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 Laporan Pertama di Sulawesi Selatan: Karakter Morfologi dan Molekuler Nematoda Puru Akar yang Berasosiasi dengan Akar Padi di Kabupaten Wajo, Sulawesi Selatan

2018 ◽  
Vol 22 (1) ◽  
pp. 58
Author(s):  
Hishar Mirsam ◽  
Fitrianingrum Kurniawati
Keyword(s):  
Polymerase Chain Reaction ◽  
Nematode Species ◽  
Morphological Characters ◽  
Rice Root ◽  
Nucleotide Sequence Analysis ◽  
Morphological Identification ◽  
Root Knot Nematode ◽  
Chain Reaction ◽  
Meloidogyne Graminicola ◽  
Polymerase Chain

Root Knot Nematode (RKN) is one of the most important cosmopolite parasitic nematode species. Reports on RKN associated with rice root in Indonesia are still limited in West Java and Yogyakarta. This study aimed to identify the RKN associated with rice root in Sub-district of Bola, District of Wajo, South Sulawesi, based on morphological and molecular characters. Sampling was carried out by purposive method based on specific criteria of sample, i.e. root knot. Identification of root knot nematode (RKN) infestation in field was done by observing the primary and secondary symptoms. Morphological identification was carried out based on characters of juvenile 2 and the female perineal pattern. Molecular identification was based on amplification of r-DNA by polymerase chain reaction technique using primers rDNA2 and rDNA 1.58s. RKN were detected associated with the incidence of root knot in rice plant. RKN was identified as Meloidogyne graminicola based on morphological characters of juvenile 2 and the female perineal pattern. PCR using primer rDNA 2 / rDNA 1.58s successfully amplified a DNA band of RKN of ± 500 bp. Nucleotide sequence analysis showed that RKN isolated from Wajo was closely related to M. graminicola isolated from Nepal, China, India, Madagascar, and USA with homology of 98.1–100.00%. IntisariNematoda puru akar (NPA) merupakan salah satu jenis nematoda parasit penting yang bersifat kosmopolit. Laporan NPA yang berasosiasi dengan akar tanaman padi di Indonesia masih terbatas di Jawa Barat dan Yogyakarta. Penelitian ini bertujuan mengidentifikasi NPA yang berasosiasi dengan akar tanaman padi di Kabupaten Wajo, Sulawesi Selatan berdasarkan karakter morfologi dan molekuler. Pengambilan sampel dilakukan secara purposif dengan memilih sampel berdasarkan pada kriteria gejala spesifik penyakit puru akar. Identifikasi serangan dilakukan dengan mengamati gejala primer dan gejala sekunder. Identifikasi morfologi dilakukan dengan pengamatan karakter morfologi juvenil 2 dan pola perineal NPA betina.Identifikasi molekuler dilakukan dengan teknik polymerase chain reaction (PCR) untuk mengamplifikasi wilayah internal transcribed spacer (ITS) ribosomal DNA (rDNA) menggunakan pasangan primer rDNA2 dan rDNA1.58s. NPA ditemukan berasosiasi dengan akar tanaman padi yang memperlihatkan gejala puru akar. NPA diidentifikasi sebagai Meloidogyne graminicola berdasarkan karakter morfologi juvenil 2 dan pola perineal NPA betina. PCR menggunakan primer rDNA2/ rDNA1.58s berhasil mengamplifikasi pita DNA NPA dengan ukuran sekitar 500 bp. Analisis runutan nukleotida menunjukkan isolat NPA asal Wajo-Indonesia memiliki tingkat kekerabatan yang sangat dekat dengan isolat M. graminicola asal Nepal, Cina, India, Madagaskar, dan Amerika Serikat dengan nilai homologi berkisar 98,1–100,0%.

