NJ Tree Research Articles

Molecular insights of mitochondrial 16S rDNA genes of the native honey bees subspecies Apis mellifera carnica and Apis mellifera jementica (Hymenoptera: Apidae) in Saudi Arabia

The honey bee Apis mellifera is of major importance for the world’s agriculture and is also suitable for environmental monitoring. It includes several recognized subspecies distinguished by using morphological and morphometric variants. Here, 200 adult worker Apis mellifera honey bees were collected from Hail region, Saudi Arabia. Mitochondrial 16S rDNA was conducted to detect molecular polymorphism among honey bee A. mellifera subspecies. The amplified and sequenced gene regions of mtDNA revealed the presence of two different subspecies of Apis mellifera carnica (gb| MH939276.1) and Apis mellifera jementica (gb| MH939277.1). The sequences were compared with each other and with others retrieved from the GenBank demonstrating a high degree of similarity (up to 72%). The NJ tree indicated that all Apis species are clustered together in one clade in addition to the genetically origin of Apis species within family Apidae as a paraphyletic group within the African lineage.

NUEVOS MARCADORES MITOCONDRIALES MEJORAN LA FILOGENIA DE LA TORTUGA CAREY Eretmochelys imbricata (TESTUDINES: CHELONIIDAE)

The sea turtles (Cheloniidae) are a group of seven species of cretaceous origin. Analyses of partial mitochondrial sequences have revealed phylogenetic inconsistences within this group. Nevertheless, these mitochondrial markers have allowed us to understand, explain and clarify population composition in areas of foraging, reproductive habits, inferences of migration patterns and, also, to define management units in the world, in order to trace conservation and monitoring plans. In this study, four methods were evaluated and compared for phylogenetic inference (Neighbor-Joining-NJ, Maximum Likelihood-ML, Maximum Parsimony-MP and Bayesian inference-BI) by using coding genes, ribosomal genes and full mitogenomes of the hawksbill, E. imbricata, and other six species of sea turtles obtained from GenBank. The sequences were analyzed independently and jointly to identify the method and marker that better explain the phylogenetic relationships among this group of reptiles. The NJ, ML, MP and BI trees showed that ND2, COX1, 16S rRNA, ND5, 12S rRNA, ND4 and COX3 are the markers that give phylogenetic trees with better resolution and support, with bootstrap values ranging from 89.0% to 99.98%. ATP6, ATP8, COX2, ND1, ND3, ND5 and ND4L genes presented polytomies. The analysis with full mitogenome often provides highly supported trees (bootstrap 98.0%) compared with single marker analysis. Trees obtained with the BI method and the ND2 gene is the one that better resolved the evolutionary relationships among the species, consolidating the position of E. imbricata within the Carettini tribe with a value of posterior probability of 0.98-1.0. The markers ND2, ND4, ND5 and COIII, not used in previous works, represent a new alternative to explain the phylogeny in this group of marine reptiles. In the present study, a complete mitogenome analysis produced robust and highly supported trees. Key words: phylogenetic relationships, Eretmochelys imbricate, mitogenoma, sea turtles, bootstrap, polytomies

Barcoding of parasitoid wasps (Braconidae and Chalcidoidea) associated with wild and cultivated olives in the Western Cape of South Africa 1.

Wild and cultivated olives harbor and share a diversity of insects, some of which are considered agricultural pests, such as the olive fruit fly. The assemblage of olive-associated parasitoids and seed wasps is rich and specialized in sub-Saharan Africa, with native species possibly coevolving with their hosts. Although historical entomological surveys reported on the diversity of olive wasp species in the Western Cape Province of South Africa, no comprehensive study has been performed in the region in the molecular era. In this study, a dual approach combining morphological and DNA-based methods was used for the identification of adult specimens reared from olive fruits. Four species of Braconidae and six species of Chalcidoidea were identified, and DNA barcoding methodologies were used to investigate conspecificity among individuals, based on randomly selected representative specimens. Morphological identifications were congruent with DNA data, as NJ and ML trees correctly placed the sequences for each species either at the genus or species level, depending on the available taxa coverage, and genetic distances strongly supported conspecificity. No clear evidence of cryptic diversity was found. Overall seed infestation and parasitism rates were higher in wild olives compared to cultivated olives, and highest for Eupelmus spermophilus and Utetes africanus. These results can be used for early DNA-based detection of wasp larvae in olives and to further investigate the biology and ecology of these species.

