Identification and genetic diversity of Meloidogyne spp. (Tylenchida: Meloidogynidae) on coffee from Brazil, Central America and Hawaii

Nematology ◽  
2004 ◽  
Vol 6 (2) ◽  
pp. 287-298 ◽  
Author(s):  
Regina Carneiro ◽  
Myrian Tigano ◽  
Onivaldo Randig ◽  
Maria Ritta Almeida ◽  
Jean-Louis Sarah
Keyword(s):  
Central America ◽  
Genetic Relationships ◽  
Phylogenetic Analyses ◽  
Good Tool ◽  
Male Characters ◽  
The Usa ◽  
Meloidogyne Spp ◽  
Species Specific ◽  
Electrophoretic Procedure ◽  
Esterase Phenotypes

Abstract The present study was based on 18 populations of Meloidogyne spp. originating from different coffee fields in Brazil, Central America and the USA (Hawaii). The identification of the main species and an outline of the diversity of root-knot nematodes parasitising coffee in these countries with respect to esterase phenotypes, morphology and molecular polymorphism, are provided. With the present electrophoretic procedure, esterase phenotypes were demonstrated to be species-specific and constitute a good tool for identifying root-knot species from coffee, viz., M. incognita (Est I1, I2), M. paranaensis (Est P1, P2), M. arenaria (Est A2), M. arabicida (Est AR2), M. exigua (Est E1), M. mayaguensis (Est M2) and two unknown populations that probably represent new species (Est SA2, SA4). The perineal pattern is often an unreliable character when used alone for making diagnostic conclusions but, when used as a complementary tool together with enzyme characterisation, is essential for checking the morphological consistency of the identification. Male characters are important for confirming the diagnosis of some species, such as M. paranaensis, M. konaensis and M. incognita. The results showed that the RAPD markers produced are consistent with other approaches (esterase phenotypes and morphological features) for confirming species identification and for estimating genetic relationships among species and isolates. Phylogenetic analyses showed that M. mayaguensis and M. exigua are more closely related to one another than they are to the other species. This was also true for M. javanica, M. arenaria and Meloidogyne spp. Low levels of intraspecific polymorphism were detected in M. exigua (8.6%), M. incognita (11.2%) and M. paranaensis (20.3%). Conversely, M. arenaria and the two unknown Meloidogyne spp. exhibited higher levels of intra- or interspecific variability (34.9 and 29.9%, respectively).

Unravelling the Habenaria repens (Orchidaceae) complex in Brazil: a biosystematic and molecular phylogenetic approach

2021 ◽  
Author(s):  
Bruna Ladeira Lau ◽  
João Aguiar Nogueira Batista ◽  
Antônio Massensini Junior ◽  
W Mark Whitten ◽  
Eduardo Leite Borba
Keyword(s):  
Species Complex ◽  
Genetic Relationships ◽  
Phylogenetic Analyses ◽  
Population Approach ◽  
Morphometric Analyses ◽  
Molecular Phylogenetic ◽  
The Usa ◽  
Morphological Variants ◽  
Floral Characters ◽  
Population Genetic Analyses

Abstract Habenaria repens (Orchidaceae) represents a species complex distributed from the southern USA to northern Argentina, including several morphological variants, here referred to as morphotypes. To investigate and clarify the morphological and genetic relationships between these morphotypes and resolve the taxonomy of the complex, we applied a biosystematic multi-population approach using molecular phylogenetic, morphometric and population genetics analyses in the group. We sampled 31 (phylogenetic analyses) and 20 (morphometric and microsatellite analyses) populations of Habenaria aranifera and H. repens from Brazil and the USA, including six morphotypes of H. repens. Bayesian and maximum parsimony phylogenetic analyses of nuclear ribosomal (ITS and ETS) and plastid (matK, trnK and rps16-trnK) markers revealed that the complex is polyphyletic, subdivided into three distantly related clades. Population genetic analyses using microsatellites showed a remarkably similar structure to the phylogenetic analyses, but both were different from the morphometric analyses of floral characters, indicating cases of diversification and convergence, probably due to pollination processes. Habenaria aranifera is embedded in a paraphyletic and polymorphic H. repens with a broad geographical distribution and other attributes of an ochlospecies, probably constituting a progenitor–derivative pair. Our results support the recognition of H. aranifera, H. repens and three or four new species.

