Search

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomics resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomics resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, antipredator strategies, and resilience and adaptive responses. They also serve as critical models for understanding widespread genomic characteristics, including evolutionary genome expansions and contractions given they have the largest range in genome sizes of any animal taxon and multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The advent of long-read sequencing technologies, along with computational techniques that enhance scaffolding capabilities and streamline computational workload is now enabling the ability to overcome some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC) in early 2023. This burgeoning community already has more than 282 members from 41 countries (6 in Africa, 131 in the Americas, 27 in Asia, 29 in Australasia, and 89 in Europe). The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and outline how the AGC can enable amphibian genomics research to "leap" to the next level.

Symbiotic interactions can determine the evolutionary trajectories of host species, influencing genetic variation through selection and changes in demography. In the context of strong selective pressures such as those imposed by infectious diseases, symbionts providing defences could contribute to increase host fitness upon pathogen emergence. Here, we generated genome-wide data of an amphibian species to find evidence of evolutionary pressures driven by two skin symbionts: a batrachochytrid fungal pathogen and an antifungal bacterium. Using demographic modelling, we found evidence of decreased effective population size, probably due to pathogen infections. Additionally, we investigated host genetic associations with infection status, antifungal bacterium abundance and overall microbiome diversity using structural equation models. We uncovered relatively lower nucleotide diversity in infected frogs and potential heterozygote advantage to recruit the candidate beneficial symbiont and fight infections. Our models indicate that environmental conditions have indirect effects on symbiont abundance through both host body traits and microbiome diversity. Likewise, we uncovered a potential offsetting effect among host heterozygosity-fitness correlations, plausibly pointing to different ecological and evolutionary processes among the three species due to dynamic interactions. Our findings revealed that evolutionary pressures not only arise from the pathogen but also from the candidate beneficial symbiont, and both interactions shape the genetics of the host. Our results advance knowledge about multipartite symbiotic relationships and provide a framework to model ecological and evolutionary dynamics in wild populations. Finally, our study approach can be applied to inform conservation actions such as bioaugmentation strategies for other imperilled amphibians affected by infectious diseases., (© 2022 John Wiley & Sons Ltd.)

While some pathogens are limited to single species, others can colonize many hosts, likely contributing to the emergence of novel disease outbreaks. Despite this biodiversity threat, traits associated with host niche expansions are not well understood in multihost pathogens. Here, we aimed to uncover functional machinery driving multihost invasion by focusing on Batrachochytrium dendrobatidis (Bd), a pathogen that infects the skin of hundreds of amphibians worldwide. We performed a meta-analysis of Bd gene expression using data from published infection experiments and newly generated profiles. We analysed Bd transcriptomic landscapes across the skin of 14 host species, reconstructed Bd isolates phylogenetic relationships, and inferred the origin and evolutionary history of differentially expressed genes under a phylogenetic framework comprising other 12 zoosporic fungi. Bd displayed plastic infection strategies when challenged by hosts with different disease susceptibility. Our analyses identified sets of differentially expressed genes under host environments with similar infection outcome. We stressed nutritional immunity and gene silencing as important processes required to overcome challenging skin environments in less susceptible hosts. Overall, Bd genes expressed during amphibian skin exploitation have arisen mainly via gene duplications with great family expansions, increasing the gene copy events previously described for this fungal species. Finally, we provide a comprehensive gene data set that can be used to further examine eco-evolutionary hypotheses for this host-pathogen system. Our study supports the idea that host environments exert contrasting selective pressures, such that gene expression plasticity could be one of the evolutionary keys leading to the success of multihost pathogens., (© 2022 John Wiley & Sons Ltd.)

