scholarly journals Molecular differentiation of the Murraya paniculata Complex (Rutaceae: Aurantioideae: Aurantieae)

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Chung Huy Nguyen ◽  
G. Andrew C. Beattie ◽  
Anthony M. Haigh ◽  
Inggit Puji Astuti ◽  
David J. Mabberley ◽  
...  

Abstract Background Orange jasmine has a complex nomenclatural history and is now known as Murraya paniculata (L.) Jack. Our interest in this common ornamental stemmed from the need to resolve its identity and the identities of closely related taxa as hosts of the pathogen ‘Candidatus Liberibacter asiaticus’ and its vector Diaphorina citri. Understanding these microbe-vector-plant relationships has been hampered by taxonomic confusion surrounding Murraya at both the generic and specific levels. Results To resolve the taxonomic uncertainty, six regions of the maternally-inherited chloroplastal genome and part of the nuclear-encoded ITS region were amplified from 85 accessions of Murraya and Merrillia using the polymerase chain reaction (PCR). Clustering used maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI). Chronograms were produced for molecular dating, and to test the monophyly of Murraya rigorously, using selected accessions of Murraya and 26 accessions of the Rutaceae and Simarubaceae. Sequence data from the ITS and chloroplastal regions suggest that Murraya paniculata (sensu (Swingle WT and Reece CR, The Citrus Industry, p. 190–430, 1967)) can be separated into four distinct but morphologically somewhat cryptic taxa: Murraya paniculata (sensu (Mabberley DJ, Taxon 65:366–371, 2016)), M. elongata, M. sumatrana and M. lucida. In addition, Murraya omphalocarpa was identified as a putative hybrid of M. paniculata and M. lucida with two geographically isolated nothovarieties representing reciprocal crosses. Murraya is monophyletic, and molecular dating suggests that it diverged from Merrillia during the Miocene (23–5 Ma) with this Murraya group speciating and dispersing during the Middle Miocene onwards. Conclusions The accessions from Asia and Australasia used in this study grouped into biogeographical regions that match herbarium specimen records for the taxa that suggest natural allopatric distributions with limited overlap and hybridity. Murraya paniculata has been distributed around the world as an ornamental plant. The division of the Murraya paniculata complex into four species with a rare hybrid also confirms morphological studies.

MycoKeys ◽  
2019 ◽  
Vol 47 ◽  
pp. 97-137 ◽  
Author(s):  
Janett Riebesehl ◽  
Eugene Yurchenko ◽  
Karen K. Nakasone ◽  
Ewald Langer

Xylodon (Hymenochaetales, Basidiomycota) is the largest segregate genus of Hyphodontia s.l. Based on molecular and morphological data, 77 species are accepted in Xylodon to date. Phylogenetic analyses of ITS and 28S sequences, including 38 new ITS and 20 28S sequences of Xylodon species, revealed four species new to science. The new taxa X.exilis, X.filicinus, X.follis and X.pseudolanatus from Taiwan, Nepal, Réunion, Belize, and USA are described and illustrated. In addition, species concepts for Odontiavesiculosa from New Zealand and Xylodonlanatus from U.S.A. are revised and the new name X.vesiculosus is proposed. Phylogenetic analyses of the ITS region placed X.spathulatus, X.bubalinus and X.chinensis in a strongly supported clade and demonstrated that they are conspecific. Palifer and Odontiopsis are synonymised under Xylodon based on morphological and sequence data. The following new combinations are proposed: X.erikssonii, X.gamundiae, X.hjortstamii, X.hyphodontinus, X.septocystidiatus and X.verecundus. Line drawings of X.cystidiatus, X.hyphodontinus, X.lanatus and X.vesiculosus, as well as photographs of X.raduloides basidiomata, are provided. A key to X.lanatus and similar species is presented.


2020 ◽  
Vol 11 (6) ◽  
pp. 613-627
Author(s):  
Gyanendra Kumar ◽  
◽  
Anuradha Singh ◽  
Sonika Pandey ◽  
Jogender Singh ◽  
...  

