scholarly journals Morphological and molecular barcode analysis of the medicinal tree Mimusops coriacea (A.DC.) Miq. collected in Ecuador

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7789 ◽  
Author(s):  
Katherine Bustamante ◽  
Efrén Santos-Ordóñez ◽  
Migdalia Miranda ◽  
Ricardo Pacheco ◽  
Yamilet Gutiérrez ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Analysis ◽  
Leaf Size ◽  
Morphological Characterization ◽  
Its2 Sequence ◽  
Morphological Description ◽  
Medicinal Tree ◽  
Molecular Barcode ◽  
Its1 And Its2 ◽  
Molecular Barcodes

Background Mimusops coriacea (A.DC.) Miq., (Sapotaceae), originated from Africa, were introduced to coastal areas in Ecuador where it is not extensively used as a traditional medicine to treat various human diseases. Different therapeutically uses of the species include: analgesic, antimicrobial, hypoglycemic, inflammation and pain relieve associated with bone and articulation-related diseases. Furthermore, Mimusops coriacea could be used as anti-oxidant agent. However, botanical, chemical or molecular barcode information related to this much used species is not available from Ecuador. In this study, morphological characterization was performed from leaves, stem and seeds. Furthermore, genetic characterization was performed using molecular barcodes for rbcL, matk, ITS1 and ITS2 using DNA extracted from leaves. Methods Macro-morphological description was performed on fresh leaves, stem and seeds. For anatomical evaluation, tissues were embedded in paraffin and transversal dissections were done following incubation with sodium hypochlorite and safranin for coloration and fixated later in glycerinated gelatin. DNA extraction was performed using a modified CTAB protocol from leaf tissues, while amplification by PCR was accomplished for the molecular barcodes rbcL, matK, ITS1 and ITS2. Sequence analysis was performed using blast in the GenBank. Phylogenetic analysis was performed with accessions queried in the GenBank belonging to the subfamily Sapotoideae. Results Leaf size was 13.56 ± 1.46 × 7.49 ± 0.65 cm; where is a macro-morphological description of the stem (see Methods). The peel of the seeds is dark brown. Sequence analysis revealed that amplicons were generated using the four barcodes selected. Phylogenetic analysis indicated that the barcodes rbcL and matK, were not discriminated between species within the same genus of the subfamily Sapotoideae. On the other hand, the ITS1 and ITS2 were discriminative at the level of genus and species of the Sapotoideae.

A new pleosporalean fungus isolated from superficial to deep human clinical specimens

2020 ◽  
Author(s):  
Nicomedes Valenzuela-Lopez ◽  
M Teresa Martin-Gomez ◽  
Ibai Los-Arcos ◽  
Alberto M Stchigel ◽  
Josep Guarro ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Rna Polymerase Ii ◽  
Pathogenic Fungus ◽  
Elongation Factor ◽  
Morphological Characterization ◽  
Morphological Description ◽  
Internal Transcribed Spacer Region ◽  
Accurate Identification ◽  
Human Patient ◽  
Opportunistic Fungal Pathogen

Abstract Human infections by pleosporalean fungi (class Dothideomycetes, phylum Ascomycota) are rarely reported. Because their identification is challenging using morphological characterization, several phylogenetic markers must be sequenced for an accurate identification and taxonomical placement of the isolates. Three isolates of clinical origin were phenotypically characterized, but due to the absence of relevant morphological traits, D1-D2 domains of the 28S nrRNA gene (LSU), the internal transcribed spacer region (ITS) of the nrRNA, and fragments of the RNA polymerase II subunit 2 (rpb2) and translation elongation factor 1-alpha (tef1) genes were sequenced to allow a phylogenetic analysis that would solve their phylogenetic placement. That analysis revealed that these isolates did not match any previously known pleosporalean genera, and they are proposed here as the new fungal genus, Gambiomyces. Unfortunately, the isolates remained sterile, which, consequently, made the morphological description of the reproductive structures impossible. Future studies should try to understand the behaviour of this fungus in nature as well as its characteristics as an opportunistic fungal pathogen. Molecular identification is becoming an essential tool for proper identification of Dothideomycetes of clinical origin. Lay Abstract We describe a new pleosporalen pathogenic fungus, Gambiomyces profunda, found in superficial to deep samples from a human patient. Because all strains remained sterile, the fungus was finally identified following a phylogenetic analysis by using four different molecular markers.

