COI Gene Data Research Articles

Three new species of the genus Amynthas (Oligochaeta: Megascolecidae) from Guangxi Zhuang Autonomous Region, China.

Three new earthworm species of the genus Amynthas Kinberg, 1867 were found in Guangxi Zhuang Autonomous Region, China: Amynthas huapingensis sp. nov., Amynthas retentus sp. nov. and Amynthas linguiensis sp. nov. Amynthas huapingensis sp. nov. belongs to Amynthas corticis-group characterized by having four pairs of spermathecal pores in 5/68/9; Amynthas retentus sp. nov., without spermathecal pores, belongs to Amynthas illotus-group; Amynthas huapingensis sp. nov. and Amynthas retentus sp. nov. have similar characteristics of male porophores medially surrounded by 23 genital papillae in a pulvinate pad within the male pore area. Amynthas linguiensis sp. nov. has variable spermathecal pores, three pairs in 6/78/9 or four pairs in 5/68/9. And its male pores each on the center of a large elliptical glandular porophore which extends from 1/4xvii to 1/4xix. The morphological comparison and COI gene data of these three new species and their similar species are given in this paper.

Telenomus gregalis Rajmohana sp. n. (Hymenoptera: Scelionidae), a gregarious egg parasitoid of the jujube lappet moth, Streblote siva (Lefèbvre) (Lepidoptera: Lasiocampidae) from India

ABSTRACT Streblote siva (Lefèbvre) (Lepidoptera: Lasiocampidae) is a polyphagous pest of many economically important crops, including moringa (Moringa oleifera Lamarck). The present study reports, for the first time, a species of Telenomus Haliday (Hymenoptera: Scelionidae) as an egg parasitoid of S. siva. The rearing data revealed that this egg parasitoid was gregarious in nature, and upon further taxonomic examination it was found that the parasitoid represented an undescribed species of Telenomus. In this study, an mt COI DNA barcode was generated for this new species from India. Additionally, with the mt COI gene data and the published 28S sequence data concatenated, a two-gene phylogenetic tree was constructed to ascertain the placement of this new species within the genus Telenomus. http://www.zoobank.org/urn:lsid:zoobank.org:pub:7F97EBD0087C4324A601-EE8194E8E577

The molecular phylogeny of cirrate octopods (Cephalopoda: Octopoda: Cirrata) using COI and 16S sequences

Contrasting accounts of taxonomic relationships between finned octopod (Octopoda: Cirrata) taxa complicate species identification and generate nomenclatural instability. A comprehensive analysis based on both 16S and COI mitochondrial gene phylogenies is presented, using all currently accepted genera and approximately 27 putative species (including type species for all genera excepting Grimpoteuthis). The goal of this is to stabilise the concepts of genera and families and identify areas needing further systematic research. Four well supported clades are consistent with families Cirroteuthidae, Cirroctopodidae, Grimpoteuthididae, and Opisthoteuthidae across both 16S and COI phylogenies. Family Stauroteuthidae resolves as a sister clade to Cirroteuthidae in some analyses of the COI gene. Combined molecular and morphological similarities suggest that the Cirrata comprises two superfamily level clades, for which Cirroteuthoidea (for Cirroteuthidae and Stauroteuthidae) and Opisthoteuthoidea (for Cirroctopodidae, Grimpoteuthididae, and Opisthoteuthidae) are proposed. The paraphyletic Cirrothauma (Cirroteuthidae) contains at least three species, while within the Grimpoteuthididae, Cryptoteuthis and Luteuthis form clades within a paraphyletic Grimpoteuthis clade, indicating a need for further taxonomic assessment. Intra-clade structure within Opisthoteuthis is better resolved with COI than 16S data. At least one potentially undescribed Opisthoteuthis occurs in the northwestern Pacific, and northeastern Pacific specimens are tentatively referred to O. bruuni, representing a significant range expansion. Lastly, using the dates of fossil stem-Octobrachians and fossil cirrates for approximate calibration, a timetree estimated from COI gene data suggests that these cirrate families and most cirrate genera arose within the Late Cretaceous, possibly as part of the Mesozoic marine revolution, between 124−62 million years ago.

