Integrative taxonomy of Meloidogyne graminicola populations with different esterase phenotypes parasitising rice in Brazil

Nematology ◽  
2020 ◽  
pp. 1-17
Author(s):  
Mayra R.C. Soares ◽  
Vanessa S. Mattos ◽  
Raycenne R. Leite ◽  
Ana Cristina M.M. Gomes ◽  
Cesar Bauer Gomes ◽  
...  
Keyword(s):  
Intraspecific Variability ◽  
Molecular Data ◽  
Integrative Taxonomy ◽  
Root Knot Nematode ◽  
Irrigated Rice ◽  
Meloidogyne Graminicola ◽  
Geographic Origins ◽  
Morphometric Features ◽  
High Level ◽  
Esterase Phenotypes

Summary The rice root-knot nematode, Meloidogyne graminicola, has been reported in Southeast Asia, China, India, South Africa, USA, Brazil, and other countries. Recent surveys in Southern Brazil showed that M. graminicola was widespread in irrigated rice in Rio Grande do Sul, Santa Catarina and Paraná states, and the presence of a species complex with a predominance of M. graminicola (Est VS1 = G1) and other variants showing similar esterase phenotypes (Est G2 = R2, G3 = R3). Meloidogyne oryzae (Est O1) and M. ottersoni (Est Ot0) were also part of this complex and were recently re-described and detected on rice. The present study provides an integrative taxonomy approach of the typical and atypical populations of M. graminicola on the basis of morphological, morphometric and molecular data. Considering morphological and morphometric features, the two atypical populations (Est G2 and G3) are in close agreement with the description of M. graminicola. Based on the molecular characterisation, populations G1, G2 and G3 were successfully amplified by M. graminicola SCAR markers, although the specificity of these markers was questioned. Phylogenetic relationships complemented and confirmed the other studies. In maximum likelihood analysis of ITS, D2-D3 rRNA and COXII-16S rRNA sequences, all populations of M. graminicola from different esterase phenotypes clustered together with other M. graminicola populations, thus confirming that these enzyme phenotypes (G1, G2 and G3) are related to the same species. A high level of intraspecific variability was detected among all populations, but no correlation between genetic variability and geographic origins occurred.

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.

An example of problems associated with DNA barcoding in tardigrades: a novel method for obtaining voucher specimens

Zootaxa ◽  
2011 ◽  
Vol 3104 (1) ◽  
pp. 42 ◽  
Author(s):  
MICHELE CESARI ◽  
ILARIA GIOVANNINI ◽  
ROBERTO BERTOLANI ◽  
LORENA REBECCHI
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Intraspecific Variability ◽  
Original Description ◽  
Morphological Characters ◽  
Molecular Data ◽  
Integrative Taxonomy ◽  
Type Locality ◽  
Moss Sample ◽  
Voucher Specimens

We have in recent papers revealed that an integrative taxonomy approach helps to solve taxonomic problems in tardigrades. However, whole tardigrades are required for DNA work, which leaves no hologenophore voucher specimens with adult morphology. Using a novel methodology for the Tardigrada, we introduce the practice of collecting high quality maximum magnification light microscopy images of recently thawed animals to act as hologenophore voucher specimens of animals later used for DNA barcode sequencing. Within the framework of a DNA barcoding project on tardigrades, we collected a moss sample from the type locality of Macrobiotus terminalis Bertolani & Rebecchi, 1993 (Castelsantangelo, Central Apennines, Italy), a species of the “Macrobiotus hufelandi group”. Within the moss sample we found several animals and eggs with a morphology that corresponded to the original description of M. terminalis, while others were attributable to Macrobiotus macrocalix Bertolani & Rebecchi, 1993. In this study, molecular (cox1 mtDNA) analyses demonstrated no intraspecific variability in M. terminalis from the type locality but very large interspecific differences when compared with M. macrocalix and GenBank data for other species within the M. “hufelandi group”. There was also a large difference between our M. terminalis sequences and the GenBank data of a specimen attributed to the same species. The GenBank sequence originated from a population in the Northern Apennines, whose morphology appeared to be like that of the specimens of the locus typicus. This confirmed the importance in utilising material from the type locality for linking molecular data to the species’ morphological characters. Our paper underlines the importance of an integrative taxonomy in species diagnoses and demonstrates a scenario where morphological observations alone are not always sufficient. Lastly, this work adds reliable information to the sequence reference library that provides a useful building block for further studies on similar and related tardigrade taxa.

