Comparative transcriptomics and gene expression in larval tiger salamander (Ambystoma tigrinum) gill and lung tissues as revealed by pyrosequencing

Mechanisms of Caspases 3/7/8/9 in the Degeneration of External Gills of Chinese Giant Salamanders (Andrias davidianus)

Metamorphosis is a critical stage in the adaptive development of amphibians from aquatic to terrestrial animals. Metamorphosis of the Chinese giant salamander is mainly manifested by the loss of external gills with consequent changes in the respiratory pattern. The loss of the external gill is regulated by the pathway of apoptosis in which caspase genes are the key factors. This study cloned and expressed the caspase 3/7/8/9 genes of the Chinese giant salamander. The main results were as follows: the complete open reading frames (ORFs) were 885 bp, 960 bp, 1461 bp and 1279 bp, respectively; caspase 3/7/8/9 genes all contained the CASc domain, and most of the motifs were located in CASc domain; and caspase 8 possessed two DED structural domains and caspase 9 possessed a CARD structural domain. Furthermore, results from the tissue distribution analysis indicated that caspase 3/7/8/9 genes were all significantly expressed in the external gill, and at 9 and 10 months of age (MOA), which is the peak time for the loss, the EXPRESSION level of caspase 3/7/8/9 genes was obviously high, which was consistent with the histological result. Moreover, the loss of external gills of the Chinese giant salamander may result from activation of both the apoptosis-related death receptor pathway and the mitochondrial pathway. Finally, it was discovered that thyroid hormone (TH) treatment could both advance the time point at which the external gills of the Chinese giant salamander began to degenerate and shorten this process. Interestingly, at the peak of its metamorphosis (9 MOA), the Chinese giant salamander further accelerated the metamorphosis rate of TH treatment, which suggested a promotive effect on the loss of external gills via the superimposition of the exogenous TH and caspase genes. The study of caspase genes in this experiment was conducive to understanding the mechanism of external gill loss in the Chinese giant salamander, as well as improving our understanding of the metamorphosis development of some Caudata species.

Towards comparative analyses of salamander limb regeneration

Among tetrapods, only salamanders can regenerate their limbs and tails throughout life. This amazing regenerative ability has attracted the attention of scientists for hundreds of years. Now that large, salamander genomes are beginning to be sequenced for the first time, omics tools and approaches can be used to integrate new perspectives into the study of tissue regeneration. Here we argue the need to move beyond the primary salamander models to investigate regeneration in other species. Salamanders at first glance come across as a phylogenetically conservative group that has not diverged greatly from their ancestors. While salamanders do present ancestral characteristics of basal tetrapods, including the ability to regenerate limbs, data from fossils and data from studies that have tested for species differences suggest there may be considerable variation in how salamanders develop and regenerate their limbs. We review the case for expanded studies of salamander tissue regeneration and identify questions and approaches that are most likely to reveal commonalities and differences in regeneration among species. We also address challenges that confront such an initiative, some of which are regulatory and not scientific. The time is right to gain evolutionary perspective about mechanisms of tissue regeneration from comparative studies of salamander species.

Multi-organ transcriptomic landscape of Ambystoma velasci metamorphosis

Metamorphosis is a postembryonic developmental process that involves morphophysiological and behavioral changes, allowing organisms to adapt into a novel environment. In some amphibians, aquatic organisms undergo metamorphosis to adapt in a terrestrial environment. In this process, these organisms experience major changes in their circulatory, respiratory, digestive, excretory and reproductive systems. We performed a transcriptional global analysis of heart, lung and gills during diverse stages of Ambystoma velasci to investigate its metamorphosis. In our analyses, we identified eight gene clusters for each organ, according to the expression patterns of differentially expressed genes. We found 4064 differentially expressed genes in the heart, 4107 in the lung and 8265 in the gills. Among the differentially expressed genes in the heart, we observed genes involved in the differentiation of cardiomyocytes in the interatrial zone, vasculogenesis and in the maturation of coronary vessels. In the lung, we found genes differentially expressed related to angiogenesis, alveolarization and synthesis of the surfactant protein. In the case of the gills, the most prominent biological processes identified are degradation of extracellular matrix, apoptosis and keratin production. Our study sheds light on the transcriptional responses and the pathways modulation involved in the transformation of the facultative metamorphic salamander A. velasci in an organ-specific manner.

