Browse
Submit Data
Databases
API
Help

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Concerted and Independent Evolution of Control Regions 1 and 2 of Water Monitor Lizards (Varanus salvator macromaculatus) and Different Phylogenetic Informative Markers.

ABSTRACT: Duplicate control regions (CRs) have been observed in the mitochondrial genomes (mitogenomes) of most varanids. Duplicate CRs have evolved in either concerted or independent evolution in vertebrates, but whether an evolutionary pattern exists in varanids remains unknown. Therefore, we conducted this study to analyze the evolutionary patterns and phylogenetic utilities of duplicate CRs in 72 individuals of Varanus salvator macromaculatus and other varanids. Sequence analyses and phylogenetic relationships revealed that divergence between orthologous copies from different individuals was lower than in paralogous copies from the same individual, suggesting an independent evolution of the two CRs. Distinct trees and recombination testing derived from CR1 and CR2 suggested that recombination events occurred between CRs during the evolutionary process. A comparison of substitution saturation showed the potential of CR2 as a phylogenetic marker. By contrast, duplicate CRs of the four examined varanids had similar sequences within species, suggesting typical characteristics of concerted evolution. The results provide a better understanding of the molecular evolutionary processes related to the mitogenomes of the varanid lineage.

SUBMITTER: Thapana W

PROVIDER: S-EPMC8772547 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Gut Bacteria of Water Monitor Lizard (Varanus salvator) Are a Potential Source of Antibacterial Compound(s).

Project description:For the past few decades, there has been limited progress in the development of novel antibacterials. Previously, we postulated that the gut microbiota of animals residing in polluted environments are a forthcoming supply of antibacterials. Among various species, the water monitor lizard is an interesting species that feeds on organic waste and the carcass of wild animals. Gut microbiota of the water monitor lizard were sequestered, identified and cultivated in RPMI-1640 to produce conditioned medium (CM). Next, the antimicrobial properties of CM were evaluated versus a selection of Gram-negative (Escherichia coli K1, Serratia marcescens, Pseudomonas aeruginosa, Salmonella enterica and Klebsiella pneumoniae) and Gram-positive bacteria (Streptococcus pyogenes, methicillin-resistant Staphylococcus aureus, and Bacillus cereus). CM were partially characterized by heat inactivation at 95°C for 10 min and tested against P. aeruginosa and S. pyogenes. CM were also tested against immortalized human keratinocytes (HaCaT) cells lines. The results demonstrated that gut microbiota isolated from water monitor lizard produced molecules with remarkable bactericidal activities. To determine the identity of the active molecules, CM were subjected to Liquid Chromatography-Mass Spectrometry. Several molecules were identified belonging to the classes of flavonoids, terpenoids, alkaloids, polyhydroxy alkaloids, polyacetylenes, bisphenols, amides, oxylipin and pyrazine derivatives with known broad-spectrum antimicrobial, anti-tumour, anti-oxidant, anti-inflammatory, and analgesic attributes. Furthermore, the detailed analysis of these molecules could lead us to develop effective therapeutic antibacterials.

| S-EPMC6963368 | biostudies-literature

Varanus salvator

Project description:Varanus salvator overview

| PRJNA930078 | ENA

Dietary Correlates of Oral and Gut Microbiota in the Water Monitor Lizard, <i>Varanus salvator</i> (Laurenti, 1768).

Project description:Numerous studies have demonstrated that food shapes the structure and composition of the host's oral and gut microbiota. The disorder of oral and gut microbiota may trigger various host diseases. Here, we collected oral and gut samples from wild water monitor lizards (Varanus salvator) and their captive conspecifics fed with bullfrogs, eggs, and depilated chicken, aiming to examine dietary correlates of oral and gut microbiota. We used the 16S rRNA gene sequencing technology to analyze the composition of the microbiota. Proteobacteria and Bacteroidota were the dominant phyla in the oral microbiota, and so were in the gut microbiota. The alpha diversity of microbiota was significantly higher in the gut than in the oral cavity, and the alpha diversity of oral microbiota was higher in captive lizards than in wild conspecifics. Comparing the relative abundance of oral and gut bacteria and their gene functions, differences among different animal groups presumably resulted from human contact in artificial breeding environments and complex food processing. Differences in gene function might be related to the absolute number and/or the taxonomic abundance of oral and gut microorganisms in the wild and the water environment. This study provides not only basic information about the oral and gut microbiota of captive and wild water monitor lizards, but also an inference that feeding on frogs and aquatic products and reducing human exposure help water monitor lizards maintain a microbiota similar to that in the wild environment.

| S-EPMC8770915 | biostudies-literature

The investigation of antibacterial properties of peptides and protein hydrolysates derived from serum of Asian water monitor (Varanus salvator).