scholarly journals Host suitability of weeds and forage species to root-knot nematode meloidogyne graminicola as a funcion of irrigation management

2014 ◽  
Vol 32 (3) ◽  
pp. 555-561
Author(s):  
R.R.D. Negretti ◽  
R. Manica-Berto ◽  
D. Agostinetto ◽  
L. Thürmer ◽  
C.B. Gomes
Keyword(s):  
Plant Species ◽  
Irrigation Management ◽  
Host Suitability ◽  
Rice Cultivation ◽  
Alternanthera Philoxeroides ◽  
Raphanus Raphanistrum ◽  
Root Knot Nematode ◽  
Irrigated Rice ◽  
Nematode Reproduction ◽  
Meloidogyne Graminicola

The irrigated rice production can be limited by various phytopathogenic agents, including root-knot nematodes (Meloidogyne spp.). Thus, the aim of this research was to check the host suitability of plant species most often found off-season and during rice cultivation, to root-knot nematode Meloidogyne graminicola, under two irrigation managements. Two experiments were conducted in a completely randomized design. In the first experiment seven plant species that occur in an area of rice cultivation, in fallow, off-season were evaluated. For the second experiment nine weed species infesting the irrigated rice culture were tested in rainfed and flooding conditions. The sixteen species, kept individually in pots with sterilized substrate, were inoculated with 5,000 eggs and second stage juveniles (J2) of nematode. BRS 410 IRGA rice plants inoculated with M.graminicola were used as control. Two months after inoculation, the root system of each plant was evaluated for number of galls and nematode reproduction factor. It was verified that the species of off-season of rice cultivation Sida rhombifolia, Raphanus raphanistrum, Spergula arvensis, Lotus corniculatus and Trifolium repens, and, during the cycle of rice cultivation, Aeschynomene denticulata, Leersia hexandra, are immune to nematode. The plant species off-season, Avena strigosa and Lolium multiflorum and of cultivation, Alternanthera philoxeroides, red rice, Echinochloa crusgalli, Cyperus difformis, Cyperus esculentus, Cyperus iria and Fimbristylis miliacea would behave as hosts of M.graminicola, mostly under rainfed conditions.

scholarly journals Shell and appendages variability in two allopatric ostracod species seen through the light of molecular data

2020 ◽  
Vol 89 (3) ◽  
pp. 247-269
Author(s):  
Ivana Karanovic ◽  
Pham Thi Minh Huyen ◽  
Hyunsu Yoo ◽  
Yuriko Nakao ◽  
Akira Tsukagoshi
Keyword(s):  
Evolutionary Biology ◽  
Intraspecific Variability ◽  
Molecular Data ◽  
Integrative Taxonomy ◽  
Shell Shape ◽  
Closely Related Species ◽  
Traditional Taxonomy ◽  
Brackish Water Species ◽  
A New Species ◽  
Water Species

Ostracod crustaceans are among the most abundant microfossil animals. Understanding intra- and interspecific variability of their shell is of pivotal importance for the interpretation of paleontological data. In comparison to appendages, ostracod shell displays more intraspecific variability (in shape, size, and ornamentation), often as a response to environmental conditions. Shell variability has been studied with sophisticated methods, such as geometric morphometrics (GM), but the conspecificity of examined specimens and populations was never tested. In addition, there are no GM studies of appendages. We build on previously published high cytochrome c oxidase subunit I (COI) divergence rates among populations of a brackish water species, Ishizakiella miurensis (Hanai, 1957). With landmark-based GM analyses of its shell and appendages, and additional genetic markers (ITS, 28S, 18S), we test if the genetic variability is structured in morphospace. This approach is the core of integrative taxonomy paradigm which has been proposed to bring the gap between traditional taxonomy and other disciplines such as evolutionary biology. The results show that it is the shell shape, and not the shape of appendages, that mirrors the molecular phylogeny, and we describe a new species. Our results suggest that the landmark-based GM studies may be useful in paleontological datasets for closely related species delineation. We implement molecular clock and population statistics to discuss speciation processes and phylogeography of the two congeners in Korea and Japan.

