mtCOI Sequences Research Articles

Genetic Characterization of the Co-Invasive Rodent Parasite Heterakis spumosa (Nematoda, Heterakidae).

Heterakis spumosa, a parasitic worm infecting rodents, is globally prevalent in black rats, brown rats, and house mice. It is hypothesized to originate from Asia due to its widespread presence in Southeast Asia in various Murinae. Previous molecular studies focused on European, African, and Japanese specimens, but none included samples from the putative native range. Rodents were collected between 2008 and 2015 across various localities in Southeast Asia and Europe, identified by morphology or genetic barcoding. Viscera were examined or preserved for later inspection. DNA was extracted from H. spumosa. PCR amplification targeting the mtCOI gene and ITS1 region was conducted in this study using newly designed primers (based on Heterakis reference sequences). PCR amplicons were subsequently sequenced and analyzed. In this study, the phylogenetic analysis using ITS1 sequences revealed that Heterakis samples from Thai and Laotian rodents belong to the species H. spumosa, exhibiting low genetic variation compared to samples from other regions. Genetic distance calculations using mtCOI sequences confirmed the marked distinction of H. spumosa from other Heterakis species. Our phylogenetic analyses using partial mtCOI and ITS1 sequences have significantly enhanced our comprehension of the genetic diversity and evolutionary history of the nematode H. spumosa.

Prevalence of strain (R and C strains) of fall armywormSpodoptera frugiperda in eastern India

An invasive alien pest, fall armyworm has been recently introduced to India. To date, two strains of FAW have been documented, viz. R strain (rice) and C strain (corn) without any clear biological attributes, even though differences are evident. A survey was conducted during 2020–22 over 18 field visits across the eastern part of India (Bihar, West Bengal, Orissa and Jharkhand) to isolate the genetic diversification of FAW populations collected from maize. This investigation was done with a mitochondrial-based ‘universal primer’ using mtCOI (mitochondrial cytochrome c oxidase subunit I) sequence analyses revealed that both strains (R strain and C strain) were present with the FAW. Interestingly, our comprehensive analysis indicates the dominance of the R strain over the C strain in the sample collected from the eastern part of India. This would be the first report from the eastern part of India, mainly the regions of Bihar, West Bengal, Orissa and Jharkhand, where FAW primarily feeds on maize. This study generates an idea about a probable incursion by a genetic asset of FAW in India, which needs dissection of the haplotype.

Reconstructed phylogeny -glimpses of polyphyly of the micro-copepod genus Oncaea- (crustacea, copepoda: cyclopoida, family: oncaeidae) using mtCOI sequences substantiated by morphology

Reconstructed phylogeny -glimpses of polyphyly of the micro-copepod genus Oncaea- (crustacea, copepoda: cyclopoida, family: oncaeidae) using mtCOI sequences substantiated by morphology

First DNA barcoding-based record of Lysiosquilla maculata (Crustacea: Stomatopoda) from Chennai coast, Tamil Nadu, India

The taxonomic identification of mantis shrimp Lysiosquilla maculata was performed through DNA barcoding analysis of specimens collected from the Kasimedu fishing port, Chennai coast, Tamil Nadu, India. The mitochondrial cytochrome oxidase subunit I (mtCOI) gene with a region of 650 bp was sequenced for phylogenetic analysis. In the present record, mitochondrial gene sequences were used to identify the mantis shrimp. This is the first confirmed DNA barcoding record from Indian waters, whose mtCOI sequence was deposited in GenBank. The Neighbor-joining method was used for phylogenetic analysis. The calculated pairwise genetic distance with five closely related species ranged from 0.01 to 0.094%. The morphological and molecular analysis confirm that the specimens collected correspond to L. maculata.

