Cytochrome Oxidase Subunit I Gene Research Articles

First Record of Aphelenchoides oryzae on Foxtail Millet (Setaria italica (L.) P. Beauv.) in Jilin Province of China.

Aphelenchoides oryzae Yokoo caused a large reduction in rice yields in Japan (1948). It was later synonymised with A. besseyi by Allen (1952), but Subbotin et al. (2021) considered it a valid species. In the main foxtail millet (Setaria italica (L.) P. Beauv.) production area of western Jilin Province, China, many plants were stunted, with thin spikes and open, smooth, shiny glumes. Severely affected spikes were noticeably shorter, fluffy at the top, and erect. In August 2023, 10 foxtail millet samples were collected and nematodes were isolated from 9 of them. A population from Songyuan City, Jilin Province (E:123.64, N:44.86) was studied. The average number of nematodes isolated per gram of ear was 510.7 ± 15.17. Female body slender, lip region rounded, lateral fields with 4 or 6 incisures, vulva located at 71.6% of the body length, post vulvar uterine sac (PUS) 3.7 times anal body width long but less than quarter distance from vulva to anus (VA), tail conical with 3 or 4 terminal spikes. The body length (L), maximum body width (W) and tail length of the female (mean, n=25) were 648 μm, 15.9 μm and 36.7 μm, respectively. PUS length / (VA)% = 23.5, L/W = 41.1, L/ tail length = 17.8. Male body tail curves like a sickle, lacks bursa and shows three pairs of copulatory papillae. Spicules typical of the genus except that the proximal end lacks a dorsal process and has only a moderately developed rostrum. Male measured (mean, n = 25): L = 525.8 μm, W = 14.8 μm, tail length = 34.0 ± 0.7 μm, spicule length = 16.4 μm; L/W = 35.6; L/tail length = 15.6 μm. Amplification of the D2-D3 expansion segments of the 28S ribosomal RNA and the cytochrome oxidase subunit I (COI) gene of mitochondrial DNA (mtDNA) with primers the forward D2A (5'-ACAAGTACCGTGAGGGAAAGTTG-3') and the reverse D3B (5'-TCGGAAGGAACCAGCTACTA-3') (Subbotin et al. 2006), and forward COI-F1 (5'-CCTACTATGATTGGTGGTTTTGGTAATTG-3') and the reverse COI-R2 (5'-GTAGCAGCAGTAAAATAAGCACG-3') (Kanzaki and Futai 2002). PCR conditions were as described by Ye et al. (2007). The sequences of 28S D2-D3 region (726 bp, PP573753- PP573761) of rDNA were 100% identical to A. oryzae (KY123700, KY123694) and COI region (698-700 bp, PP733171-PP733179), were 98.88% identical to A. oryzae (GU367867). Bayesian inference was used to construct phylogenetic tree of 28S D2-D3 region and COI gene, which showed that the Jilin populations clustered together with A. oryzae, which was a sister branch of A. besseyi. Pathogenicity was established via the infection of foxtail millet (cv. Jiyou 2). The germinated foxtail millet seeds were planted in pots containing 350 ml of sterile soil mixture. On the 15th day, every 10 seedlings were inoculated with 100 A. oryzae at the leaf sheet wounds and 3 plants were noninoculated as control. Three independent replicates were performed on different dates. Forty days post-inoculation, an average of 88.3 ± 2.26 A. oryzae were extracted from each nematode-inoculated plant, and the plants were yellowed and necrotic, uninoculated plants grew normally. The molecular and morphological identification of the nematodes obtained by re-isolation from the plants was identical to that of A. oryzae. Our findings clarify the pathogen species, which can be targeted to develop prevention and control strategies, which are important for ensuring safe grain production and helping promote sustainable local agricultural production. To our knowledge, this is the first record of A. oryzae on foxtail millet in Jilin, China.