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.

scholarly journals Characterization of a Novel Simian Immunodeficiency Virus with a vpu Gene from Greater Spot-Nosed Monkeys (Cercopithecus nictitans) Provides New Insights into Simian/Human Immunodeficiency Virus Phylogeny

2002 ◽  
Vol 76 (16) ◽  
pp. 8298-8309 ◽  
Author(s):  
Valérie Courgnaud ◽  
Marco Salemi ◽  
Xavier Pourrut ◽  
Eitel Mpoudi-Ngole ◽  
Bernadette Abela ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Simian Immunodeficiency Virus ◽  
Genomic Structure ◽  
Phylogenetic Analyses ◽  
Middle Part ◽  
Geographic Ranges ◽  
Close Phylogenetic Relationship ◽  
Immunodeficiency Virus ◽  
Relationship Of ◽  
Full Length Genome

ABSTRACT In the present study, we describe a new simian immunodeficiency virus (SIV), designated SIVgsn, naturally infecting greater spot-nosed monkeys (Cercopithecus nictitans) in Cameroon. Together with SIVsyk, SIVgsn represents the second virus isolated from a monkey belonging to the Cercopithecus mitis group of the Cercopithecus genus. Full-length genome sequence analysis of two SIVgsn strains, SIVgsn-99CM71 and SIVgsn-99CM166, revealed that despite the close phylogenetic relationship of their hosts, SIVgsn was highly divergent from SIVsyk. First of all, they differ in their genomic organization. SIVgsn codes for a vpu homologue, so far a unique feature of the members of the SIVcpz/human immunodeficiency virus type 1 (HIV-1) lineage, and detailed phylogenetic analyses of various regions of the viral genome indicated that SIVgsn might be a mosaic of sequences with different evolutionary histories. SIVgsn was related to SIVsyk in Gag and part of Pol and related to SIVcpz in Env, and the middle part of the genome did not cluster significantly with any of the known SIV lineages. When comparing the two SIVgsn Env sequences with that of SIVcpz, a remarkable conservation was seen in the V3 loop, indicating a possible common origin for the envelopes of these two viruses. The habitats of the two subspecies of chimpanzees infected by SIVcpz overlap the geographic ranges of greater spot-nosed monkeys and other monkey species, allowing cross-species transmission and recombination between coinfecting viruses. The complex genomic structure of SIVgsn, the presence of a vpu gene, and its relatedness to SIVcpz in the envelope suggest a link between SIVgsn and SIVcpz and provide new insights about the origin of SIVcpz in chimpanzees.

scholarly journals Morphometric and Molecular Diversity among Seven European Isolates of Pratylenchus penetrans

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 674
Author(s):  
Mesfin Bogale ◽  
Betre Tadesse ◽  
Rasha Haj Nuaima ◽  
Bernd Honermeier ◽  
Johannes Hallmann ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Management Strategies ◽  
Ornamental Plants ◽  
Geographic Origin ◽  
Tail Length ◽  
Nematode Species ◽  
Intraspecific Diversity ◽  
Effective Control ◽  
Pratylenchus Penetrans ◽  
The Usa

Pratylenchus penetrans is an economically important root-lesion nematode species that affects agronomic and ornamental plants. Understanding its diversity is of paramount importance to develop effective control and management strategies. This study aimed to characterize the morphological and genetic diversity among seven European isolates. An isolate from the USA was included in the molecular analyses for comparative purposes. Morphometrics of the European P. penetrans isolates generally were within the range of the original descriptions for this species. However, multiple morphometric characteristics, including body length, maximum body width, tail length and length of the post-vulval uterine sac showed discrepancies when compared to other populations. Nucleotide sequence-based analyses revealed a high level of intraspecific diversity among the isolates. We observed no correlation between D2-D3 rDNA- and COXI-based phylogenetic similarities and geographic origin. Our phylogenetic analyses including selected GenBank sequences also suggest that the controversy surrounding the distinction between P. penetrans and P. fallax remains.

scholarly journals Histological Characterization of Resistance to Different Root-Knot Nematode Species Related to Phenolics Accumulation in Capsicum annuum

2005 ◽  
Vol 95 (2) ◽  
pp. 158-165 ◽  
Author(s):  
A. Pegard ◽  
G. Brizzard ◽  
A. Fazari ◽  
O. Soucaze ◽  
P. Abad ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Capsicum Annuum ◽  
High Performance ◽  
Nematode Species ◽  
Susceptible Cultivar ◽  
Resistant Line ◽  
Root Knot Nematode ◽  
Resistance Response ◽  
Root Knot Nematodes ◽  
Chromatography Analysis