Background: The amphibian skin microbiome is an important mediator of host health and serves as a potential source of undiscovered scientifically significant compounds. However, the underlying modalities of how amphibian hosts obtain their initial skin-associated microbiome remains unclear. Here, we explore microbial transmission patterns in foam-nest breeding tree frogs from Southeast Asia (Genus: Polypedates) whose specialized breeding strategy allows for better delineation between vertically and environmentally derived microbes. To facilitate this, we analyzed samples associated with adult frog pairs taken after mating-including adults of each sex, their foam nests, environments, and tadpoles before and after environmental interaction-for the bacterial communities using DNA metabarcoding data (16S rRNA). Samples were collected from frogs in-situ in Brunei, Borneo, a previously unsampled region for amphibian-related microbial diversity., Results: Adult frogs differed in skin bacterial communities among species, but tadpoles did not differ among species. Foam nests had varying bacterial community composition, most notably in the nests' moist interior. Nest interior bacterial communities were discrete for each nest and overall displayed a narrower diversity compared to the nest exteriors. Tadpoles sampled directly from the foam nest displayed a bacterial composition less like the nest interior and more similar to that of the adults and nest exterior. After one week of pond water interaction the tadpole skin microbiome shifted towards the tadpole skin and pond water microbial communities being more tightly coupled than between tadpoles and the internal nest environment, but not to the extent that the skin microbiome mirrored the pond bacterial community., Conclusions: Both vertical influence and environmental interaction play a role in shaping the tadpole cutaneous microbiome. Interestingly, the interior of the foam nest had a distinct bacterial community from the tadpoles suggesting a limited environmental effect on tadpole cutaneous bacterial selection at initial stages of life. The shift in the tadpole microbiome after environmental interaction indicates an interplay between underlying host and ecological mechanisms that drive community formation. This survey serves as a baseline for further research into the ecology of microbial transmission in aquatic animals., (© 2021. The Author(s).)

Background: Species adaptation to laboratory conditions is a special case of domestication that has modified model organisms phenotypically and genetically. The characterisation of these changes is crucial to understand how this variation can affect the outcome of biological experiments. Yet despite the wide use of laboratory animals in biological research, knowledge of the genetic diversity within and between different strains and populations of some animal models is still scarce. This is particularly the case of the Mexican axolotl, which has been bred in captivity since 1864., Results: Using gene expression data from nine different projects, nucleotide sequence variants were characterised, and distinctive genetic background of the experimental specimens was uncovered. This study provides a catalogue of thousands of nucleotide variants along predicted protein-coding genes, while identifying genome-wide differences between pigment phenotypes in laboratory populations., Conclusions: Awareness of the genetic variation could guide a better experimental design while helping to develop molecular tools for monitoring genetic diversity and studying gene functions in laboratory axolotls. Overall, this study highlights the cross-taxa utility that transcriptomic data might have to assess the genetic variation of the experimental specimens, which might help to shorten the journey towards reproducible research.

Background: Gene expression profiles can provide insights into the molecular machinery behind tissue functions and, in turn, can further our understanding of environmental responses, and developmental and evolutionary processes. During vertebrate evolution, the skin has played a crucial role, displaying a wide diversity of essential functions. To unravel the molecular basis of skin specialisations and adaptations, we compared gene expression in the skin with eight other tissues in a phylogenetically and ecologically diverse species sample of one of the most neglected vertebrate groups, the caecilian amphibians (order Gymnophiona)., Results: The skin of the five studied caecilian species showed a distinct gene expression profile reflecting its developmental origin and showing similarities to other epithelial tissues. We identified 59 sequences with conserved enhanced expression in the skin that might be associated with caecilian dermal specialisations. Some of the up-regulated genes shared expression patterns with human skin and potentially are involved in skin functions across vertebrates. Variation trends in gene expression were detected between mid and posterior body skin suggesting different functions between body regions. Several candidate biologically active peptides were also annotated., Conclusions: Our study provides the first atlas of differentially expressed sequences in caecilian tissues and a baseline to explore the molecular basis of the skin functions in caecilian amphibians, and more broadly in vertebrates.

