Molecular characterization and phylogeny of whipworm nematodes inferred from DNA sequences of cox1 mtDNA and 18S rDNA

AbstractUrocleidoides ectoparasites are mainly found on fish of the neotropical regions. Although molecular research on monogeneans is available, no genetic data exist characterizing species in the Urocleidoides genus. Some DNA sequences have been efficacious in systematic studies and in the reconstruction of phylogenies of fish parasites. Relevant roles have been given to the sequence of the mitochondrial gene of cytochrome c oxidase I (COI). This study characterized COI sequences of the parasites Urocleidoides malabaricusi and U. cuiabai in trahira fish Hoplias aff. malabaricus of the flood plain of the Upper River Paraná, Brazil. The two species under analysis were distinguished by sequencing and analysing a 420-bp fragment of the COI gene, which suggested the existence of the cryptic species U. malabaricusi.

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Phylogeny of Meloidogyne spp. based on 18S rDNA and the intergenic region of mitochondrial DNA sequences

Nematology ◽

10.1163/156854105776186325 ◽

2005 ◽

Vol 7 (6) ◽

pp. 851-862 ◽

Cited By ~ 58

Author(s):

Regina Carneiro ◽

Don Dickson ◽

Ayyamperumal Jeyaprakash ◽

Byron Adams ◽

Myrian Tigano

Keyword(s):

Mitochondrial Dna ◽

16S Rrna ◽

Dna Sequences ◽

18S Rdna ◽

Phylogenetic Trees ◽

Optimality Criteria ◽

Cytochrome Oxidase Subunit ◽

Meloidogyne Spp ◽

Rdna Analysis ◽

Cytochrome Oxidase Subunit Ii

AbstractThe 18S rDNA of 19 populations of Meloidogyne spp. was amplified and directly sequenced. The region of mitochondrial DNA, located in the 3′ portion of the gene that codes for cytochrome oxidase subunit II (COII) through a portion of the 16S rRNA (lRNA) gene, from 16 of these populations was cloned and sequenced. Heteroplasmic sequences were identified from both rDNA and mtDNA regions for several taxa. Several sequences sampled from nominal taxa differed from previously published accounts. Phylogenetic trees based on alignments of these sequences were constructed using distance, parsimony and likelihood optimality criteria. For 18S rDNA data, three main clades were identified. One well supported clade (86–91% bootstrap) included the most common and widely disseminated species, e.g.,M. arenaria, M. javanica and M. incognita, some recently described or redescribed species (M. floridensis, M. paranaensis, and M. ethiopica) plus numerous unidentified isolates. All mitotic parthenogenetic species, except for M. oryzae, were included in this clade. Other, less well supported clades included the amphimictic and facultative meiotic species M. hapla, M. microtyla, M. maritima and M. duytsi. One such clade comprised three meiotic parthenogens (M. exigua, M. graminicola and M. chitwoodi) and M. oryzae. This clade was moderately supported (77% bootstrap) but the relationships within this clade were poor. For mitochondrial DNA data, only the species in clade I from rDNA analysis, and M. hapla were analysed. These species formed a well supported clade (100% bootstrap) to the exclusion of M. mayaguensis and M. hapla. The addition of taxa and mtDNA data to publicly available records improved the discrimination sensitivity of species and atypical, non-identified, isolates.

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Morphological and molecular characterization of Paractinolaimus sahandi n. sp. (Nematoda: Actinolaimidae) from the Sahand Mountains in Iran

Journal of Helminthology ◽

10.1017/s0022149x10000556 ◽

2010 ◽

Vol 85 (3) ◽

pp. 276-282 ◽

Cited By ~ 3

Author(s):

M. Pedram ◽

G. Niknam ◽

M.T. Vinciguerra ◽

W. Ye ◽

R.T. Robbins

Keyword(s):