In the pepper Capsicum annuum CM334, which is used by breeders as a source of resistance to Phytophthora spp. and potyviruses, a resistance gene entirely suppresses reproduction of the root-knot nematode (Meloidogyne spp.). The current study compared the histological responses of this resistant line and a susceptible cultivar to infection with the three most damaging root-knot nematodes: M. arenaria, M. incognita, or M. javanica. Resistance of CM334 to root-knot nematodes was associated with unidentified factors that limited nematode penetration and with post-penetration biochemical responses, including the hypersensitive response, which apparently blocked nematode migration and thereby prevented juvenile development and reproduction. High-performance liquid chromatography analysis suggested that phenolic compounds, especially chlorogenic acid, may be involved in CM334 resistance. The response to infection in the resistant line varied with root-knot nematode species and was correlated with nematode behavior and pathogenicity in the susceptible cultivar: nematode species that quickly reached the vascular cylinder and initiated feeding sites in the susceptible cultivar were quickly recognized in CM334 and stopped in the epidermis or cortex. After comparing our data with those from other resistant pepper lines, we suggest that timing of the resistance response and the mechanism of resistance vary with plant genotype, resistance gene, and root-knot nematode species.

Host suitability of summer cover crops to Meloidogyne arenaria, M. enterolobii, M. incognita and M. javanica

Nematology ◽  
2021 ◽  
pp. 1-9
Author(s):  
Hung X. Bui ◽  
Johan A. Desaeger
Keyword(s):  
Cover Crops ◽  
Nematode Species ◽  
Host Suitability ◽  
Parasitic Nematodes ◽  
Plant Parasitic Nematodes ◽  
Root Knot Nematode ◽  
Sunn Hemp ◽  
Host Status ◽  
Susceptible Control ◽  
Sorghum Sudangrass

Summary Cover crops can be a useful tool for managing plant-parasitic nematodes provided they are poor or non-hosts for the target nematode species. A glasshouse experiment was done to determine the host status of four common cover crops in Florida, sunn hemp, cowpea, sorghum sudangrass and sunflower, to pure populations of four common tropical root-knot nematode (RKN) species Meloidogyne javanica (Mj), M. incognita (Mi), M. enterolobii (Me) and M. arenaria (Ma). Tomato was included as a susceptible control. Eight weeks after nematode inoculation (WAI), tomato showed the highest root gall damage for all tested RKN species, with gall indices (GI) between 7 (Ma) and 8.5 (Me) and reproduction factor (RF) ranging from 20 (Ma) to 50 (Mj). No visible root galls were observed for any of the RKN species on sunn hemp and sorghum sudangrass at 8 WAI. However, Mj and Mi were able to reproduce slightly on sorghum sudangrass (RF = 0.02 and 0.79, respectively). Sunflower and cowpea were infected by all four tested RKN species, but host suitability varied. Sunflower root galling ranged from 1.1 (Me) to 4.5 (Mj) and RF = 3.2 (Me) to 28.7 (Mj), while cowpea root galling ranged from 0.6 (Mi) to 5.1 (Me) and RF = 0.8 (Mi) to 67.3 (Mj). Sunn hemp and, to a lesser extent, sorghum sudangrass were poor hosts to all four tested RKN species. Sunflower was a good host to all RKN species, but root gall damage and RF were lowest for Me. Cowpea was a good host to Mj, Me and Ma, but a poor host to Mi. Our results confirm and stress the importance of RKN species identification when selecting cover crops as an RKN management strategy.

A new species of Chlorociboria (Helotiales, Ascomycota) on herbaceous stems from China

Phytotaxa ◽  
2017 ◽  
Vol 312 (1) ◽  
pp. 111
Author(s):  
HUAN-DI ZHENG ◽  
WEN-YING ZHUANG
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Central China ◽  
Nuclear Ribosomal Dna ◽  
Light Blue ◽  
Ectal Excipulum ◽  
A New Species

A new species, namely Chlorociboria herbicola, is discovered on herbaceous stems in central China. Morphologically, the new fungus is distinctive by the combination of light blue-green apothecia, rectangular cells in ectal excipulum, and elongate-ellipsoidal ascospores with rounded ends. Phylogenetic analyses of the internal transcribed spacer and large subunit of nuclear ribosomal DNA sequences confirm its ascription in Chlorociboria and distinction from the known species of the genus.

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

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