Neighbor-joining Phylogeny Research Articles

Construction of the core germplasm of yellowhorn (Xanthoceras sorbifolium Bunge) using physiological traits and SSR markers

Yellowhorn (Xanthoceras sorbifolium Bunge) is an important ecological, economic, and ornamental plant species native to China. However, the physiological diversity, genetic variation, and core germplasms have not been revealed, which hindered the breeding process of yellowhorn. Here, we evaluated the genetic diversity of 155 yellowhorn germplasms using five physiological traits. The content of flavonoids varied significantly in different germplasms, and it was positively correlated with soluble sugar content (P < 0.01). A total of 253, 336 candidate SSR were identified from the whole genome of yellowhorn. A moderate genetic diversity was found in yellowhorn based on the mean values of the number of effective alleles (Ne = 2.307), expected heterozygosity (He = 0.527), and observed heterozygosity (Ho = 0.317) with 30 pairs of polymorphic SSR markers. Population structure, Neighbor-Joining phylogeny, and principal coordinates analyses divided all genotypes into two major groups with few admixtures. Meanwhile, we extracted 34 (21.94 %) core yellowhorn germplasms based on the variation in physiological traits (14 germplasms) and genetic diversity (23 germplasms). After multiple different analyses including genetic diversity parameters, coincidence rate of range, variance difference percentage, and coefficient of variation rate of change, there was no obvious difference between core and original germplasm, which indicated that the core germplasm could represent the original germplasm well. Our study will lay a solid foundation for future conservation and management of yellowhorn germplasms and the core collection will be valuable in molecular breeding programs.

Comparative Analysis of Genetic Structure and Diversity in Five Populations of Yellowtail Kingfish (Seriola aureovittata)

To clarify the population genetic structure, intrapopulation diversity, and interpopulation differentiation of yellowtail kingfish (Seriola aureovittata), we sampled 143 individuals from five collections of yellowtail kingfish: farmed (n = 30) and wild (n = 33) collections in China, a wild collection in Japan (n = 20), and farmed (n = 31) and wild (n = 29) collections in Australia. Using 2b-RAD simplified genome sequencing, we obtained an average of 287,594 unique tags per population, with an average sequencing depth of 27.13×. Our final genotype dataset included 48,710 SNPs (Single Nucleotide Polymorphisms). The five collections were all in Hardy–Weinberg equilibrium, and the interpopulation differentiation varied among the sample collections. The genetic differentiation coefficients (Fst) between the Chinese and Japanese yellowtail kingfish collections were low and the gene flow (Nm) values were high. These results suggest continuous gene flow occurs frequently between the collections, indicating that they belong to the same population. In contrast, genetic differentiation was high between the Australian collections and the Chinese and Japanese populations, suggesting different evolutionary origins and belonging to different populations. The farmed and wild Australian collections fell into distinct clades in a neighbor-joining phylogeny tree, suggesting farmed fish have begun to differentiate from the wild collection. A similar level of genetic diversity between the wild collections in China and Japan suggests that they originated from the same spawning ground. This, therefore, reminds us that in future aquaculture processes attention is needed regarding implementing targeted breeding strategies. In addition, our data will contribute to Chinese yellowtail kingfish genetic breeding and the sustainable use of Chinese yellowtail kingfish germplasms.

Core-Genome Multilocus Sequence Typing for Epidemiological and Evolutionary Analyses of Phytopathogenic Xanthomonas citri.