Genetics, Age Demographics, and Shell Size of Atlantic Surfclams from the Southern Edge of Their Range

The Atlantic surfclam (Spisula solidissima solidissima) is an economically valuable clam species that supports a major US fishery. Until recently, fishery efforts along the southern edge of the surfclam range were low due to clam mortalities there in the 1990s. Recent surfclam fishing efforts off Virginia raised questions of whether the surfclam population has returned in the southern region or if a single cohort is supporting the fishery there. Questions have also arisen about whether S. s. similis is among the population fished off the coast of VA. Spisula solidissima similis is a warm-water cryptic subspecies of the Atlantic surfclam. Although morphologically indistinguishable, S. s. similis grows to a smaller size and is genetically distinct. Atlantic surfclams (n = 103) were collected from the fishing grounds off the coast of VA. Each surfclam was aged, and shell length and tissue weight recorded for comparison to surfclams of the same age from the center of the population. Analyses of mitochondrial (mtCOI) sequences suggests that the two groups sampled off VA are genetically homogeneous, both groups contain two divergent mitochondrial lineages, and one surfclam sampled shares the S. s. similis mtCOI sequence. There are multiple cohorts of surfclams, suggesting that environmental conditions may have improved for surfclams in the south, or that this population has acclimated to altered conditions. Further research should investigate the potential for subspecies hybridization.

Indian record of the old-world psyllid Heterotrioza chenopodii (Reuter) (Hemiptera, Psylloidea, Triozidae) on quinoa Chenopodium quinoa (Amaranthaceae)

The Old-World Psyllid, Heterotrioza chenopodii (Hemiptera, Psylloidea, Triozidae) was found infesting quinoa, Chenopodium quinoa (Amaranthaceae) crop. The psyllids were identified using taxonomic traits and further confirmation with mitochondrial marker based molecular approach. The information on damage and its life stages is reported along with the phylogenetic information of the species. The identity, analysis in NCBI indicated that the MT-COI sequences of H. chenopodii were 96 per cent identical to the previously deposited sequences with NCBI and five submissions with accession numbers were made viz., OP735496, OP740826, OP740828, OP740829 and OP740830. The phylogenetic tree represented the similarities in the analyzed sequences Indian populations are found to be merged in between the other similar global populations.

The cotton mealybug Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae) is spreading in North Africa: first report in Tunisia

ABSTRACT Biological invasions by alien agricultural insect pests represent nowadays a major threat to the durability of agricultural systems. In this study, we report for the first time the presence of an invasive economic pest of ornamental and solanaceous crops in Tunisia: the cotton mealybug, Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae). It is native to America and has been spreading in Asia and the Mediterranean Basin. It was found in autumn 2021 forming dense colonies on Lantana camara L. (Verbenaceae) used for ornamental purposes in urban parks in the governorate of Tunis and on tomato Lycopersicon esculentum Mill. (Solanaceae) protected crops in the governorate of Sousse. Phenacoccus solenopsis was identified using an integrative approach based on morphological features and molecular analysis. Phylogenetic analysis using the mitochondrial Cytochrome Oxidase I (mtCOI) sequences of P. solenopsis populations from native and invaded areas retrieved in GenBank showed that Tunisian specimens might derive from an Asian population. We found that Nephus quadrimaculatus Herbst (Coleoptera: Coccinellidae: Scymninae) is the only natural enemy associated with this newly introduced pest so far. This is the first report of P. solenopsis attacking Lantana and tomato plants in Tunisia, and it should be considered as a potential threat to associated crops.

Molecular signatures and diagnostic nucleotides for the fishes of the tropical brackish water lake in South Asia for conservation and management

The Pulicat Lake habitat is one of the most productive and precious ecosystems in India. This study aimed to develop the species-specific molecular signatures and determine the phylogenetic relationship of fish species distributed in the Pulicat Lake. In the present study, a data set of 1008 mtCOI sequences was obtained from the published resources and used to screen character-based molecular diagnostic keys for species in silico. DNA barcodes were generated from 29 fish species fish representing 7 orders, 28 genera, and 21 families. Species-specific probes with a length range of 18–32 bp were designed on the basis of identified diagnostic nucleotide sites. The probes, developed in this study, could be used to develop DNA chips to identify fish species more quickly and accurately. The developed molecular signatures in this study will be helpful in the effective fishery management of these fish genetic resources.

Description of a new species of the genus Xyrosaris Meyrick (Lepidoptera: Yponomeutidae) from the Far East of Russia with notes on congeneric species.

