Identification Of Molecular Species Research Articles

Molecular species identification of Rockskipper (Pisces: Blenniidae) from Porok Beach (Yogyakarta, Indonesia) based on 16S rRNA and COI genes

Rockskipper belongs to the species-rich family of Blenniidae (Combtooth blenny) and is known for its cryptic and species complexes presence. Identifying cryptic species based solely on morphological features is challenging due to their similar morphological characteristics. As a result, molecular genetic techniques based on two partial mtDNA genes, COI and 16S rRNA, were employed to identify fish accurately. This study aimed to evaluate the effectiveness of COI and 16S rRNA gene for the identification of Rockskipper fish and investigate the genetic relationship between species of Rockskipper from Porok Beach. The result revealed that the thirteen Rockskipper samples from Porok Beach that belong to six species (E. vermiculatus, E. striatus, I. lineatus, I. dussumieri, I. edentulus, and B. caudolineata) with more than 99% similarity. In contrast, the 16S analysis identified five species. A Bayesian phylogenetic tree demonstrated that six species of Rockskipper from Porok Beach are genetically distinct and separated into two clusters. We also found that two samples (RS-9 and RS-10) form a monophyletic group with B. caudolineata with maximum bootstrap (NJ and ML: 100%) and posterior probability (1.00). We hypothesized that B. caudolineata is a species complex with at least two lineages: one was genetically closer to RS-8, and another was more closely related to RS-9 and RS-10. Both the COI and 16S rRNA genes were found to be capable of delineating species and revealing genetic variation among Rockskipper samples in this study. However, our findings demonstrated that the COI gene is a more accurate and reliable marker for identifying Rockskipper species from Porok Beach, Gunungkidul, Yogyakarta, Indonesia.

Identity of the numerous bloodstains at the murder scene: molecular identification of fly artifacts and fly species by CO1 analysis.

Crime scenes may contain insect artifacts as well as samples of human origin. While the presence of insects can be important evidence in forensic medicine and forensic entomology, the insect artifacts sometimes interfere with the interpretation of bloodstain pattern analysis (BPA) which can be critical for accurate crime reconstruction. Fly artifacts are especially complicated to distinguish from true bloodstains. Indeed, we encountered a murder scene with numerous bloodstains inconsistent with the cause of death and had trouble interpreting them. The morphological method has been developed to distinguish them, but this method has to rely on the analyst's experience and opinion. This study aims not only to distinguish fly artifacts from true bloodstains but also to identify fly species by detecting fly DNA in small amounts of bloodstains at the scenes. Melt curve analysis of real-time PCR (qPCR) targeting cytochrome c oxidase subunit 1 (CO1) of mitochondrial DNA (mtDNA) was able to detect fly DNA in bloodstains from a murder scene. The fly DNA was sequenced from the qPCR product, and the fly species were identified by BLAST search. Fluorescence-labeled specific primers for four species of necrophagous flies were designed based on the sequences of the CO1 region, and differences in the length of the amplification products were used to identify fly species from trace amounts of fly DNA in the artifacts.

50%, not great, not terrible: Pan-European gap-analysis shows the real status of the DNA barcode reference libraries in two aquatic invertebrate groups and points the way ahead

The essential key to routine molecular species identification (DNA barcoding/metabarcoding) is the existence of an error-free DNA barcode reference library providing full coverage of all species. Published studies generally state the need to produce more barcodes, and control their quality, but unfortunately, the number of barcoded species is still low. However, to initiate real progress, we need to know where the gaps lie, how big they are and why they persist. Our aims were to draw and understand the current state of knowledge regarding species diversity, distribution, and barcode coverage, and offer solutions for improvement. In this study, we used two groups of aquatic insects, beetles and true bugs. We have compiled and critically evaluated an essentially complete and up-to-date European list, containing 1527 species. The list served as a basis for the barcode gap analyses in the Barcode-of-Life-Data-System (BOLD) conducted in three subsequent years (2020–2022). The overall barcode coverage of the pan-European fauna was around 50 % in both groups. The lowest coverage was in the Mediterranean, the Balkans and South-eastern Europe. The coverage in each country depended significantly on the local diversity, the number of rare, endemic species and the similarity of its fauna to that of the most active barcoding European countries. Gap analyses showed a very small increase in species coverage (<1 % in European aquatic beetles) despite an ~25 % increase in the number of barcodes. Hence, it is clear that future barcoding campaigns must prioritise quality over quantity. To visibly improve reference libraries, we need to increase the involvement of taxonomic experts and focus on targeted studies and underexplored but biodiversity-rich areas.

