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Molecular diversity of Scutellonema bradys populations from Benin, based on ITS1 rDNA and COI mtDNA.

ABSTRACT: In Benin, yam production continues to face numerous production constraints, including yield and quality reduction by Scutellonema bradys. Implementation of efficient management techniques against this pest requires an improved understanding, including at the molecular level, of the pest. The current study aimed at identifying the Scutellonema spp. associated with yam in Benin and investigating the phylogenetic relationships between populations. Nematodes of the genus Scutellonema were obtained from tubers exhibiting external dry rot symptoms. DNA was extracted from nematodes belonging to 138 populations collected from 49 fields from 29 villages. For 51 of these populations, both the ITS1 and COI regions could be amplified via PCR, sequenced, compared with available sequences in the NCBI database and were identified as S. bradys. Maximum likelihood was used to construct 60% consensus phylogenetic trees based on 51 sequences. This phylogenetic analysis did not reveal any genetic separation between populations by cultivar, village, cropping system nor by agroecological zone. Neither could any subgroups within S. bradys be separated, indicating that no subspecies were present. An earlier published species-specific primer set was verified with the DNA of the 51 sequences and was considered a reliable and rapid method for S. bradys identification.

SUBMITTER: Etchiha Afoha SAP

PROVIDER: S-EPMC7370939 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Molecular diversity of Scutellonema bradys populations from Benin, based on ITS1 rDNA and COI mtDNA.

Etchiha Afoha Sètondji Alban Paterne SAP Affokpon Antoine A Waeyenberge Lieven L de Sutter Nancy N Agbangla Clément C Dansi Alexandre A Coyne Daniel L DL Viaene Nicole N

Tropical plant pathology 20180510 4

In Benin, yam production continues to face numerous production constraints, including yield and quality reduction by Scutellonema bradys. Implementation of efficient management techniques against this pest requires an improved understanding, including at the molecular level, of the pest. The current study aimed at identifying the Scutellonema spp. associated with yam in Benin and investigating the phylogenetic relationships between populations. Nematodes of the genus Scutellonem ...[more]

PMID: 32714501

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Project description:BackgroundThe Anopheles hyrcanus group, which includes at least 25 species, is widely distributed in the Oriental and Palearctic regions. Some group members have been incriminated as vectors of malaria and other mosquito-borne diseases. It is difficult to identify Hyrcanus Group members by morphological features. Thus, molecular phylogeny has been proposed as an important complementary method to traditional morphological taxonomy.MethodsBased on the GenBank database and our original study data, we used 466 mitochondrial DNA COI sequences belonging to 18 species to reconstruct the molecular phylogeny of the Hyrcanus Group across its worldwide geographic range.ResultsThe results are as follows. 1) The average conspecific K2P divergence was 0.008 (range 0.002-0.017), whereas sequence divergence between congroup species averaged 0.064 (range 0.026-0.108). 2) The topology of COI tree of the Hyrcanus Group was generally consistent with classical morphological taxonomy in terms of species classification, but disagreed in subgroup division. In the COI tree, the group was divided into at least three main clusters. The first cluster contained An. nimpe; the second was composed of the Nigerrimus Subgroup and An. argyropus; and the third cluster was comprised of the Lesteri Subgroup and other unassociated species. 3) Phylogenetic analysis of COI indicated that ancient hybridizations probably occurred among the three closely related species, An. sinensis, An. belenrae, and An. kleini. 4) The results supported An. paraliae as a probable synonym of An. lesteri, and it was possible that An. pseudopictus and An. hyrcanus were the same species, as evident from their extremely low interspecific genetic divergence (0.020 and 0.007, respectively) and their phylogenetic positions.ConclusionsIn summary, we reconstructed the molecular phylogeny and analysed genetic divergence of the Hyrcanus Group using mitochondrial COI sequences. Our results suggest that in the future of malaria surveillance, we should not only pay much attention to those known vectors of malaria, but also their closely related species.

Project description:BackgroundThe Anopheles hyrcanus group, which includes 25 species, is widely distributed in the Oriental and Palaearctic regions. Given the difficulty in identifying cryptic or sibling species based on their morphological characteristics, molecular identification is regarded as an important complementary approach to traditional morphological taxonomy. The aim of this study was to reconstruct the phylogeny of the Hyrcanus group using DNA barcoding markers in order to determine the phylogenetic correlations of closely related taxa and to compare these markers in terms of identification efficiency and genetic divergence among species.MethodsBased on data extracted from the GenBank database and data from the present study, we used 399 rDNA-ITS2 sequences of 19 species and 392 mtDNA-COII sequences of 14 species to reconstruct the molecular phylogeny of the Hyrcanus group across its worldwide range. We also compared the performance of rDNA-ITS2 against that of mtDNA-COII to assess the genetic divergence of closely related species within the Hyrcanus group.ResultsAverage interspecific divergence for the rDNA-ITS2 sequence (0.376) was 125-fold higher than the average intraspecies divergence (0.003), and average interspecific divergence for the mtDNA-COII sequence (0.055) was eightfold higher than the average intraspecies divergence (0.007). The barcoding gap ranged from 0.015 to 0.073 for rDNA-ITS2, and from 0.017 to 0.025 for mtDNA-COII. Two sets of closely related species, namely, Anophels lesteri and An. paraliae, and An. sinensis, An. belenrae and An. kleini, were resolved by rDNA-ITS2. In contrast, the relationship of An. sinensis/An. belenrae/An. kleini was poorly defined in the COII tree. The neutrality test and mismatch distribution revealed that An. peditaeniatus, An. hyrcanus, An. sinensis and An. lesteri were likely to undergo hitchhiking or population expansion in accordance with both markers. In addition, the population of an important vivax malaria vector, An. sinensis, has experienced an expansion after a bottleneck in northern and southern Laos.ConclusionsThe topology of the Hyrcanus group rDNA-ITS2 and mtDNA-COII trees conformed to the morphology-based taxonomy for species classification rather than for that for subgroup division. rDNA-ITS2 is considered to be a more reliable diagnostic tool than mtDNA-COII in terms of investigating the phylogenetic correlation between closely related mosquito species in the Hyrcanus group. Moreover, the population expansion of an important vivax malaria vector, An. sinensis, has underlined a potential risk of malaria transmission in northern and southern Laos. This study contributes to the molecular identification of the Anopheles hyrcanus group in vector surveillance.