Project description:It is well known that the Asian water monitors or Varanus salvator are both scavengers and predators. They can live and survive in the place that exposed to harmful microorganisms. Most people believe that they have some protected mechanisms to confront those infections. The aim of this study is to determine the antibacterial activities of crude peptides and protein hydrolysates extracted from serum of the Varanus salvator. Ten types of bacteria were cultured with crude peptides and protein hydrolysates which were isolated from 21 Varanus salvator's serum. The crude peptides showed some interested inhibition percentages against Enterobacter aerogenes ATCC13048 = 25.6%, Acinetobacter baumannii ATCC19606 = 33.4%, Burkholderia cepacia ATCC25416 = 35.3% and Pseudomonas aeruginosa ATCC27853 = 25.8%, whereas the protein hydrolysates had some inhibition potential on Burkholderia cepacia ATCC25416 = 24.3%. For the rest results of other tests were below 20% of inhibition. In addition, the evidences show that crude peptides have better antibacterial performances significantly than protein hydrolysates on most tested bacteria. Furthermore, antimicrobial peptides prediction shows about 10 percent hit (41/432 sequences). The interpretation shows that the best hit sequence is highly hydrophobic. It may destroy outer membrane of Gram-negative hence prevents the invasion of those bacteria. Altogether, bioinformatics and experiments show similar trends of antimicrobial peptide efficacy from Varanus salvator. Further studies need to be conducted on peptide purification and antimicrobial peptide candidate should be identified.

| S-EPMC10584125 | biostudies-literature

Unveiling the urban colonization of the Asian water monitor (<i>Varanus salvator</i>) across its distribution range using citizen science.

Project description:BackgroundThis study aims to investigate the urban colonization of the Asian water monitor (Varanus salvator) across its entire range of distribution, addressing the paucity of research on this species in urban ecosystems. The research spans the geographic range of the Asian water monitor, focusing on urbanized areas where the species accumulates more observations (Bangkok, Colombo, Jakarta, Kuala Lumpur and Singapore).MethodsWe conducted a systematic review to comprehensively assess the current knowledge of the species' presence in cities. Additionally, citizen science data from repositories like GBIF (Global Biodiversity Information facility ) were utilized to analyze the distribution patterns of V. salvator in urban environments. To elucidate urban distribution and correct collection biases, observations were weighted by sampling effort, using as a proxy all squamate occurrences available from 2010-2023, including V. salvator.ResultsDespite the widespread presence of the Asian water monitor in numerous cities within its distribution range, the available studies on the topic appear to be scarce. Existing research primarily consists of descriptive reports on diet and behavior. Our findings indicate that V. salvator predominantly colonizes green patches in urban areas, such as parks and small gardens. Larger cities exhibit higher records, potentially due to both permanent populations and increased citizen science reporting.ConclusionsThe Asian water monitor, as the largest lizard with established populations in cities, remains scarcely studied on a broader scale. However, the urban design of each city seems relevant to understand the distribution patterns within each context. Our study highlights the need for further research to explore the ecological and human dimensions associated with the species' presence in urban environments.

| S-EPMC11344998 | biostudies-literature

Varanus salvator komaini

Project description:Complete mitochondrial genome of black water monitor (Varanus salvator komaini) and water monitor (V. salvator macromaculatus)

| PRJNA865528 | ENA

Varanus salvator macromaculatus

Project description:Varanus salvator macromaculatus

| PRJNA865529 | ENA

The peripheral blood mononuclear cells preparation and the hematology of Varanus salvator.