New record of Tylodelphys metacercariae (Diplostomidae) from Perccottus glenii (Odontobutidae) and their phylogenetic assessment.

Metacercariae of Tylodelphys sp. were found in the abdominal cavity of the Chinese sleeper (Perccottus glenii) collected in Liaoning Province and Inner Mongolia Autonomous Region of China. The sequences of the mitochondrial cox1 gene and ribosomal ITS1-5.8S rDNA-ITS2 region were obtained and used for molecular identification and phylogenetic assessment of this parasite species. Results of phylogenetic analyses based on ITS and cox1 markers showed that the metacercariae of Tylodelphys sp.ex P. glenii from China were conspecific with specimens of Tylodelphys sp. collected by Sokolov etal. (2013) from the same fish-host species captured earlier in West Siberia, Russia. The examined Tylodelphys sp. ex. P. glenii is the only member of the genus whose metacercariae parasitise the abdominal cavity of fish in northern Eurasia. Tylodelphys sp. ex P. glenii clustered with T. darbyi, T. immer, T.podicipina, and Tylodelphys sp. of Soldánová etal., 2017 based on mitochondrial DNA markers, and with T. darbyi, T. immer, T. kuerepus, and T. schreuringi using nuclear DNA markers.

Super-Mitobarcoding in Plant Species Identification? It Can Work! The Case of Leafy Liverworts Belonging to the Genus Calypogeia

Molecular identification of species is especially important where traditional taxonomic methods fail. The genus Calypogeia belongs to one of the tricky taxons. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. The finding of the universal single-locus DNA barcode in plants seems to be 'the Holy Grail'; therefore, researchers are increasingly looking for multiloci DNA barcodes or super-barcoding. Since the mitochondrial genome has low sequence variation in plants, species delimitation is usually based on the chloroplast genome. Unexpectedly, our research shows that super-mitobarcoding can also work! However, our outcomes showed that a single method of molecular species delimitation should be avoided. Moreover, it is recommended to interpret the results of molecular species delimitation alongside other types of evidence, such as ecology, population genetics or comparative morphology. Here, we also presented genetic data supporting the view that C. suecica is not a homogeneous species.

Molecular Identification and Phylogenetic Relationship of Some Plant Species In Ashdagh Mountain, Sangaw, Kurdistan Of Iraq

Phylogenetic and molecular perspective of plant identification can reveal the plant composition of areas. Many new species have been identified based on morphological characters in different area of Kurdistan, but few have been identified through DNA barcoding method. In this study, Internal transcribed spacers 1 and 2 (ITS1 and ITS2) were used to identify some species in Ashdagh Mountain. The identified taxa were belonged to different families and clades and not recorded in any studies. The nucleotide sequences of identified species were 98-100% identical with species in the genebank database. The phylogenetic analysis showed diversity in phylogenetic relationships among coexisting species. In addition, the existing of Chara sp. in the acidic stream of Awa spi is a new record and not observed before. The finding of this study show the importance of using molecular and phylogenetic technique to identify and understand phylogenetic relationship among coexisting species because Kurdistan is a hot spot and need more emphasis. In addition, new species occurrence data has been added to flora of Kurdistan.

Evaluation of Candida colonization index, molecular identification, and antifungal susceptibility pattern of Candida species isolated from critically ill pediatric patients: A single-center study in Iran.