Phenotypic plasticity and local adaptations to dissolved oxygen in larvae fire salamander (Salamandra infraimmaculata)

A key environmental factor that varies both spatially and temporally in surface waters is dissolved oxygen (DO). In stagnant ephemeral freshwater ponds, DO can fluctuate diurnally and seasonally, while the constant mixing of water in streams typically maintain DO levels close to saturation with only minor fluctuations. Larvae of the Near Eastern fire salamander (Salamandra infraimmaculata) develop in a range of waterbodies that vary in flow and permanence. To study inter-population variation in larval response to environmental change, we translocated larvae between stream and pond habitats and exposed larvae sampled from different habitat types to hypoxic and normoxic conditions in the laboratory. Larvae transferred from stream to pond retain gill size, while larvae transferred from pond to stream show a reduction in gill size. Larvae that were caged within their native habitat, either stream or pond, display a decrease in gill size similar to larvae transferred from pond to stream. When exposed to experimentally manipulated levels of DO in the laboratory larvae, respectively, increase and decrease gill size under hypoxic and normoxic conditions. Habitat-type origin had a significant effect on the degree of change in gill size with larvae from permanent streams demonstrating the lowest absolute variation in gill size. There was no interaction between DO level (hypoxic/normoxic) and the larvae habitat-type origin. These results suggest that S. infraimmaculata larvae are locally adapted to their aquatic breeding habitat through the plastic ability to respond to the prevailing respiratory conditions by rapidly decreasing or increasing gill size.

Comparative expression analysis identifies the respiratory transition-related miRNAs and their target genes in tissues of metamorphosing Chinese giant salamander (Andrias davidianus)

Background

Chinese giant salamander (Andrias davidianus) undergoes a metamorphosis from aquatic larvae to terrestrial adults, with concomitant transfer of respiration from gills to lungs prior to metamorphosis. These two tissues, as well as skin, were sampled to identify the differentially expressed miRNAs.

Results

High-coverage reference transcriptome was generated from combined gill, lung and skin tissues of metamorphosing juveniles, and lung tissue of adults: 86,282 unigenes with total length of approximately 77,275,634 bp and N50 of 1732 bp were obtained. Among these, 13,246 unigenes were assigned to 288 pathways. To determine the possible involvement of miRNAs in the respiratory transition, small RNA libraries were sequenced; 282 miRNAs were identified, 65 among which were known and 217 novel. Based on the hierarchical clustering analysis, the twelve studied samples were classified into three major clusters using differentially expressed miRNAs. We have validated ten differentially expressed miRNAs and some of their related target genes using qPCR. These results largely corroborated the results of transcriptomic and miRNA analyses. Finally, an miRNA-gene-network was constructed. Among them, two miRNAs with target genes related to oxygen sensing were differentially expressed between gill and lung tissues. Three miRNAs were differentially expressed between the lungs of larvae and lungs of adults.

Conclusions

This study provides the first large-scale miRNA expression profile overview during the respiration transition from gills to lungs in Chinese giant salamander. Five differentially expressed miRNAs and their target genes were identified among skin, gill and lung tissues. These results suggest that miRNA profiles in respiratory tissues play an important role in the regulation of respiratory transition.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4662-5) contains supplementary material, which is available to authorized users.

