Genome of Spea multiplicata, a Rapidly Developing, Phenotypically Plastic, and Desert-Adapted Spadefoot Toad

Genetic Variants Underlying Plasticity in Natural Populations of Spadefoot Toads: Environmental Assessment versus Phenotypic Response

Many organisms facultatively produce different phenotypes depending on their environment, yet relatively little is known about the genetic bases of such plasticity in natural populations. In this study, we describe the genetic variation underlying an extreme form of plasticity--resource polyphenism--in Mexican spadefoot toad tadpoles, Spea multiplicata. Depending on their environment, these tadpoles develop into one of two drastically different forms: a carnivore morph or an omnivore morph. We collected both morphs from two ponds that differed in which morph had an adaptive advantage and performed genome-wide association studies of phenotype (carnivore vs. omnivore) and adaptive plasticity (adaptive vs. maladaptive environmental assessment). We identified four quantitative trait loci associated with phenotype and nine with adaptive plasticity, two of which exhibited signatures of minor allele dominance and two of which (one phenotype locus and one adaptive plasticity locus) did not occur as minor allele homozygotes. Investigations into the genetics of plastic traits in natural populations promise to provide novel insights into how such complex, adaptive traits arise and evolve.

Multi-omics resources for the Australian southern stuttering frog (Mixophyes australis) reveal assorted antimicrobial peptides

The number of genome-level resources for non-model species continues to rapidly expand. However, frog species remain underrepresented, with up to 90% of frog genera having no genomic or transcriptomic data. Here, we assemble the first genomic and transcriptomic resources for the recently described southern stuttering frog (Mixophyes australis). The southern stuttering frog is ground-dwelling, inhabiting naturally vegetated riverbanks in south-eastern Australia. Using PacBio HiFi long-read sequencing and Hi-C scaffolding, we generated a high-quality genome assembly, with a scaffold N50 of 369.3 Mb and 95.1% of the genome contained in twelve scaffolds. Using this assembly, we identified the mitochondrial genome, and assembled six tissue-specific transcriptomes. We also bioinformatically characterised novel sequences of two families of antimicrobial peptides (AMPs) in the southern stuttering frog, the cathelicidins and β-defensins. While traditional peptidomic approaches to peptide discovery have typically identified one or two AMPs in a frog species from skin secretions, our bioinformatic approach discovered 12 cathelicidins and two β-defensins that were expressed in a range of tissues. We investigated the novelty of the peptides and found diverse predicted activities. Our bioinformatic approach highlights the benefits of multi-omics resources in peptide discovery and contributes valuable genomic resources in an under-represented taxon.

Comparative genomics reveals insights into anuran genome size evolution

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.

Draft genome and multi-tissue transcriptome assemblies of the Neotropical leaf-frog Phyllomedusa bahiana

Amphibians are increasingly threatened worldwide, but the availability of genomic resources that could be crucial for implementing informed conservation practices lags well behind that for other vertebrate groups. Here, we describe draft de novo genome, mitogenome, and transcriptome assemblies for the Neotropical leaf-frog Phyllomedusa bahiana native to the Brazilian Atlantic Forest and Caatinga. We used a combination of PacBio long reads and Illumina sequencing to produce a 4.74-Gbp contig-level genome assembly, which has a contiguity comparable to other recent nonchromosome level assemblies. The assembled mitogenome comprises 16,239 bp and the gene content and arrangement are similar to other Neobratrachia. RNA-sequencing from 8 tissues resulted in a highly complete (86.3%) reference transcriptome. We further use whole-genome resequencing data from P. bahiana and from its sister species Phyllomedusa burmeisteri, to demonstrate how our assembly can be used as a backbone for population genomics studies within the P. burmeisteri species group. Our assemblies thus represent important additions to the catalog of genomic resources available from amphibians.