Morphological and molecular approaches revealed a new species of snapping shrimp genus Alpheus Fabricius, 1798 (Decapoda: Caridea: Alpheidae) from Lakshadweep Islands, India

A new species of the alpheid genus Alpheus Fabricius, 1798, Alpheus sulcipalma sp. nov., is described and illustrated based on the specimens collected from the intertidal zone of Agatti Island, Lakshadweep, India at 0.5-1.0 m depth. This species belongs to the A. edwardsii group by absences of tooth in the orbital hoods and presence of compressed major chela with dorsal and ventral notches. Alpheus sulcipalma sp. nov. is morphologically closely related with A. pacificus Dana, 1852, absence of balaeniceps crests in the minor chela and absences of spine in the merus of major pereiopod of both sexes. However, the new species differs from A. pacificus in presence of strong and broad triangular groove on the dorsolateral and dorsomesial surface of the palm of major chela; length ratio and armature of fingers and palm of minor chela, carpus segments of second and third pereiopods and telson length. The results of phylogenetic analyses using partial sequences of mitochondrial COI gene data compared between A. sulcipalma sp. nov. with congener species which strongly support the description of new species with available limited sequences. The interspecific genetic divergences of the COI gene for A. sulcipalma sp. nov. and A. pacificus were observed higher in ranges (11.1-28.9%).

Taxonomic Delineation of the Old World Species Stomphastis thraustica (Lepidoptera: Gracillariidae) Feeding on Jatropha gossypiifolia (Euphorbiaceae) that Was Collected in the New World and Imported as a Biocontrol Agent to Australia.

We provide the identification and species delineation of this biocontrol agent as Stomphastis thraustica (Meyrick in Trans Ent Soc Lond 80(1):107-120, 1908) belonging to the family Gracillariidae. We clarify the distribution pattern of S. thraustica, its host plant preferences, and present taxonomic and molecular diagnoses based on original morphological and genetic data as well as data retrieved from historic literature and genetic databases. Following our own collecting efforts in three continents Africa, South America, and Australia as well as our study of historic museum collection material, we present many new distribution records of S. thraustica for countries and territories in the world including the new discovery of this species in the Neotropical region and we report its introduction in Australia as a biocontrol agent. Using mitogenomic and COI gene data, we clarified that the closest relative of S. thraustica is Stomphastis sp. that occurs in Madagascar and Australia and feeds on the same host plant as S. thraustica - Jatropha gossypiifolia L. (Euphorbiaceae). The molecular sequence divergence in the mitochondrial DNA barcode fragment between these two closely related species S. thraustica and Stomphastis sp. is over 5.7% supporting that they are different species.

COI gene sequences confirm the taxonomic validity of the tooth-carp Aphaniops hormuzensis (Teleostei: Aphaniidae) from southern Iran

The taxonomic validity of the recently described endemic species Aphaniops hormuzensis (Cyprinodontiformes: Aphaniidae) from southern Iran has been questioned as its original description did not include data from another recently described endemic species, i.e. A. kruppi from eastern Oman. Because of the absence of mitochondrial COI gene sequences, Aphaniops hormuzensis was also not included in recent phylogenetic studies. We therefore generated COI gene data for A. hormuzensis and used the new data to construct a phylogenetic tree that also included A. kruppi (amongst other species). Bayesian and Maximum likelihood phylogenetic analyses reveal that both A. hormuzensis and A. kruppi are monophyletic, with high support values. We conclude that A. hormuzensis is a valid species, which is distinct from A. kruppi and also from A. ginaonis, another tooth-carp endemic to southern Iran. Our results add further support to the taxonomic distinctness of A. hormuzensis from southern Iran.

Towards reproducible metabarcoding data: Lessons from an international cross-laboratory experiment.