Given the high mortality rate of invasive candidiasis in hospitalized pediatric patients, it is crucial to establish a predictive system to achieve early diagnosis and treatment of patients who are likely to benefit from early antifungal treatment. This study aimed to assess the Candida colonization index, species distribution, and antifungal susceptibility pattern of Candida strains isolated from pediatric patients with high Candida colonization index (CI). This study was carried out at the Children's Medical Center in Tehran-Iran. In total, 661 samples were collected from 83 patients. The Candida CI was calculated according to the descriptions of previous studies. The isolates were identified using polymerase chain reaction-based techniques. The Clinical and Laboratory Standard Institute protocol M60 was used to conduct the antifungal susceptibility test. A colonization index greater than 0.5 was confirmed in 29 cases (58% of positive samples) with two children developing candidemia. Candida albicans (n=53, 49.5%) was the most common Candida species in patients with CI > 0.5. Except for acute lymphoblastic leukemia, no risk factors were linked to a high index in colonized children (P > 0.05). Twelve isolates (7.01%) were multi-azole resistant with high MICs against both isavuconazole and ravuconazole and seven strains (4.09%) were echinocandins resistant. In pediatric intensive care units, patients are at risk of fungal infection, particularly candidemia. In this study, more than half of the children with positive yeast cultures had CI > 0.5, and 6.8% developed candidemia.

Comparative analysis of mitochondrial genomes of Broussonetia spp. (Moraceae) reveals heterogeneity in structure, synteny, intercellular gene transfer, and RNA editing.

The genus Broussonetia (Moraceae) is comprised of three non-hybrid recognized species that all produce high quality fiber essential in the development of papermaking and barkcloth-making technology. In addition, these species also have medicinal value in several countries. Despite their important economical, medicinal, and ecological values, the complete mitogenome of Broussonetia has not been reported and investigated, which would greatly facilitate molecular phylogenetics, species identification and understanding evolutionary processes. Here, we assembled the first-reported three complete Broussonetia (B. papyrifera, B. kaempferi, and B. monoica) mitochondrial genomes (mitogenome) based on a hybrid strategy using Illumina and Oxford Nanopore Technology sequencing data, and performed comprehensive comparisons in terms of their structure, gene content, synteny, intercellular gene transfer, phylogeny, and RNA editing. Our results showed their huge heterogeneities among the three species. Interestingly, the mitogenomes of B. monoica and B. papyrifera consisted of a single circular structure, whereas the B. kaempferi mitogenome was unique and consisted of a double circular structure. Gene content was consistent except for a few transfer RNA (tRNA) genes. The Broussonetia spp. mitogenomes had high sequence conservation but B. monoica with B. kaempferi contained more synteny blocks and were more related, a finding that was well-supported in organellar phylogeny. Fragments that had been transferred between mitogenomes were detected at plastome hotspots that had integrated under potential mediation of tRNA genes. In addition, RNA editing sites showed great differences in abundance, type, location and efficiency among species and tissues. The availability of these complete gap-free mitogenomes of Broussonetia spp. will provide a valuable genetic resource for evolutionary research and understanding the communications between the two organelle genomes.

Genetic identification of submersed dodder (Cuscuta: Convolvulaceae) in Texas, U.S.A.

Cuscuta plants that were observed growing entirely submersed and parasitizing the aquatic macrophyte Hygrophila polysperma in the San Marcos and Comal Rivers in Texas, are identified genetically as C. obtusiflora. This note documents the first molecular identification of any Cuscuta species naturally growing underwater or parasitizing a submersed aquatic plant.

DNA barcoding and biomass accumulation rates of native Iranian duckweed species for biotechnological applications.

The Lemnaceae family (duckweed) consists of at least three recognized genera with six reported species in Iran that are distributed in wetlands. Duckweeds are the simplest and smallest flowering aquatic monocots with free-floating fronds that can reproduce asexually every 2-3 days. Duckweed could be a major source of balanced amino acids and high protein content, which is increasingly promising for biotechnological applications. For molecular classification and species identification of the collected samples, DNA barcoding was performed using two standard chloroplast markers, the spacer region between the ATP synthase subunits F and H (atpF-atpH) and the intron region of the ribosomal protein S16 (rps16). The results confirm the presence of four species belonging to the two genera Lemna and Spirodela. In addition, L. turionifera was detected for the first time in Iran. Due to the high growth rates of duckweed, measurement of biomass accumulation and doubling time are important factors in determining growth potential, especially for native species. The relative growth rates (RGR), doubling times (DT), biomass accumulation, and relative weekly yields (RY) of 40 distinct duckweed clones were determined under standard cultivation conditions. The dry weight-based RGR ranged from 0.149 to more than 0.600 per day, DT from 1.12 to 9 days, and RY from 7 to 108.9 per week. All values are comparable with previous studies. RGR and RY of selected clones are higher than the growth potential for a wide range of wild plants and common crops. These data support that native duckweed has high productivity value and should be further investigated as a potentially rich protein source for alternative human food, livestock feed, and recombinant protein production.