Disentangling the developmental origins of a novel phenotype: enhancement versus reversal of environmentally induced gene expression

Increasing evidence suggests that many novel traits might have originated via plasticity-led evolution (PLE). Yet, little is known of the developmental processes that underpin PLE, especially in its early stages. One such process is 'phenotypic accommodation', which occurs when, in response to a change in the environment, an organism experiences adjustments across variable parts of its phenotype that improve its fitness. Here, we asked if environmentally induced changes in gene expression are enhanced or reversed during phenotypic accommodation of a novel, complex phenotype in spadefoot toad tadpoles (Spea multiplicata). More genes than expected were affected by both the environment and phenotypic accommodation in the liver and brain. However, although phenotypic accommodation primarily reversed environmentally induced changes in gene expression in liver tissue, it enhanced these changes in brain tissue. Thus, depending on the tissue, phenotypic accommodation may either minimize functional disruption via reversal of gene expression patterns or promote novelty via enhancement of existing expression patterns. Our study thereby provides insights into the developmental origins of a novel phenotype and the incipient stages of PLE.

Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad

Genomic resources for amphibians are still hugely under-represented in vertebrate genomic research, despite being a group of major interest for ecology, evolution and conservation. Amphibians constitute a highly threatened group of vertebrates, present a vast diversity in reproductive modes, are extremely diverse in morphology, occupy most ecoregions of the world, and present the widest range in genome sizes of any major group of vertebrates. We combined Illumina, Nanopore and Hi-C sequencing technologies to assemble a chromosome-level genome sequence for an anuran with a moderate genome size (assembly span 3.09 Gb); Pelobates cultripes, the western spadefoot toad. The genome has an N50 length of 330 Mb with 98.6% of the total sequence length assembled into 14 super scaffolds, and 87.7% complete BUSCO genes. We use published transcriptomic data to provide annotations, identifying 32,684 protein-coding genes. We also reconstruct the P. cultripes phylome and identify 2,527 gene expansions. We contribute the first draft of the genome of the western spadefoot toad, P. cultripes. This species represents a relatively basal lineage in the anuran tree with an interesting ecology and a high degree of developmental plasticity, and thus is an important resource for amphibian genomic research.

Evolutionary dynamics of DIRS-like and Ngaro-like retrotransposons in Xenopus laevis and Xenopus tropicalis genomes

Anuran genomes have a large number and diversity of transposable elements, but are little explored, mainly in relation to their molecular structure and evolutionary dynamics. Here, we investigated the retrotransposons containing tyrosine recombinase (YR) (order DIRS) in the genome of Xenopus tropicalis and Xenopus laevis. These anurans show 2n = 20 and the 2n = 36 karyotypes, respectively. They diverged about 48 million years ago (mya) and X. laevis had an allotetraploid origin (around 17–18 mya). Our investigation is based on the analysis of the molecular structure and the phylogenetic relationships of 95 DIRS families of Xenopus belonging to DIRS-like and Ngaro-like superfamilies. We were able to identify molecular signatures in the 5' and 3' noncoding terminal regions, preserved open reading frames, and conserved domains that are specific to distinguish each superfamily. We recognize two ancient amplification waves of DIRS-like elements that occurred in the ancestor of both species and a higher density of the old/degenerate copies detected in both subgenomes of X. laevis. More recent amplification waves are seen in X. tropicalis (less than 3.2 mya) and X. laevis (around 10 mya) corroborating with transcriptional activity evidence. All DIRS-like families were found in both X. laevis subgenomes, while a few were most represented in the L subgenome. Ngaro-like elements presented less diversity and quantity in X. tropicalis and X. laevis genomes, although potentially active copies were found in both species and this is consistent with a recent amplification wave seen in the evolutionary landscape. Our findings highlight a differential diversity-level and evolutionary dynamics of the YR retrotransposons in X. tropicalis and X. laevis species expanding our comprehension of the behavior of these elements in both genomes during the diversification process.

Evolutionary analyses of visual opsin genes in frogs and toads: Diversity, duplication, and positive selection

