scholarly journals Genetic variability and population structure of Leucinodes orbonalis (Guenée), a severe insect pest of brinjal in India

2022 ◽  
Vol 43 (1) ◽  
pp. 59-65
Author(s):  
K.G. Padwal ◽  
◽  
S. Chakravarty ◽  
C.P. Srivastava ◽  
◽  
...  
Keyword(s):  
Genetic Variation ◽  
Insect Pest ◽  
Geographical Location ◽  
Pcr Amplification ◽  
Haplotype Network ◽  
Coi Gene ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Leucinodes Orbonalis ◽  
Coi Sequences

Aim: The present study was undertaken to provide valuable insights regarding population genetic structure of Leucinodes orbonalis from diverse agro-ecologies of India. Methodology: Molecular characterization of L. orbonalis populations collected from five major agro-climatic zones of India was carried out using mitochondrial cytochrome oxidase I (COI) gene. Collected specimens were subjected to DNA extractions, partial PCR amplification and sequencing of the target gene, and multiple sequence alignments. Results: The results showed very less diversity in the nucleotide positions of the COI sequences of 79 studied specimens, with a low number of segregating sites (30), nucleotide diversity (0.00438) and overall mean genetic distance (0.004 ± 0.001). The significant negative values of neutrality tests and unimodal mismatch distribution supported the demographic expansion theory in Indian L. orbonalis. Analysis of the molecular variance revealed that 93.13% of the genetic variation was within populations, and the variation among populations was only 6.87%. The pairwise genetic differentiation was also found to be low to moderate between most of the populations. Multiple haplotypes were recorded from all the populations, and both neighbour-joining tree as well as the haplotype network showed that clustering of the haplotypes was independent of the geographical location. Interpretation: Thus, it can be inferred that Indian populations of L. orbonalis have very low genetic variation levels concerning the COI gene. There is a possible occurrence of stable inherited gene flow among populations, thereby reducing genetic variation in India.

scholarly journals Molecular characterization of intraspecific variations in Helicoverpa armigera (Hübner) populations across India

2021 ◽  
Vol 42 (5) ◽  
pp. 1320-1329
Author(s):  
S. Chakravarty ◽  
◽  
K.G. Padwal ◽  
C.P. Srivastava ◽  
◽  
...  
Keyword(s):  
Helicoverpa Armigera ◽  
Sequence Data ◽  
Pcr Amplification ◽  
Haplotype Network ◽  
Coi Gene ◽  
Sequence Alignments ◽  
Separate Species ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Helicoverpa Armígera

Aim: The present study was undertaken to explore the genetic diversity among Helicoverpa armigera populations from varied geographic regions of India using mitochondrial cytochrome c oxidase I (COI) gene fragments. Methodology: The larval specimens of H. armigera collected from 20 locations were subjected to DNA extraction, PCR amplification of target gene, sequencing and then multiple sequence alignments. Results: Based on COI sequence data, high levels of genetic differentiation among some H. armigera populations were detected, but divergence existing was not high enough to delineate them as separate species. The Indian population as a whole exhibited similarity with global genetic assemblage. Significant negative neutrality test indices and unimodal mismatch distribution further supported that this insect experienced a demographic expansion in the past. The phylogenetic tree and median-joining haplotype network indicated that genetic similarity was not related with geographic proximity of populations. Interpretation: Differences based on genetic analyses indicate considerable subspecific level variations among H. armigera populations of India. However, there is no existence of any unidentified cryptic species of H. armigera in the country.

scholarly journals Molecular and Symptom Analysis Reveal the Presence of New Phytoplasmas Associated with Sugarcane Grassy Shoot Disease in India

Plant Disease ◽  
2007 ◽  
Vol 91 (11) ◽  
pp. 1413-1418 ◽  
Author(s):  
Kanchan Nasare ◽  
Amit Yadav ◽  
Anil K. Singh ◽  
K. B. Shivasharanappa ◽  
Y. S. Nerkar ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
Pcr Amplification ◽  
Saccharum Officinarum ◽  
23S Rrna ◽  
Rrna Gene ◽  
Sequence Alignments ◽  
High Sequence Similarity ◽  
Multiple Sequence ◽  
Very High