Comparative transcriptomics of cyprinid minnows and carp in a common wild setting: a resource for ecological genomics in freshwater communities

Comparative transcriptomics can now be conducted on organisms in natural settings, which has greatly enhanced understanding of genome–environment interactions. Here, we demonstrate the utility and potential pitfalls of comparative transcriptomics of wild organisms, with an example from three cyprinid fish species (Teleostei:Cypriniformes). We present extensively filtered and annotated transcriptome assemblies that provide a valuable resource for studies of genome evolution (e.g. polyploidy), ecological and morphological diversification, speciation, and shared and unique responses to environmental variation in cyprinid fishes. Our results and analyses address the following points: (i) ‘essential developmental genes’ are shown to be ubiquitously expressed in a diverse suite of tissues across later ontogenetic stages (i.e. juveniles and adults), making these genes are useful for assessing the quality of transcriptome assemblies, (ii) the influence of microbiomes and other exogenous DNA, (iii) potentially novel, species-specific genes, and (iv) genomic rearrangements (e.g. whole genome duplication). The data we present provide a resource for future comparative work in cypriniform fishes and other taxa across a variety of sub-disciplines, including stress response, morphological diversification, community ecology, ecotoxicology, and climate change.

Transcriptome dynamics along axolotl regenerative development are consistent with an extensive reduction in gene expression heterogeneity in dedifferentiated cells

Although in recent years the study of gene expression variation in the absence of genetic or environmental cues or gene expression heterogeneity has intensified considerably, many basic and applied biological fields still remain unaware of how useful the study of gene expression heterogeneity patterns might be for the characterization of biological systems and/or processes. Largely based on the modulator effect chromatin compaction has for gene expression heterogeneity and the extensive changes in chromatin compaction known to occur for specialized cells that are naturally or artificially induced to revert to less specialized states or dedifferentiate, I recently hypothesized that processes that concur with cell dedifferentiation would show an extensive reduction in gene expression heterogeneity. The confirmation of the existence of such trend could be of wide interest because of the biomedical and biotechnological relevance of cell dedifferentiation-based processes, i.e., regenerative development, cancer, human induced pluripotent stem cells, or plant somatic embryogenesis. Here, I report the first empirical evidence consistent with the existence of an extensive reduction in gene expression heterogeneity for processes that concur with cell dedifferentiation by analyzing transcriptome dynamics along forearm regenerative development in Ambystoma mexicanum or axolotl. Also, I briefly discuss on the utility of the study of gene expression heterogeneity dynamics might have for the characterization of cell dedifferentiation-based processes, and the engineering of tools that afforded better monitoring and modulating such processes. Finally, I reflect on how a transitional reduction in gene expression heterogeneity for dedifferentiated cells can promote a long-term increase in phenotypic heterogeneity following cell dedifferentiation with potential adverse effects for biomedical and biotechnological applications.

Morphological And Molecular Analyses of an Anatomical Novelty: The Pelvic Fin Filaments of the South American Lungfish

The pelvic fins of male South American lungfish, Lepidosiren paradoxa, are adorned with a distinctive array of filaments, which grow and become highly vascularized during the breeding season. The resemblance between these pelvic fin filaments (PFFs) and external gills of other vertebrates suggested that this gill-like structure was used for physiological gas exchange. It has been proposed that the unique pelvic fin of male L. paradoxa is used for release of oxygen from its blood into the environment in order to aerate its nesting brood, or, conversely, as an auxiliary respiratory organ by absorbing oxygen from the environment into its bloodstream. Here, we employed histology, scanning electron microscopy (SEM) and quantitative PCR (qPCR) to assess whether the morphology and molecular profile of PFFs are compatible with a role in gas exchange. First, we closely examined its external morphology and showed that PFFs develop from short papillae during the rainy season, but remain covered by a thick nonvascularized epithelium. Histological examination confirmed that capillaries within the filaments are separated from the exterior by a basement membrane and a stratified epithelium composed of four to five cell layers. In addition, SEM analysis revealed significant differences between the fin filament epithelium and typical gill epithelium. Finally, our qPCR results showed that five genes commonly expressed in gills were downregulated in PFFs relative to their expression in regular pectoral fin epidermis. Collectively, our results do not directly support a role for PFFs, commonly referred to as "limb gills", in oxygen release or uptake.