Xanthomonas citri subsp. citri is the cause of bacterial citrus canker, responsible for major economic losses to the citrus industry. X. citri subspecies and pathovars are responsible for diseases in soybean, common bean, mango, pomegranate, and cashew. X. citri disease has been tracked using several typing methods, but recent studies using genomic sequencing have been key to understanding the evolutionary relationships within the species, including fundamental differences among X. citri subsp. citri pathotypes. Here, we describe a core-genome multilocus sequence typing (cgMLST) scheme for X. citri based on 250 genomes comprising multiple examples of X. citri subsp. citri pathotypes A, A*, and Aw; X. citri subsp. malvacearum; X. citri pv. aurantifolii, pv. fuscans, pv. glycines, pv. mangiferaeindicae, pv. viticola, and pv. vignicola; and single isolates of X. citri pv. dieffenbachiae and pv. punicae. This data set included genomic sequencing of 100 novel X. citri subsp. citri isolates. cgMLST, based on 1,618 core genes across 250 genomes, is implemented at PubMLST (https://pubmlst.org/organisms/xanthomonas-citri/). GrapeTree minimum-spanning tree and Interactive Tree of Life (iTOL) neighbor-joining phylogenies generated from the cgMLST data resolved almost identical groupings of isolates to a core-genome single nucleotide polymorphism (SNP)-based neighbor-joining phylogeny. These resolved identical groupings of X. citri subsp. citri pathotypes and X. citri subspecies and pathovars. X. citri cgMLST should prove to be an increasingly valuable resource for the study of this key species of plant-pathogenic bacteria. Users can submit genomic data and associated metadata for comparison with previously characterized isolates at PubMLST to allow the rapid characterization of the local, national, and global epidemiology of these pathogens and examine evolutionary relationships. IMPORTANCE Xanthomonas citri is a plant pathogen that causes major economic losses to the citrus industry and sweet orange production in particular. Several subspecies and pathogens are recognized, with host ranges including soybean, common bean, mango, pomegranate, and cashew, among others. Recent genomic studies have shown that host-adapted X. citri subspecies and pathovars and X. citri subsp. citri pathotypes form distinct clades. In this study, we describe a core-genome multilocus sequence typing (cgMLST) scheme for this species that can rapidly and robustly discriminate among these ecologically distinct, host-adapted clades. We have established this scheme and associated databases containing genomic sequences and metadata at PubMLST, which users can interrogate with their own genome sequences to determine X. citri subspecies, pathovars, and pathotypes. X. citri cgMLST should prove to be an invaluable tool for the study of the epidemiology and evolution of this major plant pathogen.

DNA barcoding of a lesser-known catfish, Clupisoma bastari (Actinopterygii: Ailiidae) from Deccan Peninsula, India

DNA barcoding substantiates species identification, and simultaneously indicates the misnomer taxa. Based on the morphological descriptions, we identified a lesser-known catfish, Clupisoma bastari, from Godavari River basin, and contributed novel DNA barcode data to the GenBank. The Kimura 2 parameter genetic divergence between species, and the neighbour-joining phylogeny clearly depicted a distinct clade of C. bastari in the studied dataset. Clupisoma bastari maintained sufficient K2P genetic divergence (8.3% to 11.2%) with other congeners, and branched as a sister-species of C. garua. The present study highlights possible existence of a few misnomer taxa in the GenBank. We encourage further extensive sampling of different congeners of Clupisoma from a wide range of habitats to explore the species diversity and phylogenetic relationship.

Taxonomic position, antibiotic resistance and virulence factor production by Stenotrophomonas isolates from patients with cystic fibrosis and other chronic respiratory infections

BackgroundThe potential pathogenic role of Stenotrophomonas maltophilia in lung disease and in particular in cystic fibrosis is unclear. To develop further understanding of the biology of this taxa, the taxonomic position, antibiotic resistance and virulence factors of S. maltophilia isolates from patients with chronic lung disease were studied.ResultsA total of 111 isolates recovered between 2003 and 2016 from respiratory samples from patients in five different countries were included. Based on a cut-off of 95%, analysis of average nucleotide identity by BLAST (ANIb) showed that the 111 isolates identified as S. maltophilia by Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/MS) belonged to S. maltophilia (n = 65), S. pavanii (n = 6) and 13 putative novel species (n = 40), which each included 1–5 isolates; these groupings coincided with the results of the 16S rDNA analysis, and the L1 and L2 ß-lactamase Neighbor-Joining phylogeny. Chromosomally encoded aminoglycoside resistance was identified in all S. maltophilia and S. pavani isolates, while acquired antibiotic resistance genes were present in only a few isolates. Nevertheless, phenotypic resistance levels against commonly used antibiotics, determined by standard broth microbroth dilution, were high. Although putative virulence genes were present in all isolates, the percentage of positive isolates varied. The Xps II secretion system responsible for the secretion of the StmPr1–3 proteases was mainly limited to isolates identified as S. maltophilia based on ANIb, but no correlation with phenotypic expression of protease activity was found. The RPF two-component quorum sensing system involved in virulence and antibiotic resistance expression has two main variants with one variant lacking 190 amino acids in the sensing region.ConclusionsThe putative novel Stenotrophomonas species recovered from patient samples and identified by MALDI-TOF/MS as S. maltophilia, differed from S. maltophilia in resistance and virulence genes, and therefore possibly in pathogenicity. Revision of the Stenotrophomonas taxonomy is needed in order to reliably identify strains within the genus and elucidate the role of the different species in disease.

