data to a large plastid matrix restructured the recovered topology, emphasizing the importance of sampling multiple genomes and the need for new low-copy nuclear markers in bryophyte systematics. CONCLUSIONS Future genus-level phylogenies of pleurocarpous mosses should target under-utilized plastid markers such as trnK-psbA and rps4-trnL in conjunction with low-copy nuclear markers.
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Affiliation(s)
- Justin T Wynns
- Section for Organismal Biology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Rolighedsvej 21, DK-1958 Frederiksberg, Denmark
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Poczai P, Hyvönen J. Discovery of novel plastid phenylalanine (trnF) pseudogenes defines a distinctive clade in Solanaceae. SPRINGERPLUS 2013; 2:459. [PMID: 24083106 PMCID: PMC3786074 DOI: 10.1186/2193-1801-2-459] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 09/11/2013] [Indexed: 11/12/2022]
Abstract
BACKGROUND The plastome of embryophytes is known for its high degree of conservation in size, structure, gene content and linear order of genes. The duplication of entire tRNA genes or their arrangement in a tandem array composed by multiple pseudogene copies is extremely rare in the plastome. Pseudogene repeats of the trnF gene have rarely been described from the chloroplast genome of angiosperms. FINDINGS We report the discovery of duplicated copies of the original phenylalanine (trnFGAA) gene in Solanaceae that are specific to a larger clade within the Solanoideae subfamily. The pseudogene copies are composed of several highly structured motifs that are partial residues or entire parts of the anticodon, T- and D-domains of the original trnF gene. CONCLUSIONS The Pseudosolanoid clade consists of 29 genera and includes many economically important plants such as potato, tomato, eggplant and pepper.
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Affiliation(s)
- Péter Poczai
- Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, Helsinki, FIN 00014 Finland
| | - Jaakko Hyvönen
- Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, Helsinki, FIN 00014 Finland
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Pokorny L, Ho BC, Frahm JP, Quandt D, Shaw AJ. Phylogenetic analyses of morphological evolution in the gametophyte and sporophyte generations of the moss order Hookeriales (Bryopsida). Mol Phylogenet Evol 2012; 63:351-64. [PMID: 22266481 DOI: 10.1016/j.ympev.2012.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 01/03/2012] [Accepted: 01/09/2012] [Indexed: 10/14/2022]
Abstract
Morphological characters from the gametophyte and sporophyte generations have been used in land plants to infer relationships and construct classifications, but sporophytes provide the vast majority of data for the systematics of vascular plants. In bryophytes both generations are well developed and characters from both are commonly used to classify these organisms. However, because morphological traits of gametophytes and sporophytes can have different genetic bases and experience different selective pressures, taxonomic emphasis on one generation or the other may yield incongruent classifications. The moss order Hookeriales has a controversial taxonomic history because previous classifications have focused almost exclusively on either gametophytes or sporophytes. The Hookeriales provide a model for comparing morphological evolution in gametophytes and sporophytes, and its impact on alternative classification systems. In this study we reconstruct relationships among mosses that are or have been included in the Hookeriales based on sequences from five gene regions, and reconstruct morphological evolution of six sporophyte and gametophyte traits that have been used to differentiate families and genera. We found that the Hookeriales, as currently circumscribed, are monophyletic and that both sporophyte and gametophyte characters are labile. We documented parallel changes and reversals in traits from both generations. This study addresses the general issue of morphological reversals to ancestral states, and resolves novel relationships in the Hookeriales.
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Affiliation(s)
- L Pokorny
- Department of Biology, Duke University, 125 Science Drive, Durham, NC 27708-0338, USA.
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Abstract
Highly variable intergenic spacer and intron regions from nuclear and cytoplasmic DNA have been used for species identification. Noncoding internal transcribed spacers (ITSs) located in 18S-5.8S-26S, and 5S ribosomal RNA genes (rDNAs) represent suitable region for medicinal plant authentication. Noncoding regions from two cytoplasmic DNA, chloroplast DNA (trnT-F intergenic spacer region), and mitochondrial DNA (fourth intron region of nad7 gene) are also successfully applied for the proper identification of medicinal plants. Single-nucleotide polymorphism (SNP) sites obtained from the amplification of intergenic spacer and intron regions are properly utilized for the verification of medicinal plants in species level using multiplex PCR. Multiplex PCR as a variant of PCR technique used to amplify more than two loci simultaneously.