Gene Sequencing Study of Mitochondrial Cytochrome Oxidase Subunit I (COI) in Aedes aegypti Mosquito

Aedes aegypti is an important vector from the public health point of view. It transmits pathogens of Dengue and various other diseases. Controlling vector populations is key to reducing disease transmission and it is possible by understanding the taxonomic characteristics of the vectors and their genetic analysis helps in the identification of the genetic variations in species of different geographical areas. The main aim of the present study is the screening of the Aedes mosquito genome of local species as genetic studies give some insights into the vaccine for the treatment of the diseases caused by mosquito species. In the present study, the adult Ae. aegypti collected from Suryapet town where Dengue fever is endemic, used for the mitochondrial Cytochrome Oxidase subunit I (COI) gene sequencing using the techniques of polymerase chain reaction, Electrophoretic separation, spectrophotometric analysis, and BLAST. The mitochondrial COI sequence of 583 bps is published in the National Centre for Biotechnology Information (NCBI) with accession number ON413769. The sequence data was matched with the database available in the NCBI to identify variation in the gene as this gene keeps changing in the organisms and may contribute to the species establishing itself in a particular region due to congenial environmental conditions. One match with the protein called haem copper oxidase subunit I. The transmission of different pathogens in different areas can be ascertained by comparing similar sequence studies documented. Genomic studies involving genetic markers are of immense help in developing the vaccine. The mitochondrial COI gene is the marker often used for evolutionary research. The single nucleotide polymorphisms (SNP) or Restricted fragment length polymorphisms (RFLPs) that occur in DNA also contribute to the vector's adaptability to the different geographical areas and also the survival benefit which are the basis for understanding the vectors thoroughly and their role in disease transmission.

Megaselia scalaris and Senotainia tricuspis Infesting Apis mellifera: Detection by Quantitative PCR, Genotyping, and Involvement in the Transmission of Microbial Pathogens.

The Megaselia scalaris and Senotainia tricuspis parasitoid flies of the honeybee Apis mellifera were found to infest apiaries of different European and Mediterranean countries but their prevalence and impact on apiary health are little known. Therefore, in this study, quantitative PCR (qPCR)-based methods were developed for their rapid detection directly in hive matrices. The newly developed qPCR assays were targeted at the mitochondrial cytochrome oxidase subunit I (COI) gene for the M. scalaris and the cytochrome B (cytB) gene for the S. tricuspis. The tests were preliminarily applied to 64 samples of adult honeybees and hive debris collected in the Abruzzo and Molise regions, Central Italy, and the Republic of Kosovo showing that both flies occur in the two countries and more frequently in Italy. The positive apiaries in Italy were re-sampled by capturing viable forager bees and isolating emerging flies to carry out the genotyping and analyses aimed at defining if these flies can transmit honeybee pathogens. Genotyping based on the COI and cytB gene sequencing for M. scalaris and S. tricuspis, respectively, identified one S. tricuspis genotype and diverse genotypes of M. scalaris highly similar to those from distant countries. Some fly isolates harbored the DNA or RNA of honeybee microbial pathogens Paenibacillus larvae, deformed wing viruses A and B (DWVA and B), black queen cell virus (BQCV), chronic paralysis virus (CBPV), and Nosema ceranae. The results indicated that these parasites should be efficiently controlled in apiaries by using rapid detection methods to facilitate the large screening studies and early detection.

Assessment of the Genetic Diversity of the Monogenean Gill Parasite Lamellodiscus echeneis (Monogenea) Infecting Wild and Cage-Reared Populations of Sparus aurata (Teleostei) from the Mediterranean Sea.

