A multiplex PCR method for identification of two common true cutworm species (Lepidoptera: Noctuidae) tested in the central plain of Guilan province, Iran

Many species of cutworms (Lepidoptera: Noctuidae) are important agricultural pest. They feed on roots and foliage of their host plants. Traditionally these species are identified based on morphological characteristics of adults. Hence identification of specimens in poor condition, immature stages and also closely related species or cryptic species is a difficult task. The basics of biological and ecological studies largely rely on an accurate species identification; consequently these investigations are impacted by potential misidentifications. In this study, we amplified 5' region of mitochondrial c cytochrome oxidase subunit I (COI) gene (DNA barcode region) of various common true cutworm species including Agrotis ipsilon (Hufnagel, 1766), Agrotis exclamationis (Linnaeus, 1758), Peridroma saucia (Hübner, 1808) and Xestia c-nigrum (Linnaeus, 1758) from agricultural fields of Guilan province (North of Iran). We were able to detect 66 conservative Single Nucleotide Polymorphisms (SNPs) among the targeted pest species and eventually design specific primers and develop a multiplex polymerase chain reaction assay as a molecular diagnostic tool for immature stages of two the most common and abundant species including A. ipsilon and X. c-nigrum in Guilan province.

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Potential natural enemies of the invasive rugose spiraling whitefly, Aleurodicus rugioperculatus Martin in India

Journal of Biological Control ◽

10.18311/jbc/0/15598 ◽

2017 ◽

Vol 30 (4) ◽

pp. 236 ◽

Cited By ~ 2

Author(s):

K. Selvaraj ◽

R. Sundararaj ◽

T. Venkatesan ◽

Chandish R. Ballal ◽

S. K. Jalali ◽

...

Keyword(s):

Natural Enemies ◽

Tamil Nadu ◽

Ornamental Plants ◽

Coi Gene ◽

Molecular Diagnostic ◽

Pest Species ◽

Molecular Tools ◽

Accession Number ◽

Custard Apple ◽

First Time

A invasive rugose spiraling whitefly (RSW) Aleurodicus rugioperculatus Martin (Hemiptera: Aleyrodidae) was found infesting coconut, banana, custard apple and several ornamental plants in Tamil Nadu, Andhra Pradesh and Kerala for the first time in India. The identity of the pest species was determined through morphological and molecular tools. Furthermore cytochrome c oxidase-I gene (658 bp) of RSW was sequenced (GenBank accession number KY209909) which would serve as an ideal molecular diagnostic marker for its identification irrespective of its phenotypic plasticity. During the survey, several natural enemies were recorded and maximum parasitism was recorded by Encarsia guadeloupae Viggiani (Hymenoptera: Aphelinidae) and its COI gene was sequenced and deposited as Encarsia sp. (GenBank accession number KY223606). Per cent parasitism ranged from 20.0 to 60.0 % in different collection locations, highest parasitism being recorded in Kerala as compared to other states. The predators recorded were Mallada sp., few coccinellids and predatory mites. This communication is the first report of the rugose spiraling whitefly, its host plant range and associated natural enemies in India.

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DNA barcode for identification of immature stages of sand flies (Diptera: Psychodidae) collected from natural breeding sites

Zootaxa ◽

10.11646/zootaxa.4277.2.3 ◽

2017 ◽

Vol 4277 (2) ◽

pp. 228 ◽

Cited By ~ 7

Author(s):

RAFAEL JOSÉ VIVERO ◽

EDUAR ELÍAS BEJARANO ◽

LUIS GREGORIO ESTRADA ◽

FERNANDO FLÓREZ ◽

EDGAR ORTEGA-GÓMEZ ◽

...

Keyword(s):

Dna Barcode ◽

Species Level ◽

Coi Gene ◽

Bootstrap Support ◽

Sand Flies ◽

Immature Stages ◽

Phlebotomine Sand Flies ◽

Breeding Sites ◽

Natural Breeding ◽

Taxonomic Studies

Although phlebotomine sand flies breeding sites have been identified and recorded by several studies, the microhabitats exploited by these insects remain little-known and hard to find. In this context, the difficulty of finding immature stages, and the limited number of taxonomic studies to identify immature stages of phlebotomine sand flies, are considered the major obstacles when attempting a complete inventory of Lutzomyia species. The objective of this study is to validate Cytochrome Oxidase I (Barcode region) as a marker for the identification of immature stages of Lutzomyia species recovered from natural breeding sites in Colombia. Among 142 collected sand flies, 18 immature individuals that did not complete their life cycle were identified to species level through sequencing of the COI gene. Values of K2P genetic distance between 0.002–0.031 allowed the identification of larvae at species level. The bootstrap support values (96%) in the Neighbor-Joining dendrogram were consistent for the majority of the established MOTUS of Lutzomyia atroclavata, Lutzomyia micropyga, Lutzomyia serrana, Lutzomyia cayennensis, Lutzomyia rangeliana, Lutzomyia shannoni and some species of the genus Brumptomyia. The COI gene is validated as a marker for the identification of immature stages of the genus Lutzomyia.