Comparative transcriptome analyses of seven anurans reveal functions and adaptations of amphibian skin

Animal skin, which is the tissue that directly contacts the external surroundings, has evolved diverse functions to adapt to various environments. Amphibians represent the transitional taxon from aquatic to terrestrial life. Exploring the molecular basis of their skin function and adaptation is important to understand the survival and evolutionary mechanisms of vertebrates. However, comprehensive studies on the molecular mechanisms of skin functions in amphibians are scarce. In this study, we sequenced the skin transcriptomes of seven anurans belonging to three families and compared the similarities and differences in expressed genes and proteins. Unigenes and pathways related to basic biological processes and special functions, such as defense, immunity, and respiration, were enriched in functional annotations. A total of 108 antimicrobial peptides were identified. The highly expressed genes were similar in species of the same family but were different among families. Additionally, the positively selected orthologous groups were involved in biosynthesis, metabolism, immunity, and defense processes. This study is the first to generate extensive transcriptome data for the skin of seven anurans and provides unigenes and pathway candidates for further studies on amphibian skin function and adaptation.

Transposons, Genome Size, and Evolutionary Insights in Animals

The relationship between genome size and the percentage of transposons in 161 animal species evidenced that variations in genome size are linked to the amplification or the contraction of transposable elements. The activity of transposable elements could represent a response to environmental stressors. Indeed, although with different trends in protostomes and deuterostomes, comprehensive changes in genome size were recorded in concomitance with particular periods of evolutionary history or adaptations to specific environments. During evolution, genome size and the presence of transposable elements have influenced structural and functional parameters of genomes and cells. Changes of these parameters have had an impact on morphological and functional characteristics of the organism on which natural selection directly acts. Therefore, the current situation represents a balance between insertion and amplification of transposons and the mechanisms responsible for their deletion or for decreasing their activity. Among the latter, methylation and the silencing action of small RNAs likely represent the most frequent mechanisms.

The Lungfish Transcriptome: A Glimpse into Molecular Evolution Events at the Transition from Water to Land

Lungfish and coelacanths are the only living sarcopterygian fish. The phylogenetic relationship of lungfish to the last common ancestor of tetrapods and their close morphological similarity to their fossil ancestors make this species uniquely interesting. However their genome size, the largest among vertebrates, is hampering the generation of a whole genome sequence. To provide a partial solution to the problem, a high-coverage lungfish reference transcriptome was generated and assembled. The present findings indicate that lungfish, not coelacanths, are the closest relatives to land-adapted vertebrates. Whereas protein-coding genes evolve at a very slow rate, possibly reflecting a “living fossil” status, transposable elements appear to be active and show high diversity, suggesting a role for them in the remarkable expansion of the lungfish genome. Analyses of single genes and gene families documented changes connected to the water to land transition and demonstrated the value of the lungfish reference transcriptome for comparative studies of vertebrate evolution.

Transcriptome sequencing of two phenotypic mosaic Eucalyptus trees reveals large scale transcriptome re-modelling

Phenotypic mosaic trees offer an ideal system for studying differential gene expression. We have investigated two mosaic eucalypt trees from two closely related species (Eucalyptus melliodora and E. sideroxylon), which each support two types of leaves: one part of the canopy is resistant to insect herbivory and the remaining leaves are susceptible. Driving this ecological distinction are differences in plant secondary metabolites. We used these phenotypic mosaics to investigate genome wide patterns of foliar gene expression with the aim of identifying patterns of differential gene expression and the somatic mutation(s) that lead to this phenotypic mosaicism. We sequenced the mRNA pool from leaves of the resistant and susceptible ecotypes from both mosaic eucalypts using the Illumina HiSeq 2000 platform. We found large differences in pathway regulation and gene expression between the ecotypes of each mosaic. The expression of the genes in the MVA and MEP pathways is reflected by variation in leaf chemistry, however this is not the case for the terpene synthases. Apart from the terpene biosynthetic pathway, there are several other metabolic pathways that are differentially regulated between the two ecotypes, suggesting there is much more phenotypic diversity than has been described. Despite the close relationship between the two species, they show large differences in the global patterns of gene and pathway regulation.