Increasingly, large phylogenomic data sets include transcriptomic data from nonmodel organisms. This not only has allowed controversial and unexplored evolutionary relationships in the tree of life to be addressed but also increases the risk of inadvertent inclusion of paralogs in the analysis. Although this may be expected to result in decreased phylogenetic support, it is not clear if it could also drive highly supported artifactual relationships. Many groups, including the hyperdiverse Lissamphibia, are especially susceptible to these issues due to ancient gene duplication events and small numbers of sequenced genomes and because transcriptomes are increasingly applied to resolve historically conflicting taxonomic hypotheses. We tested the potential impact of paralog inclusion on the topologies and timetree estimates of the Lissamphibia using published and de novo sequencing data including 18 amphibian species, from which 2,656 single-copy gene families were identified. A novel paralog filtering approach resulted in four differently curated data sets, which were used for phylogenetic reconstructions using Bayesian inference, maximum likelihood, and quartet-based supertrees. We found that paralogs drive strongly supported conflicting hypotheses within the Lissamphibia (Batrachia and Procera) and older divergence time estimates even within groups where no variation in topology was observed. All investigated methods, except Bayesian inference with the CAT-GTR model, were found to be sensitive to paralogs, but with filtering convergence to the same answer (Batrachia) was observed. This is the first large-scale study to address the impact of orthology selection using transcriptomic data and emphasizes the importance of quality over quantity particularly for understanding relationships of poorly sampled taxa., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Background: Evolution leaves an imprint in species through genetic change. At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evolution, derived phenotypes, and ecological ranges can provide insights into adaptive radiations. Caecilians (order Gymnophiona), probably the least known of the major lineages of vertebrates, are limbless tropical amphibians, with adults of most species burrowing in soils (fossoriality). This enigmatic order of amphibians are very distinct phenotypically from other extant amphibians and likely from the ancestor of Lissamphibia, but little to nothing is known about the molecular changes underpinning their radiation. We hypothesised that colonization of various depths of tropical soils and of freshwater habitats presented new ecological opportunities to caecilians., Results: A total of 8540 candidate groups of orthologous genes from transcriptomic data of five species of caecilian amphibians and the genome of the frog Xenopus tropicalis were analysed in order to investigate the genetic machinery behind caecilian diversification. We found a total of 168 protein-coding genes with signatures of positive selection at different evolutionary times during the radiation of caecilians. The majority of these genes were related to functional elements of the cell membrane and extracellular matrix with expression in several different tissues. The first colonization of the tropical soils was connected to the largest number of protein-coding genes under positive selection in our analysis. From the results of our study, we highlighted molecular changes in genes involved in perception, reduction-oxidation processes, and aging that likely were involved in the adaptation to different soil strata., Conclusions: The genes inferred to have been under positive selection provide valuable insights into caecilian evolution, potentially underpin adaptations of caecilians to their extreme environments, and contribute to a better understanding of fossorial adaptations and molecular evolution in vertebrates.

RNA sequencing (RNA-seq) has become one of the most powerful tools to unravel the genomic basis of biological adaptation and diversity. Although challenging, RNA-seq is particularly promising for research on non-model, secretive species that cannot be observed in nature easily and therefore remain comparatively understudied. Among such animals, the caecilians (order Gymnophiona) likely constitute the least known group of vertebrates, despite being an old and remarkably distinct lineage of amphibians. Here, we characterize multi-tissue transcriptomes for five species of caecilians that represent a broad level of diversity across the order. We identified vertebrate homologous elements of caecilian functional genes of varying tissue specificity that reveal a great number of unclassified gene families, especially for the skin. We annotated several protein domains for those unknown candidate gene families to investigate their function. We also conducted supertree analyses of a phylogenomic dataset of 1,955 candidate orthologous genes among five caecilian species and other major lineages of vertebrates, with the inferred tree being in agreement with current views of vertebrate evolution and systematics. Our study provides insights into the evolution of vertebrate protein-coding genes, and a basis for future research on the molecular elements underlying the particular biology and adaptations of caecilian amphibians., (© The Author(s) 2018. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.)