The diplectanid monogenean Lamellodiscus echeneis (Wagener, 1857) is a specific and common gill parasite of the gilthead seabream Sparus aurata Linnaeus, 1758, in the Mediterranean Sea. Few isolated molecular studies of this monogenean have been conducted, and its population structure and genetic diversity are poorly understood. This study represents the first analysis of the population genetics of L. echeneis, isolated from wild and cage-reared gilthead seabream from fifteen localities in both the Southern (Tunisia) and Northern (Italy and Spain) regions of the Mediterranean Sea, using nuclear ITS rDNA markers and a partial fragment of the mitochondrial gene cytochrome oxidase subunit I (COI). The phylogenetic trees based on the newly obtained dataset and the previously published sequences of L. echeneis corroborated the spread of only a single species throughout the Mediterranean Sea. The star-like haplotypes network, inferred by COI sequences, suggested a recent population expansion of L. echeneis. This is supported by the observed high haplotype diversity (Hd = 0.918) and low nucleotide diversity (Pi = 0.01595). Population structure-based AMOVA for two groups (the Adriatic Sea and the rest of the Mediterranean Sea) attributed 35.39% of the total variation to differences within populations, 16.63% to differences among populations within groups, and 47.99% to differences among groups. Fixation indices were significant, with a high FST value (0.64612), likely related to the divergence of the parasite populations from the Adriatic Sea and other Mediterranean regions. Phylogenetic analyses grouped all samples into the main clade corresponding to L. echeneis from several localities. This study provides insight into the genetic variation between L. echeneis populations, and did not show a clear genetic structure between populations of L. echeneis throughout Tunisian, Italian, and Spanish localities, which can be attributed to the considerable gene flow between the populations favoured by the potential for host dispersion within the Mediterranean Sea. Finally, haplotypes shared between wild and cage-reared hosts provided evidence for the potential for cross-infection between wild and farmed hosts in the Mediterranean Sea.

Molecular genetic diversity analysis of the Nigerian laughing dove (Streptopelia senegalensis) and related species using selected mitochondrial genes

Nigerian laughing doves (Streptopelia senegalensis) are small birds with long tail and living in bushes of the Sub-Saharan regions of African continent, the middle East and Asia, especially India. They are used for food, medicinal and religious purposes in Nigeria. Despite their usage, there is a lack of information on the genetic diversity of laughing doves in Nigeria. This study investigates taxonomic order and diversity of Nigerian laughing doves based on the mitochondrial cytochrome oxidase subunit I (COI) and cytochrome B (CYTB). The results showed 20 haplotypes within the 28 Nigerian coupled with Global Streptopelia genus using concatenated sequences. The Nigerian laughing dove constitute 16 distinct haplotypes. The haplotype diversity was 0.743 ± 0.070, and nucleotide diversity 0.154 ± 0.101 within Nigerian population using COI sequences. Phylogenetic tree showed that Nigerian laughing doves were in the same monophyletic clade with other Streptopela orientalis, S. decocto and S. chinensis; and this confirmed that Nigerian laughing doves might have shared descendant. The median-joining network further grouped Nigerian laughing doves into two: the first group consisting of Nigerian populations only, while the second group are with Saudi Arabian and Djiboutian populations. Population expansion was revealed in Nigerian dove individuals. This study revealed 16 unique haplotypes among Nigerian laughing dove population using concatenated sequences. Interestingly, CYTB showed clustering in African laughing doves (For instance, Nigerian individuals shared haplotypes with Sao Tome and Principe, an island country in the Gulf of Guinea, the western equatorial coast of Central Africa). The current data is the first report on genetic diversity of Nigerian laughing dove using mitochondrial COI and CYTB genes.

A typical coastal plain taxon in central Brazil: Relationships and description of a new species of non-annual killifish (Cyprinodontiformes; Rivulidae) from the Paraná River basin

We describe a new species of the genus Atlantirivulus from a small first-order stream on the right margin of the Paraná River basin in the Mato Grosso do Sul, Brazil. The region of occurrence of the new species is known to be a hotspot for Melanorivulus species. This area, however, is approximately 700 km away from the record of occurrence of its closest congeners, which are distributed along the Brazilian coast in different hydrographic basins. Atlantirivulus enigmaticus, new species, is distinguished from all congeners by it s unique coloration, which consists of the flank being purplish grey with light green iridescence with brownish red dots scattered along of the body, by the neuromasts of the infraorbital series being aligned around eye, and by the presence of the short ventral process of the posttemporal. The phylogenetic position of the new species within the Atlantirivulus genus was based on molecular phylogenetic analysis using sequences of the mitochondrial gene cytochrome oxidase subunit 1. The results show that the new species is closely related to Atlantirivulus luelingi from the coastal drainages of the Brazilian state Santa Catarina. The phylogenetic position of the new species among congeners endemic to coastal river basins may be related to ancestral connections between coastal drainages and the Paraná River basin. The new species constitutes the westernmost record for the genus, and the first record of Atlantirivulus in the Paraná River basin. Insufficient collection efforts in areas of potential occurrence for the group and extinction processes in the broad region between the locality of the new species and the distribution areas of the remaining species may be a possible explanation for this disjunct distribution.