Accommodating the load: The transposable element content of very large genomes

Very large genomes, that is, those above 20 Gb, are rare but widely distributed throughout the eukaryotes. They are found within the diatoms, dinoflagellates, metazoans and green plants, but so far have not been found in the excavates. There is a known positive correlation between genome size and the proportion of the genome composed of transposable elements (TEs). Very large genomes may therefore be expected to be almost entirely composed of TEs. Of the large genomes examined, in the angiosperms, gymnosperms and the dinoflagellates only a small portion of the genome was identified as TEs, most of these genomes were unidentified and may be novel or diverse TEs. In the salamanders and lungfish, 25 to 47% of the genome were identifiable retrotransposons, that is, TEs that copy themselves before insertion. However, the predominant class of TEs found in the lungfish was not the same as that found in the salamanders. The little data we have at the moment suggests therefore that the diversity and abundance of TEs is variable between taxa with large genomes, similar to patterns found in taxa with smaller genomes. Based on results from the human genome, we suggest that the ‘missing’ portion of the lungfish and salamander genomes are old, highly divergent, and therefore inactive copies of TEs. The data available indicate that, unlike plants with large genomes, neither the lungfish nor the salamanders show an increased risk of extinction. Based on a slow rate of DNA loss in salamanders it has been suggested that the large salamander genome is the result of run-away genome expansion involving genome size increases via TE proliferation associated with reduced recombination rate. We know of no studies on DNA loss or recombination rates in lungfish genomes, however a similar scenario could describe the process of genome expansion in the lungfish. A series of waves of TE transposition and sequence decay would describe the pattern of TE content seen in both the lungfish and the salamanders. The lungfish and salamanders, therefore, may accommodate their large load of TEs because these TEs have accumulated gradually over a long period of time and have been subject to inactivation and decay.

Transcriptomic characterization of the immunogenetic repertoires of heteromyid rodents

Background

When populations evolve under disparate environmental conditions, they experience different selective pressures that shape patterns of sequence evolution and gene expression. These may be manifested in genetic and phenotypic differences such as a diverse immunogenetic repertoire in species from tropical latitudes that have greater and/or different parasite burdens than more temperate species. To test this idea, we compared the transcriptomes of one tropical species (Heteromys desmarestianus) and two species from temperate latitudes (Dipodomys spectabilis and Chaetodipus baileyi) from the Heteromyidae. We did so in a search for positive selection on sequences and/or differential expression, while controlling for phylogenetic history in our choice of species.

Results

We identified 127,812 contigs and annotated 34,878 of these, identifying immune genes associated with interleukins, cytokines, and the production of mast cells. We identified 632 genes that were upregulated in H. desmarestianus (8.7% of genes tested) and 492 (6.7%) that were downregulated. Gene ontology terms including “immune response” were associated with 31 (4.9%) of the 632 upregulated genes. We found preliminary evidence for positive selection on three genes (Palmitoyltransferase ZDHHC5 Ubiquitin-conjugating enzyme E2 N, Krueppel-like factor 10, and Spindle and kinetochore-associated protein 1) along the H. desmarestianus lineage.

Conclusions

Overall our findings pinpoint genes in species from disparate environments that are on different evolutionary trajectories in terms of expression levels and/or nucleotide sequence. Our data indicate there are significant differences in the expression of genes among the spleen transcriptomes of these species and that a number of these differentially expressed genes do not show the same pattern of differential expression in another tissue type. This points to the possibility of expression differences between these species specific to the spleen transcriptome.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-929) contains supplementary material, which is available to authorized users.