Enzyme phenotypes of Meloidogyne spp. populations

Nematology ◽  
2000 ◽  
Vol 2 (6) ◽  
pp. 645-654 ◽  
Author(s):  
Regina M.D.G. Carneiro ◽  
Patrick Quénéhervé ◽  
Maria Ritta Almeida
Keyword(s):  
Superoxide Dismutase ◽  
Esterase Activity ◽  
Intraspecific Variability ◽  
Common Species ◽  
Large Collection ◽  
Glutamate Oxaloacetate Transaminase ◽  
Major Species ◽  
The Usa ◽  
Meloidogyne Spp ◽  
Species Specific

AbstractEnzyme phenotypes, specifically esterases (EST), malate dehydrogenase (MDH), superoxide dismutase (SOD) and glutamate-oxaloacetate transaminase (GOT) were used to characterise different species of Meloidogyne, mostly from Brazil and from some American countries. Esterase activity was highly polymorphic and was the most useful in the identification of the different species. Using this enzyme it is possible to characterise and identify the four major species: M. javanica, M. incognita, M. arenaria and M. hapla from a large collection of 111 populations of Meloidogyne spp. Another seven less common species (M. coffeicola, M. paranensis, M. konaensis, M. exigua, M. graminicola, M. oryzae, M. mayaguensis), with only one or a few populations of each, were studied and exhibited species-specific EST phenotypes. The two enzymes (EST and MDH) differentiated M. graminicola and M. oryzae. It was possible to detect atypical (unidentified) phenotypes: three from Brazil, one from the USA and another from Chile. The minor bands of esterase profiles provided information to detect intraspecific variability among some populations of M. incognita and six populations of M. exigua. Profiles of MDH permitted separation of two isolates of M. javanica from Brazil. Phénotypes enzymatiques de populations de Meloidogyne - Les phénotypes enzymatiques de l'estérase (EST), la malate déshydrogènase (MDH), la superoxide dismutase (SOD) et la glutamate-oxaloacétate transaminase (GOT) ont été utilisés de manière systématique afin de caractériser plusieurs espèces de Meloidogyne provenant principalement du Brésil et de quelques pays des régions américaines. C'est l'activité estérasique qui a présenté le plus grand polymorphisme et s'est montrée la plus utile dans la caractérisation des espèces. A l'aide de cette enzyme il a été possible de caractériser et d'identifier les quatre espèces majeures de Meloidogyne: M. javanica, M. incognita, M. arenaria, et M. hapla au sein d'une collection de 111 populations de Meloidogyne spp. Sept autres espèces moins fréquentes (M. coffeicola, M. paranensis, M. konaensis, M. exigua, M. graminicola, M. oryzae, M. mayaguensis) comportant seulement quelques populations de chaque espèces ont été étudiées et ont également montré des phénotypes estérasiques spécifiques. Les deux enzymes (EST et MDH) ont permis la différenciation de M. graminicola et de M.oryzae. Il a été également possible de détecter des phénotypes atypiques non encore identifiés chez trois populations originaires du Brésil, une des USA et une du Chili. Par ailleurs, les bandes mineures des profils estérasiques ont apporté des informations sur la variabilité intra-spécifique chez quelques populations de M. incognita et six populations de M. exigua, tandis que l'observation des profils enzymatiques de la malate déshydrogènase (MDH) a permis la distinction de deux populations de M. javanica du Brésil.

scholarly journals Distribution of Meloidogyne species in carrot in Brazil

2021 ◽  
Vol 51 (5) ◽  
Author(s):  
Tiago Garcia da Cunha ◽  
Liliane Evangelista Visôtto ◽  
Letícia Mendes Pinheiro ◽  
Pedro Ivo Vieira Good God ◽  
Juliana Magrinelli Osório Rosa ◽  
...  
Keyword(s):  
Meloidogyne Incognita ◽  
Soil Samples ◽  
Molecular Techniques ◽  
Economic Losses ◽  
Specific Pcr ◽  
Meloidogyne Spp ◽  
Mixed Populations ◽  
Species Specific ◽  
Meloidogyne Species ◽  
Esterase Phenotypes

ABSTRACT: Root-knot nematodes (RKN - Meloidogyne spp.) are one of the most serious threats to carrot production worldwide. In Brazil, carrots are grown throughout the year, and economic losses due to RKN are reported. Since little is known on the distribution of RKN species in carrot fields in Brazil, we collected plant and soil samples from 35 fields across six states. Based on the morphology of perineal patterns, esterase phenotypes and species-specific PCR, three Meloidogyne species were identified: 60% of the fields were infested with Meloidogyne incognita, M. javanica was reported in 42.9% of the areas, whereas M. hapla was detected in 17.1% of carrot fields. Mixed populations were reported in 20% of the areas with a predominance of M. incognita + M. javanica. The combination of morphological, biochemical, and molecular techniques is a useful approach to identify RKN species.

