Meloidogyne lopezi n. sp. (Nematoda: Meloidogynidae), a new root-knot nematode associated with coffee (Coffea arabica L.) in Costa Rica, its diagnosis and phylogenetic relationship with other coffee-parasitising Meloidogyne species

Nematology ◽  
2014 ◽  
Vol 16 (6) ◽  
pp. 643-661 ◽  
Author(s):  
Danny A. Humphreys-Pereira ◽  
Danny A. Humphreys-Pereira ◽  
Lorena Flores-Chaves ◽  
Danny A. Humphreys-Pereira ◽  
Lorena Flores-Chaves ◽  
...  
Keyword(s):  
Costa Rica ◽  
16S Rrna ◽  
Coffea Arabica ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Restriction Enzymes ◽  
Nematode Species ◽  
Male Body ◽  
Root Knot Nematode ◽  
Pcr Rflp

Coffee (Coffea arabica L. cv. Catuai) seedlings with abundant small root galls caused by an unknown root-knot nematode were found in southern Costa Rica. Morphology, esterase and malate dehydrogenase isozyme phenotypes and DNA markers differentiated this nematode from known Meloidogyne spp. A new species, M. lopezi n. sp., with common name Costa Rican root-knot nematode, is suggested. Meloidogyne lopezi n. sp. is distinguished from other coffee-associated Meloidogyne spp. by size of female lips and stylet, male body length and stylet and second-stage juvenile body and tail morphology. The region of the mitochondrial genome between COII and 16S rRNA showed a unique amplicon size of 1370 bp, and digestions with restriction enzymes HinfI, AluI, DraI and DraIII revealed characteristic PCR-RFLP patterns that differed from the tropical root-knot nematode species M. arabicida, M. incognita, M. izalcoensis, M. javanica and M. paranaensis. Characterisation of the protein-coding map-1 gene and phylogenetic analyses suggested that M. lopezi n. sp. might reproduce by mitotic parthenogenesis. Phylogenies estimated using Bayesian analyses based on the region between the COII and 16S rRNA mitochondrial genes, as well as the 18S and 28S ribosomal nuclear genes, indicated that M. lopezi n. sp. is closely related to other tropical Meloidogyne spp. that infect coffee, especially M. arabicida, M. izalcoensis and M. paranaensis from Central and South America. Isozyme analyses and PCR-RFLP of the COII-16S rRNA mitochondrial gene region enable a clear diagnostic differentiation between these species.

Integrative taxonomy of Meloidogyne paranaensis populations belonging to different esterase phenotypes

Nematology ◽  
2020 ◽  
Vol 22 (4) ◽  
pp. 453-468
Author(s):  
Marcilene F.A. Santos ◽  
Vanessa S. Mattos ◽  
Ana Cristina M.M. Gomes ◽  
Jessica M.S. Monteiro ◽  
Daniela A. Souza ◽  
...  
Keyword(s):  
Mitochondrial Gene ◽  
Intraspecific Variability ◽  
Tail Length ◽  
Nematode Species ◽  
Integrative Taxonomy ◽  
Phylogenetic Position ◽  
Root Knot Nematode ◽  
Protein Coding ◽  
Coffee Cultivation ◽  
Esterase Phenotypes

Summary Meloidogyne paranaensis is one of the most destructive root-knot nematode species affecting coffee cultivation. This species presents different esterase phenotypes (Est): P1, P2 and P2a, previous studies showing that Est P2 and P2a populations were more aggressive to susceptible coffee cultivars than populations with Est P1, and local producers have even asked if they may be described as other species. The objective of this study was to characterise M. paranaensis populations of different esterase phenotypes (Est P1, P2 and P2a), regarding morphological, morphometric and phylogenetic relationships in distinct regions of ribosomal DNA (rDNA), mitochondrial gene cytochrome c oxidase II (COII) and nuclear protein coding gene HSP90. All populations were identified by esterase phenotype and SCAR-specific markers. Regarding morphology/morphometrics, the three populations were very similar to the description of the species, differing only in the morphology of the male stylet and second-stage juvenile hyaline tail length. Based on the phylogenetic analysis, a low intraspecific variability was detected among M. paranaensis Est P1 and Est P2 populations from Brazil; the Guatemalan population Est P2a, however, showed a genetic differentiation from the Brazilian populations, confirming the geographic genetic distance of this aggressive population. According to this multi-source approach study, in spite of the intraspecific variation, the phylogenetic position of M. paranaensis is absolute, regardless of the enzymatic phenotype and SCAR markers.