DNA methylation is mediated by a conserved family of DNA methyltransferases (Dnmts). The human genome encodes three active Dnmts (Dnmt1, Dnmt3a and Dnmt3b), the tRNA methyltransferase Dnmt2, and the regulatory protein Dnmt3L. Despite their high degree of conservation among different species, genes encoding Dnmts have been duplicated and/or lost in multiple lineages throughout evolution, indicating that the DNA methylation machinery has some potential to undergo evolutionary change. However, little is known about the extent to which this machinery, or the methylome, varies among vertebrates. Here, we study the molecular evolution of Dnmt1, the enzyme responsible for maintenance of DNA methylation patterns after replication, in 79 vertebrate species. Our analyses show that all studied species exhibit a single copy of the DNMT1 gene, with the exception of tilapia and marsupials (tammar wallaby, koala, Tasmanian devil and opossum), each of which displays two apparently functional DNMT1 copies. Our phylogenetic analyses indicate that DNMT1 duplicated before the radiation of major marsupial groups (i.e., at least ~75 million years ago), thus giving rise to two DNMT1 copies in marsupials (copy 1 and copy 2). In the opossum lineage, copy 2 was lost, and copy 1 recently duplicated again, generating three DNMT1 copies: two putatively functional genes (copy 1a and 1b) and one pseudogene (copy 1ψ). Both marsupial copies (DNMT1 copies 1 and 2) are under purifying selection, and copy 2 exhibits elevated rates of evolution and signatures of positive selection, suggesting a scenario of neofunctionalization. This gene duplication might have resulted in modifications in marsupial methylomes and their dynamics.

Infections in transplanted patients are still an important cause of morbidity and mortality. Among them, fungal infections with pathogens have become increasingly more prevalent in the last decade. We report the clinical course and management of disseminated Scedosporium apiospermum infection in a kidney transplant recipient, with microbiological isolation of the fungus in cerebrospinal fluid culture. S apiospermum is a fungus that is distributed worldwide and can be grown from soil samples or stagnant water. Disseminated infection is the most frequent form of infection, with cerebral involvement in most cases, which leads to a very high mortality (around 75%). Post-transplant renal infections require a thorough evaluation. Specifically, a high suspicion index is necessary, considering Scedosporium infection among the differential diagnosis of invasive fungal diseases in renal transplantation patients. It is essential to confirm the microbiological diagnosis for an adequate diagnosis and treatment., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Objective: To determine in patients with autosomal dominant polycystic kidney disease the relationship between total renal volume (the sum of both kidneys, TRV) as measured by magnetic resonance and renal function; and its behaviour according to sex and the presence of arterial hypertension, hypercholesterolaemia and hyperglycemia., Method: Cross-sectional study including patients with autosomal dominant polycystic kidney disease who underwent periodic reviews at Nephrology external consultations at Hospital de las Nieves de Granada, and who underwent an magnetic resonance to estimate renal volume between January 2008 and March 2011., Results: We evaluated 67 patients (59.7% women, average age of 48±14.4 years) and found a significant positive association between TRV and serum creatinine or urea, which was reversed compared with estimated glomerular filtration by MDRD-4 and Cockcroft-Gault. Women showed an average serum creatinine level and a significantly lower TRV level compared with males. Subgroups affected by arterial hypertension and hyperuricemia presented average values for serum creatinine and urea, higher for TRV and lower for estimated glomerular filtration. The hypercholesterolaemia subgroup showed higher average values for urea and lower for estimated glomerular filtration, without detecting significant differences compared with TRV., Conclusion: The volume of polycystic kidneys measured by magnetic resonance is associated with renal function, and can be useful as a complementary study to monitor disease progression. The presence of arterial hypertension, hyperuricemia or hypercholesterolaemia is associated with a poorer renal function., (Copyright © 2015 Elsevier España, S.L.U. y Sociedad Española de Medicina Interna (SEMI). All rights reserved.)