Survey for Yellow Mosaic Disease Occurring on Blackgram [Vigna mungo (L.) Hepper] and Weed Hosts in Four Major Blackgram Growing Districts of Andhra Pradesh and Characterization of Associated Viruses using Coat Protein Gene

Background: Yellow mosaic disease (YMD) caused by Yellow mosaic virus is one of the major constraints in the pulse production in Andhra Pradesh (A.P.) due to fast evolution of strains, like Mungbean yellow mosaic India virus (MYMIV). Keeping this in view, a survey was undertaken in the major blackgram growing districts of A.P. to know the YMD incidence in blackgram and weed hosts and were characterized based on genetic features by comparing with other YMV isolates from different hosts and locations across the world. Methods: Roving survey was conducted during rabi 2019-20 in major blackgram growing districts of A.P. viz., Krishna, Guntur, West Godavari and Prakasam districts for YMD incidence. Blackgram plants showing characteristic symptoms were collected as representative samples from each mandal along with the suspected weed plants and were subjected to amplification using coat protein (CP) specific primers followed by molecular characterization. Phylogenetic tree for coat protein (CP) gene was constructed using aligned sequences with 1000 bootstrap replicates following neighbor-joining phylogeny. Result: Out of the four districts surveyed, the highest disease incidence was recorded at Machavaram village of Prakasam district (43.22%), whereas least disease incidence was recorded at Chinaganjam village of Praksam district (2.4%). Six weeds viz., Ageratum conyzoides, Amaranthus viridis, Parthenium hysterophporus, Vigna trilobata, Abelmoscus moschatus, Desmodium laxiflorum have showed positive result in PCR amplification with MYMIV specific coat protein primers. Four isolates from blackgram samples and two from weed plants shared 94.85 to 99.58% nucleotide identity among themselves.

Discovery of potential phytases of the purple acid phosphatase family in a wide range of photosynthetic organisms and insights into their structure and evolution

PAPhys are phytases that belong to the family of purple acid phosphatases (PAPs). Currently, there is limited information about how to distinguish a PAPhy sequence from a PAP without phytase activity. PAPhys have only been identified in angiosperm plants; therefore, it is unknown how prevalent they are in other photosynthetic organisms and what their phylogenetic relationships are. Therefore, the purpose of this research is to discover potential PAPhys using novel PAPhy-associated motifs and provide new information on their phylogeny. Experimentally validated PAPhys were identified and analyzed using the neighbor-joining phylogeny, and from each clade, a consensus sequence (CS) was generated. CSs were analyzed with the Multiple Em for Motif Elicitation (MEME) tool to identify characteristic motifs; with these motifs, potential PAPhys were searched in a broad range of photosynthetic organisms using the Motif Alignment & Search Tool (MAST). Genes encoding potential PAPhys were analyzed by maximum-likelihood phylogeny. Twenty-one PAPhys were identified in the literature and resolved into five clades. The MEME analysis generated four PAPhy-associated motifs (M1 to M4). A total of 160 potential PAPhys were identified with MAST. The phylogeny of these potential PAPhys revealed 11 major clades, among which six clades do not possess any experimentally studied PAPhy. The PAPhy motifs identified in this work were useful for identifying potential PAPhys. Phylogenetic analysis suggested that PAPhys are an ancient class of proteins in photosynthetic organisms. These new insights have provided valuable information on the evolution of this class of phytases and may assist in the cloning of novel PAPhys, which could lead to biotechnological applications.