Mass Spectrometry Analysis of the Human Brain Sphingolipidome.

In recent decades, mass spectrometry-based lipidomics has provided a fertile environment for scientific investigations of biochemical and mechanistic processes in biological systems. Notably, this approach has been used to characterize physiological and pathological processes relevant to the central nervous system by identifying changes in the sphingolipid content in the brain, cerebral spinal fluid, and blood plasma. However, despite a preponderance of studies identifying correlations between specific lipids and disease progression, this powerful resource has not yet substantively translated into clinically useful diagnostic assays. Part of this gap may be explained by insufficient depth of the lipidomic profiles in many studies, by lab-to-lab inconsistencies in methodology, and a lack of absolute quantification. These issues limit the identification of specific molecular species and the harmonization of results across independent studies. In this chapter, we contextualize these issues with recent reports identifying correlations between brain lipids and neurological diseases, and we describe the workflow our group has optimized for analysis of the blood plasma sphingolipidome, adapted to the characterization of the human brain tissue.

First detection of Cryptosporidium proventriculi from wild birds in Cyprus.

Cryptosporidium is an important intestinal zoonotic pathogen that can infect various hosts and cause diarrheal disease. There are no reports on the prevalence and molecular characterization of Cryptosporidium in wild birds in Cyprus. Therefore, the present study aimed to determine the prevalence of Cryptosporidium spp. and genotypes in wild birds found at Phassouri Reedbeds (Akrotiri Wetlands), Cyprus. Fecal samples of 75 wild birds (Eurasian coot Fulica atra, N = 48; Eurasian teal Anas crecca, N = 20; duck - Anas spp., Ν = 7) were screened for Cryptosporidium by PCR amplification and sequencing. Only one sample (1.3%) belonging to a Eurasian coot was PCR-positive for Cryptosporidium. Based on sequencing of the 18S rRNA locus, this species was identified as Cryptosporidium proventriculi. This is the first report on the molecular identification of this Cryptosporidium species in a Eurasian coot.

Molecular Identification of Non-tuberculous Mycobacterial Species in Fecal samples from Cattle and Buffaloes

Abstract: The non-tuberculous mycobacteria (NTM) are ‘atypical mycobacteria’ belonging to species other than those classified in the Mycobacterium tuberculosis complex. NTM species have been reported to cause cross-reactive immune responses that interfere with the diagnosis of tuberculosis in both livestock and wildlife and are considered as potential pathogens for animals and humans. The present study was conducted for detection of non- tuberculous mycobacterial species (NTM) in fecal samples with a history of intermittent diarrhea from cattle and buffaloes. Polymerase Chain Reaction and PRA (PCR-RFLP) was performed on 30 fecal samples collected from cattle and buffaloes of organized dairy farms in Ludhiana, for detection of non - tuberculous mycobacterial species (NTM). In the present studyM. fortuitum was detected in two out of 30 fecal samples by PCR and PCR-RFLP (PRA).

Molecular Phylogeny of Dermestidae (Coleoptera) Reveals the Polyphyletic Nature of Trogoderma Latreille and the Taxonomic Placement of the Khapra Beetle Trogoderma granarium Everts