This study was carried out to identify and characterize Trichoderma species isolated from rhizospheric soil of Uttar Pradesh, India, by using single spore technique. Morphological, cultural and molecular characterization were done with sequence analysis of the internal transcribed spacer (ITS) region. The classes were compared with morphological identification and rDNA sequence data for every class of all Trichoderma strains were of the same identity. These strains belonged to T. harzianum (Th azad), T. viride (01PP), T. asperellum (Tasp/CSAU), T. Koningii [TK (CSAU)], T. atroviride (71L), T. longibrachiatum (21PP), T. virens [Tvi (CSAU)], T. reesei [Tr (CSAU)], T. aggressivum [T.agg(CSAU)], T. aureoviride [T. avi (CSAU)], T. citrinoviride [T. cvi (CSAU)], T. erinaceum [T. eri (CSAU)], T. koningiopsis [T. kop (CSAU)], T. tomentosum [T. tos (CSAU)], T. mintisporum [T. mip (CSAU)], T. pubscenes [T. sce (CSAU)], T. saturnisporum [T. ssp (CSAU)], T. spirale [T. sp. (CSAU)]. Morphological studies were based on the colony appearance, growth rate and microscopic features such as branching patterns of conidiophores, the arrangement of phialospores and their shape, size and color. The 5.8S-ITS regions of the Trichoderma strains were amplified using ITS1 and ITS4 primers. The rRNA based analysis is a central method used not only to explore microbial diversity but also to identify new strains. Validations of ITS marker with 18 Trichoderma sp. were done and their sequences were deposited at NCBI GenBank their permanent accession no. were allotted.


2006 ◽  
Vol 54 (5) ◽  
pp. 353 ◽  
Author(s):  
Denise Raterman ◽  
Robert W. Meredith ◽  
Luis A. Ruedas ◽  
Mark S. Springer

The family Phalangeridae comprises approximately two dozen extinct and extant species that include the brushtail possums (Trichosurus), scaly-tailed possum (Wyulda) and cuscuses (Phalanger, Strigocuscus, Spilocuscus and Ailurops). Morphological studies have suggested that Ailurops ursinus is the sister taxon to all other phalangerids. Another species of interest is Strigocuscus celebensis, whose morphologically based taxonomic affinity has habitually been with trichosurins. Mitochondrial 12S rRNA results, however, found moderate support for an Ailurops and Strigocuscus celebensis clade and placed A. ursinus and S. celebensis as sister to Phalanger and Spilocuscus. This study uses nuclear sequence data from the breast cancer and ovarian cancer susceptibility gene 1 (BRCA1) to test previous mitochondrial DNA results and uses relaxed molecular clock methods to estimate divergence dates. The results support Ailurops as sister taxon to S. celebensis and this clade as sister to Phalangerini. Relaxed molecular-dating methods suggest a date of 23–29 million years for the split between Trichosurini and the remaining phalangerids and 19–24 million years for the split between Ailurops + Strigocuscus celebensis and Phalangerini. Several vicariant/dispersal events are necessary to explain the geographic distribution of the Phalangeridae and our estimated molecular divergence dates are congruent with previously proposed south-east Asian geological events.


2002 ◽  
Vol 15 (1) ◽  
pp. 49 ◽  
Author(s):  
Dorothy A. Steane ◽  
Dean Nicolle ◽  
Gay E. McKinnon ◽  
René E. Vaillancourt ◽  
Brad M. Potts

This expanded survey of ITS sequences represents the largest analysis of molecular data ever attempted on Eucalyptus. Sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA were included in an analysis of 90 species of Eucalyptus s.s. and 28 species representing eight other genera (Allosyncarpia, Angophora, Arillastrum, Corymbia, Eucalyptopsis, Stockwellia, Lophostemon and Metrosideros). The results of the study indicate that Angophora and Corymbia form a well-supported clade that is highly differentiated from Eucalyptus s.s. Corymbia species are divided between two clades, one of which may be the sister to Angophora. Allosyncarpia, Arillastrum, Eucalyptopsis and ‘Stockwellia’ are also highly differentiated from Eucalyptus s.s. If the genus Eucalyptus is to be expanded to include Angophora and Corymbia(sensu Brooker 2000), ITS data suggest that Allosyncarpia, Eucalyptopsis, ‘Stockwellia’ and potentially Arillastrum should also be included in Eucalyptus s.l. The ITS data suggest that subg. Symphyomyrtus is paraphyletic and that subg. Minutifructus should be included within it. Within subg.Symphyomyrtus, only sect. Maidenaria appears to be monophyletic. Sections Adnataria and Dumaria are probably monophyletic; sections Exsertaria and Latoangulatae are very close and probably should be combined in a single section. Section Bisectae is polyphyletic and is divided into two distinct lineages. The phylogenetic groups depicted by ITS data are consistent with the frequency of natural inter-specific hybridisations as well as data from controlled crosses within subgenus Symphyomyrtus. The ITS data illustrate that subg. Idiogenes and western Australian monocalypts are early evolutionary lines relative to E. diversifolia, E. rubiginosa (monotypic subg. Primitiva) and the eastern monocalypts and that subg. Primitiva should be sunk into subg. Eucalyptus. Subgenus Eudesmia may be monophyletic, grouping with subgenera Idiogenes and Eucalyptus. Further work is required to confirm the phylogenetic positions of the monotypic subgenera Alveolata, Cruciformes, Acerosae and Cuboidea.