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Affiliation(s)
- Ok Ran Lee
- Department of Oriental Medicinal Materials and Processing, College of Life Science, Kyung Hee University, Suwon, South Korea
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Korotkova N, Borsch T, Quandt D, Taylor NP, Müller KF, Barthlott W. What does it take to resolve relationships and to identify species with molecular markers? An example from the epiphytic Rhipsalideae (Cactaceae). AMERICAN JOURNAL OF BOTANY 2011; 98:1549-1572. [PMID: 21900612 DOI: 10.3732/ajb.1000502] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY The Cactaceae are a major New World plant family and popular in horticulture. Still, taxonomic units and species limits have been difficult to define, and molecular phylogenetic studies so far have yielded largely unresolved trees, so relationships within Cactaceae remain insufficiently understood. This study focuses on the predominantly epiphytic tribe Rhipsalideae and evaluates the utility of a spectrum of plastid genomic regions. • METHODS We present a phylogenetic study including 52 of the 53 Rhipsalideae species and all the infraspecific taxa. Seven regions (trnK intron, matK, rbcL, rps3-rpl16, rpl16 intron, psbA-trnH, trnQ-rps16), ca. 5600 nucleotides (nt) were sequenced per sample. The regions used were evaluated for their phylogenetic performance and performance in DNA-based species recognition based on operational taxonomic units (OTUs) defined beforehand. • KEY RESULTS The Rhipsalideae are monophyletic and contain five clades that correspond to the genera Rhipsalis, Lepismium, Schlumbergera, Hatiora, and Rhipsalidopsis. The species-level tree was well resolved and supported; the rpl16 and trnK introns yielded the best phylogenetic signal. Although the psbA-trnH and trnQ-rps16 spacers were the most successful individual regions for OTU identification, their success rate did not significantly exceed 70%. The highest OTU identification rate of 97% was found using the combination of psbA-trnH, rps3-rpl16, trnK intron, and trnQ-rps16 as a minimum possible marker length (ca. 1660 nt). • CONCLUSIONS The phylogenetic performance of a marker is not determined by the level of sequence variability, and species discrimination power does not necessarily correlate with phylogenetic utility.
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Affiliation(s)
- Nadja Korotkova
- Nees-Institut für Biodiversität der Pflanzen, Universität Bonn, Germany.
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Identification and characterization of plastid trnF(GAA) pseudogenes in four species of Solanum (Solanaceae). Biotechnol Lett 2011; 33:2317-23. [PMID: 21833547 DOI: 10.1007/s10529-011-0701-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 07/04/2011] [Indexed: 01/05/2023]
Abstract
Non-functional trnF pseudogenes that rarely occur in embryophytes have been found in Solanaceae. We have sequenced the trnL-F intergenic spacer of four species of Solanum, and found duplicated regions of the original trnF gene. These repeats were 94-260 bp long causing large length variation in the trnL-F intergenic spacer resulting from differences in pseudogene copy number (2-4). The duplicated trnF regions are comprised of several highly structured motifs, which were partial residues, or entire parts of the Anticodon, T- and D-domains of the original gene, but all lacked the acceptor stems at the 5'- or 3'-end. Pseudogenes included several transitions and transversions in their sequences compared to the original trnF gene. Among pseudogene copies, T-domains were more frequent and fragmented than D-domain elements. Our results demonstrate that although chloroplast evolution is uniform such structural duplications in the sequences used for phylogenetic reconstructions should be treated with great caution.