Intraspecific variability of the facultative meiotic parthenogenetic root-knot nematode (Meloidogyne graminicola) from rice fields in Vietnam

2015 ◽  
Vol 338 (7) ◽  
pp. 471-483 ◽  
Author(s):  
Stéphane Bellafiore ◽  
Claire Jougla ◽  
Élodie Chapuis ◽  
Guillaume Besnard ◽  
Malyna Suong ◽  
...  
Keyword(s):  
Intraspecific Variability ◽  
Rice Fields ◽  
Root Knot Nematode ◽  
Meloidogyne Graminicola

Intraspecific variability of morphological characters in the species-rich deep-sea genus Acantholaimus Allgén, 1933 (Nematoda: Chromadoridae)

Nematology ◽  
2016 ◽  
Vol 18 (4) ◽  
pp. 455-473 ◽  
Author(s):  
Dmitry M. Miljutin ◽  
Maria A. Miljutina
Keyword(s):  
Deep Sea ◽  
Intraspecific Variability ◽  
Morphological Characters ◽  
Molecular Data ◽  
Species Discrimination ◽  
Species Differentiation ◽  
Lateral Field ◽  
Operational Taxonomic Units ◽  
General Arrangement ◽  
Taxonomic Approach

Acantholaimusis a species-rich genus of deep-sea nematodes, often with dozens of species found at the same locality but each represented by single or few individuals. Species discrimination by morphological characters in this genus is therefore often difficult due to transitional forms that may be referred to several species because of lack of data on intraspecific variability. The aim of this study was to evaluate the intraspecific variability of morphological characters that are most often used inAcantholaimustaxonomy, in order to distinguish those which are most informative for species differentiation. A reverse taxonomic approach was applied for initial species discrimination. Two loci, one each from small and large subunits of rRNA, were sequenced for 59Acantholaimusspecimens from two deep-sea locations. Twenty-seven Molecular Operational Taxonomic Units (MOTU) were identified, of which 12 were represented by more than one individual. These were then analysed for intraspecific variability in morphological characters. Some of the examined characters showed high intraspecific variability; specifically: length of cephalic setae; distance from anterior end to amphid; shape of anterior setae; position and arrangement of cervical setae. In the absence of genetic data, these characters should be used with caution for differential diagnoses or species discrimination. Other characters were more conservative within the same MOTU: body proportions; length of outer labial setae; amphidial diam.; appearance of lateral field; general arrangement of cervical setae; and shape of tail. These characters may be successfully used for species discrimination in the absence of molecular data.

scholarly journals Colouration, chaetotaxy and molecular data provide species-level resolution in a species complex of Dicranocentrus (Collembola : Entomobryidae)

2018 ◽  
Vol 32 (6) ◽  
pp. 1298 ◽  
Author(s):  
Feng Zhang ◽  
Daoyuan Yu ◽  
Mark I. Stevens ◽  
Yinhuan Ding
Keyword(s):  
Species Complex ◽  
Instar Larva ◽  
Molecular Data ◽  
Integrative Taxonomy ◽  
Species Level ◽  
Integrative Approach ◽  
Gene Markers ◽  
Late Neogene ◽  
Taxonomic Approach ◽  
Colour Patterns

Integrative taxonomic approaches are increasingly providing species-level resolution to ‘cryptic’ diversity. In the absence of an integrative taxonomic approach, formal species validation is often lacking because of inadequate morphological diagnoses. Colouration and chaetotaxy are the most commonly used characters in collembolan taxonomy but can cause confusion in species diagnoses because these characters often have large intraspecific variation. Here, we take an integrative approach to the genus Dicranocentrus in China where four species have been previously recognised, but several members of the genus have been morphologically grouped as a species complex based on having paired outer teeth on unguis and seven colour patterns. Molecular delimitations based on distance- and evolutionary models recovered four candidate lineages from three gene markers and revealed that speciation events likely occurred during the late Neogene (4–13million years ago). Comparison of intact dorsal chaetotaxy, whose homologies were erected on the basis of first instar larva, further validated these candidates as formal species: D. gaoligongensis, sp. nov., D. similis, sp. nov., D. pallidus, sp. nov. and D. varicolor, sp. nov., and increase the number of Dicranocentrus species from China to eight. Our study further highlights the importance of adequate taxonomy in linking morphological and molecular characters within integrative taxonomy.