Plant Disease ◽  
2003 ◽  
Vol 87 (11) ◽  
pp. 1329-1332 ◽  
Author(s):  
J. Roux ◽  
H. Myburg ◽  
B. D. Wingfield ◽  
M. J. Wingfield

Cryphonectria cubensis is an economically important pathogen of commercial Eucalyptus spp. Differences have been reported for disease symptoms associated with Cryphonectria canker in South Africa and other parts of the world, and recent DNA-based comparisons have confirmed that the fungus in South Africa is different from that in South America and Australasia. During a disease survey in the Republic of Congo, Cryphonectria canker was identified as an important disease on Eucalyptus grandis and E. urophylla. In this study, we compared Congolese and South African isolates of C. cubensis using DNA sequence data and pathogenicity under greenhouse conditions. The β-tubulin and internal transcribed spacer (ITS) region sequences show that C. cubensis in Congo is different from the fungus in South Africa and that Congolese isolates group most closely with South American isolates. Furthermore, pathogenicity tests showed that a South African isolate was more aggressive than two Congolese isolates. We conclude that two distinct Cryphonectria spp. occur in Africa and hypothesize that the fungus in the Congo probably was introduced into Africa from South America. Both fungi are important pathogens causing disease and death of economically important plantation trees. However, they apparently have different origins and must be treated separately in terms of disease management and quarantine considerations.


2004 ◽  
Vol 50 (11) ◽  
pp. 985-988 ◽  
Author(s):  
Maria Helena Pelegrinelli Fungaro ◽  
Marciane Magnani ◽  
Laurival Antônio Vilas-Boas ◽  
Patrícia Cristina Vissotto ◽  
Márcia Cristina Furlaneto ◽  
...  

Ochratoxin A (OA) is a mycotoxin that has been found in coffee beans and coffee beverages. Its toxicological profile includes carcinogenicity, nephrotoxicity, and immunotoxicity. Aspergillus ochraceus is the major species responsible for OA production in Brazilian coffee beans. The genetic relationships among 25 A. ochraceus strains collected from Brazilian coffee-bean samples were determined based on RAPD and internal transcribed spacer (ITS) sequence data. The isolates were resolved into 2 distinct groups, one with 4 strains (group A) and the other with 21 strains (group B). Specific nucleotide variations characterizing group A and B were found for both ITS1 and ITS2 regions. Group B is a new group proposed here to accommodate the majority of the Brazilian isolates. Each group was found to contain both toxigenic and nontoxigenic strains, indicating that there is no association between molecular genotypes and the ability to produce OA.Key words: Aspergillus ochraceus, ochratoxin A, ITS region (ITS1–5.8S–ITS2), RAPD.


Plant Disease ◽  
2014 ◽  
Vol 98 (10) ◽  
pp. 1442-1442 ◽  
Author(s):  
R. Félix-Gastélum ◽  
G. Herrera-Rodríguez ◽  
C. Martínez-Valenzuela ◽  
I. E. Maldonado-Mendoza ◽  
F. R. Quiroz-Figueroa ◽  
...  