Low depth sequencing reveals the critically endangered Batagur kachuga (Red-crowned roofed turtle) mitochondrial genome and its evolutionary implications

The Batagur kachuga (B. kachuga), commonly known as the Red-crowned roofed turtle, is a critically endangered species native to India and its neighboring countries like Bangladesh, and Nepal. The present study is the first report of the complete mitochondrial genome of B. kachuga (16,517 bp) construed via the next-generation sequencing (NGS) approach from eggshell DNA. There are 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), 13 protein-coding genes (PCGs), and one putative control region (CR/D-loop) in the mitogenome. The CR region from the current study reveals conserved TAS, CD, and CSB domains and two AT-rich tandem repeat regions. Most genes are encoded in the heavy strand except the NADH dehydrogenase subunit 6 (ND6) gene and seven tRNA genes. Most PCGs start with the initiation codon ATG, except the COI (Cytochrome Oxidase Subunit-I) gene, which starts with the GTG codon. The present investigation also predicts the distinctive cloverleaf structures of tRNAs except for tRNA-Ser1 and tRNA-Ser-2, which lack a DHU arm. The comparative analysis of Ka/Ks with other 33 species from Order Testudines, in relation to B. kachuga, revealed negative selection in most PCGs, indicating a process of preservation and purification that aids in eliminating undesirable or detrimental substitutes. Phylogenetic analysis of this species has been analysed using the complete mitogenome of 33 turtle species. The maximum likelihood phylogenetic tree strongly supports each family in different clades and also reveals a close relationship between the Pangashura and Batagur genera. Our study suggests the generation of genome-wide molecular data, in terms of mitogenomes, SNPs, and SSRs, is needed to improve the understanding of this species and their phylogenetics and evolutionary relationships, which will help to improve the conservation efforts of this species.

Population Genetics of Culex tritaeniorhynchus (Diptera: Culicidae) in Türkiye

PurposeMosquitoes are important vectors of pathogens that can affect humans and animals. Culex tritaeniorhynchus is an important vector of arboviruses such as Japanese encephalitis virus, West Nile virus among various human and animal communities. These diseases are of major public health concern and can have huge economic and health burdens in prevalent countries. Although populations of this important mosquito species have been detected in the Mediterranean and Aegean regions of Türkiye; little is known about its population structure. Our study is to examine the population genetics and genetic composition of Cx. tritaeniorhynchus mosquitoes collected from several localities using cytochrome oxidase subunit I (COI) and the NADH dehydrogenase subunit 5 genes (ND5). This is the first extensive study of Cx. tritaeniorhynchus in the mainland Türkiye with sampling spanning many of provinces.MethodsIn this study, DNA extraction, amplification of mitochondrial COI and ND5 genes and population genetic analyses were performed on ten geographic populations of Culex tritaeniorhynchus in the Aegean and Mediterranean region of Türkiye.ResultsBetween 2019 and 2020, 96 samples were collected from 10 geographic populations in the Aegean and Mediterranean regions; they were molecularly analyzed and 139 sequences (50 sequence for COI and 89 sequence for ND5) were used to determine the population structure and genetic diversity. For ND5 gene region, the samples produced 24 haplotypes derived from 15 variable sites and for COI gene region, 43 haplotypes were derived from 17 variable sites. The haplotype for both gene regions was higher than nucleotide diversity. Haplotype phylogeny revealed two groups present in all populations. AMOVA test results show that the geographical populations were the same for all gene regions. Results suggest that Cx. tritaeniorhynchus is a native population in Türkiye, the species is progressing towards speciation and there is no genetic differentiation between provinces and regions.ConclusionThis study provides useful information on the molecular identifcation and genetic diversity of Cx. tritaeniorhynchus; these results are important to improve mosquito control programs.