scholarly journals The molecular diversity of different isolates of Beauveria bassiana (Bals.) Vuill. as assessed using intermicrosatellites (ISSRs)

2007 ◽  
Vol 12 (2) ◽  
Author(s):  
M. Estrada ◽  
Manuel Camacho ◽  
César Benito
Keyword(s):  
Beauveria Bassiana ◽  
The Other ◽  
Caribbean Region ◽  
Pcr Markers ◽  
Issr Primer ◽  
Geographic Origins ◽  
The Caribbean ◽  
Beauveria Bassiana Isolates ◽  
High Level ◽  
Issr Pcr

AbstractInter-microsatellite PCR (ISSR-PCR) markers were used to identify and to examine the genetic diversity of eleven Beauveria bassiana isolates with different geographic origins. The variability and the phylogenetic relationships between the eleven strains were analyzed using 172 ISSR-PCR markers. A high level of polymorphism (near 80%) was found using these molecular markers. Seven different isolates showed exclusive bands, and ISSR primer 873 was able to distinguish between all the strains. The dendrogram obtained with these markers is robust and in agreement with the geographical origins of the strains. All the isolates from the Caribbean region were grouped together in a cluster, while the other isolates grouped in the other cluster. The similarity exhibited between the two clusters was less than 50%. This value of homology shows the high genetic variability detected between the isolates from the Caribbean region and the other isolates. ISSR-PCR markers provide a quick, reliable and highly informative system for DNA fingerprinting, and allowed the identification of the different B. bassiana isolates studied.

scholarly journals Evaluation of Organic Amendments against Rice Root-KnotNematode at Seedling Stage of Rice

1970 ◽  
Vol 9 ◽  
pp. 21-27 ◽  
Author(s):  
Nabin Kumar Dangal ◽  
D. Sharma Poudyal ◽  
S. M. Shrestha ◽  
C. Adhikari ◽  
J. M. Duxbury ◽  
...  
Keyword(s):  
Block Design ◽  
Organic Amendments ◽  
Severity Index ◽  
Rice Root ◽  
Chicken Manure ◽  
Root Weight ◽  
Root Knot Nematode ◽  
Meloidogyne Graminicola ◽  
Shoot Weight ◽  
Lesion Severity

Pot experiment was conducted during July-September 2006 to evaluate some organic amendments such as sesame (Sesamum indicum) biomass, buckwheat (Fagopyrum esculentum) biomass, neem (Azadirachta indica) leaves, chinaberry (Melia azedarch) leaves and chicken manure @ 1, 2 and 3 t ha-1 each against the rice root-knot nematode (Meloidogyne graminicola Golden & Birchfield) in direct seeded rice. The treatments were replicated five times in a randomized complete block design. The number of second stage juveniles (J2) of M. graminicola was significantly low in chicken manure @ 3 t ha-1. The root knot severity index was significantly low in sesame @ 3 t ha-1, chinaberry @ 3, 2 or 1 t ha-1, neem @ 3 t ha-1 and chicken manure @ 2 or 3 t ha-1 amended soil but root lesion severity index was lower only in chicken manure @ 2 t ha-1 treated plots. The fresh shoot weight and length were significantly high in chicken manure amendment @ 2 or 3 t ha-1 at 45th day after seeding. However, the fresh root weight, length, number of leaves and number of J2 recovered from the roots were non-significant. Key words: biomass; juveniles; Meloidogyne graminicola; root-knot severity index; root lesion severity index DOI: 10.3126/njst.v9i0.3160 Nepal Journal of Science and Technology 9 (2008) 21-27

Sign in / Sign up

Export Citation Format

Share Document