Rose (Rosa spp.) is the most important ornamental plant cultivated in greenhouse and open fields in Mexico but its quality has been limited by powdery mildew (PM). High incidence and disease damage is common during winter in Sinaloa, Mexico (temperature range 18 to 25°C and prolonged episodes of relative humidity ≥90%). The fungus attacks leaves and flowers and grows abundantly on the pedicels, sepals, and receptacles, especially when the flower bud is unopened (2). Field advisors in Mexico have referred to Sphaerotheca pannosa (Wallr. ex Fr.) Lév. as a causal agent of the disease. However, there has not been solid scientific evidence to support this statement. Morphometric and molecular analysis were conducted to elucidate the identity of the fungal isolates collected from 2012 through 2013 in northern Sinaloa. PM specimens included eight different rose varieties. Conidiophores and conidia were observed under a compound microscope. The mycelium had a mean diameter of 4.7 to 6.0 μm; conidiophores (Euoidium type) 2 to 5 celled, occasionally 6 celled emerged from the superficial mycelium; conidiophores were unbranched with conidia produced in chains from the apex. The average length of the conidiophores was 54.9 to 98.0 μm; the foot cell of the conidiophores was straight and was 24.9 to 53.6 μm long with a diameter from 8.2 to 9.8 μm across its medium part. Conidia originated from unswollen conidiogenous cells, with fibrosin bodies, formed in long chains, and were cylindrical to ovoid, 25.8 to 30.4 μm long and 13.9 to 17.3 μm wide. The outline of the conidial chains was crenate. Conidia exhibited a slight constriction at one end. The germ tubes emerged from a shoulder of the conidia. The outer wall of partially collapsed conidia showed longitudinal and transversal wrinkling and slight constrictions at the ends; the terminal end of the conidia was concentrically ridged. For molecular characterization, the ITS region of the specimens was amplified with primers ITS1F and ITS4. Phylogenetic analysis was performed with MEGA 6.0 (bootstrap = 1,000) using Kimura 2 parameter (K2P) substitution model. The resulting phylogeny grouped our specimens (GenBank KM001665 to 69) within a clade of Podosphaera pannosa (Wall.: Fr.) de Bary (formerly known as Sphaerotheca pannosa) sequences (e.g., AB525938; bootstrap (1,000) = 98). Phylogenetic and morphometric data are in agreement with descriptions of the anamorphic P. pannosa (1,3). Morphological studies indicate that P. macularis (previously known as S. humuli) and P. pannosa are not indistinctly different (2). Phylogenetic analysis showed relationship to P. pannosa, but not to P. macularis. Typical symptoms caused by P. pannosa were observed. Morphological studies (4) reported the anamorph of P. pannosa on Rosa spp. in central Mexico. To date, no report exists on the molecular identification of P. pannosa associated to roses in northern Sinaloa, Mexico. Future research directions should focus on finding the teleomorph of the fungus to support its identity, and to explore disease management tools such as effective fungicides and developing resistant rose cultivars. References: (1) U. Braun et al. Page 13 in: The Powdery Mildews: A Comprehensive Treatise. APS Press, St. Paul, MN, 2002. (2) R. K. Horst. Compendium of Rose Diseases. APS Press, St. Paul, MN, 1983. (3) L. Leus et al. J. Phytopathol. 154:23, 2006. (4) Yañez-Morales et al. Some new reports and new species of powdery mildew from Mexico. Schlechtendalia 19:46, 2009.


HortScience ◽  
2017 ◽  
Vol 52 (1) ◽  
pp. 31-39 ◽  
Author(s):  
Godfrey P. Miles ◽  
Ed Stover ◽  
Chandrika Ramadugu ◽  
Manjunath L. Keremane ◽  
Richard F. Lee

In a Fort Pierce, FL, field planting, plant growth, and Huanglongbing (HLB) severity were assessed as indicators of HLB tolerance on progenies of 83 seed-source accessions of Citrus and Citrus relatives mainly from the Riverside, CA, genebank. The HLB-associated pathogen [Candidatus Liberibacter asiaticus (CLas)] and vector [asian citrus psyllid (ACP), Diaphorina citri] were abundant, and trees were naturally challenged for 6 years before metrics (leaf mottle, percent canopy mottle, overall health, canopy density, canopy width, canopy height, and trunk diameter) were collected in Oct. and Nov. 2015. The healthiest trees with low or no HLB symptoms were distant citrus relatives: Balsamocitrus dawei, Bergera koenigii, Casimiroa edulis, Clausena excavata, Murraya paniculata, and one accession of Severinia buxifolia. Within Citrus, most of the healthiest trees with densest canopies, little leaf loss, and greater growth were those with pedigrees that included Citrus medica (citron). These included progenies of Citrus hybrid (‘Limon Real’), Citrus limetta, Citrus limettioides, Citrus limonia, C. medica, Citrus volkameriana, and some Citrus limon accessions. Trees in this category exhibited distinct leaf-mottle characteristic of HLB and substantial pathogen titers, but maintained dense canopies and exhibited good growth. Trees from seed-source accessions in the genus Citrus without citron in their background were generally among the least healthy overall with less dense canopies. The exceptions were progenies of two Citrus aurantium accessions, which were markedly healthier than progenies of other Citrus seed-source accessions not derived from citron. Linear regression analysis, between metrics collected and pedigree of seed parent, indicated that percentage of citron in the pedigree significantly correlated with measures of tolerance. Although no commercial Citrus genotypes yielded progenies with strong HLB resistance, in this field experiment several progenies maintained dense canopies and good growth, and may be useful for breeding HLB tolerant cultivars.