scholarly journals On the Close Relatedness of Two Rice-Parasitic Root-Knot Nematode Species and the Recent Expansion of Meloidogyne graminicola in Southeast Asia

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 175 ◽  
Author(s):  
Guillaume Besnard ◽  
Ngan Thi-Phan ◽  
Hai Ho-Bich ◽  
Alexis Dereeper ◽  
Hieu Trang Nguyen ◽  
...  
Keyword(s):  
Genomic Structure ◽  
Phylogenetic Analyses ◽  
Nuclear Genome ◽  
Nematode Species ◽  
Intraspecific Diversity ◽  
Nuclear Ribosomal Dna ◽  
Genomic Sequences ◽  
Root Knot Nematode ◽  
Meloidogyne Graminicola ◽  
Close Phylogenetic Relationship

Meloidogyne graminicola is a facultative meiotic parthenogenetic root-knot nematode (RKN) that seriously threatens agriculture worldwide. We have little understanding of its origin, genomic structure, and intraspecific diversity. Such information would offer better knowledge of how this nematode successfully damages rice in many different environments. Previous studies on nuclear ribosomal DNA (nrDNA) suggested a close phylogenetic relationship between M. graminicola and Meloidogyne oryzae, despite their different modes of reproduction and geographical distribution. In order to clarify the evolutionary history of these two species and explore their molecular intraspecific diversity, we sequenced the genome of 12 M. graminicola isolates, representing populations of worldwide origins, and two South American isolates of M. oryzae. k-mer analysis of their nuclear genome and the detection of divergent homologous genomic sequences indicate that both species show a high proportion of heterozygous sites (ca. 1–2%), which had never been previously reported in facultative meiotic parthenogenetic RKNs. These analyses also point to a distinct ploidy level in each species, compatible with a diploid M. graminicola and a triploid M. oryzae. Phylogenetic analyses of mitochondrial genomes and three nuclear genomic sequences confirm close relationships between these two species, with M. graminicola being a putative parent of M. oryzae. In addition, comparative mitogenomics of those 12 M. graminicola isolates with a Chinese published isolate reveal only 15 polymorphisms that are phylogenetically non-informative. Eight mitotypes are distinguished, the most common one being shared by distant populations from Asia and America. This low intraspecific diversity, coupled with a lack of phylogeographic signal, suggests a recent worldwide expansion of M. graminicola.

scholarly journals Characterization of X-Disease Phytoplasmas in Chokecherry from North Dakota by PCR-RFLP and Sequence Analysis of the rRNA Gene Region

Plant Disease ◽  
2000 ◽  
Vol 84 (11) ◽  
pp. 1235-1240 ◽  
Author(s):  
Y. H. Guo ◽  
Z.-M. Cheng ◽  
J. A. Walla
Keyword(s):  
16S Rrna ◽  
North Dakota ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Pcr Rflp

Genetic variation of X-disease phytoplasma strains from chokecherry (ChX) in North Dakota and nearby sites, and their relatedness with three standard strains of the X-disease phytoplasma group, eastern X-disease (CX), western X-disease (WX), and goldenrod yellows (GR1) phyto-plasmas, were studied. Primer pairs were developed to amplify the 23S ribosomal RNA (rRNA) gene and the 16S/23S spacer region. The rRNA genes (16S rRNA, 23S rRNA, and two ribosomal protein [rp] genes) and the 16S/23S spacer region were amplified by polymerase chain reactions. The restriction fragment length polymorphism (RFLP) patterns of 16S rRNA, 23S rRNA, and rp genes, generated by digestion with four restriction enzymes (AluI, HpaII, MseI, and RsaI), showed no difference among 43 ChX phytoplasma isolates. Sequencing of the 441-bp 16S/23S spacer region revealed variation at four positions among 12 ChX phytoplasma strains. A tRNAIle and other conserved sequences were identified in the spacer region. Among X-disease subgroups, RFLP analysis indicated that ChX is similar to WX, closely related to CX, and easily distinguished from GR1. Sequencing indicated that ChX is closer to CX than to WX. Together, the analyses indicated that ChX phytoplasmas are genetically different from the standard strains of other X-disease phytoplasma subgroups.

scholarly journals Epidemics of Meloidogyne brasilensis in Central Brazil on Processing Tomato Hybrids That Have the Root-Knot Nematode Mi Resistance Gene