Advances in high-throughput sequencing (HTS) are revolutionizing monitoring in marine environments by enabling rapid, accurate and holistic detection of species within complex biological samples. Research institutions worldwide increasingly employ HTS methods for biodiversity assessments. However, variance in laboratory procedures, analytical workflows and bioinformatic pipelines impede the transferability and comparability of results across research groups. An international experiment was conducted to assess the consistency of metabarcoding results derived from identical samples and primer sets using varying laboratory procedures. Homogenized biofouling samples collected from four coastal locations (Australia, Canada, New Zealand and the USA) were distributed to 12 independent laboratories. Participants were asked to follow one of two HTS library preparation workflows. While DNA extraction, primers and bioinformatic analyses were purposefully standardized to allow comparison, many other technical variables were allowed to vary among laboratories (amplification protocols, type of instrument used, etc.). Despite substantial variation observed in raw results, the primary signal in the data was consistent, with the samples grouping strongly by geographical origin for all data sets. Simple post hoc data clean-up by removing low-quality samples gave the best improvement in sample classification for nuclear 18S rRNA gene data, with an overall 92.81% correct group attribution. For mitochondrial COI gene data, the best classification result (95.58%) was achieved after correction for contamination errors. The identified critical methodological factors that introduced the greatest variability (preservation buffer, sample defrosting, template concentration, DNA polymerase, PCR enhancer) should be of great assistance in standardizing future biodiversity studies using metabarcoding.

DNA barcoding and phylogenetic relationship of two fish species of genus Garra (Family: Cyprinidae) from Aravalli region of Southern Rajasthan based on mtDNA COI sequences

The genus Garra (stone sucker), Family Cyprinidae, consists of a group of species that are remarkably similar in morphology. These species are often difficult to distinguish based on external morphological approach. To resolve the existing uncertainty about the relationships and groups of these fishes, an attempt has been made to study the phylogenetic relationships of Garra gotyla and Garra mullya using mtDNA COI gene sequences from Aravalli region of Southern Rajasthan. The sequences were submitted to NCBI GenBank to establish and validate the taxonomical identification of the samples. A total of 5 COI sequences were generated. The overall GC content of Garra gotyla and Garra mullya were 44.13 and 43.00% respectively. The genetic distance within groups was 0.001 and 0.01 for G. gotyla and G. mullya respectively. The Neighbour-joining tree of two fish species using COI gene data revealed two distinct groups with 0.157 divergence. DNA barcode discriminated congeneric species without any confusion. The study strongly validated the efficiency of COI as an ideal marker for DNA barcoding of Indian freshwater fishes.

Detection and characterization of wolbachia endosimbiont in wild bee (apis cerena) using the cytohrome C oxidase subunit I gene

Apis cerena; is as wild bee or honey bee, widespread in almost all regions of Indonesia, these bee economic value as the honey it produces. Indonesian people, especially in Tanjung Peropa Southeast Sulawesi who use bees as a honey-producing source maintain honey bees with a honeycomb claim system that lives in hives in forested trees or found in people’s homes. Until now, there is no breeding or breeding business. Wobachia is endosimbiont which was infected Artrophoda, including insects, which can influence the dynamics of these insects population and can reduce insect perform and viability. Therefore, molecular detection of the presence of Wolbachia in Apiscerena is important. The COI gene is a gene proposed as an animal barcode. There is evidence of primer use of the COI gene as a barcode which is often contaminated with Wolbachia COI gene which is not a target. The individual bee was extracted the genome DNA using the CTAB (cetyltrimethyl ammonium bromide) method, and then the cytochrome oxidase gene (COI) was umplified using an animal barcode primer. The amplification results are then sequenced and then characterized. Using Wolbachia COI gene data available on GenBank as a comparison, reconstruction of phylogenetic tree of Wobachian base on COI nucleotide sequences, so the position taxon of Wolbachia shall be determine. Phylogenetic tree reconstruction make with a Neiberjoining method with the Kimura 2-meter models and 1000x boostrapped. The results showed that the Wobachi COI gene was successfully amplified by these primer animal barcode, along 701bp. A proof that wild bees have been infected by Wolbachia. The findings of this study prove that PCR method are very sensitive to be used to detect existenceWolbachia in bees. This also means that the primer used to reveal animal barcodes, specifically vertebrates, can also amplify the Wolbachia gene; a Rickettsia. The gene has special characteristics, namely 633 base pairs (bp) conserved, and 24 bp variable nucleotides. Of these there are 12 nucleotides which unique for Wobachians who infected A.cerena from Tanjung Peropa, Kendari Southeast Sulawesi. Base N composition dominated of Timine. The phylogenetic tree showed that Wolbachia from Apis cerena, is closely related to Wolbachia endosymbiont Hymenoptera, with 99% of boostrapped value.