A new species, Xyrosaris insularis sp. n., was found in the Far East of Russia. Most of the specimens were obtained through the rearing of larvae that fed on Celastrus orbiculatus Thunb. (Celastraceae). The genetic distances between the mtCOI sequences in X. insularis and congeneric species are in the range 1.2-13.9%. Minimal genetic distance (1.2%) was discovered between new species and X. lichneuta Meyrick from Shaanxi (China), which is lower than the standard mtCOI barcoding threshold of 2% for species delineation, but both taxa differ well in the genital morphology. The description of a new species is accompanied by illustrations of variations in the pattern, by the genitalia of both sexes, and by larva on its host plant.

Mitochondrial DNA Corroborates the Genetic Variability of Clarias Catfishes (Siluriformes, Clariidae) from Cameroon.

The airbreathing walking catfish (Clariidae: Clarias) comprises 32 species that are endemic to African freshwater systems. The species-level identification of this group is challenging due to their complex taxonomy and polymorphism. Prior to this study, the biological and ecological studies were restricted to a single species, Clarias gariepinus, resulting in a biased view of their genetic diversity in African waters. Here, we generated the 63-mitochondrial Cytochrome c oxidase subunit 1 (COI) gene sequences of Clarias camerunensis and Clarias gariepinus from the Nyong River in Cameroon. Both C. camerunensis and C. gariepinus species maintained adequate intra-species (2.7% and 2.31%) and inter-species (6.9% to 16.8% and 11.4% to 15.1%) genetic distances with other Clarias congeners distributed in African and Asian/Southeast Asian drainages. The mtCOI sequences revealed 13 and 20 unique haplotypes of C. camerunensis and C. gariepinus, respectively. The TCS networks revealed distinct haplotypes of C. camerunensis and shared haplotypes of C. gariepinus in African waters. The multiple species delimitation approaches (ABGD and PTP) revealed a total of 20 and 22 molecular operational taxonomic units (MOTUs), respectively. Among the two Clarias species examined, we found more than one MOTU in C. camerunensis, which is consistent with population structure and tree topology results. The phylogeny generated through Bayesian Inference analysis clearly separated C. camerunensis and C. gariepinus from other Clarias species with high posterior probability supports. The present study elucidates the occurrence of possible cryptic diversity and allopatric speciation of C. camerunensis in African drainages. Further, the present study confirms the reduced genetic diversity of C. gariepinus across its native and introduced range, which might have been induced by unscientific aquaculture practices. The study recommends a similar approach to the same and related species from different river basins to illuminate the true diversity of Clarias species in Africa and other countries.

Meloidogyne paramali n. sp. (Nematoda: Meloidogyninae) and First Report of M. marylandi in maple and yacca tree from Japan.

Meloidogyne paramali n. sp. was detected from Japanese maple trees (Acer palmatum) from Chiba, Japan during quarantine inspections in China. This species is characterized by second-stage juveniles (J2) with short tail length 32.2 (24-36.8) μm, finely rounded to broadly pointed tail terminus with extremely short hyaline tail terminus 4.3 (3.0-4.9) μm; perineal patterns of females characterized by an oval or irregular appearance, with round and low dorsal arch, and fine and smooth striae. M. paramali n. sp. is very similar to M. mali in that the perineal pattern has fine, smooth striae and both J2 have a short tail, but it can be distinguished from the latter by perineal pattern of the female (lateral field distinct vs. indistinct), shorter J2 hyaline tail terminus (4.3 [3.0-4.9] μm vs. 8.2 [4.8-12.7] μm, and by J2 tail with finely rounded to broadly pointed tail terminus, never sharply pointed vs. finely rounded and almost pointed. The polytomous key codes of the new species are as follows: Female: A21, B2, C32, D4; Male: A21, B3, C2, D1, E2, F2; J2: A2, B23, C43, D34, E12, F34. Detailed phylogenetic analysis based on partial 18S, ITS, D2-D3 28S, and partial mtCOI sequences also confirmed it as a new species, which is very close to M. mali and M. vitis and forms molecular group VIII. M. marylandi and other Meloidogyne species detected from plants from Japan in China are also discussed.