Abstract The hide, larder, and carpet beetles (Coleoptera: Dermestidae) are a family of mainly scavenger beetles, with numerous species such as the khapra beetle (Trogoderma granarium Everts, 1898), the black carpet beetle [Attagenus unicolor (Brahm, 1791)] and the hide beetle (Dermestes maculatus De Geer, 1774) being widely recognized as serious economic pests of stored products and museum collections. A stable classification and reliable identification of genera and species of these pests and their 1,700 relatives are of great relevance for trade restrictions, biosecurity, pest management, forensics, and biodiversity surveys. In this study, we examined and sequenced mitochondrial genomes of 477 dermestid specimens, representing all subfamilies and 90% of the globally recognized tribes and subtribes. Our study provides the most comprehensive, taxonomically verified, and vouchered resource of mitochondrial reference sequences linked to specimen images and occurrence records of pests and their relatives, enabling eDNA surveys, metabarcoding and molecular species identification. It also reconstructs the phylogeny of Dermestidae based on molecular and morphological data for the first time, thereby providing robust phylogenetic hypotheses for a stable classification system from family to genus-level. Accordingly, a revised classification of Dermestidae with formal nomenclatural changes is proposed, recognizing six subfamilies: Orphilinae, Trinodinae, Trogoparvinae subfam. nov. (type genus TrogoparvusHáva, 2001), Dermestinae, Attageninae, and Megatominae. Trinodinae is recovered towards the base of Dermestidae with three tribes: Trinodini (=Trinoparvini syn. nov.), Thylodriini, and Trichelodini. Dermestinae is the only subfamily with adults lacking a median ocellus, and it includes the tribes Thorictini stat. nov. (that is downgraded from Thorictinae), Marioutini, and Dermestini. The endemic Australian genus Derbyana Lawrence and Ślipiński was recovered within Holarctic Dermestes Linnaeus. Attageninae is strongly supported and includes the monogeneric Adelaidiini and polygenic Attagenini. Former subgenera of Attagenus Latreille, i.e., Lanorus Mulsant and Rey (= Paranovelsis Casey syn. nov.), Telopes Redtenbacher and Aethriostoma Motschulsky, are elevated to generic level. The largest clade, Megatominae, is confirmed as monophyletic and is divided into three tribes: Anthrenini, Ctesiini, and Megatomini. Megatomini is divided into three subtribes: Megatomina, Orphinina subtribe nov. (type genus Orphinus Motschulsky), and Trogodermina. Within the economically important lineage Trogodermina, Trogoderma Latreille is delimited to contain only Holarctic species including the Khapra beetle T. granarium Everts, while a Southern Hemisphere clade is here recognized as Eurhopalus Solier in Gay, 1849 (= AnthrenocerusArrow, 1915; Myrmeanthrenus Armstrong, 1945; Neoanthrenus Armstrong, 1941; SodaliatomaHáva, 2013; Reesa Beal, 1967 syn. nov.). A revised classification of the extant genera of Dermestidae is also provided.

European and Mediterranean Myzocallidini Aphid Species: DNA Barcoding and Remarks on Ecology with Taxonomic Modifications in An Integrated Framework.

The genus Myzocallis Passerini (Hemiptera, Aphididae, Calaphidinae, Myzocallidini) is a rather primitive group of aphids currently comprising 45 species and 3 subspecies, subdivided into ten subgenera, three of them having a West Palaearctic distribution. The majority of the species inhabit Fagales plants and some of them are considered pests. Despite their ecological interest and the presence of some taxonomic controversies, there are only a few molecular studies on the group. Here, the main aims were to develop a DNA barcodes library for the molecular identification of West Palaearctic Myzocallis species, to evaluate the congruence among their morphological, ecological and DNA-based delimitation, and verify the congruence of the subgeneric subdivision presently adopted by comparing the results with those obtained for other Panaphidini species. These study findings indicate that Myzocallis (Agrioaphis) leclanti, originally described as a subspecies of M. (A.) castanicola and M. (M.) schreiberi, considered as a subspecies of M. (M.) boerneri, should be regarded at a rank of full species, and the subgenera Agrioaphis,&amp;nbsp;Lineomyzocallis,&amp;nbsp;Neomyzocallis, Pasekia were elevated to the rank of genus, while Myzocallis remain as such.

