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BMC Genomics Jul 2023Amphibians, particularly anurans, display an enormous variation in genome size. Due to the unavailability of whole genome datasets in the past, the genomic elements and...
BACKGROUND
Amphibians, particularly anurans, display an enormous variation in genome size. Due to the unavailability of whole genome datasets in the past, the genomic elements and evolutionary causes of anuran genome size variation are poorly understood. To address this, we analyzed whole-genome sequences of 14 anuran species ranging in size from 1.1 to 6.8 Gb. By annotating multiple genomic elements, we investigated the genomic correlates of anuran genome size variation and further examined whether the genome size relates to habitat types.
RESULTS
Our results showed that intron expansions or contraction and Transposable Elements (TEs) diversity do not contribute significantly to genome size variation. However, the recent accumulation of transposable elements (TEs) and the lack of deletion of ancient TEs primarily accounted for the evolution of anuran genome sizes. Our study showed that the abundance and density of simple repeat sequences positively correlate with genome size. Ancestral state reconstruction revealed that genome size exhibits a taxon-specific pattern of evolution, with families Bufonidae and Pipidae experiencing extreme genome expansion and contraction events, respectively. Our result showed no relationship between genome size and habitat types, although large genome-sized species are predominantly found in humid habitats.
CONCLUSIONS
Overall, our study identified the genomic element and their evolutionary dynamics accounting for anuran genome size variation, thus paving a path to a greater understanding of the size evolution of the genome in amphibians.
Topics: Animals; Genome Size; DNA Transposable Elements; Genomics; Anura; Evolution, Molecular
PubMed: 37415107
DOI: 10.1186/s12864-023-09499-8 -
PloS One 2023The lack of information regarding biodiversity status hampers designing and implementing conservation strategies and achieving future targets. Northern Pakistan consists...
The lack of information regarding biodiversity status hampers designing and implementing conservation strategies and achieving future targets. Northern Pakistan consists of a unique ecoregion mosaic which supports a myriad of environmental niches for anuran diversity in comparison to the deserts and xeric shrublands throughout the rest of the country. In order to study the niche suitability, species overlap and distribution patterns in Pakistan, we collected observational data for nine anuran species across several distinct ecoregions by surveying 87 randomly selected locations from 2016 to 2018 in Rawalpindi District and Islamabad Capital Territory. Our model showed that the precipitation of the warmest and coldest quarter, distance to rivers and vegetation were the greatest drivers of anuran distribution, expectedly indicating that the presence of humid forests and proximity to waterways greatly influences the habitable range of anurans in Pakistan. Sympatric overlap between species occurred at significantly higher density in tropical and subtropical coniferous forests than in other ecoregion types. We found species such as Minervarya spp., Hoplobatrachus tigerinus and Euphlyctis spp. preferred the lowlands in proximal, central and southern parts of the study area proximal to urban settlements, with little vegetation and higher average temperatures. Duttaphrynus bengalensis and D. stomaticus had scattered distributions throughout the study area with no clear preference for elevation. Sphaerotheca pashchima was patchily distributed in the midwestern extent of the study area as well as the foothills to the north. Microhyla nilphamariensis was widely distributed throughout the study area with a preference for both lowlands and montane terrain. Endemic frogs (Nanorana vicina and Allopaa hazarensis) were observed only in locations with higher elevations, higher density of streams and lower average temperatures as compared to the other seven species sampled. It is recommended to provide legal protection to amphibians of Pakistan, especially endemic species, through revision in the existing wildlife laws. We suggest studying the effectiveness of existing amphibian tunnels and corridors or designing new ones tailored to the needs of our species to prevent their local extinction due to ongoing or proposed urban development which might affect their dispersal and colonization.
Topics: Animals; Pakistan; Anura; Biodiversity; Forests; Bufonidae; Ecosystem
PubMed: 37319174
DOI: 10.1371/journal.pone.0285867 -
Toxins Mar 2024Toad Venom (TV) is the dried product of toxic secretions from Cantor (BgC) or Schneider (BmS). Given the increasing medical demand and the severe depletion of wild...