Systematic study of the genus Compsilura Bouché in Southeast and East Asia with morphological and molecular data (Diptera, Tachinidae)

• Three new species of Compsilura are described from Southeast and East Asia. • Compsilura samoaensis is treated as a junior synonym of C . concinnata . • The genetic differences in the COI gene of four Compsilura species are examined . • The piercing female postabdomens are compared to consider the alliances to Compsilura . Compsilura concinnata (Meigen) is one of the most famous, most polyphagous and most widely distributed tachinid flies (Diptera, Tachinidae) in the world. This species is well known as a biocontrol agent of some injurious pests of cultural and wild plants and has been introduced from Europe to the United States to control mainly the gypsy moth. Recently we found three new species very closely resembling C. concinnata from Southeast and East Asia: C . lobata sp. nov. (Japan and Thailand), C . malayana sp. nov. (Malaysia) and C . pauciseta sp. nov. (Japan and Taiwan). Additionally, C . samoaensis Malloch is treated as a junior synonym of C . concinnata based on the examination of the type specimen. The genetic differences in the mitochondrial COI gene data are examined to assess the accuracy of species delimitation of Compsilura . The male postabdominal characters of these species are illustrated. The piercing female postabdomen of C . concinnata is illustrated and compared to those of other members belonging to the Blondelia group including Blondelia Robineau-Desvoidy , Celatoria Coquillett, Eucelatoria Townsend and Vibrissina Rondani.

Evidence for population expansion of Cotton pink bollworm Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae) in India

Pink bollworm, Pectinophora gossypiella (Saunders) infestation on Bt cotton is a major concern to cotton production in India. The genetic diversity and phylogeographic structure of the insect in light of PBW resistance needs to be revisited. The objective of this study was to identify different haplotypes of pink bollworm and their distribution in India. To achieve this we studied the population structure in 44 cotton growing districts of India. The partial mitochondrial COI sequence analyses of 214 pink bollworm populations collected from 44 geographical locations representing 9 cotton growing states of India were analysed. Genetic diversity analysis exhibited presence of 27 haplotypes, among them Pg_H1 and Pg_H2 were the most common and were present in 143 and 32 populations, respectively. Distributions of pairwise differences obtained with partial COI gene data from the overall Indian populations are unimodal, suggesting population expansion in India. Significant neutrality test on the basis of Tajima’ D and Fu’s Fs presented a star-shaped haplotype network together with multiple haplotypes. The unimodal mismatch distribution, rejection of neutrality test with significant negative values supported the theory of demographic expansion in cotton pink bollworm populations in India. Genetic data not only provides us with a perspective of population genetics, but also that the two populations of pink bollworm, those occurring early in the season are genetically close to the late season populations with respect to their partial CO1 region. Resistance to Cry toxins does not seem to have had an impact on this region of the mt DNA in populations of pink bollworm.

What can be Concluded from COI Gene Data in Limited History Specimen: A sample analysis of a forest pest,Lymantria dispar

Nowadays, more and more biodiversity and biogeography studies are conducted with the help of gene sequences. Fresh samples obtained using consistent collection methods can provide DNA for analysis and yield the current status of target species. As there are often no historical samples providing a timescale, it is often difficult to draw conclusions and to provide an evolutionary explanation of the observed biogeographical patterns because of a lack of evidence. The huge natural history specimen collections in museums could possibly provide this information. The gypsy moth, Lymantria dispar (Linnaeus) is a worldwide forest pest species. Our analyses of mitochondrial COI gene sequencing data in specimens from disparate locations revealed previously unknown genetic relationships in gypsy moth populations across space (in and around China) and time (1955–2012). We recovered 103 full-length COI gene sequences from eight fresh samples and from 95 Lymantria dispar collection specimens that had been captured between 1955 and 1996. Combining 103 full-length COI gene sequences with 146 COI gene sequences from Genbank (https://www.ncbi.nlm.nih.gov) or DNA barcode libraries, we analyzed the genetic differentiation, gene flow and haplotypes (special sequences from individuals) within the gypsy moth populations in order to reflect the genetic structure and population dynamics of this pest. Twenty-five previously unknown haplotypes were discovered. Regional populations from the same location, but collected at different times, showed high genetic diversity. In some geographical populations (Heilongjiang, Liaoning and Beijing populations), the genetic differentiation was greatest in 1979, but much lower in 1992 and 2012. This study is an example that shows how specimen collections can be useful to complete gaps in biodiversity studies carried out through genetic sequencing.