Plant Disease ◽  
2010 ◽  
Vol 94 (6) ◽  
pp. 781-781 ◽  
Author(s):  
J. M. Charchar ◽  
M. E. N. Fonseca ◽  
J. B. Pinheiro ◽  
L. S. Boiteux ◽  
J. D. Eisenback
Keyword(s):  
Federal District ◽  
Nematode Species ◽  
Resistance Locus ◽  
Male Body ◽  
Root Knot Nematode ◽  
Sources Of Resistance ◽  
Vegetative Development ◽  
Tomato Crop ◽  
Central Brazil ◽  
Mi Gene

The species Meloidogyne brasilensis Charchar & Eisenback 2002 was described as causing root rot, severe wilt, and numerous galls in pea (Pisum sativum L.) in Brasília-Federal District and tomato (Solanum lycopersicum L.) cv. Rossol (known to have the root-knot nematode resistance Mi gene) in Londrina-Paraná State, Brazil. To our knowledge, this current work is the first report of the epidemics on tomato hybrids that have the Mi gene caused by infection of M. brasilensis in central Brazil. Samples were obtained from fields with two commercial hybrids that have the Mi gene (‘Calroma’ and ‘Nemapride’) that were cultivated under center-pivot irrigation in Silvânia, Goiás State. These hybrids exhibited slow vegetative development and malformed roots because of the high number of large galls. Symptomatic plants were collected from a tomato crop area of more than 100 ha. Random sampling indicated field sectors with up to 100% of symptomatic plants. Morphological and morphometric evaluations of this Meloidogyne population were carried out with the female perineal pattern, stylet, and excretory pore and also with the male body traits, labial disc, and stylet. The esterase phenotype was unique for this population with four clear bands (J. M. Charchar, unpublished data). Altogether, the morphological and biochemical characteristics of this population were in agreement with that reported for M. brasilensis (1). Koch's postulates were fulfilled using tomato ‘Rutgers’ (susceptible) and ‘Rossol' (with the Mi resistance locus) under greenhouse conditions. The massive use of tomato hybrids with the Mi gene could be a strong selection factor favoring this pathogen under growing conditions in central Brazil. Germplasm screen searching for sources of resistance specific to this nematode species is advisable. Reference: (1) J. M. Charchar and J. D. Eisenback. Nematology 4:629, 2002.

scholarly journals Molecular Characterization of Functional and Phylogenetic Genes from Natural Populations of Methanotrophs in Lake Sediments

1999 ◽  
Vol 65 (11) ◽  
pp. 5066-5074 ◽  
Author(s):  
Andria M. Costello ◽  
Mary E. Lidstrom
Keyword(s):  
16S Rrna ◽  
Phylogenetic Analyses ◽  
Natural Populations ◽  
Restriction Enzymes ◽  
Clone Libraries ◽  
Operational Taxonomic Units ◽  
Methane Oxidizing Bacteria ◽  
Lake Washington ◽  
Pcr Products ◽  
Total Community

ABSTRACT The 16S rRNA and pmoA genes from natural populations of methane-oxidizing bacteria (methanotrophs) were PCR amplified from total community DNA extracted from Lake Washington sediments obtained from the area where peak methane oxidation occurred. Clone libraries were constructed for each of the genes, and approximately 200 clones from each library were analyzed by using restriction fragment length polymorphism (RFLP) and the tetrameric restriction enzymesMspI, HaeIII, and HhaI. The PCR products were grouped based on their RFLP patterns, and representatives of each group were sequenced and analyzed. Studies of the 16S rRNA data obtained indicated that the existing primers did not reveal the total methanotrophic diversity present when these data were compared with pure-culture data obtained from the same environment. New primers specific for methanotrophs belonging to the generaMethylomonas, Methylosinus, andMethylocystis were developed and used to construct more complete clone libraries. Furthermore, a new primer was designed for one of the genes of the particulate methane monooxygenase in methanotrophs, pmoA. Phylogenetic analyses of both the 16S rRNA and pmoA gene sequences indicated that the new primers should detect these genes over the known diversity in methanotrophs. In addition to these findings, 16S rRNA data obtained in this study were combined with previously described phylogenetic data in order to identify operational taxonomic units that can be used to identify methanotrophs at the genus level.

scholarly journals Calochaete gen. nov. (Cyanobacteria, Nostocales), a new cyanobacterial type from the “páramo” zone in Costa Rica