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DNA barcoding to resolve the confusion in identifying Tribolium confusum and Tribolium castaneum

Bangladesh Journal of Zoology ◽

10.3329/bjz.v47i2.44344 ◽

2019 ◽

Vol 47 (2) ◽

pp. 333-342

Author(s):

Abu Faiz Md Aslam ◽

Sharmin Sultana ◽

Sumita Rani Das ◽

Abdul Jabber Howlader

Keyword(s):

Dna Barcoding ◽

Tribolium Castaneum ◽

Life Stage ◽

Dna Barcode ◽

Tribolium Confusum ◽

Likelihood Method ◽

Coi Gene ◽

Pest Species ◽

Stored Grain ◽

Accurate Identification

Tribolium confusum and Tribolium castaneum (Coleoptera: Tenebrionidae) are two very confusing pest species while identification is done on the basis of morphology only. Such pests are discovered in stored grain as immature stages, which further complicates the identification process. Accurate identification of these pests is urgently required for integrated pest management. In this research, DNA barcoding was used to identify these pests accurately at any life stage. A 658 bp fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene was analyzed. DNA barcode dataset of T. confusum (GeneBank Acc. no. MK120453.1) and T. castaneum (Acc. no. MK411585.1) were constructed. The nucleotide composition reveals that average AT contents (59.9%) were higher than the GC contents (38.6%). Phylogenetic analysis by maximum likelihood method showed that both the species were originated from a common major clade. About 17.13% nucleotide differences were noted between the CO1 sequences by multiple sequence alignment. The interspecies nucleotide genetic distance (0.200) was calculated using Kimura 2 parameter. Haplotype analysis showed high genetic diversity (112 mutaional steps) among them. Bangladesh J. Zool. 47(2): 333-342, 2019

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Molecular characterization and identification of three stored grain pests based on mitochondrial cytochrome C oxidase subunit I (COI) gene sequences

Bangladesh Journal of Zoology ◽

10.3329/bjz.v47i1.42016 ◽

2019 ◽

Vol 47 (1) ◽

pp. 1-11

Author(s):

Abu Faiz Md Aslam ◽

Sharmin Sultana ◽

Faria Farhana Rain ◽

Sumita Rani Das ◽

Ayesha Siddika ◽

...

Keyword(s):

Insect Pests ◽

Sitophilus Oryzae ◽

Dna Barcode ◽

Control Measures ◽

Coi Gene ◽

Composition Analysis ◽

Callosobruchus Chinensis ◽

Pest Species ◽

Stored Grain ◽

Stored Grain Pests

Stored grain pests are discovered in food as immature stages, which further complicates the identification process. A DNA barcode dataset of some important pests that can be used for easy and confirm identification in stages of life is constructed. COI genes of three stored grain insect pests i.e,, Sitophilus oryzae, Callosobruchus chinensis and Oryzaephilus surinamensis were sequenced. The sequenced genes were submitted to NCBI GenBank and obtained accession numbers MG967331.1, MG967332.1, MG967333.1 and MK041216.1. BLAST analysis showed 99 to 100% homology with existing GenBank sequences. The nucleotide composition analysis revealed that the value of A+T (64.8%) is greater than G+C (35.2%). Genetic distance among four sequences of three store pests were ranged from 0.00293-0.32807. Phylogenetic analysis showed that these three species are originated from different clades. Haplotype analysis of mitochondrial COI gene of the stored grain insect pests showed high genetic diversity among them. C. chinensis, O. surinamensis and S. oryzae were separated from their common ancestor by 80, 73 and 64 mutational steps. These information may be helpful for attempting any successful control measures against the pest species. In conclusion, present author established the first DNA barcode dataset of three store grain pests and confirmed its efficiency for identifying these pests. Bangladesh J. Zool. 47(1): 1-11, 2019

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DNA barcoding of razor clam Solen spp. (Solinidae, Bivalva) in Indonesian beaches

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d210207 ◽

2020 ◽

Vol 21 (2) ◽

Author(s):

Ninis trisyani Margono ◽

DWI ANGGOROWATI RAHAYU

Keyword(s):