Effect of agricultural intensification on the genetic diversity of Helicoverpa armigera

AbstractAgricultural intensification affects natural and crop ecosystems, and increases the risk of agricultural pests in agroecosystems. Helicoverpa armigera Hübner (Lepidoptera: Noctuidae) is an important pest that damages a wide range of crops. However, the effect of agricultural intensification on the genetic diversity of this pest is still unclear. In this study, we investigated the effects of the composition and configuration of the landscape on the genetic diversity of the agricultural pest H. armigera based on cytochrome oxidase subunit I (COI) analyses. In total, 10 haplotypes were found in 2016 and 15 haplotypes in 2021 based on COI genes. The haplotype diversity and nucleotide diversity were the highest in the Anqiu (AQ) region during 2016 and in the Bincheng (BC) region during 2021. Haplotype 2 and haplotype 3 (Hap2 and Hap3) were the dominant haplotypes in the H. armigera population. Agricultural intensification had no effect on the genetic diversity of H. armigera between 2016 and 2021. Our study highlights the effect of agricultural intensification on the genetic diversity of H. armigera. Understanding the genetic consequences of agricultural intensification is essential for the green control of agricultural pests and the sustainable development of agriculture.

Dataset of barcoded Reticulariaceae: ten years of DNA sequencing.

As a result of the ten years (2012-2022) work under the critical revision of the genera of Reticulariaceae, a set of papers was published. Collection data of hundreds of specimens, used as a material for these studies, were provided as supplements of corresponding papers, but remained unpublished in biodiversity databases. Here, we represent an occurrence dataset "Barcoded Reticulariaceae of the World", published in GBIF. It includes data on 523 myxomycete collections (including 36 types) gathered from five continents and spanning 24 countries. The dataset encompasses 43 distinct species and one subspecies of myxomycetes, including rare, endemic, and recently-described taxa. Species included to the database mainly belong to the genera Alwisia, Lycogala, Reticularia, Siphoptychium, Thecotubifera and Tubifera (Reticulariaceae), but as well Lindbladia and Licaethalium (Cribrariaceae). Nearly all of the research material, with the exception of several old collections, underwent molecular barcoding, primarily involving the 18S rDNA gene, but also the elongation factor 1α gene and mitochondrial cytochrome oxidase subunit I gene. For those sequences that are stored in the NCBI GenBank, accession numbers are provided in the dataset. Newly-described species make up a significant part of the studied herbarium collections; many of them can be characterised as common for their region. A particularly high level of taxonomic novelty is observed in Australia, which may be explained by the endemism of the local myxomycete biota.

Molecular and morphological characterisation of larvae of the genus Diamesa Meigen, 1835 (Diptera: Chironomidae) in Alpine streams (Ötztal Alps, Austria).

Diamesa species (Diptera, Chironomidae) are widely distributed in freshwater ecosystems, and their life cycles are closely linked to environmental variables such as temperature, water quality, and sediment composition. Their sensitivity to environmental changes, particularly in response to pollution and habitat alterations, makes them valuable indicators of ecosystem health. The challenges associated with the morphological identification of larvae invoke the use of DNA barcoding for species determination. The mitochondrial cytochrome oxidase subunit I (COI) gene is regularly used for species identification but faces limitations, such as similar sequences in closely related species. To overcome this, we explored the use of the internal transcribed spacers (ITS) region in addition to COI for Diamesa larvae identification. Therefore, this study employs a combination of molecular markers alongside traditional morphological identification to enhance species discrimination. In total, 129 specimens were analysed, of which 101 were sampled from a glacier-fed stream in Rotmoostal, and the remaining 28 from spring-fed streams in the neighbouring valleys of Königstal and Timmelstal. This study reveals the inadequacy of utilizing single COI or ITS genes for comprehensive species differentiation within the genus Diamesa. However, the combined application of COI and ITS markers significantly enhances species identification resolution, surpassing the limitations faced by traditional taxonomists. Notably, this is evident in cases involving morphologically indistinguishable species, such as Diamesa latitarsis and Diamesa modesta. It highlights the potential of employing a multi-marker approach for more accurate and reliable Diamesa species identification. This method can be a powerful tool for identifying Diamesa species, shedding light on their remarkable adaptations to extreme environments and the impacts of environmental changes on their populations.