Toad Venom (TV) is the dried product of toxic secretions from Cantor (BgC) or Schneider (BmS). Given the increasing medical demand and the severe depletion of wild toads, a number of counterfeit TVs appeared on the market, posing challenges to its quality control. In order to develop an efficient, feasible, and comprehensive approach to evaluate TV quality, a thorough analysis and comparison of chemical compounds among legal species BgC and BmS, as well as the main confusion species Schmidt (BaS) and Strauch (BrS), were conducted by ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS), high performance liquid chromatography (HPLC), sodium dodecylsulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and Nano LC-MS/MS analyses. We identified 126 compounds, including free or conjugated bufadienolides, indole alkaloids and amino acids, among the four species. The content of main bufadienolides, such as gamabufotalin, bufotalin, bufalin, cinobufagin, and resibufogenin, and the total protein contents varied widely among 28 batches of TV due to their origin species. The sum of the five bufadienolides within the BgC, BmS, BaS, and BrS samples were 8.15-15.93%, 2.45-4.14%, 11.15-13.50%, and 13.21-14.68%, respectively. The total protein content of BgC (6.9-24.4%) and BaS (19.1-20.6%) samples were higher than that of BmS (4.8-20.4%) and BrS (10.1-13.7%) samples. Additionally, a total of 1357 proteins were identified. There were differences between the protein compositions among the samples of the four species. The results indicated that BgC TV is of the highest quality; BaS and BrS TV could serve as alternative resources, whereas BmS TV performed poorly overall. This research provides evidence for developing approaches to evaluate TV quality and selecting the proper species as the origin source of TV listed in the Chinese pharmacopoeia.
Topics: Animals; Amino Acids; Bufanolides; Bufonidae; Tandem Mass Spectrometry
PubMed: 38535825
DOI: 10.3390/toxins16030159 -
ELife Dec 2023Environmental seasonality can promote the evolution of larger brains through cognitive and behavioral flexibility but can also hamper it when temporary food shortage is...
Environmental seasonality can promote the evolution of larger brains through cognitive and behavioral flexibility but can also hamper it when temporary food shortage is buffered by stored energy. Multiple hypotheses linking brain evolution with resource acquisition and allocation have been proposed for warm-blooded organisms, but it remains unclear how these extend to cold-blooded taxa whose metabolism is tightly linked to ambient temperature. Here, we integrated these hypotheses across frogs and toads in the context of varying brumation (hibernation) durations and their environmental correlates. We showed that protracted brumation covaried negatively with brain size but positively with reproductive investment, likely in response to brumation-dependent changes in the socio-ecological context and associated selection on different tissues. Our results provide novel insights into resource allocation strategies and possible constraints in trait diversification, which may have important implications for the adaptability of species under sustained environmental change.
Topics: Animals; Hibernation; Brain; Anura; Bufonidae; Cold Temperature; Biological Evolution
PubMed: 38085091
DOI: 10.7554/eLife.88236 -
Scientific Reports Sep 2023The host-microbiome community is influenced by several host and environmental factors. In order to disentangle the individual effects of host and environment, we...
The host-microbiome community is influenced by several host and environmental factors. In order to disentangle the individual effects of host and environment, we performed a laboratory experiment to assess the effects of the exposure to different water sources on the skin and gut microbiome of two amphibian species (Pelophylax perezi and Bufo spinosus). We observed that the bacterial communities greatly varied with water environment and host identity. Tadpoles of B. spinosus collected from a waterbody with poorer bacterial diversity exhibited a more diverse skin and gut microbiome after exposed to a richer water source. Tadpoles of P. perezi, originally collected from a richer water environment, exhibited less marked alterations in diversity patterns independently of the water source but showed alterations in gut composition. These results highlight that environment alterations, such as the water source, combined with the host effect, impact the microbiome of amphibian species in different ways; the population history (e.g., previous water environment and habitat) of the host species may also influence future alterations on tadpole microbiome.