Over the last two decades, there has been increasing interest in new techniques for the percutaneous treatment of coronary chronic total occlusions (CTO), which have a success rate that is much higher than that of a few years ago. The rise in percutaneous treatment for these lesions is due to its ability to improve the symptoms and prognosis of patients in the chronic and stable phase of coronary disease. Current data suggest that successful percutaneous coronary intervention for CTO is associated with improvement in patient symptoms, quality of life, left ventricular function, and survival, compared with those with unsuccessful CTO PCI. However, all the scientific evidence supporting this treatment comes from observational studies, and no randomized study comparing percutaneous treatment with medical treatment has yet been published. A major limitation of these studies is their observational design, with limited information with regard to potential baseline differences between the successful vs unsuccessful cohorts. Pending randomized studies, patients should be selected very carefully, especially if they are asymptomatic or very few symptoms, and the benefits obtained in terms of complications during the procedure, the quality of life obtained and further ischemic events avoided should be evaluated systematically. In this review, we will consider the available information supporting percutaneous treatment for chronic occlusions, as well as the areas of uncertainty where more research projects are required.

A 56-year-old woman, non-smoker, who complained of dry cough and dyspnea during the last month came to the emergency department due to increased dyspnea. The chest X-ray showed areas of poorly defined, bilateral alveolar opacities, leading to the diagnosis of bronchopneumonia with partial respiratory failure. During admission, she experienced an exacerbation of the dyspnea. A high-resolution computed tomography scan was performed, showing areas of ground glass opacities with interlobular septal thickening ("crazy-paving" pattern), predominantly in lower lobes. She required mechanical ventilation and she was admitted to the intensive care unit. Subsequently, an open lung biopsy was performed. The following questions should be proposed:, (Copyright © 2013 Elsevier España, S.L. All rights reserved.)

Objective: To describe the technique of stereotactic body radiation therapy (SBRT) of lung lesions after the computed tomography (CT) guided placement of an internal fiducial marker and to assess the results, complications and secondary effects of these procedures., Material and Method: A series of 39 lesions (8 primary and 31 metastases) in 25 patients treated using this procedure were analysed. A CT-guided percutaneous transthoracic puncture was performed for placing the internal marker in the lesion or near to it. The procedure did not require sedation. The marker serves as a guide for the treatment of the lesion using SBRT with respiratory synchronism, which allows the movement of the tumour to be controlled and to decrease the radiation volume, giving high doses with precision to the tumour, and minimal to the surrounding healthy tissue., Results: The only complication of the percutaneous fiducial placement was a pneumothorax in 6 (24%) patients. A pleural drain had to be placed in 3 patients. Local control was achieved in 96.7% of the lesions. The radiation produced a grade 1 asthenia in 1 patient, a grade 2 pneumonitis in one patient and a grade 1 pneumonitis in the remainder., Conclusions: The CT-guided placement of internal markers in lung lesions is a safe technique that may be performed as ambulatory procedure. SBRT with respiratory synchronism allows the dose to the tumour to be increased, and reduces the volume of healthy lung treated, with few secondary effects., (Copyright © 2011 SERAM. Published by Elsevier Espana. All rights reserved.)

Susceptibility to erythromycin and clindamycin was determined in 860 consecutive clinical isolates of beta-haemolytic streptococci belonging to groups A (GAS, n = 134), B (GBS, n = 689), C (GCS, n = 19) and G (GGS, n = 18). Erythromycin resistance was 26.1% in GAS, 15.7% in GBS, 5.3% in GCS and 33.3% in GGS. The highest rate of clindamycin resistance (33.3%) was in GGS, followed by GBS (15.8%), GCS (15.8%) and GAS (5.2%). The M phenotype was predominant in GAS (80%), the constitutive MLS(B) phenotype was predominant in GBS (75%), and all GGS isolates showed the inducible MLS(B) phenotype. The uncommon erythromycin-susceptible and clindamycin-resistant phenotype was found in four GBS and two GCS isolates.