Characterisation of Meloidogyne spp. (Tylenchida: Meloidogynidae) from coffee plantations in Central America and Brazil

Nematology ◽  
2004 ◽  
Vol 6 (2) ◽  
pp. 193-204 ◽  
Author(s):  
Adan Hernandez ◽  
Mireille Fargette ◽  
And Jean-Louis Sarah
Keyword(s):  
Costa Rica ◽  
El Salvador ◽  
Central America ◽  
Central American ◽  
Meloidogyne Hapla ◽  
Coffee Plantations ◽  
Meloidogyne Spp ◽  
Growing Conditions ◽  
Esterase Phenotype ◽  
Esterase Phenotypes

Abstract Isozymes (Esterases, MDH, SOD, GOT) and perineal patterns were studied in 29 isolates of Meloidogyne spp. collected on coffee (Coffea arabica) plantations in four Central American countries and on one isolate collected in Brazil. Five species were clearly diagnosed and six new multi-enzyme phenotypes were also revealed corresponding to within-species diversity or possible new species. Meloidogyne exigua was found in Costa Rica, Nicaragua and Honduras, M. arenaria in El Salvador and M. incognita ('M1a' esterase phenotype) in Brazil. Meloidogyne arabicida was found in Costa Rica and has a new esterase phenotype, 'M1F1b'. Nematodes with the 'F1' esterase phenotype were found in Guatemala and their specific status is discussed. Two isolates from El Salvador displayed unknown esterase phenotypes ('M1F1a' and 'Sa4'). One isolate from northern Guatemala was clearly identified as Meloidogyne hapla and another from the same area was related to M. enterolobii or M. mayaguensis. Neither of these latter isolates was able to develop in coffee roots under our growing conditions. The diversity of root-knot nematodes parasitising coffee roots in this region is discussed.

scholarly journals Multilocus phylogenies reveal three new truffle-like taxa and the traces of interspecific hybridization in Octaviania (Boletaceae, Boletales)

IMA Fungus ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Takamichi Orihara ◽  
Rosanne Healy ◽  
Adriana Corrales ◽  
Matthew E. Smith
Keyword(s):  
Rna Polymerase Ii ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Gene Tree ◽  
Phylogenetic Network ◽  
Elongation Factor ◽  
Morphological Observation ◽  
Tree Comparison ◽  
Unknown Species ◽  
The Usa

ABSTRACTAmong many convergently evolved sequestrate fungal genera in Boletaceae (Boletales, Basidiomycota), the genus Octaviania is the most diverse. We recently collected many specimens of Octaviania subg. Octaviania, including several undescribed taxa, from Japan and the Americas. Here we describe two new species in subgenus Octaviania, O. tenuipes and O. tomentosa, from temperate to subtropical evergreen Fagaceae forests in Japan based on morphological observation and robust multilocus phylogenetic analyses (nrDNA ITS and partial large subunit [LSU], translation elongation factor 1-α gene [TEF1] and the largest subunit of RNA polymerase II gene [RPB1]). Based on specimens from the Americas as well as studies of the holotype, we also taxonomically re-evaluate O. asterosperma var. potteri. Our analysis suggests that O. asterosperma var. potteri is a distinct taxon within the subgenus Octaviania so we recognize this as O. potteri stat. nov. We unexpectedly collected O. potteri specimens from geographically widespread sites in the USA, Japan and Colombia. This is the first verified report of Octaviania from the South American continent. Our molecular analyses also revealed that the RPB1 sequence of one O. tenuipes specimen was identical to that of a closely related species, O. japonimontana, and that one O. potteri specimen from Minnesota had an RPB1 sequence of an unknown species of O. subg. Octaviania. Additionally, one O. japonimontana specimen had an unusually divergent TEF1 sequence. Gene-tree comparison and phylogenetic network analysis of the multilocus dataset suggest that these heterogenous sequences are most likely the result of previous inter- and intra-specific hybridization. We hypothesize that frequent hybridization events in Octaviania may have promoted the high genetic and species diversity found within the genus.

scholarly journals Uncovering two phases of early intercontinental COVID-19 transmission dynamics

2020 ◽  
Vol 27 (8) ◽  
Author(s):  
Jing Yang ◽  
Juan Li ◽  
Shengjie Lai ◽  
Corrine W Ruktanonchai ◽  
Weijia Xing ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
International Travel ◽  
Contact Tracing ◽  
Genetic Sequencing ◽  
Response Strategies ◽  
The World ◽  
Containment Measures ◽  
The Usa ◽  
Community Transmission ◽  
Two Phases