scholarly journals Short communication: Morphological description and molecular detection of Pestalotiopsis sp. on hazelnut in Serbia

2017 ◽  
Vol 15 (3) ◽  
pp. e10SC02 ◽  
Author(s):  
Tanja Vasić ◽  
Darko Jevremović ◽  
Vesna Krnjaja ◽  
Aleksandar Leposavić ◽  
Snežana Anđelković ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Detection ◽  
Short Communication ◽  
Pathogenic Fungi ◽  
Morphological Characterization ◽  
Leaf Blight ◽  
Morphological Description ◽  
Morphological Identification ◽  
Pathogenicity Tests ◽  
Genomic Regions

In autumn 2015, hazelnut plants with leaf blight symptoms were noticed in a commercial plantation in the Province of Vojvodina, Serbia. Symptomatic samples were collected and submitted to laboratory analysis. Based on morphological characterization, the fungus isolated from the material was initially identified as Pestalotiopsis sp. Pathogenicity tests showed that two selected isolates infected hazelnut leaves and fruits that developed symptoms after artificial inoculation. The pathogen was re-isolated from diseased leaves and fruits, confirming Koch’s postulates. Molecular identification was performed with sequence and phylogenetic analysis of ITS, EF1-α, and TUB genomic regions. Phylogenetic analysis confirmed the results of the morphological identification. The detection of Pestalotiopsis sp., a causal agent of leaf blight on hazelnut in Serbia, is one of a few reports of these pathogenic fungi on hazelnut.

scholarly journals Extensive Phylogenetic Analysis of Piscine Orthoreovirus Genomic Sequences Shows the Robustness of Subgenotype Classification

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 41
Author(s):  
Marcos Godoy ◽  
Daniel A. Medina ◽  
Rudy Suarez ◽  
Sandro Valenzuela ◽  
Jaime Romero ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Sequence Analysis ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Genomic Segment ◽  
Double Stranded Rna ◽  
The Family ◽  
Original Classification

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which differentiates PRV into two major genotypes, I and II, and each of these into two subgenotypes, designated as Ia and Ib, and IIa and IIb, respectively. Moreover, some clusters of country- and host-specific PRV subgenotypes were observed in the subset of sequences used. This work strengthens the subgenotype classification of PRV based on the S1 segment and can be used to enhance research on the virulence of PRV.

scholarly journals Genetic Diversity and Pathogenic Variability Among Isolates of Colletotrichum Species from Strawberry

2003 ◽  
Vol 93 (2) ◽  
pp. 219-228 ◽  
Author(s):  
Béatrice Denoyes-Rothan ◽  
Guy Guérin ◽  
Christophe Délye ◽  
Barbara Smith ◽  
Dror Minz ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Sequence Data ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Data ◽  
Its2 Sequence ◽  
Host Specialization ◽  
Pathogenicity Tests ◽  
Colletotrichum Spp ◽  
Rapd Polymorphism ◽  
Pathogenic Variability