Topics: Animals; Gastrointestinal Microbiome; Larva; Water; Microbiota; Bufonidae; RNA, Ribosomal, 16S
PubMed: 37770544
DOI: 10.1038/s41598-023-43340-2 -
Toxins Mar 2024Antimicrobial peptides (AMPs) are key molecules in the innate immune defence of vertebrates with rapid action, broad antimicrobial spectrum, and ability to evade...
Antimicrobial peptides (AMPs) are key molecules in the innate immune defence of vertebrates with rapid action, broad antimicrobial spectrum, and ability to evade pathogen resistance mechanisms. To date, amphibians are the major group of vertebrates from which most AMPs have been characterised, but most studies have focused on the bioactive skin secretions of anurans (frogs and toads). In this study, we have analysed the complete genomes and/or transcriptomes of eight species of caecilian amphibians (order Gymnophiona) and characterised the diversity, molecular evolution, and antimicrobial potential of the AMP repertoire of this order of amphibians. We have identified 477 candidate AMPs within the studied caecilian genome and transcriptome datasets. These candidates are grouped into 29 AMP families, with four corresponding to peptides primarily exhibiting antimicrobial activity and 25 potentially serving as AMPs in a secondary function, either in their entirety or after cleavage. In silico prediction methods were used to identify 62 of those AMPs as peptides with promising antimicrobial activity potential. Signatures of directional selection were detected for five candidate AMPs, which may indicate adaptation to the different selective pressures imposed by evolutionary arms races with specific pathogens. These findings provide encouraging support for the expectation that caecilians, being one of the least-studied groups of vertebrates, and with ~300 million years of separate evolution, are an underexplored resource of great pharmaceutical potential that could help to contest antibiotic resistance and contribute to biomedical advance.
Topics: Humans; Animals; Antimicrobial Peptides; Anura; Bufonidae; Evolution, Molecular; Anti-Infective Agents
PubMed: 38535816
DOI: 10.3390/toxins16030150 -
Ecotoxicology and Environmental Safety Nov 2023The impacts of lead/Pb on ecosystems have received widespread attention. Growth suppression is a major toxic effect of Pb compounds on aquatic animals, however, some...
The impacts of lead/Pb on ecosystems have received widespread attention. Growth suppression is a major toxic effect of Pb compounds on aquatic animals, however, some studies have also reported their growth-promoting effects. These complex outcomes may be explained by anions that accompany Pb or by the multiple toxic mechanisms/pathways of Pb. To examine these hypotheses, we tested how Bufo gargarizans tadpoles responded to Pb(NO) (100 and 200 μg/L Pb) using transcriptomics and microbiomics, with NaNO and blank groups as controls. Tadpoles exposed to Pb(NO) showed delayed development while increased somatic growth in a dose-dependent manner, which can be attributed to the effects of NO and Pb, respectively. Tadpole transcriptomics revealed that exposure to NO downregulated the MAPK pathway at transcriptional level, explaining the development-suppressing effect of NO; while Pb upregulated the transcription of detoxification pathways (e.g., xenobiotics metabolism by cytochrome P450 and glutathione metabolism), indicating cellular stress and thus contradicting the growth advantage of Pb-exposed tadpoles. Pb exposure changed the tadpole gut microbiota drastically, characterized by increased polysaccharides and carbohydrate utilization while decreased fatty acid and amino acid consumption according to microbial functional analysis. Similar gut microbial variations were observed in field-collected tadpoles from different Pb environments. This metabolic shift in gut microbiota likely improved the overall food utilization efficiency and increased the allocation of fatty acids and amino acids to the host, explaining the growth advantage of Pb-exposed tadpoles. In summary, our results suggest multiple toxic pathways of Pb, and the gut microbiota may affect the pollution outcomes on animals.
Topics: Animals; Larva; Gastrointestinal Microbiome; Lead; Ecosystem; Bufonidae
PubMed: 37890260
DOI: 10.1016/j.ecoenv.2023.115601 -
PeerJ 2023Hybridization following secondary contact may produce different outcomes depending on the extent to which genetic diversity and reproductive barriers have accumulated...