Among major vertebrate groups, anurans (frogs and toads) are understudied with regard to their visual systems, and little is known about variation among species that differ in ecology. We sampled North American anurans representing diverse evolutionary and life histories that likely possess visual systems adapted to meet different ecological needs. Using standard molecular techniques, visual opsin genes, which encode the protein component of visual pigments, were obtained from anuran retinas. Additionally, we extracted the visual opsins from publicly available genome and transcriptome assemblies, further increasing the phylogenetic and ecological diversity of our dataset to 33 species in total. We found that anurans consistently express four visual opsin genes (RH1, LWS, SWS1, and SWS2, but not RH2) even though reported photoreceptor complements vary widely among species. The proteins encoded by these genes showed considerable sequence variation among species, including at sites known to shift the spectral sensitivity of visual pigments in other vertebrates and had conserved substitutions that may be related to dim-light adaptation. Using molecular evolutionary analyses of selection (dN/dS) we found significant evidence for positive selection at a subset of sites in the dim-light rod opsin gene RH1 and the long wavelength sensitive cone opsin LWS. The function of sites inferred to be under positive selection are largely unknown, but a few are likely to affect spectral sensitivity and other visual pigment functions based on proximity to previously identified sites in other vertebrates. We also found the first evidence of visual opsin duplication in an amphibian with the duplication of the LWS gene in the African bullfrog, which had distinct LWS copies on the sex chromosomes suggesting the possibility of sex-specific visual adaptation. Taken together, our results indicate that ecological factors, such as habitat and life history, as well as behavior, may be driving changes to anuran visual systems.

Pseudogenized Amelogenin Reveals Early Tooth Loss in True Toads (Anura: Bufonidae)

Extant anurans (frogs and toads) exhibit reduced dentition, ranging from a lack of mandibular teeth to complete edentulation, as observed in the true toads of the family Bufonidae. The evolutionary time line of these reductions remains vague due to a poor fossil record. Previous studies have demonstrated an association between the lack of teeth in edentulous vertebrates and the pseudogenization of the major tooth enamel gene amelogenin (AMEL) through accumulation of deleterious mutations and the disruption of its coding sequence. In this study, we have harnessed the pseudogenization of AMEL as a molecular dating tool to correlate loss of dentition with genomic mutation patterns during the rise of the family Bufonidae. Specifically, we have utilized AMEL pseudogenes in three members of the family as a tool to estimate the putative date of edentulation in true toads. Comparison of AMEL sequences from Rhinella marina, Bufo gargarizans and Bufo bufo, with nine extant, dentulous frogs, revealed mutations confirming AMEL inactivation in Bufonidae. AMEL pseudogenes in modern bufonids also exhibited remarkably high 86-93% sequence identity among each other, with only a slight increase in substitution rate and relaxation of selective pressure, in comparison with functional copies in other anurans. Moreover, using selection intensity estimates and synonymous substitution rates, analysis of functional and pseudogenized AMEL resulted in an estimated inactivation window of 46-60 million years ago in the lineage leading to modern true toads, a time line that coincides with the rise of the family Bufonidae.

Transcriptomic bases of a polyphenism

Polyphenism-in which multiple distinct phenotypes are produced from a single genotype owing to differing environmental conditions-is commonplace, but its molecular bases are poorly understood. Here, we examine the transcriptomic bases of a polyphenism in Mexican spadefoot toads (Spea multiplicata). Depending on their environment, their tadpoles develop into either a default "omnivore" morph or a novel "carnivore" morph. We compared patterns of gene expression among sibships that exhibited high versus low production of carnivores when reared in conditions that induce the carnivore morph versus those that do not. We found that production of the novel carnivore morph actually involved changes in fewer genes than did the maintenance of the default omnivore morph in the inducing environment. However, only body samples showed this pattern; head samples showed the opposite pattern. We also found that changes to lipid metabolism (especially cholesterol biosynthesis) and peroxisome contents and function might be crucial for establishing and maintaining differences between the morphs. Thus, our findings suggest that carnivore phenotype might have originally evolved following the breakdown of robustness mechanisms that maintain the default omnivore phenotype, and that the carnivore morph is developmentally regulated by lipid metabolism and peroxisomal form, function, and/or signaling. This study also serves as a springboard for further exploration into the nature and causes of plasticity in an emerging model system.