Morphological and molecular characterisation of Cymothoa eremita (Brunnich, 1783) (Isopoda: Cymothoidae) from the South China Sea

A morphological description and molecular characterisation of the parasitic isopod Cymothoa eremita Brünnich, 1783, collected off the fish host Nemipterus furcosus (Valenciennes, 1830) from the South China Sea, is presented here. Since most cymothoid descriptions are primarily based on females, this paper highlights the morphological characteristics from 20 ovigerous female and 20 male C. eremita cymothoids, isolated from 300 fish individuals. Furthermore, our findings indicated significant variations in the morphological features of C. eremita, including: 1) average length and width dimensions, 2) the presence or absence of eyes, 3) the length of pleotelson, 4) the configuration of its posterior and lateral margins, and 5) the structure of the cephalon. These characteristics were compared among diverse fish host species reported in different geographical regions. Twenty one of 300 N. furcosus were infested with C. eremita, with a prevalence of 7%, and mean intensity of 1.9 (two cymothoids per individual fish) respectively. A total of 687 base pairs (bp) from the mitochondrial cytochrome oxidase subunit I (COI) gene were sequenced for C. eremita as a complementary measure to the morphological analysis undertaken in this study. These sequences were utilized to reconstruct a phylogenetic tree, incorporating our sequenced specimens and relevant sequences sourced from the GenBank database. The Maximum Likelihood (ML) phylogenetic tree comprised 45 cymothoid species, with partial COI gene sequences showing monophyletic clustering of most species within the same genus, which is in congruence with their morphological divergence. Continued efforts to conduct studies on the biology, taxonomy, ecology and genetics of both cymothoid and fish host are crucial to better understand the patterns of host-parasite specificity and co-evolutionary changes, which may indirectly contribute towards cymothoid speciation and diversification.

Long-Term Population Genetic Features of the Rhopilema nomadica Jellyfish from the Israeli Mediterranean Coasts

The rhizostomatid scyphozoan Rhopilema nomadica is one of the most notorious marine invasive species established in the eastern Mediterranean Sea. Using seven microsatellite loci, here, we examined the population genetic structures on 587 individual tissue samples collected from 21 sites along the Mediterranean coast of Israel over a period of 16 years. The results indicate unique microsatellite landscapes for all samples, which belong to a single unstructured population. The >20 alleles found in most loci, low fixation index (F) values (average 0.106), and high heterozygosity (average 0.667) suggest random or assortative mating. Additionally, the low overall differentiation (Fst) values (0.043) and pairwise Fst values between the samples collected in different years indicated gene flow and random mating over the years, potentially due to the long-lasting podocytes, scyphistomae, and adults causing a population overlap between the sampled months/years. Likewise, analyses were conducted between seasons, sites, and early/intermediate/late periods of collecting years. These results support the previous analyses performed on the mitochondrial gene cytochrome oxidase subunit I (COI) sequences, altogether indicating a highly polymorphic single unstructured R. nomadica population in the Levant, possibly backed by independent introductions. The results hint to the existence of highly functional connectivity with a genetically highly diverse source population.

A new species of lungworm from the Atlantic Forest: Rhabdias megacephala n. sp. parasite of the endemic anuran Proceratophrys boiei.

Rhabdias are lung-dwelling parasites of anurans and some reptiles. Currently, 93 species are known to exist worldwide. The identification of Rhabdias species is based mainly on morphological traits of hermaphroditic females that generally have a very conserved morphology. However, different approaches, such as the combination of morphological, molecular, and ecological data, have provided advances in identifying and delimiting rhabdiasid species. Here, we describe a new species of Rhabdias from the south of Brazil, with morphological and molecular data. The new species is distinguished from its congeners by having an elongated body, evident cephalic dilation, larger buccal capsule, and large esophagus. In addition to morphological characteristics, we observed significant genetic divergence among the cytochrome oxidase subunit I (COI) sequence of the new species and the closest available sequence, Rhabdias fuelleborni (10.24%-10.87%). Furthermore, phylogenetic reconstructions based on the COI gene indicated that the new species represents a different lineage, constituting an outgroup of the species complexes Rhabdias cf. stenocephala and Rhabdias fuelleborni with Rhabdias sp. 4. Thus, Rhabdias megacephala is the 24th nominal species of the Neotropical region, the 14th Brazilian, and the fourth species described from south of Brazil.