Phylogenetic Analysis ◽

Genetic Distance ◽

Dna Barcoding ◽

Dna Barcode ◽

Morphological Characteristics ◽

Wide Distribution ◽

Coi Gene ◽

Razor Clam ◽

Molecular Phylogenetic ◽

Solen Grandis

Abstract. Trisyani N, Rahayu DA. 2020. DNA barcoding of razor clam Solen spp. (Solinidae, Bivalva) in Indonesian beaches. Biodiversitas 21: 478-484. Solen spp. are shells with various morphological characteristics with a wide distribution of tropical and subtropical beaches, including Indonesia. The identification of Solen spp. is generally based on its morphological characteristics. This method is very problematic due to specimens share similarity in morphology and color. This study was using DNA barcode as a molecular identification tool. The bivalve COI sequence was amplified using PCR and molecular phylogenetic analysis using the Neighbor-Joining method. The amplified COI gene has a length of about 665 bp. The purpose of this study was to evaluate genetic variation and compare the phylogenetic Solen spp. in Indonesian waters. The composition of the nucleotide bases of Solen spp. the comparative species are A = 26.79%, C = 23.16%, G = 19.17% and T = 30.93%. The total nucleotide base A + T was 57.72%, while G + C was 42.33%. The results of phylogenetic analysis showed that Solen spp. Cirebon and Jambi are in one clade with Solen regularis with genetic distance 0.000 - 0.002. Solen spp. Surabaya, Bangkalan, Pamekasan, and Sumenep are in separate clades and are related to Solen grandis, Solen stricus and Solen lamarckii with genetic distance from 0.146 - 0.156. The diversity of nucleotide was 0.9780 and was divided into 12 haplotypes.

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Identification of Neoceratitis asiatica (Becker) (Diptera: Tephritidae) based on morphological characteristics and DNA barcode

Zootaxa ◽

10.11646/zootaxa.4363.4.7 ◽

2017 ◽

Vol 4363 (4) ◽

pp. 553

Author(s):

SHAOKUN GUO ◽

JIA HE ◽

ZIHUA ZHAO ◽

LIJUN LIU ◽

LIYUAN GAO ◽

...

Keyword(s):

Dna Sequences ◽

Phylogenetic Trees ◽

Gap Analysis ◽

Dna Barcode ◽

Morphological Characteristics ◽

Coi Gene ◽

Economic Losses ◽

Morphological Identification ◽

Lycium Barbarum ◽

Accurate Identification

Neoceratitis asiatica (Becker), which especially infests wolfberry (Lycium barbarum L.), could cause serious economic losses every year in China, especially to organic wolfberry production. In some important wolfberry plantings, it is difficult and time-consuming to rear the larvae or pupae to adults for morphological identification. Molecular identification based on DNA barcode is a solution to the problem. In this study, 15 samples were collected from Ningxia, China. Among them, five adults were identified according to their morphological characteristics. The utility of mitochondrial DNA (mtDNA) cytochrome c oxidase I (COI) gene sequence as DNA barcode in distinguishing N. asiatica was evaluated by analysing Kimura 2-parameter distances and phylogenetic trees. There were significant differences between intra-specific and inter-specific genetic distances according to the barcoding gap analysis. The uncertain larval and pupal samples were within the same cluster as N. asiatica adults and formed sister cluster to N. cyanescens. A combination of morphological and molecular methods enabled accurate identification of N. asiatica. This is the first study using DNA barcode to identify N. asiatica and the obtained DNA sequences will be added to the DNA barcode database.

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DNA barcodes and reliable molecular identifications in a diverse group of invasive pests: lessons from Bactrocera fruit flies on variation across the COI gene, introgression, and standardization

10.1101/2020.11.23.394510 ◽

2020 ◽

Author(s):

Camiel Doorenweerd ◽

Michael San Jose ◽

Luc Leblanc ◽

Norman Barr ◽

Scott Geib ◽

...

Keyword(s):