Seasonal change in species composition and target-site mutations in Anopheles gambiae s.l. in the severe drought area of Kandi, North-eastern Benin

The persistence of malaria transmission in areas with very arid environmental conditions remains enigmatic. The present study investigated seasonal variation of mosquito species composition and Kdr and Ace-1 mutations in Anopheles gambiae s.l. in the very arid district of Kandi in North-eastern Benin.Adult mosquitoes were sampled over 1 year using both human landing catches (HLC) and pyrethrum spray catches in 4 villages belonging to 2 areas of different levels of aridity. The collections were carried out on a bi-monthly basis in the wet season, and once every month in the dry season to better capture the entomological situation in drought period. Females An. gambiae sl specimens were kept aside and analysed by PCR for species identification. Presence of kdr and Ace-1 mutations was also assessed in the An. gambiae s.l. collection.A total of 2,211 host-seeking mosquitoes belonging to 15 species were collected in the study area. An. gambiae s.l. was the most abundant species and represented 67% of the collection. Other Anopheles species were found at very low frequency among which An. funestus, An. pharoensis, An. broheri and An. coustani. Molecular species identification showed in dry season a significantly higher frequency of An. coluzzii over An. gambiae s. s. in both less dry (70% vs 29% with p < 0.001) and driest (70% vs 30% and p = 0.034) areas of the district of Kandi. In the rainy season, there was similar frequency of An. coluzzii and An. gambiae s. s. in the less arid area (53% vs 45%; p = 0.153), while An. coluzzii remained significantly predominant (62% vs 38%; p = 0.012) in the driest zone. The frequency of kdr mutation was significantly higher in dry season than in rainy season (93% vs 84%; p

Dispersal direction of Malaysian Fasciola gigantica from neighboring southeast Asian countries inferred using mitochondrial DNA analysis.

Fasciola gigantica and hybrid Fasciola flukes, responsible for the disease fasciolosis, are found in Southeast Asian countries. In the present study, we performed molecular species identification of Fasciola flukes distributed in Terengganu, Malaysia using multiplex PCR for phosphoenolpyruvate carboxykinase (pepck) and PCR-restriction fragment length polymorphism (RFLP) for DNA polymerase delta (pold). Simultaneously, phylogenetic analysis based on mitochondrial NADH dehydrogenase subunit 1 (nad1) was performed for the first time on Malaysian Fasciola flukes to infer the dispersal direction among neighboring countries. A total of 40 flukes used in this study were identified as F. gigantica. Eight nad1 haplotypes were identified in the F. gigantica population of Terengganu. Median-joining network analysis revealed that the Malaysian population was related to those obtained from bordering countries such as Thailand and Indonesia. However, genetic differentiation was detected using population genetics analyses. Nevertheless, the nucleotide diversity (π) value suggested that F. gigantica with the predominant haplotypes was introduced into Malaysia from Thailand and Indonesia. The dispersal direction suggested by population genetics in the present study may not be fully reliable since Fasciola flukes were collected from a single location in one state of Malaysia. Further studies analyzing more samples from many locations are required to validate the dispersal direction proposed herein.

Potential biocontrol agent of indigenous Bacillus sp. EG6.4: Molecular identification, larvicidal toxicity, and mechanism of actions

Abstract. Salamun, Susetyo RD, Nafidiastri FA, Zain RA, Sari RP, Geraldi A, Fatimah, Ni’matuzahroh. 2022. Potential biocontrol agent of indigenous Bacillus sp. EG6.4: Molecular identification, larvicidal toxicity, and mechanism of actions Biodiversitas 23: 5431-5438. This research was carried out for molecular identification, as well as the determination and mechanism of action of larvicidal toxicity of Bacillus sp. EG6.4 isolated from breeding sites of Aedes aegypti from Gresik, East Java, Indonesia. Bacillus sp. EG6.4 was a Gram-positive endospore-forming bacteria. Molecular species identification using 16S rRNA gene sequencing showed that isolate had 97.89% similarity with Bacillus mojavensis. The isolate showed larvicidal toxicity against A. aegypti larvae. The lethal concentration 50% (LC50) values ??at 24 and 48hours exposure were 8.99±1.01 ×107 cells/mL and 8.43±1.01 ×107 cells/mL, respectively, while lethal time 50% (LT50) value was 11.9±1.1 hours. Production of chitinolytic enzymes or biosurfactants, chitinolytic and hemolytic assays were conducted to determine the larvicidal mechanism. As a result, Bacillus sp. EG6.4 showed hemolytic, but not chitinolytic activity, indicating its potency to produce biosurfactants. Transmission Electron Microscopy (TEM) result showed that isolate had oval-shaped endospores located subterminal with massive-shape parasporal inclusions. The detection of srfA-D gene showed that isolate produced surfactin biosynthesis thioesterase. Thus, Bacillus sp. EG6.4 produced biosurfactant that potentially to be developed as a biocontrol agent for disease vectors and plant pathogens.