Hybridization following secondary contact may produce different outcomes depending on the extent to which genetic diversity and reproductive barriers have accumulated during isolation. The Japanese toad, , is distributed on the main islands of Japan. In the present study, we applied multiplexed inter-simple sequence repeat genotyping by sequencing to achieve the fine-scale resolution of the genetic cluster in and . We also elucidated hybridization patterns and gene flow degrees across contact zones between the clusters identified. Using SNP data, we found four genetic clusters in and and three contact zones of the cluster pairs among these four clusters. The two oldest diverged lineages, and , formed a narrow contact zone consistent with species distinctiveness. Therefore, we recommend that these two subspecies be elevated to the species level. In contrast, the less diverged pairs of two clusters in and , respectively, admixed over a hundred kilometers, suggesting that they have not yet developed strong reproductive isolation and need to be treated as conspecifics. These results will contribute to resolving taxonomic confusion in Japanese toads.
Topics: Animals; Bufonidae; Genetics, Population; Hybridization, Genetic; Japan
PubMed: 37901459
DOI: 10.7717/peerj.16302 -
International Journal of Molecular... Jun 2023Amplexus is a type of mating behavior among toads that is essential for successful external fertilization. Most studies have primarily focused on the behavioral...
Amplexus is a type of mating behavior among toads that is essential for successful external fertilization. Most studies have primarily focused on the behavioral diversity of amplexus, and less is known regarding the metabolic changes occurring in amplectant males. The aim of this study was to compare the metabolic profiles of amplectant Asiatic toad () males in the breeding period (BP group) and the resting males in the non-breeding period (NP group). A metabolomic analysis was conducted on the flexor carpi radialis (FCR), an essential forelimb muscle responsible for clasping during courtship. A total of 66 differential metabolites were identified between the BP and NP groups, including 18 amino acids, 12 carbohydrates, and 8 lipids, and they were classified into 9 categories. Among these differential metabolites, 13 amino acids, 11 carbohydrates, and 7 lipids were significantly upregulated in the BP group compared to the NP group. In addition, a KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis identified 17 significant metabolic pathways, including ABC transporters, aminoacyl-tRNA biosynthesis, arginine biosynthesis, pantothenate and CoA biosynthesis, and fructose and mannose metabolism. These results suggest that amplectant male toads are metabolically more active than those during the non-breeding period, and this metabolic adaptation increases the likelihood of reproductive success.
Topics: Animals; Male; Adaptation, Physiological; Amino Acids; Bufonidae; Carbohydrate Metabolism; Carbohydrates; Energy Metabolism; Forelimb; Lipid Metabolism; Metabolome; Muscle, Skeletal; Sexual Behavior, Animal
PubMed: 37373324
DOI: 10.3390/ijms241210174 -
Scientific Reports Jul 2023Facultative colour change is widespread in the animal kingdom, and has been documented in many distantly related amphibians. However, experimental data testing the...
Facultative colour change is widespread in the animal kingdom, and has been documented in many distantly related amphibians. However, experimental data testing the extent of facultative colour change, and associated physiological and morphological implications are comparatively scarce. Background matching in the face of spatial and temporal environmental variation is thought to be an important proximate function of colour change in aquatic amphibian larvae. This is particularly relevant for species with long larval periods such as the western spadefoot toad, Pelobates cultripes, whose tadpoles spend up to six months developing in temporary waterbodies with temporally variable vegetation. By rearing tadpoles on different coloured backgrounds, we show that P. cultripes larvae can regulate pigmentation to track fine-grained differences in background brightness, but not hue or saturation. We found that colour change is rapid, reversible, and primarily achieved through changes in the quantity of eumelanin in the skin. We show that this increased eumelanin production and/or maintenance is also correlated with changes in morphology and oxidative stress, with more pigmented tadpoles growing larger tail fins and having an improved redox status.
Topics: Animals; Larva; Antioxidants; Melanins; Bufonidae; Anura; Pigmentation
PubMed: 37495600
DOI: 10.1038/s41598-023-39107-4