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Definition of Eight Mulberry Species in the Genus Morus by Internal Transcribed Spacer-Based Phylogeny. PLoS One 2015; 10:e0135411. [PMID: 26266951 PMCID: PMC4534381 DOI: 10.1371/journal.pone.0135411] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/21/2015] [Indexed: 11/19/2022] Open
Abstract
Mulberry, belonging to the order Rosales, family Moraceae, and genus Morus, has received attention because of both its economic and medicinal value, as well as for its important ecological function. The genus Morus has a worldwide distribution, however, its taxonomy remains complex and disputed. Many studies have attempted to classify Morus species, resulting in varied numbers of designated Morus spp. To address this issue, we used information from internal transcribed spacer (ITS) genetic sequences to study the taxonomy of all the members of generally accepted genus Morus. We found that intraspecific 5.8S rRNA sequences were identical but that interspecific 5.8S sequences were diverse. M. alba and M. notabilis showed the shortest (215 bp) and the longest (233 bp) ITS1 sequence length, respectively. With the completion of the mulberry genome, we could identify single nucleotide polymorphisms within the ITS locus in the M. notabilis genome. From reconstruction of a phylogenetic tree based on the complete ITS data, we propose that the Morus genus should be classified into eight species, including M. alba, M. nigra, M. notabilis, M. serrata, M. celtidifolia, M. insignis, M. rubra, and M. mesozygia. Furthermore, the classification of the ITS sequences of known interspecific hybrid clones into both paternal and maternal clades indicated that ITS variation was sufficient to distinguish interspecific hybrids in the genus Morus.
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Ghada B, Ahmed BA, Messaoud M, Amel SH. Genetic diversity and molecular evolution of the internal transcribed spacer (ITSs) of nuclear ribosomal DNA in the Tunisian fig cultivars (Ficus carica L.; Moracea). BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2012.11.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Bargues MD, Artigas P, Khoubbane M, Mas-Coma S. DNA sequence characterisation and phylogeography of Lymnaea cousini and related species, vectors of fascioliasis in northern Andean countries, with description of L. meridensis n. sp. (Gastropoda: Lymnaeidae). Parasit Vectors 2011; 4:132. [PMID: 21749718 PMCID: PMC3168421 DOI: 10.1186/1756-3305-4-132] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 07/12/2011] [Indexed: 11/25/2022] Open
Abstract
Background Livestock fascioliasis is a problem throughout Ecuador, Colombia and Venezuela, mainly in Andean areas where the disease also appears to affect humans. Transmission patterns and epidemiological scenarios of liver fluke infection have shown to differ according to the lymnaeid vector snail species involved. These Andean countries present the vectors Lymnaea cousini, L. bogotensis and L. ubaquensis, unknown in the rest of Latin America. An exhaustive combined haplotype study of these species is performed by means of DNA sequencing of the nuclear ribosomal 18S RNA gene, ITS-2 and ITS-1, and mitochondrial DNA cox1 gene. Results The conserved 5.8S rDNA sequence corroborated that no pseudogenes are involved in the numerous non-microsatellite/minisatellite-related indels appearing between the ITS-2 and ITS-1 sequences when comparing different L. cousini - L. bogotensis populations. Sequence analyses and phylogenetic reconstruction methods including other lymnaeid vector species show that (i) L. bogotensis is a synonym of L. cousini, (ii) L. ubaquensis is a synonym of Pseudosuccinea columella, and (iii) populations of L. cousini hitherto known from Venezuelan highlands indeed belong to a new species for which the name L. meridensis n. sp. is proposed. This new species is described and a complete phenotypic differentiation provided. Conclusions ITS-2, ITS-1 and cox1 prove to be good markers for specimen classification and haplotype characterisation of these morphologically similar lymnaeids in endemic areas. Analysis of the 18S gene and phylogenetic reconstructions indicate that L. cousini and L. meridensis n. sp. cluster in an evolutionary line different from the one of P. columella, despite their external resemblance. This suggests an evolutionary phenotypic convergence related to similar environments and which has given rise to frequent specimen misclassification. Body size and phylogenetic relationships of L. meridensis n. sp. with well-known vectors as Lymnaea cousini and P. columella, as well as with Galba/Fossaria species, suggest that the new species may participate in disease transmission to both animals and humans in altitude areas during the yearly window in which temperatures are higher than the F. hepatica minimum development threshold. The involvement of L. cousini and P. columella in the transmission and geographical/altitudinal distribution of fascioliasis in these Andean countries is analysed.
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Affiliation(s)
- M Dolores Bargues
- Departamento de Parasitología, Facultad de Farmacia, Universidad de Valencia, 46100 Burjassot, Valencia, Spain
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Gustinelli A, Caffara M, Florio D, Otachi EO, Wathuta EM, Fioravanti ML. First description of the adult stage of Clinostomum cutaneum Paperna, 1964 (Digenea: Clinostomidae) from grey herons Ardea cinerea L. and a redescription of the metacercaria from the Nile tilapia Oreochromis niloticus niloticus (L.) in Kenya. Syst Parasitol 2010; 76:39-51. [PMID: 20401577 DOI: 10.1007/s11230-010-9231-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 09/24/2009] [Indexed: 11/26/2022]
Abstract
The combined use of morphological and molecular studies allowed for the first time the recognition and description of the adult stage of Clinostomum cutaneum Paperna, 1964 from the grey heron Ardea cinerea L. in Kenya. A redescription of the metacercaria that infect Nile tilapia Oreochromis niloticus niloticus (L.) from the same aquatic environment is also presented. C. cutaneum differs from all other species of Clinostomum Leidy, 1856 in the shape of its uterus. Sequencing the rRNA confirmed the morphological similarity between adults from the grey heron and the metacercarial stage from tilapia, and a level of genetic similarity with the other previously sequenced Clinostomum spp. was observed. The need for a reorganisation of Clinostomum using both morphological and molecular methods is highlighted.