Four New Species of the Genus Eoneureclipsis (Trichoptera: Psychomyiidae) from China Inferred from Morphology and DNA Barcodes.

Four new species of the genus Eoneureclipsis Kimmins, 1955 from China are described, illustrated, and diagnosed based on male genitalia: Eoneureclipsis jianfenglingensis sp. nov. from Hainan, E. foraminulatus sp. nov. from Guangxi, E. spinosus sp. nov. from Guangxi and Guangdong, and E. gei sp. nov. from Fujian. A dichotomous key to Chinese adult males of Eoneureclipsis is provided. A distribution map for all Eoneureclipsis species is also presented. The DNA barcodes (partial mtCOI sequences) of E. jianfenglingensis sp. nov., E. gei sp. nov., and E. hainanensis Mey, 2013 have been generated and compared with all existing sequences of Eoneureclipsis species.

Morphological and molecular characterisation of Trachactinolaimus nanjingensis n. sp. (Dorylaimida: Actinolaimidae) from Nanjing, China

Summary Trachactinolaimus nanjingensis n. sp. isolated from mosses at the Yangshan Quarry Park in Nanjing, P.R. China, is described. It is characterised by 3.01 (2.64-3.42) mm long female and 2.84 (2.50-3.22) mm long male, four onchia with numerous mural denticles (>100), vulva with a transverse slit, 15-19 contiguous ventromedian supplements, spicules length of 61.5 (54.6-64.3) μm, and female and male both having long tail, with c′ values equal to 5.0-9.2 and 2.3-3.5, respectively. The new species was morphologically compared with T. brevicaudatus, T. dominicus, T. montanus and T. radulatus. The sequences of 18S and 28S rRNA genes of the new species were obtained using regular PCR amplification, while the ITS and mtCOI sequences were extracted from the whole genome sequencing assembly. The phylogenetic relationships of the new species were reconstructed using 18S and 28S sequences and the status of the new species was discussed. The 18S and 28S sequences of a population of genus Westindicus recovered during the present study were also obtained. This is the first time to present the ITS and mtCOI sequences of family Actinolaimidae.

A method for DNA extraction and molecular identification of Aphids

Aphid species (Insecta, Hemiptera) are economically important invasive pest throughout the world, though their identification is intricate due to tiny size and inconspicuous nature of morphology. Mitochondrial cytochrome c oxidase I (mtCOI) region has been proven to be a standard barcode to identify the diverse array of insect groups. Isolation of good quality DNA is a fundamental first step in insect DNA barcoding which is obtained by standardizing the DNA isolation method. In this study, we demonstrate a modified CTAB method for the isolation of DNA to maximize the quality and yield from small aphids. This method will help the researchers to efficiently isolate DNA from small aphid and the method can be utilized for other small insects as well. We evaluated the quality of the isolated DNA and the mtCOI gene region were subjected to PCR amplification. Further, the gene segment was sequenced and gene annotation was done by NCBI BLAST program through which the insect was found to be Aphis gossypii. This study provides a set of molecular tools that can be used for identification of insect at species level through DNA barcoding and biodiversity analysis.•Detailed method to maximize quality and quantity of genomic DNA isolated from aphids.•Molecular identification of aphids using mtCOI gene amplification and sequence validation.•First report on Aphis gossypii infecting Solanum trilobatum provides insights of pest identification and management.

First Report of a Paucibranchia (Polychaeta, Eunicidae) Species without Lateral Palps in Korean Subtidal Waters, with Genetic Evidence for Its Taxonomic Position

An undescribed species belonging to the family Eunicidae was detected in a sublittoral habitat of the southern coast of Korea. This Korean eunicid species was initially thought to belong to the genus Lysidice based on its general appearance, including the absence of prostomial lateral palps and peristomial cirri. However, a more detailed characterization of the morphological features of the maxillae and mandible coupled with mtCOI and 18S rRNA gene sequence analyses confirmed that this species is a member of the genus Paucibranchia. The absence of lateral palps found in the intact adult specimens with 153 segments is a unique feature not previously reported in species belonging to Paucibranchia. Thus, the new species, Paucibranchia triantennata sp. nov., can be easily distinguished from other known congeneric species. Except for the absence of lateral palps, P. triantennata sp. nov. resembled P. conferta, P. gathofi, and P. patriciae in the shape of the prostomium, brief location and shape of branchiae, and absence of compound spinigers. However, P. triantennata could be clearly distinguished from these species by the shorter prostomial antennae, a large number of subacicular hooks, and the morphological features of the maxillae and compound falcigers.