A total of 240 sugarcane (Saccharum officinarum) plants showing phenotypic symptoms of sugarcane grassy shoot (SCGS) disease were collected from three states of India, Maharashtra, Karnataka, and Uttar Pradesh. Phytoplasmas were detected in all symptomatic samples by the polymerase chain reaction (PCR) amplification of phytoplasma-specific 16S rRNA gene and 16S-23S rRNA spacer region (SR) sequences. No amplification was observed when DNA from asymptomatic plant samples was used as a template. Sixteen samples were selected on the basis of phenotypic symptoms and geographic location, and cloning and sequencing of the 16S rRNA and spacer regions were performed. Multiple sequence alignments of the 16S rRNA sequences revealed that they share very high sequence similarity with phytoplasmas of rice yellow dwarf, 16SrXI. However, the 16S-23S rRNA SR sequence analysis revealed that while the majority of phytoplasmas shared very high (>99%) sequence similarity with previously reported sugarcane phytoplasmas, two of them, namely BV2 (DQ380342) and VD7 (DQ380343), shared relatively low sequence similarity (79 and 84%, respectively). Therefore, these two phytoplasmas may be previously unreported ones that cause significant yield losses in sugarcane in India.

scholarly journals Primeiro registro de Rachiplusia nu (Guenée, 1852) (Lepidoptera: Noctuidae) sobrevivendo em soja Bt no Brasil

2021 ◽  
Vol 3 ◽  
pp. ec03028
Author(s):  
Adriana C. Nardon ◽  
Sandra M. Mathioni ◽  
Leandro V. dos Santos ◽  
Daniel D. Rosa
Keyword(s):  
Control Strategies ◽  
Insect Pest ◽  
Amplicon Sequencing ◽  
Management Control ◽  
Coi Gene ◽  
Sequencing Analysis ◽  
Crop Species ◽  
Soybean Leaf ◽  
Coi Sequences ◽  
Soybean Leaves

Loopers are important defoliators in several crop species. Among the loopers attacking non-Bt soybean cultivars, Chrysodeixis includens (Walker, [1858]) was the most common. The use of trangenic Bt soybean in appromately 70% of the soybean fields in Brazil led to a decrease in the loopers in these fields. However, technical field specialists and soybean producers recently observed Plusiinae larvae damaging transgenic Bt soybean, posing a risk over the Bt technology. Therefore, the aim of this study was to identify and confirm the catterpillar species feeding on transgenic Bt soybean fields in Brazil. Larvae and soybean leaf samples were collected in 12 soybean-producing locations from four Brazillian States. Soybean leaf samples were tested to confirm whether they were transgenic Bt. Larvae were reared in artificial diet and submitted to feeding trials on non-transgenic and transgenic Bt soybean leaves. The species identification was perfomed by amplicon sequencing of the cytochrome oxidase I (COI) gene of eight larvae per local. All 12 populations fed in the transgenic Bt soybean and the sequencing analysis of COI determined that they belong to Rachiplusia nu (Guenée, 1852) with 100% similarity to the COI sequences available in NCBI for this species. These results suggest that the R. nu species is not controlled by the genetic modification event present in the tested soybean variety and highlights the need for additional looper management control strategies, such as insecticide application, for controlling this insect pest in transgenic Bt soybean.

scholarly journals Establishment of Culex modestus in Belgium and a glance into the virome of Belgian mosquito species

2020 ◽  
Author(s):  
Lanjiao Wang ◽  
Ana Lucia Rosales Rosas ◽  
Lander De Coninck ◽  
Chenyan Shi ◽  
Johanna Bouckaert ◽  
...  
Keyword(s):  
Disease Transmission ◽  
Mosquito Species ◽  
Haplotype Network ◽  
Coi Gene ◽  
Relevant Role ◽  
Surveillance Programs ◽  
Belgian Population ◽  
Risk Of Disease ◽  
Coi Sequences ◽  
The Uk