Cactodera xinanensis n. sp. (Nematoda: Heteroderinae), a new species of cyst-forming nematode from Southwest China, with a key to the Genus Cactodera.

The cyst nematodes, subfamily Heteroderinae, are plant pathogens of worldwide economic significance. A new cyst nematode of the genus Cactodera within the Heteroderinae, Cactodera xinanensis n. sp., was isolated from rhizospheres of crops in the Guizhou and Sichuan provinces of southwest China. The new species was characterized by having the cyst with a length/width = 1.3 ± 0.1 (1.1-1.6), a fenestral diameter of 28.1 ± 4.3 (21.3-38.7) μm, vulval denticles present; second-stage juvenile with stylet 21.5 ± 0.5 (20.3-22.6) μm long, tail 59.4 ± 2.0 (55.9-63.8) μm long and hyaline region 28.7 ± 2.7 (25.0-36.3) μm long, lateral field with four incisures; the eggshell with punctations. The new species can be differentiated from other species of Cactodera by a longer tail and hyaline region of second-stage juveniles. Phylogenetic relationships within populations and species of Cactodera are given based on the analysis of the internal transcribed spacer (ITS-rRNA), the large subunit of the nuclear ribosomal RNA (28S-rRNA) D2-D3 region and the partial cytochrome oxidase subunit I (COI) gene sequences here. The ITS-rRNA, 28S-rRNA and COI gene sequences clearly differentiated Cactodera xinanensis n. sp. from other species of Cactodera. A key and a morphological identification characteristic table for the species of Cactodera are included in the study.

An analysis of morphological and genetic diversity of mango fruit flies in Pakistan.

Fruit flies of genus Bactrocera are important insect pests of commercially cultivated mangos in Pakistan limiting its successful production in the country. Despite the economic risk, the genetic diversity and population dynamics of this pest have remained unexplored. This study aimed to morphologically identify Bactrocera species infesting Mango in major production areas of the country and to confirm the results with insect DNA barcode techniques. Infested mango fruits from the crop of 2022, were collected from 46 locations of 11major production districts of Punjab and Sindh provinces, and first-generation flies were obtained in the laboratory. All 10,653 first generation flies were morphologically identified as two species of Bactrocera; dorsalis and zonata showing geography-based relative abundance in the two provinces; Punjab and Sindh. Morphological identification was confirmed by mitochondrial cytochrome oxidase gene subunit I (mt-COI) based DNA barcoding. Genetic analysis of mtCOI gene region of 61 selected specimens by the presence of two definite clusters and reliable intraspecific distances validated the results of morphological identification. This study by morphological identification of a large number of fruit fly specimens from the fields across Pakistan validated by insect DNA barcode reports two species of Bactrocera infesting mango in the country.

Phylogenetic and population genetic analyses of Thrips tabaci Lindeman (Thysanoptera: Thripidae) on Allium host in India.

Onion thrips (Thrips tabaci) is a complex of cryptic species with subtle morphological differences and distinct genetic backgrounds; thus, species identification using traditional methods remains challenging. The existence of different haplotypes and genotypes within a species can significantly influence various aspects of its biology, including host preference, reproductive capacity, resistance to pesticides, and vector competence for plant viruses. Understanding the genetic diversity and population structure of cryptic species within T. tabaci will not only aid in the development of more effective control strategies tailored to specific genetic variants but also in monitoring population dynamics, tracking invasive species, and implementing quarantine measures to prevent the spread of economically damaging thrips biotypes. This study aims to explore intraspecies genetic diversity and molecular evolutionary relationships of the mitochondrial cytochrome oxidase gene subunit I (mtCOI) in T. tabaci populations from India. To capture diversity within the Indian T. tabaci populations, amplicon sequencing was performed for the thrips mtCOI gene from eight diverse localities in India. A total of 48 sequences retrieved for the mtCOI gene from the NCBI Nucleotide database were analysed. Multiple insertions and deletions were detected at various genomic positions across the populations from different localities, with the highest variation observed in the 300-400 genome position range. Molecular diversity analyses identified 30 haplotypes within the population, with certain subpopulations exhibiting higher gene flow. Analysis of single nucleotide polymorphism patterns within the mtCOI gene across diverse Indian locales revealed significant intrapopulation genetic heterogeneity and its potential repercussions on gene functionality. Elevated F statistics (Fst) values in the northern-western subpopulations suggested high genetic variability, particularly evident in haplotype networks originating mainly from the northern region, notably Delhi. While most populations displayed stable and ancient evolutionary histories, thrips populations from northern, western, and north-eastern regions indicated rapid growth.