Abstract Background The COVID-19 pandemic has posed an ongoing global crisis, but how the virus spread across the world remains poorly understood. This is of vital importance for informing current and future pandemic response strategies. Methods We performed two independent analyses, travel network-based epidemiological modelling and Bayesian phylogeographic inference, to investigate the intercontinental spread of COVID-19. Results Both approaches revealed two distinct phases of COVID-19 spread by the end of March 2020. In the first phase, COVID-19 largely circulated in China during mid-to-late January 2020 and was interrupted by containment measures in China. In the second and predominant phase extending from late February to mid-March, unrestricted movements between countries outside of China facilitated intercontinental spread, with Europe as a major source. Phylogenetic analyses also revealed that the dominant strains circulating in the USA were introduced from Europe. However, stringent restrictions on international travel across the world since late March have substantially reduced intercontinental transmission. Conclusions Our analyses highlight that heterogeneities in international travel have shaped the spatiotemporal characteristics of the pandemic. Unrestricted travel caused a large number of COVID-19 exportations from Europe to other continents between late February and mid-March, which facilitated the COVID-19 pandemic. Targeted restrictions on international travel from countries with widespread community transmission, together with improved capacity in testing, genetic sequencing and contact tracing, can inform timely strategies for mitigating and containing ongoing and future waves of COVID-19 pandemic.

scholarly journals Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints

2019 ◽  
Vol 15 ◽  
pp. 117693431988994
Author(s):  
Shulin Zhang ◽  
Yaling Cai ◽  
Jinggong Guo ◽  
Kun Li ◽  
Renhai Peng ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Genetic Relationships ◽  
Phylogenetic Analyses ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Association Analyses ◽  
Genome Wide ◽  
Candidate Gene Locus

Determining the genetic rearrangement and domestication footprints in Gossypium hirsutum cultivars and primitive race genotypes are essential for effective gene conservation efforts and the development of advanced breeding molecular markers for marker-assisted breeding. In this study, 94 accessions representing the 7 primitive races of G hirsutum, along with 9 G hirsutum and 12 Gossypium barbadense cultivated accessions were evaluated. The genotyping-by-sequencing (GBS) approach was employed and 146 558 single nucleotide polymorphisms (SNP) were generated. Distinct SNP signatures were identified through the combination of selection scans and association analyses. Phylogenetic analyses were also conducted, and we concluded that the Latifolium, Richmondi, and Marie-Galante race accessions were more genetically related to the G hirsutum cultivars and tend to cluster together. Fifty-four outlier SNP loci were identified by selection-scan analysis, and 3 SNPs were located in genes related to the processes of plant responding to stress conditions and confirmed through further genome-wide signals of marker-phenotype association analysis, which indicate a clear selection signature for such trait. These results identified useful candidate gene locus for cotton breeding programs.

scholarly journals Genetic Differentiation Associated with Fumonisin and Gibberellin Production in JapaneseFusarium fujikuroi

2018 ◽  
Vol 85 (1) ◽  
Author(s):  
Haruhisa Suga ◽  
Mitsuhiro Arai ◽  
Emi Fukasawa ◽  
Keiichi Motohashi ◽  
Hiroyuki Nakagawa ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Genetic Relationships ◽  
Pathogenic Fungus ◽  
Phylogenetic Analyses ◽  
Aflp Markers ◽  
Fusarium Fujikuroi ◽  
Rice Seedlings ◽  
Bakanae Disease ◽  
Content Type ◽  
Gibberellin Production