Animal Species ◽

Sequence Data ◽

Dna Barcode ◽

Fruit Fly ◽

Coi Gene ◽

Pest Species ◽

Base Pairs ◽

Invasive Pests ◽

Population Sampling ◽

Species Complexes

AbstractThe utility of a universal DNA ‘barcode’ fragment of 658 base pairs of the Cytochrome C Oxidase I (COI) gene for the recognition of all animal species has been a widely debated topic on theoretical and practical levels. Regardless of its challenges, large amounts of COI sequence data have been produced in the last two decades. To optimally use the data towards reliable species identification will require further steps to validate the method and reference libraries. The fruit fly tribe Dacini holds about a thousand species, of which eighty are pests of economic concern, including some of the world’s foremost fruit and vegetable pests, and there are many morphologically cryptic species complexes in the tribe. Where previous studies showed limited success in using COI to identify Dacini, our results with a highly curated morphological dataset indicate high congruence between morphology and COI: 90% of the species in our 5,576 sequences, 262-species global dataset can be identified with COI alone based on a monophyly criterion. However, in some key pest species belonging to complexes that were previously thought diagnosable with COI, we found that expanded sampling and independent validation of identifications using genomic data revealed introgression of mitochondrial DNA. We find that the informative SNPs are uniformly distributed across the COI gene, and we provide recommendations for standardization. We conclude that reliable molecular identifications with COI require extensive species coverage, population sampling, and genomics-supported reference identifications before they can be validated as a “diagnostic” marker for specific groups.

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Potential natural enemies of the invasive rugose spiraling whitefly, Aleurodicus rugioperculatus Martin in India

Journal of Biological Control ◽

10.18311/jbc/2016/15598 ◽

2017 ◽

Vol 30 (4) ◽

pp. 236

Author(s):

K. Selvaraj ◽

R. Sundararaj ◽

T. Venkatesan ◽

Chandish R. Ballal ◽

S. K. Jalali ◽

...

Keyword(s):

Natural Enemies ◽

Tamil Nadu ◽

Ornamental Plants ◽

Coi Gene ◽

Molecular Diagnostic ◽

Pest Species ◽

Molecular Tools ◽

Accession Number ◽

Custard Apple ◽

First Time

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Redescription of immature stages of the soybean looper (Lepidoptera: Noctuidae: Plusiinae)

The Canadian Entomologist ◽

10.4039/tce.2015.62 ◽

2015 ◽

Vol 148 (3) ◽

pp. 247-259 ◽

Cited By ~ 4

Author(s):

Maria J. Barrionuevo ◽

German San Blas

Keyword(s):

Economic Value ◽

Western Hemisphere ◽

Correct Identification ◽

Pest Species ◽

Immature Stages ◽

Preimaginal Stages ◽

Control Procedures ◽

Plant Families ◽

Lepidoptera Noctuidae ◽

Chrysodeixis Includens

AbstractChrysodeixis includens (Walker) is a characteristic Plusiinae (Lepidoptera: Noctuidae) species from the Western Hemisphere. The larva have already been found feeding on several different plant families, including economic value crops such as soybeans. This species coexists and can be confused with Rachiplusia nu (Guenée) (Lepidoptera: Noctuidae) in soybean crops. Furthermore, some studies indicate that C. includens shows tolerance to various insecticides, leading to differentiation among these two species to be most important in relation to control procedures to be undertaken. To contribute to the correct identification of C. includens we made detailed redescriptions of all preimaginal stages (egg, larva, and pupa). Immature stages of C. includens were reared in laboratory under controlled conditions of 27±2 °C, 70–75% relative humidity, and 14:10 (light/dark) photoperiod. We consider opportune detection of preimaginal stages of Chrysodeixis includens will help to control this pest species, especially at admissible economical levels.

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COLD TOLERANCE OF PSEUDALETIA UNIPUNCTA AND PERIDROMA SAUCIA (LEPIDOPTERA: NOCTUIDAE)

The Canadian Entomologist ◽

10.4039/ent1171055-8 ◽

1985 ◽

Vol 117 (8) ◽

pp. 1055-1060 ◽

Cited By ~ 8

Author(s):

G.L. Ayre

Keyword(s):

Cold Tolerance ◽

Genetic Differences ◽

Immature Stages ◽

Egg Survival ◽

Pseudaletia Unipuncta ◽

Canadian Prairies ◽

Peridroma Saucia ◽

Larval Stages ◽

Cold Tolerant ◽

Lepidoptera Noctuidae

AbstractPupae and 3rd-instar larvae of Pseudaletia unipuncta (Haw.) survived longer at 0 and −2°C than other immature stages, and insects reared at 15°C were more cold tolerant than those reared at 20°C. Egg survival at 0°C varied greatly among replicates suggesting genetic differences among females. No adults survived 2 weeks at 0°C. Peridroma saucia (Hub.) would not rear satisfactorily at 15°C and, other than eggs, all stages tested were from rearings at 20°C. Eggs from adults at 15°C were more cold tolerant than those from adults at 20°C. There were no differences in survival among any of the larval stages or pupae. Some adults survived 6 weeks at 0°C. No stage of either species survived over 8 weeks at 0°C nor 4 weeks at −2°C indicating that overwintering on the Canadian prairies is unlikely.

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