Ninety-five isolates of Colletotrichum including 81 isolates of C. acutatum (62 from strawberry) and 14 isolates of C. gloeosporioides (13 from strawberry) were characterized by various molecular methods and pathogenicity tests. Results based on random amplified polymorphic DNA (RAPD) polymorphism and internal transcribed spacer (ITS) 2 sequence data provided clear genetic evidence of two subgroups in C. acutatum. The first subgroup, characterized as CA-clonal, included only isolates from strawberry and exhibited identical RAPD patterns and nearly identical ITS2 sequence analysis. A larger genetic group, CA-variable, included isolates from various hosts and exhibited variable RAPD patterns and divergent ITS2 sequence analysis. Within the C. acutatum population isolated from strawberry, the CA-clonal group is prevalent in Europe (54 isolates of 62). A subset of European C. acutatum isolates isolated from strawberry and representing the CA-clonal and CA-variable groups was assigned to two pathogenicity groups. No correlation could be drawn between genetic and pathogenicity groups. On the basis of molecular data, it is proposed that the CA-clonal subgroup contains closely related, highly virulent C. acutatum isolates that may have developed host specialization to strawberry. C. gloeosporioides isolates from Europe, which were rarely observed were either slightly or nonpathogenic on strawberry. The absence of correlation between genetic polymorphism and geographical origin in Colletotrichum spp. suggests a worldwide dissemination of isolates, probably through international plant exchanges.

scholarly journals Agro morphological characterization of cashew trees (Anacardium occidental L.), in improvement for the high yield and high quality of raw nuts in Burkina Faso

2021 ◽  
Vol 14 (9) ◽  
pp. 3188-3199
Author(s):  
Windpouiré Vianney Tarpaga ◽  
Larbouga Bourgou ◽  
Moussa Guira ◽  
Albert Rouamba
Keyword(s):  
Burkina Faso ◽  
Core Collection ◽  
Morphological Diversity ◽  
Morphological Characterization ◽  
High Yield ◽  
Morphological Description ◽  
Average Weight ◽  
In Situ Collection

The cashew sector has taken a great economic interest, due to the strong global demand for raw nuts. However, in Burkina Faso, the productivity of orchards still remains low, a consequence of a lack of breeding program on the species. In order to increase yields and improve the quality of the raw nut, efficient clones must be developed. Surveys were carried out and a primary in situ collection was made from which a core collection of 15 trees was extracted. An agro-morphological description of the selected trees and an analysis of the structuration of the variability within them were carried out. The study revealed appreciable agro-morphological diversity through shape, size and color of apple, type of inflorescence, fruiting period and the health of trees. A structure of diversity based on agronomic criteria led to identify 5 groups of trees, characterized by an average weight of the nut between 6.64 and 8.32 g, a kernel rate between 28.10 and 31.26% and a yield per tree between 34.27 and 104.42 kg. Performing trees will be erected as heads of clones for the production of grafted plants. La filière anacarde a pris un grand intérêt économique, suite à la forte demande mondiale en noix brutes. Cependant, au Burkina Faso, la productivité des vergers demeure encore faible, conséquence d’une absence de sélection variétale du matériel végétal. En vue d’accroître les rendements et d’améliorer la qualité de la noix brute, une recherche de clones performants était indispensable. Des prospections ont été conduites et une collection primaire in situ a été constituée dont une core collection de 15 arbres a été extraite. Une description agro-morphologique des arbres sélectionnés et une analyse de la structuration de la variabilité en son sein ont été conduites. L’étude a révélé une diversité agro morphologique appréciable à travers la forme, le calibre et la couleur de la pomme, le type d’inflorescence, la période de fructification et l’état sanitaire des arbres. Une structuration de la diversité basée sur les critères agronomiques a permis d’identifier 5 groupes d’arbres, caractérisés par un poids moyen de la noix compris entre 6,64 et 8,32 g, un taux d’amande compris entre 28,10 et 31,26% et un rendement par arbre compris entre 34,27 et 104,42 kg. Les arbres les plus performants constitueront des têtes de clones pour la production de plants par greffage.

Protubera beijingensis sp. nov. (Protophallaceae, Phallales) from China

Phytotaxa ◽  
2018 ◽  
Vol 348 (2) ◽  
pp. 133
Author(s):  
GUOJIE LI ◽  
DEJIANG DENG ◽  
JINKANG WEI ◽  
CHULONG ZHANG ◽  
RUILIN ZHAO ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
North China ◽  
Morphological Description ◽  
Similar Species ◽  
Multigene Phylogenetic Analysis ◽  
Globally Distributed ◽  
A New Species