Geographical distribution and phylogenic relationships of Hirschmanniella diversa Sher (Nematoda: Pratylenchidae) in Japan

Summary Hirschmanniella diversa and H. imamuri parasitise the lotus, Nelumbo nucifera. Hirschmanniella spp. are the most important pests of lotus cultivation in Japan, but the distribution and species dominancy are not fully understood. In this study, we aimed to collect Hirschmanniella spp. individuals from lotus roots in the major lotus cultivation areas in Japan and identify them morphologically and molecularly using the 18S, D2-D3 regions of rRNA and mitochondrial cytochrome c oxidase subunit I (mtCOI). Hirschmanniella oryzae, commonly known to cause damage on rice in Japan, was also obtained and analysed for inter- and intraspecies sequence variations. All individuals of the genus Hirschmanniella extracted from lotus roots in 16 fields in ten prefectures were identified as H. diversa morphologically and molecularly. This result revealed that H. diversa is a dominant Hirschmanniella species parasitising lotus in Japan. Meanwhile, intraspecific sequence variations in H. diversa were relatively higher in the mtCOI (1-21 bases, ≦5.3%) than in the 18S rRNA and D2-D3 of 28S rRNA (0.0-0.3% and 0.0-0.4%, respectively) and in those of H. oryzae. Based on the mtCOI sequences, five haplotypes were identified and each haplotype was distributed in relatively close regions or regions in which the same lotus cultivars were grown, although further studies are required to verify this assertion. The morphological and genetic variations were higher in H. diversa than in H. oryzae (no intraspecific sequence variation in mtCOI), suggesting that H. diversa was not a recent invasive species.

Species-specific molecular signatures for the commercially important scombrids using mitochondrial gene analysis; a tool for fisheries management

The family Scombridae, comprising of commercially important marine fishes, which are widely distributed across tropical, subtropical, and temperate waters. Scombrids constitute an important fishery and are exploited across their range of distribution. Accurate identification of species is important for effective fisheries management and forensics purposes. In the present study, commercially important species of scombrids distributed in Indian waters were selected for molecular phylogeny and development of species-specific diagnostic keys using mitochondrial cytochrome c oxidase I (COI) gene. In addition to morphological identification, the species were identified using molecular-based identification approach and character-based identification system. Molecular phylogeny for 16 species of scombrids was ascertained using mitochondrial COI analyses. The character-based molecular diagnostic keys for 16 species of scombrids were developed in-silico from data set comprising 603 mtCOI sequences generated in the present study as well as collected from published resources. The study uncovered 39 unambiguous molecular keys, capable of distinguishing all reference taxa under study. The development of species-specific sequences and key diagnostic nucleotides for scombrid fish species will be helpful in effective forensic applications, enforcement of fisheries regulations, and for sustainable utilization of this commercially important group of species.

Genetic Diversity and Geographic Distribution of Bemisia tabaci Species Complex Infecting Soybean in Northern Hills and North Western Plains of India

Background: The Silverleaf whitefly, Bemisia tabaci (Gennadius), is a pest of global significance causing huge economic loss to a wide range of agricultural crops. The pest is regarded as a cryptic species complex which differs in its adaptability to host, fecundity and resistance to insecticides. The expected outcome of the investigation is updated information on prevalence of cryptic species of B. tabaci in the major soybean growing areas in the region. Methods: A roving survey was carried out to assess the occurrence of B. tabaci in the major soybean growing areas of Northern Hills and North Western Plain zones during three consecutive crop seasons from 2018 to 2020. The survey locations were divided in to two broad groups viz., Hills and Plains (Tarai region) and a total of 76 villages were visited during the survey. Cryptic species composition was analyzed using the mtCOI sequence through PCR amplification. Result: The mean whitefly population per plant for the three years in hills and plains were 0.53 and 3.55, respectively. The highest whitefly population was observed in 2019 (1.79 per plant) followed by 2018 (1.50 per plant) and 2020 (1.11 per plant). There was significant (p less than 0.0001) negative correlation (r= -0.749) with altitude. Phylogenetic relationships indicated the existence of two cryptic species Asia-1 and Asia-II-1. Of these, Asia-II-1 was found to be prominent especially in the North Western Plain Zone. In the Northern Hill Zone both Asia 1 and Asia-II-1 were detected.