Unveiling the close relationship between Betta burdigala and Betta uberis through DNA barcoding based on COI Gene

A Wild Betta burdigala is only known from Bangka Island, while a Wild Betta uberis resides in Kalimantan Tengah and Kalimantan Barat in Indonesia. Both species share numerous physical characteristics, particularly in the meristic count, body color, and specific habitat. In this study, we estimate the degree of similarity between Betta burdigala and Betta uberis using DNA barcoding based on the Cytochrome Oxidase Sub Unit I (COI) gene. The COI gene is a unique and small gene which found in mitochondrial DNA and is used in the DNA barcoding approach to identify species. This approach allows for the analysis of species similarities and the learning of the evolutionary histories of those species. Based on the COI gene, Betta burdigala and Betta uberis have a close genetic distance and a DNA similarity of 96.66%, much higher than other bettas. They differ by eight nucleotide bases, and their genetic distance is 0.04, while a genetic distance between 0.010 and 0.099 is considered to be low and indicative of high similarity. According to the phylogenetic tree, these species are descended from a single, closely related ancestor on the same branch. Based on the COI gene, we assume that they are identical. Additionally, we advise conducting additional research using the mitochondrial DNA complex and in-depth morphological examination to confirm the accuracy of the study’s findings.

Morphological and molecular identification of java barb (Barbonymus gonionotus) from East Java Province

This study aims is compare the identification of Java barb fish (Barbonymus gonionotus) in East Java Province by morphometric and molecular identification. Molecular identification was conducted using mitochondrial DNA based on the Cytochrome Oxidase Sub Unit I (COI) region. Java barb fish samples were collected from various regions in East Java Province including Gresik, Mojokerto, Madiun, Malang, and Banyuwangi. The identification results by morphological and molecular methods showed the same results, namely Barbonymus gonionotus. Based on the morphological identification, Barbonymus gonionotus has a long and flat body shape with a raised back, terminal mouth position, silver body colour with a darker dorsal area, dorsal fin shape with weakly hardened rays, and homocercal caudal fin shape. The morphometric measurements of Java barb fish using the one-way ANOVA test showed that the five locations differed significantly. The results of the molecular research showed that all java barb fish sequences were successfully amplified with the COI gene (648 bp). The BLASTN results show the percentage identity ranges from 99.85-100%.

The threat of a non-native oligochaete species in Iran's freshwater: assessment of the diversity and origin of Eiseniella tetraedra (Savigny, 1826) and its response to climate change.

Oligochaetes are the most abundant benthic taxa in aquatic ecosystems that play an important role in food webs. The present study aims to assess the diversity and origin of Eiseniella tetraedra as a non-native species in the Lar National Park of Iran and also its response to current and future climate change. We obtained the specimen from rivers and sequenced the mitochondrial gene Cytochrome Oxidase subunit I (COI) and combined them with 117 sequences from the Jajroud and Karaj rivers in Iran and native regions from GenBank (NCBI). We also ran Species Distribution Modelings (SDMs) using an ensemble model approach that was estimated according to two shared socio-economic pathways (SSPs): 126 and 585 of the MRI-ESM2 based on CMIP6. According to the results, all the samples examined in the current study originated from Spanish rivers, and no unique haplotype was found in the Lar National Park. Moreover, the results also show high haplotype diversity that can positively affect the success of this non-native species in different freshwater. Also, the results of SDMs depict that climate change would remarkably affect the distribution of E. tetraedra and it verifies the invasion power of E. tetraedra in Iran's freshwater ecosystems over time.