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Jagarlamudi S, G R, Kurapati RK, Pinnamaneni R. Molecular identification of Mango, Mangifera indica L.var. totupura. Bioinformation 2011; 5:405-9. [PMID: 21423885 PMCID: PMC3055156 DOI: 10.6026/97320630005405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 01/10/2011] [Indexed: 11/23/2022] Open
Abstract
Mango (>Mangifera indica) belonging to Anacardiaceae family is a fruit that grows in tropical regions. It is considered as the King of fruits. The present
work was taken up to identify a tool in identifying the mango species at the molecular level. The chloroplast trnL-F region was amplified from extracted
total genomic DNA using the polymerase chain reaction (PCR) and sequenced. Sequence of the dominant DGGE band revealed that Mangifera indica in
tested leaves was Mangifera indica (100% similarity to the ITS sequences of Mangifera indica). This sequence was deposited in NCBI with the accession
no. GQ927757.
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Affiliation(s)
| | - Rosaiah G
- Department of Botany, Acharya Nagarjuna University, Nagarjuna Nagar, Andhra Pradesh, India
| | | | - Rajasekhar Pinnamaneni
- Department of Biotechnology, Sreenidhi Institute of Science and Technology, Yamnampet, Ghatkesar, R.R.District, Andhra Pradesh,India
- Rajasekhar Pinnamaneni:
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Whitlock BA, Hale AM, Groff PA. Intraspecific inversions pose a challenge for the trnH-psbA plant DNA barcode. PLoS One 2010; 5:e11533. [PMID: 20644717 PMCID: PMC2903610 DOI: 10.1371/journal.pone.0011533] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 06/17/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The chloroplast trnH-psbA spacer region has been proposed as a prime candidate for use in DNA barcoding of plants because of its high substitution rate. However, frequent inversions associated with palindromic sequences within this region have been found in multiple lineages of Angiosperms and may complicate its use as a barcode, especially if they occur within species. METHODOLOGY/PRINCIPAL FINDINGS Here, we evaluate the implications of intraspecific inversions in the trnH-psbA region for DNA barcoding efforts. We report polymorphic inversions within six species of Gentianaceae, all narrowly circumscribed morphologically: Gentiana algida, Gentiana fremontii, Gentianopsis crinita, Gentianopsis thermalis, Gentianopsis macrantha and Frasera speciosa. We analyze these sequences together with those from 15 other species of Gentianaceae and show that typical simple methods of sequence alignment can lead to misassignment of conspecifics and incorrect assessment of relationships. CONCLUSIONS/SIGNIFICANCE Frequent inversions in the trnH-psbA region, if not recognized and aligned appropriately, may lead to large overestimates of the number of substitution events separating closely related lineages and to uniting more distantly related taxa that share the same form of the inversion. Thus, alignment of the trnH-psbA spacer region will need careful attention if it is used as a marker for DNA barcoding.
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Volkmar U, Knoop V. Introducing intron locus cox1i624 for phylogenetic analyses in Bryophytes: on the issue of Takakia as sister genus to all other extant mosses. J Mol Evol 2010; 70:506-18. [PMID: 20473660 DOI: 10.1007/s00239-010-9348-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Accepted: 04/13/2010] [Indexed: 11/30/2022]
Abstract
Liverworts are well supported as the sister group to all other land plants (embryophytes) by molecular data. Observations strongly supporting this earliest dichotomy in embryophyte evolution are the strikingly different introns occurring in the mitochondrial DNAs of liverworts versus non-liverwort embryophytes (NLE), including the mosses. A final conclusion on the most basal lineages of mosses, for which genera such as Sphagnum and Takakia are the most likely candidates, is lacking. We have now investigated cox1i624, a mitochondrial group I intron conserved between the moss Physcomitrella patens and the liverwort Marchantia polymorpha. Focusing on a sampling of liverwort and moss genera, which had previously been identified as early branching taxa in their respective clades, we find that group I intron cox1i624 is universally conserved in all 33 mosses and 11 liverworts investigated. The group I intron core secondary structure is well conserved between the two ancient land plant clades. However, whereas dramatic size reductions are seen in the moss phylogeny, exactly the opposite is observed for liverworts. The cox1i624g1 locus was used for phylogenetic tree reconstruction also in combination with data sets of nad5i753g1 as well as chloroplast loci rbcL and rps4. The phylogenetic analyses revealed (i) very good support for the Treubiopsida as sister clade to all other liverworts, (ii) a sister group relationship of the nematodontous Tetraphidopsida and Polytrichopsida and (iii) two rivalling hypotheses about the basal-most moss genus with mitochondrial loci suggesting an isolated Takakia as sister to all other mosses and chloroplast loci indicating a Takakia-Sphagnum clade.