New Species ◽

Molecular Characterization ◽

Outer Layer ◽

18S Rdna ◽

Soil Samples ◽

28S Rdna ◽

First Report ◽

Morphological And Molecular Characterization

AbstractParactinolaimus sahandi n. sp., found in wet soil samples collected from the rhizosphere of grasses of Sahand Mountains, Iran, is described. This new species is characterized by its long body (3.5–4.7 mm), high a value (74.5–88.5), anterior location of posterior subventral nuclei, occupying 62.5–68.0% of glandularium distance, the presence of 1–4 pre- and 1–3 post-vulval papillae and numerous tiny, not innervated papillae in front and behind the vulva in the outer layer of cuticle; common functional males in the population, with 62.5–81.3 μm long spicules and 15–17 ventromedian supplements. The new species, which is the only one in the genus showing the advulval cuticular tiny papillae and is unusually slender, is compared to four species of Paractinolaimus, namely P. macrolaimus, P. longidrilus, P. spanithelus and P. rafiqi. The ribosomal 18S rDNA (1246 bp sequenced) and 28S rDNA D2/D3 region (844 bp sequenced) of P. sahandi n. sp. were sequenced for molecular characterization. Sequences of the 18S and 28S D2/D3 of P. sahandi n. sp. have distinct differences from those of the only sequenced P. macrolaimus, with 6 bp differences in 18S and 38 bp differences and five gaps in 28S. This is the first report of the occurrence of members of Actinolaimidae in Iran.

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Characterization of Three Species of Thrips on Weeping Fig, Nutmeg, and Marine Seruni Plants Based on Mtcoi DNA Sequences

Biosaintifika Journal of Biology & Biology Education ◽

10.15294/biosaintifika.v8i2.5448 ◽

2016 ◽

Vol 8 (2) ◽

pp. 185

Author(s):

Nia Kurniawaty ◽

Purnama Hidayat ◽

Aunu Rauf

Keyword(s):

Pest Management ◽

Molecular Characterization ◽

Dna Sequences ◽

Biology Education ◽

Morphological Data ◽

Coi Gene ◽

Molecular Characteristics ◽

Vegetable Crops ◽

Total Extraction

Thrips are widely reported as pests in vegetable crops. However, the existence of Phlaeothripidae members has a less concern in Indonesia. Phlaeothripidae is the only family of Tubulifera Suborder and some reports suggested that they had potential to be pests in several crops due to their ability to roll up and to make galls on leaves. The first step in pest management attempt is to identify the pest accurately and quickly, so the pest management can be on target and more efficient. One of the identification methods is the molecular identification using DNA barcoding techniques. This study aimed to characterize and to compare species thrips in banyan, nutmeg, and marine seruni based on their molecular characteristics. This research was conducted in Bogor and Kuningan. The process of molecular characterization consisteds of four steps DNA total extraction, amplification by using PCR, COI gene sequence, and data analysis. PCR programme was succesfully to amplified mtCOI gene fragment at 710 bp. The length of mtCOI gene of Gynaikothrips uzeli, Haplothrips ganglbaueri, and Pseudophilothrips ichini were 704, 686, and 702 bp dominated by A and T bases with nucleotide variation value of 27.8%. This results confirmed that molecular characterization using mtCOI gene mitochondrial had successfully supported the morphological data. How to CiteKurniawaty, N., Hidayat, P. & Rauf, A. (2016). Characterization of Three Species of Thrips on Banyan, Nutmeg, and Marine Seruni Plants Based on Coi Gene. Biosaintifika: Journal of Biology & Biology Education, 8(2), 185-192.

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The molecular characterization of the short interspersed repeated DNA sequences in the bovine genome

10.31274/rtd-180813-4382 ◽

1983 ◽

Author(s):

Katherine Anne Koren Richardson

Keyword(s):

Molecular Characterization ◽

Dna Sequences ◽

Bovine Genome ◽

Repeated Dna ◽

Repeated Dna Sequences

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