Novel brain gene-expression patterns are associated with a novel predaceous behaviour in tadpoles

Novel behaviours can spur evolutionary change and sometimes even precede morphological innovation, but the evolutionary and developmental contexts for their origins can be elusive. One proposed mechanism to generate behavioural innovation is a shift in the developmental timing of gene-expression patterns underlying an ancestral behaviour, or molecular heterochrony. Alternatively, novel suites of gene expression, which could provide new contexts for signalling pathways with conserved behavioural functions, could promote novel behavioural variation. To determine the relative contributions of these alternatives to behavioural innovation, I used a species of spadefoot toad, Spea bombifrons. Based on environmental cues, Spea larvae develop as either of two morphs: 'omnivores' that, like their ancestors, feed on detritus, or 'carnivores' that are predaceous and cannibalistic. Because all anuran larvae undergo a natural transition to obligate carnivory during metamorphosis, it has been proposed that the novel, predaceous behaviour in Spea larvae represents the accelerated activation of gene networks influencing post-metamorphic behaviours. Based on comparisons of brain transcriptional profiles, my results reject widespread heterochrony as a mechanism promoting the expression of predaceous larval behaviour. They instead suggest that the evolution of this trait relied on novel patterns of gene expression that include components of pathways with conserved behavioural functions.

A bird-like genome from a frog: Mechanisms of genome size reduction in the ornate burrowing frog, Platyplectrum ornatum

The diversity of genome sizes across the tree of life is of key interest in evolutionary biology. Various correlates of variation in genome size, such as accumulation of transposable elements (TEs) or rate of DNA gain and loss, are well known, but the underlying molecular mechanisms driving or constraining genome size are poorly understood. Here, we study one of the smallest genomes among frogs characterized thus far, that of the ornate burrowing frog (Platyplectrum ornatum) from Australia, and compare it to other published frog and vertebrate genomes to examine the forces driving reduction in genome size. At ∼1.06 gigabases (Gb), the P. ornatum genome is like that of birds, revealing four major mechanisms underlying TE dynamics: reduced abundance of all major classes of TEs; increased net deletion bias in TEs; drastic reduction in intron lengths; and expansion via gene duplication of the repertoire of TE-suppressing Piwi genes, accompanied by increased expression of Piwi-interacting RNA (piRNA)-based TE-silencing pathway genes in germline cells. Transcriptomes from multiple tissues in both sexes corroborate these results and provide insight into sex-differentiation pathways in Platyplectrum Genome skimming of two closely related frog species (Lechriodus fletcheri and Limnodynastes fletcheri) confirms a reduction in TEs as a major driver of genome reduction in Platyplectrum and supports a macroevolutionary scenario of small genome size in frogs driven by convergence in life history, especially rapid tadpole development and tadpole diet. The P. ornatum genome offers a model for future comparative studies on mechanisms of genome size reduction in amphibians and vertebrates generally.

Comparative genomics of Glandirana rugosa using unsupervised AI reveals a high CG frequency

Genome sequencing of a unique frog (Glandirana rugosa) having XY/ZW systems within the species and comparative genomics with other six frogs were performed using a batch-learning self-organizing map, which is unsupervised AI for oligonucleotide compositions, to clarify its genome characteristics.

The Japanese wrinkled frog (Glandirana rugosa) is unique in having both XX-XY and ZZ-ZW types of sex chromosomes within the species. The genome sequencing and comparative genomics with other frogs should be important to understand mechanisms of turnover of sex chromosomes within one species or during a short period. In this study, we analyzed the newly sequenced genome of G. rugosa using a batch-learning self-organizing map which is unsupervised artificial intelligence for oligonucleotide compositions. To clarify genome characteristics of G. rugosa, we compared its short oligonucleotide compositions in all 1-Mb genomic fragments with those of other six frog species (Pyxicephalus adspersus, Rhinella marina, Spea multiplicata, Leptobrachium leishanense, Xenopus laevis, and Xenopus tropicalis). In G. rugosa, we found an Mb-level large size of repeat sequences having a high identity with the W chromosome of the African bullfrog (P. adspersus). Our study concluded that G. rugosa has unique genome characteristics with a high CG frequency, and its genome is assumed to heterochromatinize a large size of genome via methylataion of CG.