Natural selection and the genetic basis of osmoregulation in heteromyid rodents as revealed by RNA-seq

One adaptation of ecological and evolutionary interest is the extraordinary ability of desert rodents to retain water during waste production. Much is known regarding the unique kidney physiology of kangaroo rats (Dipodomys spp.) and their ability to retain water during waste production, yet the genetic basis of these physiological adaptations is relatively unknown. Herein, we utilized RNA-seq data to conduct a comparative study to identify osmoregulatory genes expressed in heteromyid rodents. We sequenced kidney tissue from two temperate desert species (Dipodomys spectabilis and Chaetodipus baileyi) from two separate subfamilies of the Heteromyidae and compared these transcriptomes to a tropical mesic species (Heteromys desmarestianus) from a third subfamily. The evolutionary history of these subfamilies provided a robust phylogenetic control that allowed us to separate shared evolutionary history from convergence. Using two methods to detect differential expression (DE), we identified 1890 genes that showed consistent patterns of DE between the arid and mesic species. A three-species reciprocal BLAST analysis revealed 3511 sets of putative orthologues that, upon comparison to known Mus musculus sequences, revealed 323 annotated and full-length genic regions. Selection tests displayed evidence of positive selection (dn/ds > 1) on six genes in the two desert species and remained significant for one of these genes after correction for multiple testing. Thus, our data suggest that both the coding sequence and expression of genes have been shaped by natural selection to provide the genetic architecture for efficient osmoregulation in desert-adapted heteromyid rodents.

Microsatellite analyses across three diverse vertebrate transcriptomes (Acipenser fulvescens, Ambystoma tigrinum, and Dipodomys spectabilis)

Historically, many population genetics studies have utilized microsatellite markers sampled at random from the genome and presumed to be selectively neutral. Recent studies, however, have shown that microsatellites can occur in transcribed regions, where they are more likely to be under selection. In this study, we mined microsatellites from transcriptomes generated by 454-pyrosequencing for three vertebrate species: lake sturgeon (Acipenser fulvescens), tiger salamander (Ambystoma tigrinum), and kangaroo rat (Dipodomys spectabilis). We evaluated (i) the occurrence of microsatellites across species; (ii) whether particular gene ontology terms were over-represented in genes that contained microsatellites; (iii) whether repeat motifs were located in untranslated regions or coding sequences of genes; and (iv) in silico polymorphism. Microsatellites were less common in tiger salamanders than in either lake sturgeon or kangaroo rats. Across libraries, trinucleotides were found more frequently than any other motif type, presumably because they do not cause frameshift mutations. By evaluating variation across reads assembled to a given contig, we were able to identify repeat motifs likely to be polymorphic. Our study represents one of the first comparative data sets on the distribution of vertebrate microsatellites within expressed genes. Our results reinforce the idea that microsatellites do not always occur in noncoding DNA, but commonly occur in expressed genes.

Differences in gene expression within a striking phenotypic mosaic Eucalyptus tree that varies in susceptibility to herbivory

BACKGROUND

Long-lived trees can accumulate mutations throughout their lifetimes that may influence biotic and abiotic interactions. For example, some Eucalyptus trees display marked variation in herbivore defence within a single canopy. These "mosaic" trees support foliage with distinct chemotypes which are differentially favoured by insect and vertebrate herbivores, resulting in susceptible and resistant branches within a single canopy. These mosaic trees provide a unique opportunity to explore the biosynthesis and genetic regulation of chemical defences in the foliage. The biosynthesis of the principal defence compounds, terpenoid-dominated essential oils, is well understood. However, the regulation of the genes involved and thus the control of phenotypic variation within a single tree canopy remains a mystery.

RESULTS

We sequenced the transcriptomes of the leaves of the two different chemotypes of a chemically mosaic Eucalyptus melliodora tree using 454 pyrosequencing technology. We used gene set enrichment analysis to identify differentially expressed transcripts and found the proportion of differentially expressed genes in the resistant and susceptible foliage similar to the transcript difference between functionally distinct tissues of the same organism, for example roots and leaves. We also investigated sequence differences in the form of single nucleotide polymorphisms and found 10 nucleotides that were different between the two branches. These are likely true SNPs and several occur in regulatory genes.