Complete genome sequence and probiotic properties of Lactococcus petauri LZys1 isolated from healthy human gut.

Introduction. Lactococcus petauri LZys1 (L. petauri LZys1) is a type of lactic acid bacteria (LAB), which was initially isolated from healthy human gut.Hypothesis/Gap Statement. It was previously anticipated that L. petauri LZys1 has potential characteristics of probiotic properties. The genetic structure and the regulation functions of L. petauri LZys1 need to be better revealed.Aim. The aim of this study was to detect the probiotic properties L. petauri LZys1 and to reveal the genome information related to its genetic adaptation and probiotic profiles.Methodology. Multiple in vitro experiments were carried out to evaluate its lactic acid-producing ability, resistance to pathogenic bacterial strains, auto-aggregation and co-aggregation ability, and so on. Additionally, complete genome sequencing, gene annotation, and probiotic associated gene analysis were performed.Results. The complete genome of L. petauri LZys1 comprised of 1 985 765 bp, with a DNA G+C content of 38.07 %, containing 50 tRNA, seven rRNA, and four sRNA. A total of 1931 genes were classified into six functional categories by Kyoto Encyclopaedia of Genes and Genomes (KEGG) database. The neighbour-joining phylogeny tree based on the whole genome of L. petauri LZys1 and other probiotics demonstrated that L. petauri LZys1 has a significant similarity to Lactococcus garvieae. The functional genes were detected to expound the molecular mechanism and biochemical processes of its potential probiotic properties, such as atpB gene.Conclusion. All the results described in this study, together with relevant information previously reported, made L. prtauri LZys1 a very interesting potential strain to be considered as a prominent candidate for probiotic use.

De novo transcriptome assembly of the green alga Ankistrodesmus falcatus.

Ankistrodesmus falcatus is a globally distributed freshwater chlorophyte that is a candidate for biofuel production, is used to study the effects of toxins on aquatic communities, and is used as food in zooplankton research. Each of these research fields is transitioning to genomic tools. We created a reference transcriptome for of A. falcatus using NextGen sequencing and de novo assembly methods including Trinity, Velvet-Oases, and EvidentialGene. The assembled transcriptome has a total of 17,997 contigs, an N50 value of 2,462, and a GC content of 64.8%. BUSCO analysis recovered 83.3% of total chlorophyte BUSCOs and 82.5% of the eukaryotic BUSCOs. A portion (7.9%) of these supposedly single-copy genes were found to have transcriptionally active, distinct duplicates. We annotated the assembly using the dammit annotation pipeline, resulting in putative functional annotation for 68.89% of the assembly. Using available rbcL sequences from 16 strains (10 species) of Ankistrodesmus, we constructed a neighbor-joining phylogeny to illustrate genetic distances of our A. falcatus strain to other members of the genus. This assembly will be valuable for researchers seeking to identify Ankistrodesmus sequences in metatranscriptomic and metagenomic field studies and in experiments where separating expression responses of zooplankton and their algal food sources through bioinformatics is important.

A Disjunctive Marginal Edge of Evergreen Broad-Leaved Oak (Quercus gilva) in East Asia: The High Genetic Distinctiveness and Unusual Diversity of Jeju Island Populations and Insight into a Massive, Independent Postglacial Colonization.