AbstractCulex modestus is a mosquito species with a relevant role in the transmission of West Nile virus and Usutu virus. Its presence has been reported across Europe, yet it is absent in Belgium. Field mosquitoes in the city of Leuven and surroundings were collected in the summer of 2019 and 2020. Species identification was performed by morphological features and partial sequences of the mitochondrial cytochrome oxidase subunit 1 (COI) gene. In order to examine the genetic structure of the Cx. modestus population found in Leuven, mitochondrial sequences of Cx. modestus mosquitoes collected in other 8 countries across Europe were retrieved from GenBank and confronted to the COI sequences from Belgian mosquitoes to construct a haplotype network.Hereby, we confirmed the new establishment of Cx. modestus in the surroundings of Leuven, Belgium. Haplotype network analysis showed that the Belgian population is rather diverse, suggesting that it must have been establish in Belgium for some time. The Belgian population was most closely related to Cx. modestus populations from the UK and Germany. The NetoVIR protocol was used to study the virome of 8 pools of mosquitoes. At least 33 eukaryotic viral species were identified. Nine (near-)complete genomes belonging to 6 viral species were identified, named Culex totivirus Leu1, Leu2 and Leu3, Alphamesonivirus Leu4, Iflavirus Leu5 and Leu6, Negevirus Leu7 and Leu8, and Rhabdovirus Leu9, all of which were closely related to known viruses. In conclusion, with the introduction of Cx. modestus in Belgium, the evaluation of its potential role in the transmission of arboviruses that could cause disease in animals and humans is necessary.Importance for non-specialistCulex modestus is a mosquito species that plays a role in nature as a ‘bridge’ vector, being able to transmit pathogens between birds, as well as from birds to mammals, including humans. In Belgium, this species was considered absent. Field mosquitoes were collected in urban, peri-urban and wetland areas in the summer of 2019 and 2020 in Leuven, and morphological and molecular methods were performed to confirm the presence of Cx. modestus in this region. The ability of mosquitoes to transmit pathogens can depend on a lot of factors, one of them being the natural virus composition in their bodies. For this purpose, we aimed to identify the whole virus group harbored by Belgian mosquitoes. This could provide more insight for mosquito and, therefore, disease control. Besides, the introduction of Cx. modestus may increase the risk of disease transmission. It is advisable to implement mosquito surveillance programs monitoring this species.

scholarly journals Phylogeography of cliff racer (Platyceps rhodorachis Jan, 1865) from Punjab, Pakistan

2023 ◽  
Vol 83 ◽  
Author(s):  
S. Malik ◽  
A. Javid ◽  
Hamidullah ◽  
M. A. Iqbal ◽  
A. Hussain ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Species Identification ◽  
Dna Sequences ◽  
Large Scale ◽  
Coi Gene ◽  
Gene Sequences ◽  
Field Surveys ◽  
Coi Sequences

Abstract The present study reports the existence of cliff racer, Platyceps rhodorachis from the plains of Punjab, Pakistan. A total of 10 specimens were captured during the field surveys from June to September, 2018 from different sites of Punjab. Platyceps rhodorachis was identify on the basis of morphology and confirmed through COI gene sequences. The obtained DNA sequences have shown reliable and exact species identification. Newly produced DNA sequences of Platyceps rhodorachis were submitted to GenBank and accession numbers were obtained (MK936174.1, MK941839.1 and MT790210.1). N-J tree based on COI sequences of Platyceps rhodorachis clearly separated as out-group with other members of family Colubridae based on p-distance. The intra-specific genetic variation ranges from 12% to 18%. The DNA sequences of Platyceps rhodorachis kashmirensis, Platyceps rhodorachis ladacensis, Platyceps ventromaculatus, Platyceps ventromaculatus bengalensis and Platyceps ventromaculatus indusai are not available at NCBI to validate their taxonomic positions. In our recommendations, a large scale molecular based identification of Pakistan’s herpetofauna is required to report more new or subspecies from country.

scholarly journals Human Missense Variation is Constrained by Domain Structure and Highlights Functional and Pathogenic Residues