2019 ◽  
Author(s):  
Joshua I Brian ◽  
Simon K Davy ◽  
Shaun P Wilkinson

Coral reefs rely on their intracellular dinoflagellate symbionts (family Symbiodiniaceae) for nutritional provision in nutrient-poor waters, yet this association is threatened by thermally stressful conditions. Despite this, the evolutionary potential of these symbionts remains poorly characterised. In this study, we tested the potential for divergent Symbiodiniaceae types to sexually reproduce (i.e. hybridise) within Cladocopium, the most ecologically prevalent genus in this family. With sequence data from three organelles (cob gene, mitochondria; psbAncr region, chloroplast; and ITS2 region, nucleus), we utilised the Incongruence Length Difference test, Approximately Unbiased test, tree hybridisation analyses and visual inspection of raw data in stepwise fashion to highlight incongruences between organelles, and thus provide evidence of reticulate evolution. Using this approach, we identified three putative hybrid Cladocopium samples among the 158 analysed, at two of the seven sites sampled. These samples were identified as the common Cladocopium types C40 or C1 with respect to the mitochondria and chloroplasts, but the rarer types C3z, C3u and C1# with respect to their nuclear identity. These five Cladocopium types have previously been confirmed as evolutionarily distinct and were also recovered in non-incongruent samples multiple times, which is strongly suggestive that they sexually reproduced to produce the incongruent samples. A concomitant inspection of Next Generation Sequencing data for these samples suggests that other plausible explanations, such as incomplete lineage sorting, are much less likely. The approach taken in this study allows incongruences between gene regions to be identified with confidence, and brings new light to the evolutionary potential within Symbiodiniaceae.


Phytotaxa ◽  
2021 ◽  
Vol 516 (3) ◽  
Author(s):  
KURTULUŞ ÖZGİŞİ ◽  
BURCU TARIKAHYA-HACIOĞLU

Symphytum is regarded one of the most complicated genera in terms of the classification of its members among the Boraginaceae. In addition to different infrageneric classification methods, several species complex or aggregates have been proposed to deal with the taxonomical problem of genus members. Symphytum asperum aggregate was first introduced by Kurtto, who proposed six taxa within this aggregate. However, according to further studies by different researchers based on morphological data, total number of species of the complex was variable. The number of species was reduced to three, comprising S. asperum, S. savvalense, and S. sylvaticum, after the phylogenetic and morphological studies of Tarıkahya-Hacıoğlu and Erik. However, the taxonomical status of some of these species (i.e., S. savvalense and S. sylvaticum, and S. sepulcrale), which was assigned as a member of this complex by Kurtto, has been regarded as unresolved. To solve this uncertainty, different species delimitation methods were used, including statistical parsimony network analysis (TCS), generalized mixed Yule coalescent (GMYC), and Bayesian Phylogenetics and Phylogeography (BPP) of the ITS, trnL-F and trnS-G sequence data. In addition to members of this complex, S. ibericum, which is phylogenetically nested within the S. asperum aggregate, was also used. The TCS and GMYC analyses demonstrated more complicated clusters, whereas high posterior probabilities of BPP clusters were more compatible with the morphological data. In accordance with the morphological approach of Tarıkahya-Hacıoğlu and Erik, the species delimitation analyses based on molecular data support the recognition of S. asperum, S. ibericum, S. savvalense, and S. sylvaticum as different species.


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