New epidemic cluster of pre-extensively drug resistant isolates of Mycobacterium tuberculosis Ural family emerging in Eastern Europe

BackgroundUral genetic family is a part of the Euro-American lineage of Mycobacterium tuberculosis and is endemic in Northern Eurasia (former Soviet Union [FSU]). These strains were long described as drug susceptible and of low virulence, but recent studies reported an increasing circulation of the multidrug-resistant (MDR) and extensively drug-resistant (XDR) Ural strains. Here, we analyzed all publicly available whole genome sequence data of Ural genotype isolates, in order to elucidate their phylogenomic diversity with a special focus on MDR and potentially epidemic clones.ResultsA total of 149 M. tuberculosis genomes of Ural isolates from FSU countries were mined from the GMTV database and TB-ARC project. We identified 6002 variable amino acid positions that were assessed for functional significance and used to build ML, NJ trees and for Bayesian TMRCA estimation. Three robust monophyletic clades were identified: Clade A (31 isolates from Russia, Belarus, Moldova), Clade B (52 isolates from Russia), and Clade C (37 isolates from Moldova, 2 from Belarus). Clade C was significantly associated with XDR or pre-XDR status compared to the pooled Clades A and B (33/39 versus 5/83, P < 0.0001). Time of origin was estimated for Clade A at 77.7–137 years ago and for Clade B at 56.3–99.2 years ago compared to the significantly more recent origin for Clade C. in silico spoligotyping identified signatures specific of the Clade A (spoligotype SIT35), and Clades B and C (both SIT262).ConclusionsA genetically compact and evolutionarily young Ural Clade C, likely originated after collapse of the Soviet Union, and reached epidemic proportions in Moldova in the last 20 years. This epidemic pre-XDR clone (mostly rifampin, isoniazid and kanamycin resistant) is characterized by a specific combination of mutations: KatG Ser315Thr, fabG1 -15C > T, RpoB Ser450Leu, RpsL Lys88Arg, eis -12G > A and EmbB Ser297Ala/T > G. Its further dissemination may occur towards both Russia and European Union and should be taken into consideration by health authorities. The identified spoligotyping signatures can serve for rapid preliminary detection and surveillance of the more hazardous pre-XDR associated strains of the Ural family, both in populations from countries of their endemic circulation and migrant communities.

English

Inter Simple Sequence Repeat (ISSR) markers were employed to reveal genetic diversity and relatedness among 27 chickpea (Cicer arietinum L.) cultivars in Ethiopia. Four di-nucleotide repeat primers amplified 24 clear and reproducible bands of which 22 were polymorphic (91.67%). The genetic variation among 27 chickpea cultivars including 12 kabuli and 15 desi verities is high; in which desi type exhibited a genetic diversity of 75% with Shannon index of 0.47, while the kabuli type chickpea had 91.67% genetic diversity and Shannon index of 0.50. Unweighted Pair Group of Arithmetic mean (UPGMA) dendrogram and NJ trees with Jaccard’s similarity coefficient showed three major clusters. This was also recovered by 3D principal coordinates analysis, although some cultivars were intermixed. Analysis of molecular variance (AMOVA) demonstrated highly significant (p < 0.001) genetic diversity within cultivars (97.71%) than among cultivars (2.29%). The distinct cultivars (Aererti, Tejie, Fetenech and Maryie) can serve as parents for future genetic resources conservation and Chickpea breeding program in Ethiopia. Key word: Chickpea cultivars, genetic diversity, ISSR markers, Ethiopia.

Diversity of The Ornate Lorikeet (Trichoglossus ornatus) Birds Based on Mitochondrial DNA Protein Coding Gene

Ornate lorikeet (Trichoglossus ornatus) is an endemic bird in Sulawesi. Endemism is one of the factors in declining bird’s population. In the case of the birds conservation programme, information about gene diversity is important for basic strategy. Mitochondrial DNA of animals consists of protein coding genes including ND2 gene. This study informs diversity of the Ornate Lorikeet (Trichoglossus ornatus) birds based on DNA sequences of ND2 gene. DNA total was extracted from blood samples of 21 birds. PCR (Polymerase Chain Reaction) was performed and successfully amplified a single DNA fragment of ND2 gene for all birds. DNA fragments were sequenced and totally 997 base pairs were analyzed. NJ tree was constructed using MEGA5. All DNA sequence data showed that between the birds there were 20 polymorphic (segregating) sites with mean genetic distance was 0.004 ± 0.002 (ranged from 0,000 – 0,008), and had 17 sequence haplotypes (HTor1- HTo17). Haplotype diversity (Hd) was 0.967 ± 0.30387 and nucleotide diversity (Pi) was 0.00439 ± 0.0012. Genetic diversity information could be potential relevance to the breeding management for conservation of the birds.