Phytotaxa ◽  
2013 ◽  
Vol 109 (1) ◽  
pp. 36 ◽  
Author(s):  
TOMÁŠ HAUER ◽  
MARKÉTA BOHUNICKÁ ◽  
RADKA MÜHLSTEINOVÁ
Keyword(s):  
Costa Rica ◽  
16S Rrna ◽  
Type Species ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Soil Material ◽  
Similar Morphology ◽  
Rdna Sequences ◽  
16S Rdna Sequences

A new tapered and false branched morphotype of filamentous heterocytous cyanobacterium was isolated from soil material collected on a massif of Chirripó Mountain, Costa Rica. The strain was analyzed morphologically and a sequence of its 16S rRNA gene was compared with available 16S rDNA sequences of organisms with similar morphology, especially those with heteropolar tapering filaments. Phylogenetic analyses revealed that the strain was significantly different from Rivulariaceae, but was closely related to several strains designated as Tolypothrix. However, according to the original descriptions in the literature, members of the genus Tolypothrix possess only very slightly tapering filaments. With regard to all these differences, we decided to describe a new genus—Calochaete gen. nov. with type species C. cimrmanii.

A new Cosmocercoides species (Ascaridida: Cosmocercidae), C. wuyiensis n. sp., from the Asiatic frog Amolops wuyiensis (Amphibia: Anura)

2019 ◽  
Vol 94 ◽  
Author(s):  
Y. Liu ◽  
Q. Yu ◽  
Y.-L. Shu ◽  
J.-H. Zhao ◽  
J.-Y. Fang ◽  
...  
Keyword(s):  
18S Rdna ◽  
Phylogenetic Analyses ◽  
Nematode Species ◽  
Coi Gene ◽  
Male Body ◽  
Lizard Species ◽  
Nucleotide Divergence ◽  
Distinguishing Features ◽  
Morphological And Molecular Characterization

Abstract We identified and characterized a new cosmocercid nematode species, Cosmocercoides wuyiensis n. sp., through microscopic examination and sequencing of the partial small ribosomal RNA gene (18S rDNA), internal transcribed spacer (ITS) and mitochondrial cytochrome c oxidase subunit 1 (COI) genes. The new species was isolated from the intestine of the Asiatic frog Amolops wuyiensis Liu and Hu, 1975 captured from four localities of the Anhui province in south-east China. Among the 25 recorded species of the Cosmocercoides genus, the morphology of C. wuyiensis n. sp. is closest to that of C. kiliwai and C. malayensis, which were isolated from various Mexican frog and Malaysian lizard species, respectively. However, C. wuyiensis n. sp. displayed several distinguishing features, such as small size of the male body, two spicules of unequal lengths in the male, small gubernaculum, pre-, ad- and post-cloacal caudal rosette papillae in the ratio of 18–24:2:6 and simple papillae in the ratio of 14:multiple:4, circle and number of punctation in each rosette at 1:11–16, sharply conical tail-end and the presence of lateral alae and somatic papillae in both sexes. BLAST and the phylogenetic analyses of the 18S rDNA and ITS sequences indicated that C. wuyiensis n. sp. belonged to the genus Cosmocercoides, while that of the COI gene sequence of C. wuyiensis n. sp. showed 16.36% nucleotide divergence with C. pulcher and 47.99% nucleotide divergence with C. qingtianensis. The morphological and molecular characterization of C. wuyiensis n. sp. provides new taxonomic data for this genus.

A Re-analysis of the phylogeny of the genus Protobothrops (Reptilia: Viperidae), with particular reference to the systematic position of P. xiangchengensis

2006 ◽  
Vol 27 (3) ◽  
pp. 433-439 ◽  
Author(s):  
Peng Guo ◽  
Ermi Zhao ◽  
Yaping Zhang ◽  
Junfeng Pang
Keyword(s):  
Maximum Likelihood ◽  
16S Rrna ◽  
Cytochrome B ◽  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Systematic Position ◽  
Valid Species ◽  
12S Rrna

AbstractBased on three mitochondrial gene fragments (12S rRNA, 16S rRNA, cytochrome b), the phylogeny of Protobothrops is re-analyzed using Maximum-parsimony (MP), Maximum-likelihood (ML), and Bayesian (BI) approaches. All phylogenetic analyses indicate that all putative Protobothrops species examined formed a monophyletic group; however, the intrageneric relationships are still unresolved. The phylogenetic relationships further confirm that P. xiangchengensis is a valid species distinct from P. mucrosquamatus and that it is closely related to P. jerdonii.

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

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