ABSTRACTFusarium fujikuroiis a pathogenic fungus that infects rice. It produces several important mycotoxins, such as fumonisins. Fumonisin production has been detected in strains of maize, strawberry, and wheat, whereas it has not been detected in strains from rice seedlings infested with bakanae disease in Japan. We investigated the genetic relationships, pathogenicity, and resistance to a fungicide, thiophanate-methyl (TM), in 51 fumonisin-producing strains and 44 nonproducing strains. Phylogenetic analyses based on amplified fragment length polymorphism (AFLP) markers and two specific genes (a combined sequence of translation elongation factor 1α [TEF1α] and RNA polymerase II second-largest subunit [RPB2]) indicated differential clustering between the fumonisin-producing and -nonproducing strains. One of the AFLP markers, EATMCAY107, was specifically present in the fumonisin-producing strains. A specific single nucleotide polymorphism (SNP) between the fumonisin-producing and nonproducing strains was also detected inRPB2, in addition to an SNP previously found inTEF1α. Gibberellin production was higher in the nonproducing than in the producing strains according to anin vitroassay, and the nonproducing strains had the strongest pathogenicity with regard to rice seedlings. TM resistance was closely correlated with the cluster of fumonisin-nonproducing strains. The results indicate that intraspecific evolution in JapaneseF. fujikuroiis associated with fumonisin production and pathogenicity. Two subgroups of JapaneseF. fujikuroi, designated G group and F group, were distinguished based on phylogenetic differences and the high production of gibberellin and fumonisin, respectively.IMPORTANCEFusarium fujikuroiis a pathogenic fungus that causes rice bakanae disease. Historically, this pathogen has been known asFusarium moniliforme, along with many other species based on a broad species concept. Gibberellin, which is currently known as a plant hormone, is a virulence factor ofF. fujikuroi. Fumonisin is a carcinogenic mycotoxin posing a serious threat to food and feed safety. Although it has been confirmed thatF. fujikuroiproduces gibberellin and fumonisin, production varies among strains, and individual production has been obscured by the traditional appellation ofF. moniliforme, difficulties in species identification, and variation in the assays used to determine the production of these secondary metabolites. In this study, we discovered two phylogenetic subgroups associated with fumonisin and gibberellin production in JapaneseF. fujikuroi.

scholarly journals Taxonomic revision of Russula subsection Amoeninae from South Korea

MycoKeys ◽  
2020 ◽  
Vol 75 ◽  
pp. 1-29
Author(s):  
Komsit Wisitrassameewong ◽  
Myung Soo Park ◽  
Hyun Lee ◽  
Aniket Ghosh ◽  
Kanad Das ◽  
...  
Keyword(s):  
New Species ◽  
South Korea ◽  
Central America ◽  
North American ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Taxonomic Revision ◽  
Molecular Phylogenetic ◽  
Pileus Surface ◽  
A New Species

Russula subsection Amoeninae is morphologically defined by a dry velvety pileus surface, a complete absence of cystidia with heteromorphous contents in all tissues, and spores without amyloid suprahilar spot. Thirty-four species within subsection Amoeninae have been published worldwide. Although most Russula species in South Korea have been assigned European or North American names, recent molecular studies have shown that Russula species from different continents are not conspecific. Therefore, the present study aims to: 1) define which species of Russula subsection Amoeninae occur on each continent using molecular phylogenetic analyses; 2) revise the taxonomy of Korean Amoeninae. The phylogenetic analyses using the internal transcribed spacer (ITS) and multilocus sequences showed that subsection Amoeninae is monophyletic within subgenus Heterophyllidiae section Heterophyllae. A total of 21 Russula subsection Amoeninae species were confirmed from Asia, Australia, Europe, North America, and Central America, and species from different continents formed separate clades. Three species were recognized from South Korea and were clearly separated from the European and North American species. These species are R. bella, also reported from Japan, a new species described herein, Russula orientipurpurea, and a new species undescribed due to insufficient material.

scholarly journals Optimizing the location of watercraft inspection stations to slow the spread of aquatic invasive species

2021 ◽  
Author(s):  
Robert G. Haight ◽  
Amy C. Kinsley ◽  
Szu-Yu Kao ◽  
Denys Yemshanov ◽  
Nicholas B. D. Phelps
Keyword(s):  
Invasive Species ◽  
Optimal Policy ◽  
Program Design ◽  
Programming Model ◽  
Aquatic Invasive Species ◽  
Management Objectives ◽  
Large Numbers ◽  
The Usa ◽  
Species Specific ◽  
Infestation Status

AbstractThe accidental spread of aquatic invasive species (AIS) by recreational boaters is a major concern of state and county environmental planners in the USA. While programs for watercraft inspection to educate boaters and slow AIS spread are common practice, large numbers of boats and waterbodies, together with limited budgets, make program design difficult. To facilitate program design, we developed an integer programming model for allocation of scarce inspection resources among lakes. Our model uses species-specific infestation status of lakes and estimates of boat movement between lakes. The objective is to select lakes for inspection stations to maximize the number of risky boats inspected, where risky boats are ones that move from infested to uninfested lakes. We apply our model in Stearns County in central Minnesota, USA, to prioritize lakes for inspection stations and evaluate alternative management objectives. With an objective of protecting uninfested lakes within and outside Stearns County, the optimal policy is to locate stations at infested lakes having the most boats departing for uninfested lakes inside and outside the county. With an objective of protecting only Stearns County lakes, the optimal policy is to locate stations at both infested and uninfested lakes having the riskiest boats arriving from within and outside the county and departing to in-county lakes. The tradeoff between these objectives is significant.

Sign in / Sign up

Export Citation Format

Share Document