DNA barcoding of Cloridopsis immaculata: genetic distance and phylogeny of stomatopods

The changes of coastal topography might have genetically altered the extant species diversity in Chilika Lake. The genetic assessment of stomatopods has never been attempted from this ecosystem. The study generate the first genetic information (mtCOI) of Cloridopsis immaculata. DNA sequences of C. immaculata shows 12.9% genetic divergence with Harpiosquilla harpax and clade as sister species in NJ tree. Alima, Harpiosquilla, and Oratosquilla shows high congeneric/conspecific genetic divergence (20.9%, 15.7%, and 7.2%) and cladded separately in the phylogeny; correlate to their diverse populations. We recommend more extensive survey of stomatopods and generation of molecular data to resolve the taxonomic uncertainty.

The complete mitochondrial genome of Hyporhamphus quoyi (Beloniformes; Hemiramphidae)

The complete mitogenome of Hyporhamphus quoyi was sequenced, which is a closed double-stranded circular molecule of 16,511 bp, and we analyzed the main features in terms of the genome organization, gene arrangement and codon usage. The overall base composition includes A(27.4%), T(26.0%), C(30.4%) and G(16.2%). Moreover, the 13 protein-coding genes (PCGs) encode 3804 amino acids in total, 12 of which use the initiation codon ATG except COI uses GTG, most of them have a complete stop codon, whereas Cytb ends with the incomplete stop codon represented as a single T. The phylogenetic tree based on the neighbor-Joining method was conducted to provide relationship within Beloniformes, based on 12 PCGs encoded by the heavy strand, the NJ tree demonstrated that H. quoyi has a closest relationship with Hyporhamphus intermedius, which could be a useful basis for propagation of this species.

Isolation, identification, and molecular diversity of indigenous isolates of Beauveria bassiana from Taif region, Saudi Arabia

The entomopathogenic fungus, Beauveria bassiana causes a disease known as the white muscadine disease in insects. Most of the entomopathogenic fungi are soil borne nature an attempt was made to collect the soil samples from various ecosystems. Therefore, the present study aimed to isolate native strains of B. bassiana and study their genetic diversity at Taif region, Saudi Arabia, using ITS of nuclear DNA and COI gene analysis by comparing of different isolates from occasional localities through the world. Ninety-four soil samples were collected from different regions at Taif. Only 11 samples had B. bassiana fungus with a ratio of 11.7%. Sequences of ITS (593 bp), and partial COI (437 bp) of these isolates were carried out and revealed that four differed in their genetics. These sequences were deposited in the DDBJ GenBank database with eight accession numbers. Consequently, the three analytical methods (MP, NJ, and ML) executed a single tree with identical topology. The tree identified the studied isolates into two main clusters; the first contained Uzbekistan and USA isolates. The Chinese isolate clustered with this group in the MP tree and was diverged as a single cluster in the NJ tree. The second clade included the newly studied four isolates from Taif and the Italian isolate. The pairwise genetic distances among the four studied isolates (D ranged between 0.002 and 0.008) showed that they were genetically closely related. Further studies are needed to indicate more differentiation among these isolates and to evaluate their efficacy against the important insect pests in Saudi Arabia.

The complete mitochondrial genome of the larval Bombay duck Harpodon nehereus (Aulopiformes, Synodontidae) from Yangtze estuary and the phylogenetic relationship of Synodontidae species

The complete mitochondrial genome of the larvae Harpodon nehereus collected from Yangtze estuary was determined by next-generation sequencing. The mitogenome is a circular molecule 16,536 bp in length, including the typical structure of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region. The TAS, central CSB and CSB were detected in the control region. The gene contents of the mitogenome are identical to those observed in most marine bony fishes. The NJ tree showed that H. nehereus clustered in a branch close to the species from the same genus.