Project description:The objectives of this study were to evaluate the proper anticoagulants coated in blood-collecting tube for the peripheral blood mononuclear cells (PBMCs) isolation and to evaluate the proper culture temperature for the Varanus salvator's PBMCs, in addition, the hematological characteristics also reported. The heparin treated blood (n = 10) and EDTA treated blood (n = 10) from Varanus salvator were obtained for PBMCs evaluation. The PBMCs obtained from the heparin treated blood was significantly higher than that of EDTA treated blood during the culture period (P < 0.05) indicated heparin would be more appropriated anticoagulant for blood collection. The PBMCs cultured under 37°C and 27°C were not significantly difference on first three days but 37°C showed significantly higher effect in the following days (P < 0.05) indicated both temperatures can be used which 37°C should be an optimal for PBMCs preparation. The peripheral blood cells of Varanus salvator (n = 49) were analyzed for hematological profiles and characteristics which the number of erythrocytes 1.19 ± 0.04 x 1012/L (1.17-1.35 x 1012/L) and WBC 2.41 ± 0.13 x 109/L (2.29-2.81 x 109/L) with absolute differential count of heterophils 0.92 ± 0.02 x 109/L (0.87-0.95 x 109/L), lymphocytes 1.17 ± 0.01 x 109/L (1.15-1.23 x 109/L), azurophils 0.40 ± 0.01 x 109/L (0.37-0.42 x 109/L), basophils 0.000 ± 0.001 x 109/L (0.004-0.011 x 109/L) and monocytes 0.027 ± 0.002 x 109/L (0.028-0.039 x 109/L). These results would play an important role on the cell immunological studies of the Varanus salvator in the future.

| S-EPMC9307208 | biostudies-literature

Morphometric dataset of Varanus salvator for non-invasive sex identification using machine learning.

Project description:Reliable sex identification in Varanus salvator traditionally relied on invasive methods like genetic analysis or dissection, as less invasive techniques such as hemipenes inversion are unreliable. Given the ecological importance of this species and skewed sex ratios in disturbed habitats, a dataset that allows ecologists or zoologists to study the sex determination of the lizard is crucial. We present a new dataset containing morphometric measurements of V. salvator individuals from the skin trade, with sex confirmed by dissection post- measurement. The dataset consists of a mixture of primary and secondary data such as weight, skull size, tail length, condition etc. and can be used in modelling studies for ecological and conservation research to monitor the sex ratio of this species. Validity was demonstrated by training and testing six machine learning models. This dataset has the potential to streamline sex determination, offering a non-invasive alternative to complement existing methods in V. salvator research, mitigating the need for invasive procedures.

| S-EPMC10997747 | biostudies-literature

Revision of Varanus marathonensis (Squamata, Varanidae) based on historical and new material: morphology, systematics, and paleobiogeography of the European monitor lizards.

Project description:Monitor lizards (genus Varanus) inhabited Europe at least from the early Miocene to the Pleistocene. Their fossil record is limited to about 40 localities that have provided mostly isolated vertebrae. Due to the poor diagnostic value of these fossils, it was recently claimed that all the European species described prior to the 21st century are not taxonomically valid and a new species, Varanus amnhophilis, was erected on the basis of fragmentary material including cranial elements, from the late Miocene of Samos (Greece). We re-examined the type material of Varanus marathonensis Weithofer, 1888, based on material from the late Miocene of Pikermi (Greece), and concluded that it is a valid, diagnosable species. Previously unpublished Iberian material from the Aragonian (middle Miocene) of Abocador de Can Mata (Vallès-Penedès Basin, Barcelona) and the Vallesian (late Miocene) of Batallones (Madrid Basin) is clearly referable to the same species on a morphological basis, further enabling to provide an emended diagnosis for this species. Varanus amnhophilis appears to be a junior subjective synonym of V. marathonensis. On the basis of the most complete fossil Varanus skeleton ever described, it has been possible to further resolve the internal phylogeny of this genus by cladistically analyzing 80 taxa coded for 495 morphological and 5729 molecular characters. Varanus marathonensis was a large-sized species distributed at relatively low latitudes in both southwestern and southeastern Europe from at least MN7+8 to MN12. Our cladistic analysis nests V. marathonensis into an eastern clade of Varanus instead of the African clade comprising Varanus griseus, to which it had been related in the past. At least two different Varanus lineages were present in Europe during the Neogene, represented by Varanus mokrensis (early Miocene) and V. marathonensis (middle to late Miocene), respectively.

| S-EPMC6281198 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data