2017 ◽  
Author(s):  
Stuart A. MacGowan ◽  
Fábio Madeira ◽  
Thiago Britto-Borges ◽  
Melanie S. Schmittner ◽  
Christian Cole ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Prediction Models ◽  
Domain Architecture ◽  
Ring Finger ◽  
Missense Variant ◽  
Protein Domain ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Functional Studies ◽  
Pathogenic Variants

Human genome sequencing has generated population variant datasets containing millions of variants from hundreds of thousands of individuals1-3. The datasets show the genomic distribution of genetic variation to be influenced on genic and sub-genic scales by gene essentiality,1,4,5 protein domain architecture6 and the presence of genomic features such as splice donor/acceptor sites.2 However, the variant data are still too sparse to provide a comparative picture of genetic variation between individual protein residues in the proteome.1,6 Here, we overcome this sparsity for ∼25,000 human protein domains in 1,291 domain families by aggregating variants over equivalent positions (columns) in multiple sequence alignments of sequence-similar (paralagous) domains7,8. We then compare the resulting variation profiles from the human population to residue conservation across all species9 and find that the same tertiary structural and functional pressures that affect amino acid conservation during domain evolution constrain missense variant distributions. Thus, depletion of missense variants at a position implies that it is structurally or functionally important. We find such positions are enriched in known disease-associated variants (OR = 2.83, p ≈ 0) while positions that are both missense depleted and evolutionary conserved are further enriched in disease-associated variants (OR = 1.85, p = 3.3×10-17) compared to those that are only evolutionary conserved (OR = 1.29, p = 4.5×10-19). Unexpectedly, a subset of evolutionary Unconserved positions are Missense Depleted in human (UMD positions) and these are also enriched in pathogenic variants (OR = 1.74, p = 0.02). UMD positions are further differentiated from other unconserved residues in that they are enriched in ligand, DNA and protein binding interactions (OR = 1.59, p = 0.003), which suggests this stratification can identify functionally important positions. A different class of positions that are Conserved and Missense Enriched (CME) show an enrichment of ClinVar risk factor variants (OR = 2.27, p = 0.004). We illustrate these principles with the G-Protein Coupled Receptor (GPCR) family, Nuclear Receptor Ligand Binding Domain family and In Between Ring-Finger (IBR) domains and list a total of 343 UMD positions in 211 domain families. This study will have broad applications to: (a) providing focus for functional studies of specific proteins by mutagenesis; (b) refining pathogenicity prediction models; (c) highlighting which residue interactions to target when refining the specificity of small-molecule drugs.

scholarly journals Studies on DNA barcoding of sacred plant - Ficus religiosa L.

2016 ◽  
Vol 1 (1) ◽  
pp. 29
Author(s):  
D. Sivalingam ◽  
R. Rajendran ◽  
K. Anbarasan
Keyword(s):  
Dna Barcoding ◽  
Pcr Amplification ◽  
Evolutionary Trend ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Ficus Religiosa ◽  
Multiple Sequence Alignments ◽  
Ctab Method ◽  
Pcr Products ◽  
Study Species

In the present investigation, DNA barcoding were made for the sacred trees of Main (Big) Temples in Cuddalore district, namely Ficus religiosa, to document their reliable identification, discrimination, similarities and evolutionary trend among them and with their related taxa for future use.  DNA isolation from leaf samples of present study species was carried out by using a modified CTAB method and good isolation was got for the species studied. Gradient PCR amplification was performed for the isolated DNA using matK gene and the primers matK472F & matK1248R.  The amplification success was 90-95%. PCR amplification was tested with 1 % agarose gel electrophoresis using ethidium bromide and the products were confirmed.  The PCR products were sent to Xcelris Labs Ltd. Sydney House, Premchand Nagar Road, Bodakdev, Ahmedabad 380054, India, for DNA sequencing and sequences were got for the species with the success rate of 95 %.  Pairwise sequence alignments were made with BLAST and multiple sequence alignments are made with ClustalW, and based on the sequence alignments, dentrograms were constructed using software Mega 5 and Neighbor joining method to study the phylogenetic aspects of the species studied and with their related taxa.

scholarly journals Distribution of Two Strains of Leptoglossus zonatus (Dallas) (Hemiptera: Coreidae) in the Western Hemisphere: Is L. zonatus a Potential Invasive Species in California?