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MESH Headings
- Animals
- Birds/parasitology
- Cichlids/parasitology
- DNA, Helminth/chemistry
- DNA, Helminth/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Kenya
- Microscopy
- Microscopy, Electron, Scanning
- Molecular Sequence Data
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 28S/genetics
- Sequence Analysis, DNA
- Trematoda/anatomy & histology
- Trematoda/classification
- Trematoda/isolation & purification
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Affiliation(s)
- Andrea Gustinelli
- Department of Veterinary Public Health and Animal Pathology, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, BO, Italy.
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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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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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Genomic Configuration of the Autotetraploid Oat Species Avena macrostachya Inferred from Comparative Analysis of ITS1 and ITS2 Sequences: on the Oat Karyotype Evolution during the Early Events of the Avena Species Divergence. RUSS J GENET+ 2005. [DOI: 10.1007/s11177-005-0120-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Won H, Renner SS. The internal transcribed spacer of nuclear ribosomal DNA in the gymnosperm Gnetum. Mol Phylogenet Evol 2005; 36:581-97. [PMID: 16099382 DOI: 10.1016/j.ympev.2005.03.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2004] [Revised: 03/08/2005] [Accepted: 03/11/2005] [Indexed: 11/17/2022]
Abstract
We analyze the structure of the internal transcribed spacers ITS1 and ITS2 of the nuclear ribosomal DNA in the gymnosperm Gnetum, using a phylogenetic framework derived mainly from an intron in the nuclear low-copy LEAFY gene. Gnetum comprises 25-35 species in South America, Africa, and Asia, of which we sampled 16, each with two to six clones. Criteria used to assess ITS functionality were highly divergent nucleotide substitution, GC content, secondary structure, and incongruent phylogenetic placement of presumed paralogs. The length of ITS1 ranged from 225 to 986 bp and that of ITS2 from 259 to 305 bp, the largest ranges so far reported from seed plants. Gnetum ITS1 contains two informative sequence motifs, but different from other gymnosperms, there are only few and short (7-13 bp) tandem repeats. Gnetum ITS2 contains two structural motifs, modified in different clades by shortening of stems and loops. Conspecific sequences grouped together except for two recombinant pseudogenes that had ITS1 of one clade and ITS2 of another. Most of the pseudogenic ITS copies, paralogs, and putative chimeras occurred in a clade that according to a fossil-calibrated chloroplast-DNA clock has an age of a few million years. Based on morphology and chromosome numbers, the most plausible causes of the observed high levels of ITS polymorphism are hybridization, allopolyploidy, and introgression.
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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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Bakker FT, Olsen JL, Stam WT. Evolution of nuclear rDNA ITS sequences in the Cladophora albida/sericea clade (Chlorophyta). J Mol Evol 1995; 40:640-51. [PMID: 7643415 DOI: 10.1007/bf00160512] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Ribosomal DNA ITS sequences were compared among 13 different species and biogeographic isolates from the monophyletic "albida/sericea clade" in the green algal genus Cladophora. Six distinct ITS sequence types were found, characterized by multiple insertions and deletions and high levels of nucleotide substitution. Conserved domains within the ITS regions indicate the presence of ITS secondary structure. Low transition/transversion ratios among the six types and nearly symmetrical tree-length frequency distributions indicate some saturation, and low phylogenetic signal. Although branching order among five of the six ITS sequence types could not be resolved, estimates of ITS sequence divergence as compared with 18S divergence in a subset of the taxa suggests that the origin of the different ITS types is probably in the mid-Miocene (12 Ma ago) but that biogeographic isolates within a single ITS type (including both Pacific and Atlantic representatives) have probably dispersed on a time scale of thousands rather than millions of years.
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Affiliation(s)
- F T Bakker
- Department of Marine Biology, University of Groningen, Haren, The Netherlands
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Liu JS, Schardl CL. A conserved sequence in internal transcribed spacer 1 of plant nuclear rRNA genes. PLANT MOLECULAR BIOLOGY 1994; 26:775-8. [PMID: 7948932 DOI: 10.1007/bf00013763] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
A highly conserved sequence was found in rRNA gene internal transcribed spacer 1 (ITS1) among flowering plant species. The sequence, GGCRY-(4 to 7 n)-GYGYCAAGGAA (where Y = C or T; R = G or A) is located in the central region of ITS1, and is present in published sequences from a wide range of flowering plants. The rest of ITS1 is highly variable in sequence. Therefore, the conserved motif within ITS1 may have a key function in the processing of rRNA gene transcripts. Furthermore, identification of such a conserved motif will help facilitate alignment of sequences for phylogenetic analysis.
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MESH Headings
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Base Sequence
- Conserved Sequence
- DNA, Plant/genetics
- DNA, Plant/metabolism
- DNA, Ribosomal/genetics
- DNA, Ribosomal/metabolism
- Genes, Plant
- Molecular Sequence Data
- Nucleic Acid Conformation
- Plants/genetics
- Plants/metabolism
- RNA, Ribosomal/biosynthesis
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- Sequence Homology, Nucleic Acid
- Species Specificity
- Transcription, Genetic
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Affiliation(s)
- J S Liu
- Department of Plant Pathology, University of Kentucky, Lexington 40546-0091
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