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Project description:Around 300 different plant species are infected by the plant-parasitic reniform nematode (Rotylenchulus reniformis), including cotton. This is a devasting nematode with a preference for cotton; it is commonly found in Alabama farms and causes severe reduction in yields. Its first internal transcribed spacer (ITS1) region can be sequenced, and potential mutations can be found in order to study the population dynamics of the reniform nematode. The goal of our study was to sequence the ITS1 rDNA region in male and female RNs that were collected from BelleMina, Hamilton, and Lamons locations in Alabama. After separating the single male and female RNs from the samples collected from the three selected listed sites above, the ITS1 region was amplified selectively using specific primers, and the resulting products were cloned and sequenced. Two distinct bands were observed after DNA amplification of male and female nematodes at 550 bp and 730 bp, respectively. The analysis of sequenced fragments among the three populations showed variation in average nucleotide frequencies of female and male RNs. Singletons within the female and male Hamilton populations ranged from 7.8% to 10%, and the variable sites ranged from 13.4% to 26%. However, female and male BelleMina populations had singletons ranging from 7.1% to 19.7% and variable regions in the range of 13.9% to 49.3%. The female and male Lamons populations had singletons ranging from 2.5% to 8.7% and variable regions in the range of 2.9% to 14.2%. Phylogenetic (neighbor-joining) analysis for the two ITS1 fragments (ITS-550 and ITS-730) showed relatively high intra-nematode variability. Different clone sequences from an individual nematode often had greater similarity with other nematodes than with their own sequences. RNA fold analysis of the ITS1 sequences revealed varied stem and loop structures, suggesting both conserved and variable regions in the variants identified from female and male RNs, thus underscoring the presence of significant intra- and inter-nematodal variation among RN populations in Alabama.

Project description:BackgroundChinese grass shrimp (Palaemonetes sinensis) is an important species widely distributed throughout China, which is ecologically relevant and possesses ornamental and economic value. These organisms have experienced a sharp decline in population due to overfishing. Therefore interest in P. sinensis aquaculture has risen in an effort to alleviate fishing pressure on wild populations. Therefore, we investigated the genetic diversity and variation of P. sinensis to verify the accuracy of previous research results, as well as to assess the risk of diversity decline in wild populations and provide data for artificial breeding.MethodsPalaemonetes sinensis specimens from seven locations were collected and their genetic variability was assessed based on mitochondrial COI gene segments. DNA sequence polymorphisms for each population were estimated using DNASP 6.12. The demographic history and genetic variation were evaluated using Arlequin 3.11. At last, the pairwise genetic distance (Ds) values and dendrograms were constructed with the MEGA 11 software package.ResultsOur study obtained sequences from 325 individuals, and 41 haplotypes were identified among the populations. The haplotype diversity (Hd) and nucleotide diversity (π) indices ranged from 0.244 ± 0.083 to 0.790 ± 0.048 and from 0.0004 ± 0.0001 to 0.0028 ± 0.0006, respectively. Haplotype network analyses identified haplotype Hap_1 as a potential maternal ancestral haplotype for the studied populations. AMOVA results indicated that genetic variations mainly occurred within populations (73.07%). Moreover, according to the maximum variation among groups (FCT), analysis of molecular variance using the optimal two-group scheme indicated that the maximum variation occurred among groups (53.36%). Neutrality and mismatch distribution tests suggested that P. sinensis underwent a recent population expansion. Consistent with the SAMOVA analysis and haplotype network analyses, the Ds and FST between the population pairs indicated that the JN population was distinctive from the others.ConclusionsOur study conducted a comprehensive characterization of seven wild P. sinensis populations, and our findings elucidated highly significant differences within populations. The JN population was differentiated from the other six populations, as a result of long-term geographical separation. Overall, the present study provided a valuable basis for the management of genetic resources and a better understanding of the ecology and evolution of this species.

Dataset Information

Molecular diversity of Scutellonema bradys populations from Benin, based on ITS1 rDNA and COI mtDNA.

Publications

Molecular diversity of <i>Scutellonema bradys</i> populations from Benin, based on ITS1 rDNA and COI mtDNA.

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