The complete mitochondrial genome of long-tailed whiskered bat, Myotis frater (Myotis, Vespertilionidae)

Here, we report the complete mitogenome of Myotis frater with the GenBank accession number MH177276 as a first step to elucidate genetic characteristics of this species. Its mitogenome was 17,089 bp long and consisted of 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and a control region. The gene order and composition of M. frater was similar to that of most other vertebrates. The base composition of the 13 PCG in descending order was A (33.8%), C (22.7%), T (30.4%), and G (13.1%), with an AT content of 64.2%. Four overlapping regions in ATP8/ATP6, ATP6/COX3, ND4L/ND4, and ND5/ND6, among the 13 PCGs were found. The 935 bp long control region is located between tRNA-Pro and tRNA-Phe with 4 ATTACATAATACATTATATGTATAATCGTACATTAAATTAACTCCCACATGAATATTAAGCATGTCCATACTAATATTAAT-repeat at 5′ region and 45 ACGCAT-repeat at 3′ terminus. Phylogenetic analysis suggested that M. frater is most closely related to M. bechsteinii (KX757757), it was supported by 100% bootstrap under both ML and NJ tree.

Emerging risks in the European seafood chain: Molecular identification of toxic Lagocephalus spp. in fresh and processed products

Pufferfish may be responsible for human intoxications due to the accumulation of a potentially lethal neurotoxin, called tetrodotoxin (TTX). While traditionally some species of pufferfish are consumed in Japan, their marketing is banned in the EU. However, their illegal presence in mislabelled products has been reported. Moreover, some species of the genus Lagocephalus spread in the Mediterranean Sea during the last decades due to the Lessepsian migration phenomenon and they may represent a significant emerging risk within the European seafood chain. This study aimed at finding a suitable molecular marker for quickly identifying Lagocephalus species in fresh and processed products. All available sequences of COI and cytb mitochondrial genes were used to create different length datasets (long and short fragments) to be used to produce NJ trees depicting genetic relationships for Lagocephalus spp. On the basis of its higher variability, cytb gene was selected as the molecular target and 17 new complete sequences of 6 Lagocephalus species, deriving from reference samples, were produced and included in the datasets. Then, a primer pair for amplifying a 130bp cytb polymorphic fragment from all of the Lagocephalus spp. was designed for identifying sixteen mislabelled commercial products containing pufferfish with degraded DNA. Cytb dataset's phylogenetic analysis supported the most recent species classification of the Lagocephalus genus and highlighted the presence of toxic L. spadiceus in the products. The analysis of the proposed short fragment could represent a reliable tool to protect European consumers from the emerging risk associated to toxic Lagocephalus spp.

Taxonomic assessment of the Oxytropis species from South-East of Kazakhstan

The genus Oxytropis DC. is one of the largest genera in the Fabaceae family. The most plant species belonging to the Oxytropis genus have an important medicinal value. Currently the botanical taxonomy of the genus is complicated due to existence of many subgenera and sections that developed based on morphological traits. Also, in the literature there is luck of knowledge on phylogeny of Oxytropis species from Central Asian region. Therefore, the purpose of the present study was the clarification of taxonomic relationship of two Oxytropis species from SouthEast of Kazakhstan (O. almaatensis Bajt. and O. glabra DC.). The study was based on using phylogenetic analysis and haplotype network assessment based on sequences ITS (internal transcribed spacers), which is DNA marker of nuclear genome. Plant materials of O. almaatensis were collected from 2 populations in two neighboring Gorges in Trans Ili Alatau Mountains, O. glabra plant material was obtained from Herbarium of the Department of Biodiversity and Bioresources, al-Farabi Kazakh National University. Based on DNA sequences of ITS the phylogenetic and network relationships were investigated by using Neighbor Joining and Median Joining methods, respectively. The nucleotide sequences of ITS of O. almaatensis and O. glabra were aligned with sequences of 29 Oxytropis references found in the NCBI database. Out of the 601 aligned positions of ITS 33 (5.6 %) sites were found to be polymorphic nucleotides and used in evaluation of the genetic relationship of species. Constructed MJ haplotype network showed a very high congruence with the NJ phylogenetic tree. MJ network provided valuable additional hints in clarification of the taxonomic relationship among species involved in the analysis. In this study phylogenetic NJ tree and MJ network based on the variation of ITS sequences confirmed the monophyletic origin of the genus. The ITS haplotype network suggested that O. glabra is very diverse species and possibly played important role in the evolutionary processes of the genus in Central Asian region. The study is additional contribution in the molecular taxonomy of complex Oxytropis genus.

Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae).

Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for phylogenetic comparative analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.

Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae)

Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for comparative phylogenetic analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.

Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae)

Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for phylogenetic comparative analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.

Forensic parameters and admixture in Mestizos from five geographic regions of Mexico based on 20 autosomal STRs (Powerplex 21 system).