The genus Protubera includes gasteroid species. Its members are globally distributed in tropical, subtropical, and temperate areas, and presently, six species are recognized. In this paper, Protubera beijingensis from North China is described as a new species. Its morphological description and illustration are provided in detail and compared with morphologically similar species. A multigene phylogenetic analysis based on nLSU, atp6, and rpb2 sequences of the genus Protubera also identifies this organism as a new species within Protubera.

scholarly journals Molecular characterization of Ribosomal DNA (ITS2) of hard ticks in Iran: understanding the conspecificity of Dermacentor marginatus and D. niveus

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Parisa Soltan-Alinejad ◽  
Zahra Ramezani ◽  
Hamideh Edalat ◽  
Zakkyeh Telmadarraiy ◽  
Farrokh Dabiri ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Tick Species ◽  
Morphological Characteristics ◽  
Blood Feeding ◽  
Its2 Sequence ◽  
Hard Tick ◽  
Dermacentor Marginatus ◽  
Hard Ticks ◽  
Morphological Studies ◽  
Veterinary Importance

Abstract Objectives Hard ticks (Acari: Ixodidae) are ectoparasites of medical and veterinary importance. They are obligate blood-feeding vectors with the ability to transmit a wide variety of pathogens. Standard morphological keys are normally used for the identification of tick species. However, considering the importance of accurate species identification and the determination of bio-ecological characteristics of species, relying on morphological keys alone can be questionable. In this study, two DNA fragments (ITS2 and COI) were selected for phylogenetic evaluation of Iranian hard tick species belonging to the genera Dermacentor, Hyalomma, and Rhipicephalus. Results 1229 specimens of Dermacentor marginatus, D. niveus, Hyalomma anatolicum, Rhipicephalus bursa, and R. sanguineuss.l constituting 11 populations were collected from three different climatic and zoogeographical zones in Iran. Morphological studies revealed notable differences in important morphological characteristics between different populations of D. marginatus. The results of ITS2 sequence analysis provided additional evidence which supports the conspecificity of D. niveus and D. marginatus. Contrary to this finding, the sequence analysis of COI and phylogeny favored the separation of the two species. Given the greater importance of COI in identifying and discriminating species, a possibility heterospecificity between the two species should be considered.

scholarly journals Genomic Characterization and Phylogenetic Classification of Bovine Coronaviruses Through Whole Genome Sequence Analysis

Viruses ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 183 ◽  
Author(s):  
Tohru Suzuki ◽  
Yoshihiro Otake ◽  
Satoko Uchimoto ◽  
Ayako Hasebe ◽  
Yusuke Goto
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Analysis ◽  
Molecular Characterization ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Wild Ruminant ◽  
Genome Sequence Analysis ◽  
Genomic Characterization

Bovine coronavirus (BCoV) is zoonotically transmissible among species, since BCoV-like viruses have been detected in wild ruminants and humans. BCoV causing enteric and respiratory disease is widespread in cattle farms worldwide; however, limited information is available regarding the molecular characterization of BCoV because of its large genome size, despite its significant economic impact. This study aimed to better understand the genomic characterization and evolutionary dynamics of BCoV via comparative sequence and phylogenetic analyses through whole genome sequence analysis using 67 BCoV isolates collected throughout Japan from 2006 to 2017. On comparing the genomic sequences of the 67 BCoVs, genetic variations were detected in 5 of 10 open reading frames (ORFs) in the BCoV genome. Phylogenetic analysis using whole genomes from the 67 Japanese BCoV isolates in addition to those from 16 reference BCoV strains, revealed the existence of two major genotypes (classical and US wild ruminant genotypes). All Japanese BCoV isolates originated from the US wild ruminant genotype, and they tended to form the same clusters based on the year and farm of collection, not the disease type. Phylogenetic trees on hemagglutinin-esterase protein (HE), spike glycoprotein (S), nucleocapsid protein (N) genes and ORF1 revealed clusters similar to that on whole genome, suggesting that the evolution of BCoVs may be closely associated with variations in these genes. Furthermore, phylogenetic analysis of BCoV S genes including those of European and Asian BCoVs and human enteric coronavirus along with the Japanese BCoVs revealed that BCoVs differentiated into two major types (European and American types). Moreover, the European and American types were divided into eleven and three genotypes, respectively. Our analysis also demonstrated that BCoVs with different genotypes periodically emerged and predominantly circulated within the country. These findings provide useful information to elucidate the detailed molecular characterization of BCoVs, which have spread worldwide. Further genomic analyses of BCoV are essential to deepen the understanding of the evolution of this virus.