Perspectives on studying molecular adaptations of amphibians in the genomic era

Understanding the genetic mechanisms underlying particular adaptations/phenotypes of organisms is one of the core issues of evolutionary biology. The use of genomic data has greatly advanced our understandings on this issue, as well as other aspects of evolutionary biology, including molecular adaptation, speciation, and even conservation of endangered species. Despite the well-recognized advantages, usages of genomic data are still limited to non-mammal vertebrate groups, partly due to the difficulties in assembling large or highly heterozygous genomes. Although this is particularly the case for amphibians, nonetheless, several comparative and population genomic analyses have shed lights into the speciation and adaptation processes of amphibians in a complex landscape, giving a promising hope for a wider application of genomics in the previously believed challenging groups of organisms. At the same time, these pioneer studies also allow us to realize numerous challenges in studying the molecular adaptations and/or phenotypic evolutionary mechanisms of amphibians. In this review, we first summarize the recent progresses in the study of adaptive evolution of amphibians based on genomic data, and then we give perspectives regarding how to effectively identify key pathways underlying the evolution of complex traits in the genomic era, as well as directions for future research.

Identification of candidate loci for adaptive phenotypic plasticity in natural populations of spadefoot toads

Phenotypic plasticity allows organisms to alter their phenotype in direct response to changes in the environment. Despite growing recognition of plasticity's role in ecology and evolution, few studies have probed plasticity's molecular bases-especially using natural populations. We investigated the genetic basis of phenotypic plasticity in natural populations of spadefoot toads (Spea multiplicata). Spea tadpoles normally develop into an "omnivore" morph that is favored in long-lasting, low-density ponds. However, if tadpoles consume freshwater shrimp or other tadpoles, they can alternatively develop (via plasticity) into a "carnivore" morph that is favored in ephemeral, high-density ponds. By combining natural variation in pond ecology and morph production with population genetic approaches, we identified candidate loci associated with each morph (carnivores vs. omnivores) and loci associated with adaptive phenotypic plasticity (adaptive vs. maladaptive morph choice). Our candidate morph loci mapped to two genes, whereas our candidate plasticity loci mapped to 14 genes. In both cases, the identified genes tended to have functions related to their putative role in spadefoot tadpole biology. Our results thereby form the basis for future studies into the molecular mechanisms that mediate plasticity in spadefoots. More generally, these results illustrate how diverse loci might mediate adaptive plasticity.

A draft genome assembly of the eastern banjo frog Limnodynastes dumerilii dumerilii (Anura: Limnodynastidae)

Amphibian genomes are usually challenging to assemble due to their large genome size and high repeat content. The Limnodynastidae is a family of frogs native to Australia, Tasmania and New Guinea. As an anuran lineage that successfully diversified on the Australian continent, it represents an important lineage in the amphibian tree of life but lacks reference genomes. Here we sequenced and annotated the genome of the eastern banjo frog Limnodynastes dumerilii dumerilii to fill this gap. The total length of the genome assembly is 2.38 Gb with a scaffold N50 of 285.9 kb. We identified 1.21 Gb of non-redundant sequences as repetitive elements and annotated 24,548 protein-coding genes in the assembly. BUSCO assessment indicated that more than 94% of the expected vertebrate genes were present in the genome assembly and the gene set. We anticipate that this annotated genome assembly will advance the future study of anuran phylogeny and amphibian genome evolution.

Variation in hybrid gene expression: Implications for the evolution of genetic incompatibilities in interbreeding species

Interbreeding species often produce low-fitness hybrids due to genetic incompatibilities between parental genomes. Whether these incompatibilities reflect fixed allelic differences between hybridizing species, or, alternatively, standing variants that segregate within them, remains unknown for many natural systems. Yet, evaluating these alternatives is important for understanding the origins and nature of species boundaries. We examined these alternatives using spadefoot toads (genus Spea), which naturally hybridize. Specifically, we contrasted patterns of gene expression in hybrids relative to pure-species types in experimentally produced tadpoles from allopatric parents versus those from sympatric parents. We evaluated the prediction that segregating variation should result in gene expression differences between hybrids derived from sympatric parents versus hybrids derived from allopatric parents, and found that 24% of the transcriptome showed such differences. Our results further suggest that gene expression in hybrids has evolved in sympatry owing to evolutionary pressures associated with ongoing hybridization. Although we did not measure hybrid incompatibilities directly, we discuss the implications of our findings for understanding the nature of hybrid incompatibilities, how they might vary across populations over time, and the resulting effects on the evolutionary maintenance - or breakdown - of reproductive barriers between species.