CONCLUSION

We found three lines of evidence that suggest changes to a 'master switch' can result in large scale phenotypic changes: 1. We found differential expression of terpene biosynthetic genes between the two chemotypes that could contribute to chemical variation within this plant. 2. We identified many genes that are differentially expressed between the two chemotypes, including some unique genes in each branch. These genes are involved in a variety of processes within the plant and many could contribute to the regulation of secondary metabolism, thus contributing to the chemical variation. 3. We identified 10 SNPs, some of which occur in regulatory genes that could influence secondary metabolism and thus contribute to chemical variation. Whilst this research is inherently limited by sample size, the patterns we describe could be indicative of other plant genetic mosaics.

A priori and a posteriori approaches for finding genes of evolutionary interest in non-model species: osmoregulatory genes in the kidney transcriptome of the desert rodent Dipodomys spectabilis (banner-tailed kangaroo rat)

One common goal in evolutionary biology is the identification of genes underlying adaptive traits of evolutionary interest. Recently next-generation sequencing techniques have greatly facilitated such evolutionary studies in species otherwise depauperate of genomic resources. Kangaroo rats (Dipodomys sp.) serve as exemplars of adaptation in that they inhabit extremely arid environments, yet require no drinking water because of ultra-efficient kidney function and osmoregulation. As a basis for identifying water conservation genes in kangaroo rats, we conducted a priori bioinformatics searches in model rodents (Mus musculus and Rattus norvegicus) to identify candidate genes with known or suspected osmoregulatory function. We then obtained 446,758 reads via 454 pyrosequencing to characterize genes expressed in the kidney of banner-tailed kangaroo rats (Dipodomys spectabilis). We also determined candidates a posteriori by identifying genes that were overexpressed in the kidney. The kangaroo rat sequences revealed nine different a priori candidate genes predicted from our Mus and Rattus searches, as well as 32 a posteriori candidate genes that were overexpressed in kidney. Mutations in two of these genes, Slc12a1 and Slc12a3, cause human renal diseases that result in the inability to concentrate urine. These genes are likely key determinants of physiological water conservation in desert rodents.

The effects of contig length and depth on the estimation of SNP frequencies, and the relative abundance of SNPs in protein-coding and non-coding transcripts of tiger salamanders (Ambystoma tigrinum)

BACKGROUND

Next-generation sequencing methods have contributed to rapid progress in the fields of genomics and population genetics. Using this high-throughput and cost-effective technology, a number of studies have estimated single nucleotide polymorphism (SNP) frequency by calculating the mean number of SNPs per unit sequence length (e.g., mean SNPs/kb). However, both read length and contig depth are highly variable and thus raise doubt about simple methods of SNP frequency estimation.

RESULTS

We used 454 pyrosequencing to identify 2,980 putative SNPs in the eastern tiger salamander (Ambystoma tigrinum tigrinum) transcriptome, then constructed analytical models to estimate SNP frequency. The model which considered only contig length (i.e., the method employed in most published papers) was evaluated with very poor likelihood. Our most robust model considered read depth as well as contig length, and was 7.5 × 10⁵⁵ times more likely than the length-only model. Using this novel modeling approach, we estimated SNP frequency in protein-coding (mRNA) and non-coding transcripts (e.g., small RNAs). We found little difference in SNP frequency in the contigs, but we found a trend of a higher frequency of SNPs in long contigs representing non-coding transcripts relative to protein-coding transcripts. These results support the hypothesis that long non-coding transcripts are less conserved than long protein-coding transcripts.

CONCLUSIONS

A modeling approach (i.e., using multiple model construction and model selection approaches) can be a powerful tool for identifying selection on specific functional sequence groups by comparing the frequency and distribution of polymorphisms.