Phylogenetic Analysis of Burkholderia Species by Multilocus Sequence Analysis

2013 ◽  
Vol 67 (1) ◽  
pp. 51-60 ◽  
Author(s):  
Paulina Estrada-de los Santos ◽  
Pablo Vinuesa ◽  
Lourdes Martínez-Aguilar ◽  
Ann M. Hirsch ◽  
Jesús Caballero-Mellado
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Analysis ◽  
Multilocus Sequence Analysis ◽  
Burkholderia Species

scholarly journals Natural Merodiploidy of the lux-rib Operon of Photobacterium leiognathi from Coastal Waters of Honshu, Japan

2007 ◽  
Vol 189 (17) ◽  
pp. 6148-6158 ◽  
Author(s):  
Jennifer C. Ast ◽  
Henryk Urbanczyk ◽  
Paul V. Dunlap
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Analysis ◽  
Coastal Waters ◽  
Efflux Pump ◽  
Bacterial Species ◽  
Genomic Analysis ◽  
Multidrug Efflux Pump ◽  
Photobacterium Leiognathi ◽  
Content Organization ◽  
Luminous Bacteria

ABSTRACT Sequence analysis of the bacterial luminescence (lux) genes has proven effective in helping resolve evolutionary relationships among luminous bacteria. Phylogenetic analysis using lux genes, however, is based on the assumptions that the lux genes are present as single copies on the bacterial chromosome and are vertically inherited. We report here that certain strains of Photobacterium leiognathi carry multiple phylogenetically distinct copies of the entire operon that codes for luminescence and riboflavin synthesis genes, luxCDABEG-ribEBHA. Merodiploid lux-rib strains of P. leiognathi were detected during sequence analysis of luxA. To define the gene content, organization, and sequence of each lux-rib operon, we constructed a fosmid library of genomic DNA from a representative merodiploid strain, lnuch.13.1. Sequence analysis of fosmid clones and genomic analysis of lnuch.13.1 defined two complete, physically separate, and apparently functional operons, designated lux-rib 1 and lux-rib 2. P. leiognathi strains lelon.2.1 and lnuch.21.1 were also found to carry lux-rib 1 and lux-rib 2, whereas ATCC 25521T apparently carries only lux-rib 1. In lnuch.13.1, lelon.2.1, lnuch.21.1, and ATCC 25521T, lux-rib 1 is flanked upstream by lumQ and putA and downstream by a gene for a hypothetical multidrug efflux pump. In contrast, transposase genes flank lux-rib 2 of lnuch.13.1, and the chromosomal location of lux-rib 2 apparently differs in lnuch.13.1, lelon.2.1, and lnuch.21.1. Phylogenetic analysis demonstrated that lux-rib 1 and lux-rib 2 are more closely related to each other than either one is to the lux and rib genes of other bacterial species, which rules out interspecies lateral gene transfer as the origin of lux-rib 2 in P. leiognathi; lux-rib 2 apparently arose within a previously unsampled or extinct P. leiognathi lineage. Analysis of 170 additional strains of P. leiognathi, for a total of 174 strains examined from coastal waters of Japan, Taiwan, the Philippine Islands, and Thailand, identified 106 strains that carry only a single lux-rib operon and 68 that carry multiple lux-rib operons. Strains bearing a single lux-rib operon were obtained throughout the geographic sampling range, whereas lux-rib merodiploid strains were found only in coastal waters of central Honshu. This is the first report of merodiploidy of lux or rib genes in a luminous bacterium and the first indication that a natural merodiploid state in bacteria can correlate with geography.

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