First Description of the Mitogenome Features of Neofoleyellides Genus (Nematoda: Onchocercidae) Isolated from a Wild Bird (Pyrrhocorax pyrrhocorax).

Simple SummaryFilarioidea, a superfamily of nematodes, presently includes 42 species divided into six genera, mainly in the family Onchocercidae, which have been reported to infect a wide range of hosts, including reptiles, birds, and mammals. Current limitations in molecular characterization methods and species identification are the main obstacles to a better understanding of the biology of Onchocercidae species, particularly in wildlife. Thus, the objective of the present study was to sequence and analyze the complete mt genome of Neofoleyellides sp. isolated from a wild bird (Pyrrhocorax pyrrhocorax) and to assess its phylogenetic position in the Onchocercidae family. The evaluated Neofoleyellides sp. mt genome was consistent with the molecular pattern of the Onchocercidae family: 36 subunits consisting of 12 PCGs, 2 rRNAs, and 22 tRNAs. Phylogenetic analyses based on the 18S rRNA gene, cox1 gene, and 12 PCGs showed consistent results, which strongly supported monophyly of the genus Neofoleyellides. These findings enriched the gene database and improved our knowledge of the molecular characteristics of the Onchocercidae family, which provide useful genetic markers to study the population genetics, molecular biology, and phylogenetics of these Onchocercidae nematodes.The Onchocercidae family is composed of more than 30 valid nematode species with notable zoonotic potential. Current limitations in molecular characterization methods and species identification are the main obstacles to a better understanding of the biology of Onchocercidae species, particularly in wildlife. This study describes for the first time the complete mitochondrial (mt) genome sequence of Neofoleyellides sp. isolated from a wild bird (Pyrrhocorax pyrrhocorax) and belonging to the Neofoleyellides genus (Nematoda: Onchocercidae). The mt genome of Neofoleyellides sp. (GenBank accession number: ON641583) was a typical circular DNA molecule of 13,628 bp in size with an AT content of 76.69%. The complete mt genome comprised 36 functional subunits, including 12 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. The most common start codon was ATT/ATG except for nad2 with TTG, and TAA was the termination codon for all protein-coding genes (PCGs). Phylogenetic analysis of the concatenated and aligned amino acid sequences of the 12 PCGs showed that the trees generated using different methods (Bayesian inference and maximum likelihood) with different partition schemes shared similar topologies. The isolated Neofoleyellides sp. was placed in the Onchocercidae family and formed a sister branch with the genera Onchocerca and Dirofilaria. The entire mt genome of Neofoleyellides sp. presented in this study could provide useful data for studying the population genetics and phylogenetic relationships of Onchocercidae species.

Molecular Identfication of Bacillus pumilus BY 16S rRNA from Abattoir Wastewater

Abattoir is one of the most pronounced but yet ignored sources of highly recalcitrant wastewater that pose many environmental challenges and cause harm to mankind. However, little was reported on the molecular identification of bacterial committee from the abattoir wastewater. This study aimed at isolation and molecular identification of most abundant bacterium species from wastewater of abattoir. Wastewater sample was collected, isolate and identify the most abundant bacterium by gram staining and microscopy. Genomic DNA (gDNA) was extracted from the isolated bacterium and conducted 16S rRNA PCR amplification. Multiple sequence and phylogenetic relationship among other 8 Bacillus species and 1 outgroup were inferred by comparing the sequence data sets from NBCI. The biochemical identification analyses indicated that the bacterium is gram positive with Bacillus shape and cream-yellow colour. 16S rRNA and bioinformatics analyses demonstrated that the most abundant isolated bacterium is Bacillus pumilus with 99% identification. Moreover, the phylogenetic tree analysis discovered that the identified bacterium from this study is more closely related to Bacillus species as they share the same clade. The sequence is partial as compared with the other deposited sequences in the GeneBank. This study provides an insight on the microbial species of Nigeria abattoir wastewater which was identified using molecular approach. As well, gave a clue for potential treatment of the wastewater.