We analyzed Mestizo (admixed) population samples from different geographic regions of Mexico (n= 1283) with 20 autosomal STRs (PowerPlex® 21, Promega Corp.). Allele frequencies and forensic parameters from the Northwest, Northeast, West, Center, and Southeast regions are reported, as well as from the pooled Mexican population sample. The combined PD and PE for this 20 STR system were > 0.9999999999 and > 0.99999996593% in all five population samples, respectively. Analysis of molecular variance (AMOVA) of these Mexican population samples, plus Monterrey (Northeast) and Mexico (Center) Cities, showed low but significant differences among Mexican-Mestizos from the seven populations (Fst = 0.20%; p = 0.0000). Structure analysis showed the highest proportion of Native American ancestry in Mexico City, Center, and Southeast regions, respectively, which was in agreement with the estimated genetic distances represented in a MDS plot and a NJ tree. The best fit of population clusters (K = 4) obtained with the Structure software indicates that Mexican-Mestizos are mainly composed by European, African, and two Native American ancestries. The European and Native American ancestries displayed a contrary gradient, increasing toward the North-West and South-Southeast, respectively. These 20 autosomal STR loci improved the admixture estimation regarding previous studies with the 13 CODIS-STRs, as supported by the higher similarity with previous estimates based on genome-wide SNP. In brief, this study validates the confident use of the PowerPlex® 21 system for human identification purposes in Mestizo populations throughout the Mexican territory.

Phylogeographic pattern of Liza affinis populations in Chinese coastal waters: estimation of larval dispersal potential

To examine phylogeographic pattern of Liza affinis populations in Chinese coastal waters, eight geographic populations were collected and analyzed using sequence analysis based on the first hypervariable region of mitochondrial control region. A total of 117 haplotypes from eight populations were obtained from 223 individuals and 22 of them were shared among different populations. High values of haplotype diversity and nucleotide diversity were observed for eight populations. The topology of the NJ tree was shallow, and there were no significant genealogical branches or clusters corresponding to sampling localities. The values of pairwise Fst ranged from −0.009 to 0.171 and most of them were not statistically significant after sequential Bonferroni correction. The results of LAMARC also indicated no significant population genetic structure in L. affinis along the Chinese coast. The demographic history of Liza affinis examined by neutrality tests and mismatch distribution analysis suggested a population expansion event dating back to late Pleistocene. The potential larval dispersal ability coupled with the present ocean currents and the late Pleistocene environment should be responsible for the present phylogeographic pattern of Liza affinis.

Identification of bear bile powder and its adulterants by using DNA barcoding technology

To identify the precious bile powder and its adulterants by DNA barcoding, and establish its standard experimental process to ensure the safe and effective utilization. Total twelve sequences from samples of bear bile powder which come from Ursus thibetanus for DNA extraction, PCR(polymerase chain reaction) and sequence, then using CodonCode Aligner V 7.0.1 shear primer region to obtain COI sequence. The COI sequences of U. arctos and their adulterants were obtained from GenBank. MEGA7.0 software was applied for analyzing mutation, calculating intraspecific and interspecific K2P(Kimura 2-Parameter) genetic distance and constructing the Neighbor-joining tree(NJ). The results showed that the maximum K2P genetic distance of bear bile powder of U. thibetanus and U. arctos are far less than minimum K2P genetic distance within its adulterants species, and the results of NJ tree demonstrated that each species could be distinguished from the counterfeits obviously. DNA barcoding is a safe, convenient and reliable technique for species identification, and it is important to establish the standard sequence of COI sequences for animal medicines.

Identification of penaeid shrimp from Chilika Lake through DNA barcoding

Chilika Lake is one of the prolific habitats of shrimps in India and offers tons of commercial trading every year. The genetic diversity of penaeid shrimp species in this oldest and largest brackish water lagoon is unknown so far. The DNA barcoding is emerging as an essential supportive tool for morphology-based species identification. In this study, we have generated DNA barcode data of morphologically identified six penaeid shrimps from Chilika Lake. Most of the generated sequences revealed 99–100% similarities with the conspecific database sequences (GenBank and BOLD). More than one distinct clade in NJ tree and high-genetic variability were resulted in P. monodon (6.5% to 8.8%), L. vannamei (3.2% to 5.8%) and M. monoceros (2.3% to 3.5%). The resulted genetic variation within the species depicted different population correlate with the different sampling locations. Thus, more extensive survey and generation of more DNA barcode data of penaeid shrimp from the diverse geographical area might resolve the uncertain genetic distance within the species.