Genetic diversity of whitefly species of the Bemisia tabaci Gennadius (Hemiptera: Aleyrodidae) species complex, associated with vegetable crops in Côte d'Ivoire.

Since several years, whiteflies of the species complex of Bemisia tabaci (Gennadius) are causing several damages on vegetable crops in Côte d'Ivoire. These sap-sucking insects are the main vector of many viruses on tomato and several species of this complex have developed resistances against insecticides. Nevertheless, there is very little information about whitefly species on vegetable crops in Côte d'Ivoire. Here, we investigated the species diversity and their genetic diversity and structuring on samples from vegetable crops in the major tomato production areas of Côte d'Ivoire. To assess this diversity, 535 whitefly samples from different localities and plant species were collected and analysed with nuclear (microsatellite) and mitochondrial (mtCOI) markers. In each site, and ecological data were recorded, including whiteflies abundance and plant species colonised by B. tabaci. The analysis of mtCOI sequences of whiteflies indicated the presence of four cryptic species on tomato and associated crops in Côte d'Ivoire. These were MED ASL, MED Q1, SSA 1 and SSA3. The MED ASL species dominated over all samples in the different regions and plant species. One haplotype of MED ASL out of the 15 identified predominated on most plant species and most sites. These results suggested that MED ASL is probably the main phytovirus vector in the Ivorian vegetable cropping areas. In contrast, only five haplotypes of MED Q1 were identified on vegetables but in the cotton-growing areas of the country. Its low prevalence, low nuclear and mitochondrial diversity might indicate a recent invasion of this species on vegetable crops in Côte d'Ivoire. The Bayesian nuclear analysis indicated the presence of hybrid genotypes between the two main species MED ASL and MED Q1, however in low prevalence (10%). All these results highlight the need to maintain whitefly populations monitoring for a more effective management in Côte d'Ivoire.

Mitochondrial Genetic Diversity of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) Associated with Cassava in Lao PDR.

Simple SummaryThe whitefly species Bemisia tabaci is a known pest of cassava and a vector of cassava geminiviruses in Africa and India, but its role in the recent spread of Cassava Mosaic Disease (CMD) in Southeast Asia is not well known. This is in part due to a lack of data on the occurrence and distribution of B. tabaci in this region. We show here the first results of any country-wide survey and identification of B. tabaci colonizing cassava in Lao PDR.Cassava Mosaic Disease (CMD) caused by Sri Lankan cassava mosaic virus (SLCMV), has rapidly spread in Southeast Asia (SEA) since 2016. Recently it has been documented in Lao PDR. Previous reports have identified whitefly species of B. tabaci as potential vectors of CMD in SEA, but their occurrence and distribution in cassava fields is not well known. We conducted a countrywide survey in Lao PDR for adult whiteflies in cassava fields, and determined the abundance and genetic diversity of the B. tabaci species complex using mitochondrial cytochrome oxidase I (mtCOI) sequencing. In order to expedite the process, PCR amplifications were performed directly on whitefly adults without DNA extraction, and mtCOI sequences obtained using nanopore portable-sequencing technology. Low whitefly abundances and two cryptic species of the B. tabaci complex, Asia II 1 and Asia II 6, were identified. This is the first work on abundance and genetic identification of whiteflies associated with cassava in Lao PDR. This study indicates currently only a secondary role for Asia II in spreading CMD or as a pest. Routine monitoring and transmission studies on Asia II 6 should be carried out to establish its potential role as a vector of SLCMV in this region.