Jeju Island is located at a marginal edge of the distributional range of East Asian evergreen broad-leaved forests. The low genetic diversity of such edge populations is predicted to have resulted from genetic drift and reduced gene flow when compared to core populations. To test this hypothesis, we examined the levels of genetic diversity of marginal-edge populations of Quercus gilva, restricted to a few habitats on Jeju Island, and compared them with the southern Kyushu populations. We also evaluated their evolutionary potential and conservation value. The genetic diversity and structure were analyzed using 40 polymorphic microsatellite markers developed in this study. Ecological Niche Modeling (ENM) has been employed to develop our insights, which can be inferred from historical distribution changes. Contrary to our expectations, we detected a similar level of genetic diversity in the Jeju populations, comparable to that of the southern Kyushu populations, which have been regarded as long-term glacial refugia with a high genetic variability of East Asian evergreen trees. We found no signatures of recent bottlenecks in the Jeju populations. The results of STRUCTURE, neighbor-joining phylogeny, and Principal Coordinate Analysis (PCoA) with a significant barrier clearly demonstrated that the Jeju and Kyushu regions are genetically distinct. However, ENM showed that the probability value for the distribution of the trees on Jeju Island during the Last Glacial Maximum (LGM) converge was zero. In consideration of these results, we hypothesize that independent massive postglacial colonization from a separate large genetic source, other than Kyushu, could have led to the current genetic diversity of Jeju Island. Therefore, we suggest that the Jeju populations deserve to be separately managed and designated as a level of management unit (MU). These findings improve our understanding of the paleovegetation of East Asian evergreen forests, and the microevolution of oaks.

Applicability of inter-simple sequence repeat (ISSR), start codon targeted (SCoT) markers and ITS2 gene sequencing for genetic diversity assessment in Moringa oleifera Lam

Moringa oliefera Lam. is the most widely cultivated species among the members of Moringa genus in tropics for its nutritional and medicinal values. Almost all plant parts have been used in human's nutrition and therapy. The molecular characterizations are required for effective improvement for better utilization. In the present study, genetic variation in ten individual Moringa oleifera plants were investigated using ten primers of each inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) markers. In current study, SCoT is used for the first time to assess the genetic diversity in moringa. The results of ISSR and SCoT analysis for the ten local M. oleifera revealed approximately 91 and 108 different banding patterns, 73 and 87 of them consider as monomorphic bands and other 18 and 21 fragments consider as polymorphic bands with a percentage about 19.7 and 19.4%, respectively. Low levels of polymorphism were observed between ISSR and SCoT which means that they are useful tools for genetic similarity detection in M. oleifera species. Sequence identity of M. oleifera plants in relation to NCBI data base were 96, 100, 99 and 99 with ITS2, matK, psbA and rbcL genes, respectively, with lower E value (≤1e). Moreover, the phylogenetic Neighbor-joining (NJ) tree was constructed using rbcL, matK, psbA and ITS gene sequences. M. oleifera clustered into two clades with 99% similarity. The results suggest that the neighbor-joining phylogeny tree could effectively identify M. oleifera from its adulterants, including its closely related species. M. oleifera showed a sister relationship to M. oleifera MG548808.1 and M. oleifera KT737756.1. The results confirmed the usefulness of molecular techniques such ISSR, SCoT and ITS barcoding markers to assess the genetic diversity among the selected M. oleifera types for genetic conservation and plant improvement.

The genetic diversity and population structure of Sophora alopecuroides (Faboideae) as determined by microsatellite markers developed from transcriptome.

Sophora alopecuroides (Faboideae) is an endemic species, mainly distributed in northwest China. However, the limited molecular markers range for this species hinders breeding and genetic studies. A total of 20,324 simple sequence repeat (SSR) markers were identified from 118,197 assembled transcripts and 18 highly polymorphic SSR markers were used to explore the genetic diversity and population structure of S. alopecuroides from 23 different geographical populations. A relatively low genetic diversity was found in S. alopecuroides based on mean values of the number of effective alleles (Ne = 1.81), expected heterozygosity (He = 0.39) and observed heterozygosity (Ho = 0.55). The results of AMOVA indicated higher levels of variation within populations than between populations. Bayesian-based cluster analysis, principal coordinates analysis and Neighbor-Joining phylogeny analysis roughly divided all genotypes into four major groups with some admixtures. Meanwhile, geographic barriers would have restricted gene flow between the northern and southern regions (separated by Tianshan Mountains), wherein the two relatively ancestral and independent clusters of S. alopecuroides occur. History trade and migration along the Silk Road would together have promoted the spread of S. alopecuroides from the western to the eastern regions of the northwest plateau in China, resulting in the current genetic diversity and population structure. The transcriptomic SSR markers provide a valuable resource for understanding the genetic diversity and population structure of S. alopecuroides, and will assist effective conservation management.

Genetic Diversity, Population Structure, and Linkage Disequilibrium of Pearl Millet.