First record of Vallonia costata (O. F. Müller, 1774) (Gastropoda, Eupulmonata, Valloniidae) from British Columbia, Canada, confirmed by partial-COI gene sequence

The minute terrestrial snail Vallonia costata (O. F. Müller, 1774) is reported for the first time from the province of British Columbia, Canada. The identification was based on shell morphology and confirmed by COI gene data. This species is presumed to be introduced to the province.

Exploring malaria vector diversity on the Amazon Frontier

BackgroundDeforestation in the Amazon and the social vulnerability of its settler communities has been associated with increased malaria incidence. The feeding biology of the most important malaria vectors in the region, notably Nyssorhynchus darlingi, compounds efforts to control vectors and reduce transmission of what has become known as “Frontier Malaria”. Exploring Anophelinae mosquito diversity is fundamental to understanding the species responsible for transmission and developing appropriate management and intervention strategies for malaria control in the Amazon River basin.MethodsThis study describes Anophelinae mosquito diversity from settler communities affected by Frontier Malaria in the states of Acre, Amazonas and Rondônia by analysing COI gene data using cluster and tree-based species delimitation approaches.ResultsIn total, 270 specimens from collection sites were sequenced and these were combined with 151 reference (GenBank) sequences in the analysis to assist in species identification. Conservative estimates found that the number of species collected at these sites was between 23 (mPTP partition) and 27 (strict ABGD partition) species, up to 13 of which appeared to be new. Nyssorhynchus triannulatus and Nyssorhynchus braziliensis displayed exceptional levels of intraspecific genetic diversity but there was little to no support for putative species complex status.ConclusionsThis study demonstrates that Anophelinae mosquito diversity continues to be underestimated in poorly sampled areas where frontier malaria is a major public health concern. The findings will help shape future studies of vector incrimination and transmission dynamics in these areas and support efforts to develop more effective vector control and transmission reduction strategies in settler communities in the Amazon River basin.

DNA barcoding and molecular phylogeny in Ranidae

The family Ranidae has the widest distribution compared with other frog family. The phylogeny of the Ranidae is still a matter of dispute. In the present study, we analyzed the COI barcodes of 29 species from six genera belonging to the family Ranidae. Twenty-seven species (93.10% of all the species) were correctly identified by their DNA barcodes. Pelophylax lessonae and Pelophylax ridibundus shared the same one barcode sequence. Kimura two-parameter distances were calculated between barcodes. Pair-wise comparisons among-species were distributed from 0.16% (between Pelophylax lessonae and Pelophylax esculenta) to 29.13% (between Rana warszewitschii and Rana dybowskii). The average genetic distance between species was 28 times higher than the average genetic distance within species. The neighbor-joining method was used to construct a phylogenetic tree, which grouped all the genera into two divergent clades. The results indicated that some currently recognized genera of Ranidae may not be monophyletic. COI gene data supported the hypothesis of polyphyly for Rana, Amolops, Babina, and Hylarana. DNA barcoding is an effective molecular tool for Ranidae species identification and phylogenetic inference.

Pelacakan Gen Sitokrom Oksidase Sub Unit I (COI) DNA Mitokondria Itik Tegal (Anas domesticus) Menggunakan Primer Universal

Currently local ducks are generally quite difficult to find in a big farm in Inonesia, including Tegal ducks. Tegal ducks is one of the genetic resources native to Indonesia with it’s advantages in terms of high and large egg production. Conservation and development of local ducks have strived to maintain our existence of Indonesian livestock germplasm. If such information is not superior to native species exist, the opportunity to increase his lead further also getting smaller. Tracking the mitochondrial COI gene DNA of Tegal ducks may underlie the process of an organism's genetic characterization. Information about Tegal duck mitochondrial DNA has not been done. The information obtained can be used for optimization of duck products native to Indonesia both in physiological aspects, phylogeny and genetic engineering. The research method used in this research is tracking COI gene data from Gen Bank with the programs Clustal X and Genedoc. Tracking then continued using universal primers HCO and LCO. The results of the data followed up with the isolation and amplification of COI gene mitochondrial DNA as well as the optimization of PCR conditions. The results showed mitochondrial DNA COI gene Tegal ducks were amplified with primer LCO obtain DNA fragments of length less than 250 bp. Kata kunci: duck’s from Tegal, COI gene, mitochondrial DNA