Insects ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1094
Author(s):  
Andrea L. Joyce ◽  
Hannah Parolini ◽  
Harry Brailovsky
Keyword(s):  
Nucleotide Diversity ◽  
Phylogenetic Analyses ◽  
Insect Pest ◽  
Haplotype Diversity ◽  
Haplotype Network ◽  
Western Hemisphere ◽  
Coi Gene ◽  
Mtdna Coi ◽  
New Genotype ◽  
Economic Pest

The leaffooted plant bug, Leptoglossus zonatus (Dallas) (Hemiptera: Coreidae) is polyphagous and widely distributed in the Western Hemisphere. Although it has been recorded in California since around 1900, it has become a more common pest in almonds in the last decade. Other studies have shown that an established insect can become a pest when a new genotype is introduced. This study investigated the distribution of two lineages (strains) of L. zonatus in the Western Hemisphere. Specimens from the Leptoglossus collection in the national insect collection in Mexico were used to extract DNA and sequence the mitochondrial DNA cytochrome oxidase I (mtDNA COI) gene, for use in population genetic and phylogenetic analyses. New sequences from Mexico, Central and South America were combined with those available in GenBank, from California and Brazil. Two lineages (strains) of L. zonatus were uncovered. One lineage occurs in California, Mexico and Ecuador. The second lineage is more widespread and found in California, Mexico, Guatemala, Nicaragua, Bolivia and Brazil. The haplotype number and diversity, and nucleotide diversity, were found for samples from California, Mexico, and Brazil, for the two lineages, and for all 118 sequences combined. All sequences combined produced five haplotypes, and a haplotype diversity of 0.54. California and Brazil had 3 haplotypes each, with one haplotype shared (5 total). Haplotype diversity in California and in Brazil were 0.526 and 0.505, respectively. A haplotype network found that one haplotype was most abundant and widespread. The small number of haplotypes, a range expansion, and economic pest status of L. zonatus in California, all contribute to this insect being a potentially invasive insect pest.

scholarly journals Genetic Diversity Analysis of Cultivated Kappaphycus in Indonesian Seaweed Farms using COI Gene

2020 ◽  
Vol 15 (2) ◽  
pp. 65
Author(s):  
Pustika Ratnawati ◽  
Nova F Simatupang ◽  
Petrus R Pong-Masak ◽  
Nicholas A Paul ◽  
Giuseppe C Zuccarello
Keyword(s):  
Genetic Variation ◽  
Kappaphycus Alvarezii ◽  
Coi Gene ◽  
Morphological Examination ◽  
Bottom Line ◽  
Yield And Quality ◽  
Major Player ◽  
Coi Sequences ◽  
Trade Names ◽  
Prime End

Indonesia is a major player in the aquaculture of red algae, especially carrageenan producing ‘eucheumatoids’ such as Kappaphycus and Eucheuma. However, many current trade names do not reflect the evolutionary species and updated taxonomy, this is especially the case for eucheumatoid seaweeds that are highly variable in morphology and pigmentation. Genetic variation is also not known for the cultivated eucheumatoids in Indonesia. Therefore, this study aimed to determine the species and the level of genetic variation within species of cultivated eucheumatoids from various farms across Indonesia, spanning 150-1500 km, using the DNA barcoding method. Samples of seaweed were randomly collected at 14 farmed locations between April 2017 and May 2018. For this study the 5-prime end (~ 600 bp) of the mitochondrial-encoded cytochrome oxidase subunit one (COI) was amplified and sequenced. Morphological examination showed that the samples were quite variable in branching pattern and color. All samples collected from farms with floating line cultivation were identified based on COI sequences as Kappaphycus alvarezii and showed no variation in the COI gene. One farm sample with bottom-line cultivation was identified as K. striatus. The low genetic variation is in contrast to the phenotypic variation of samples, indicating that variation and phenotypic responses to environments is still found in samples with implications for growth rates and carrageenan yield and quality. Information about the genetic variation in stocks is important base knowledge for maintaining, expanding and continuing seaweed aquaculture.

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