Mapping of GBS reads of 398 accessions to the draft genome sequence identified 82,112 SNPs Model-based clustering analysis revealed a hierarchical genetic structure of six subgroups Greater LD decay in the west-African subpopulation is likely due to long history of recombination Genetic differentiation analysis among subpopulations revealed variation in selection signatures Pearl millet [Cenchrus americanus (L.) Morrone syn. Pennisetum glaucum (L.) R. Br.] is one of the most extensively cultivated cereals in the world, after wheat (Triticum aestivum L.), maize (Zea mays L.), rice (Oryza sativa L.), barley (Hordeum vulgare L.), and sorghum [Sorghum bicolor (L.) Moench]. It is the main component of traditional farming systems and a staple food in the arid and semiarid regions of Africa and southern Asia. However, its genetic improvement is lagging behind other major cereals and the yield is still low. Genotyping-by-sequencing (GBS)-based single-nucleotide polymorphism (SNP) markers were screened on a total of 398 accessions from different geographic regions to assess genetic diversity, population structure, and linkage disequilibrium (LD). By mapping the GBS reads to the reference genome sequence, 82,112 genome-wide SNPs were discovered. The telomeric regions of the chromosomes have the higher SNP density than in pericentromeric regions. Model-based clustering analysis of the population revealed a hierarchical genetic structure of six subgroups that mostly overlap with the geographic origins or sources of the genotypes but with differing levels of admixtures. A neighbor-joining phylogeny analysis revealed that germplasm from western Africa rooted the dendrogram with much diversity within each subgroup. Greater LD decay was observed in the west-African subpopulation than in the other subpopulations, indicating a long history of recombination among landraces. Also, genome scan of genetic differentiatation detected different selection histories among subpopulations. These results have potential application in the development of genomic-assisted breeding in pearl millet and heterotic grouping of the lines for improved hybrid performance.

Genome-Wide Analysis of Carboxylesterases (COEs) in the Whitefly, Bemisia tabaci (Gennadius).

The whitefly (Bemisia tabaci), an important invasive pest that causes severe damage to crops worldwide, has developed resistance to a variety of insecticides. Carboxylesterases (COEs) are important multifunctional enzymes involved in the growth, development, and xenobiotic metabolism of insects. However, systematic studies on the COEs of B. tabaci are scarce. Here, 42 putative COEs in different functional categories were identified in the Mediterranean species of B. tabaci (B. tabaci MED) based on a genome database and neighbor-joining phylogeny. The expression patterns of the COEs were affected by the development of B. tabaci. The expression levels of six COEs were positively correlated with the concentration of imidacloprid to which B. tabaci adults were exposed. The mortality of B. tabaci MED adults fed dsBTbe5 (67.5%) and dsBTjhe2 (58.4%) was significantly higher than the adults fed dsEGFP (41.1%) when treated with imidacloprid. Our results provide a basis for functional research on COEs in B. tabaci and provide new insight into the imidacloprid resistance of B. tabaci.

DNA Barcoding Reveals Association of Glossiphoniidae Species on Endangered Freshwater Turtles in Northeast India.

The identification of Glossiphoniidae species is often confusing due to the lack of both morphological and molecular data worldwide. The study aimed to identify the collected leech specimens from two endangered freshwater turtles, Chitra indica and Pangshura sylhetensis from northeast India. We generated DNA barcode sequences and estimated the genetic distances and phylogenetic relationship of the studied taxa with another 14 Glossiphoniidae genera (114 barcode sequences). The high genetic distinctiveness (17.9 to 26.3%) and distinct clustering in Neighbor-Joining (NJ) phylogeny, we identified the studied specimens as Glossiphoniidae sp. We assumed that the studied specimens might be a new member of Glossiphoniidae or an extant species without DNA information. Hence, the study recommends further sampling of leeches from the similar host as well as from same and various localities and also generates the molecular data to perceive the exact diversity. The aimed study is also helpful to encourage the awareness and conservation management of freshwater turtles and other threatened animals.