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Affiliation(s)
- Ute Volkmar
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abt. Molekulare Evolution, Universität Bonn, Kirschallee 1, Bonn, Germany.
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Phylogeny of the moss class Polytrichopsida (BRYOPHYTA): Generic-level structure and incongruent gene trees. Mol Phylogenet Evol 2010; 55:381-98. [DOI: 10.1016/j.ympev.2010.02.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Revised: 01/27/2010] [Accepted: 02/04/2010] [Indexed: 11/23/2022]
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The phylogeny of mosses – Addressing open issues with a new mitochondrial locus: Group I intron cobi420. Mol Phylogenet Evol 2010; 54:417-26. [DOI: 10.1016/j.ympev.2009.09.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2009] [Revised: 09/12/2009] [Accepted: 09/22/2009] [Indexed: 11/15/2022]
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17
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18
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Watts CD, Fisher AE, Shrum CD, Newbold WL, Hansen S, Liu C, Kelchner SA. The D4 set: primers that target highly variable intron loops in plant chloroplast genomes. Mol Ecol Resour 2008; 8:1344-7. [PMID: 21586041 DOI: 10.1111/j.1755-0998.2008.02229.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Chloroplast group II introns offer high-quality, rapidly evolving single-copy loci for comparative sequence analysis. These introns feature diagnostic secondary structures with loops that are among the least evolutionarily constrained sequence in plastomes. We exploited these structures to develop universal primers that amplify and sequence the large Domain IV (D4) loop in several angiosperm introns. With a single sequence read, we recover 300-600 nucleotides of highly variable sequence across angiosperms, with rates of change that are equal to or higher than many of the best known intergenic spacers in plant chloroplast genomes.
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Affiliation(s)
- Chad D Watts
- Department of Biological Sciences, Idaho State University, Pocatello, ID 83209-8007, USA
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Hernández-Maqueda R, Quandt D, Werner O, Muñoz J. Phylogeny and classification of the Grimmiaceae/Ptychomitriaceae complex (Bryophyta) inferred from cpDNA. Mol Phylogenet Evol 2008; 46:863-77. [DOI: 10.1016/j.ympev.2007.12.017] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Revised: 10/26/2007] [Accepted: 12/20/2007] [Indexed: 11/25/2022]
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Miyata Y, Sugita C, Maruyama K, Sugita M. RNA editing in the anticodon of tRNA Leu (CAA) occurs before group I intron splicing in plastids of a moss Takakia lepidozioides S. Hatt. & Inoue. PLANT BIOLOGY (STUTTGART, GERMANY) 2008; 10:250-255. [PMID: 18304199 DOI: 10.1111/j.1438-8677.2007.00027.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
RNA editing of cytidine (C) to uridine (U) transitions occurs in plastids and mitochondria of most land plants. In this study, we amplified and sequenced the group I intron-containing tRNA Leu gene, trnL-CAA, from Takakia lepidozioides, a moss. DNA sequence analysis revealed that the T. lepidozioides tRNA Leu gene consisted of a 35-bp 5' exon, a 469-bp group I intron and a 50-bp 3' exon. The intron was inserted between the first and second position of the tRNA Leu anticodon. In general, plastid tRNA Leu genes with a group I intron code for a TAA anticodon in most land plants. This strongly suggests that the first nucleotide of the CAA anticodon could be edited in T. lepidozioides plastids. To investigate this possibility, we analysed cDNAs derived from the trnL-CAA transcripts. We demonstrated that the first nucleotide C of the anticodon was edited to create a canonical UAA anticodon in T. lepidozioides plastids. cDNA sequencing analyses of the spliced or unspliced tRNA Leu transcripts revealed that, while the spliced tRNA was completely edited, editing in the unspliced tRNAs were only partial. This is the first experimental evidence that the anticodon editing of tRNA occurs before RNA splicing in plastids. This suggests that this editing is a prerequisite to splicing of pre-tRNA Leu.