DNA barcoding reveals distinct population of Plotosus canius (Siluriformes: Plotosidae) in Sundarbans waters

The Gray eel-catfish, Plotosus canius is a widely distributed species in Indo-West Pacific region and predominantly found in marine and brackish water. Although the recent genetics study evidenced the different population of P. canius from Southeast Asia, sampling from Indian water is required to assess the ample population structure. Hence, the current study is aimed to generate the DNA sequences of P. canius from Sundarban to recognize the genetic distinctiveness of the Indian population. Both P. canius and P. lineatus showed more than one clade in neighbor-joining (NJ) phylogeny. Further, the high genetic divergences in P. canius (5.2–11%) and P. lineatus (3.6–11%) depicted cryptic and diverse population. The median-joining network with 21 haplotypes also suggested unique haplogroup of P. canius from Sundarbans. However, more sampling of P. canius from diverse geographical locations and involving additional molecular markers would substantiate the conservation genetics and proper management.

DNA barcoding adjudicate two different morphs of Bascanichthys deraniyagalai (Anguilliformes: Ophichthidae): re-description and first record from Chilika lagoon, India

Morphological characters and distribution pattern of the snake eel, Bascanichthys deraniyagalai is debatable during the past half-century. Thus, the species is re-described herewith by morphometry, vertebrae, and molecular data. In recent Chilika expedition in India, we have collected 10 specimens and observed a vertebral count dimorphism. The present study distinctly detected two vertebral groups of B. deraniyagalai: first group with 5 predorsal vertebrae, 81–83 preanal vertebrae, 190–196 total vertebrae in females; however, the sex of the second group with 5 predorsal vertebrae, 72–74 preanal vertebrae, 176–178 total vertebrae was not able to confirm. Further, the molecular data of morphologically identified two distinct groups of B. deraniyagalai shows negligible Kimura 2 parameter genetic divergence and cohesive clustering in Neighbor-Joining phylogeny proved to be the two different morphs of the same species. Hence, the present study indicated there might be vertebral count or sexual dimorphism in B. deraniyagalai, which need further sampling and taxonomic revision to unwrap the fact.

DNA barcoding identified two endangered dolphins: threats on living aquatic mammals in India

DNA barcode data of both endangered dolphin species, Platanista gangetica, and Orcaella brevirostris are lacking in the global database. The study generated partial mitochondrial cytochrome c oxidase subunit I (mtCOI) gene sequences of the two highly threatened dolphin species from India. The family Platanistidae with one species and family Delphinidae with 12 species were showed 1.2%–19.7% between species genetic divergence in the studied dataset. Both P. gangetica and O. brevirostris were revealed distinct clade in neighbor-joining (NJ) phylogeny. Further, D. delphis, S. coeruleoalba, and T. truncatus have shown more than one clade and comparatively high genetic divergence within the species suggested prominent genetic variation between different populations. The study recommends generating more DNA barcode data from diverse habitats of P. gangetica and O. brevirostris to evaluate the exact population structure and adopting better conservation strategies thereafter.

Organizing hematologic gene sequence data using neighbor joining phylogeny method

There are a number of methods to spot orthologous genes from homologous genes. Since identifying orthologous genes are main problem and play a major role in the hematologic genetic disorders. In this paper, we propose different approaches to discover orthologs of homologous hereditary diseases of the hematological system and find the evolutionary relationship between hereditary genetic diseases of the hematological system by adjoining the joining method of contiguous merging trees.

DNA testing of edible crabs from seafood shops on the Odisha coast, India.

Seafood consumption is highly demanding due to the important source of protein it contains, as well as being rich in omega-3 fatty acids. However, the adulteration of seafood is an alarming issue worldwide, including India. This study deals with edible crabs from seafood shops on the Odisha state coast in eastern India. The generated DNA barcode sequences successfully identified most of the studied brachyuran crab species by similarity search results in global databases. The species were also delimited by significant genetic divergence and Neighbour-Joining phylogeny. Additionally, the study detected the contamination of unknown organisms in the commercialized crab recipes from seafood shops. The DNA based species detection of brachyuran crab may be useful to resolve many ambiguities in species identification and monitoring of commercialized seafood concerning food safety.