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Affiliation(s)
- Y Miyata
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
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Quandt D, Stech M. Molecular evolution of the trnL(UAA) intron in bryophytes. Mol Phylogenet Evol 2005; 36:429-43. [PMID: 16005648 DOI: 10.1016/j.ympev.2005.03.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2004] [Revised: 02/09/2005] [Accepted: 03/07/2005] [Indexed: 11/20/2022]
Abstract
Structure, variability, and molecular evolution of the trnL(UAA) intron in bryophytes (mosses and liverworts) is analyzed based on more than 1000 sequences representing all classes, including comparisons of lengths and GC-contents, sequence similarities, evolutionary rates and ti/tv ratios of the major lineages and selected genera. Secondary structure analyses of the more variable stem-loop regions facilitated recognition of sequence repeats and minute inversions that often occurred independently in non-related lineages, thus supporting alignment construction and homology assessment. The most length-variable stem-loop region P8 does not share a common evolutionary history across all major bryophyte lineages. Independent nucleotide additions such as internally repeated sequence segments resulted in non-homologous P8 sequences that cannot be folded into a common P8 secondary structure, neither for all bryophytes nor for liverworts or mosses. To address evolutionary patterns, separate analyses of P6/P8 and the remaining intron (core) have to be performed, as overall values of the complete intron are misleading. It is argued that a transition bias observed above the genus level in the core structure is caused by structural constraints, not by its higher GC-content in comparison to the more AT-rich P6 and P8. Compensating base pair changes detected in highly conserved elements are often characteristic of the major bryophyte lineages (classes). Sequence divergence and evolutionary rates are generally higher in liverworts than in mosses, resulting in ambiguous alignments of P6 and P8 even within classes. In mosses, trends towards length reduction of P8 and lower evolutionary rates of the intron are observed. Average intraspecific variation is less than 1%, corresponding to 2-3 mutations in the complete intron.
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Affiliation(s)
- Dietmar Quandt
- Nees Institut für Biodiversität der Pflanzen, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 170, D-53115 Bonn, Germany.
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Quandt D, Huttunen S, Streimann H, Frahm JP, Frey W. Molecular phylogenetics of the Meteoriaceae s. str.: focusing on the genera Meteorium and Papillaria. Mol Phylogenet Evol 2004; 32:435-61. [PMID: 15223029 DOI: 10.1016/j.ympev.2003.12.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2003] [Revised: 12/10/2003] [Indexed: 11/20/2022]
Abstract
In order to delimit and understand the evolution of the Meteoriaceae, we provide phylogenetic analyses using the internal transcribed spacer 2 (ITS2) of nuclear ribosomal DNA in combination with two plastid markers, trnL-F and psbT-H. In contrast to the widely used trnL-F region, the psbT-H gene cluster, coding for proteins of photosystem II, has been rarely used to address systematic questions among the different land plant lineages. To overcome the problem of potential ambiguous alignments of non-coding DNA regions, the data were independently analyzed using direct optimization. The comparison and evaluation of the obtained results showed that the inferred cladograms based on the different phylogenetic approaches are very similar, with only minor differences. In combination with morphological characters, generic relationships as well as taxonomic and nomenclatural problems, especially regarding the key genera Meteorium and Papillaria are discussed in detail. New insights into generic relationships of the Meteoriaceae are provided, such as the exclusion of the monospecific southern South American genera Ancistrodes and Cryphaeophilum, which are subsequently transferred to the Hookeriaceae and Cryphaeaceae, respectively. Phylogenetic reconstructions using maximum likelihood as well as parsimony approaches reveal that at the familial level the Meteoriaceae s. l. are polyphyletic, if the formerly recognized "Trachypodaceae" are considered as a separate family. Based on our results we favor the synonym of the Trachypodaceae with the Meteoriaceae.
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