Specific nuclear DNA amounts in toads of the genus Bufo

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 assembly of the invasive cane toad, Rhinella marina

Background

The cane toad (Rhinella marina formerly Bufo marinus) is a species native to Central and South America that has spread across many regions of the globe. Cane toads are known for their rapid adaptation and deleterious impacts on native fauna in invaded regions. However, despite an iconic status, there are major gaps in our understanding of cane toad genetics. The availability of a genome would help to close these gaps and accelerate cane toad research.

Findings

We report a draft genome assembly for R. marina, the first of its kind for the Bufonidae family. We used a combination of long-read Pacific Biosciences RS II and short-read Illumina HiSeq X sequencing to generate 359.5 Gb of raw sequence data. The final hybrid assembly of 31,392 scaffolds was 2.55 Gb in length with a scaffold N50 of 168 kb. BUSCO analysis revealed that the assembly included full length or partial fragments of 90.6% of tetrapod universal single-copy orthologs (n = 3950), illustrating that the gene-containing regions have been well assembled. Annotation predicted 25,846 protein coding genes with similarity to known proteins in Swiss-Prot. Repeat sequences were estimated to account for 63.9% of the assembly.

Conclusions

The R. marina draft genome assembly will be an invaluable resource that can be used to further probe the biology of this invasive species. Future analysis of the genome will provide insights into cane toad evolution and enrich our understanding of their interplay with the ecosystem at large.

In vivo genotoxicity of atrazine to anuran larvae

Atrazine has been an environmental contaminant for more than two decades. While there can be little dispute as to the presence of atrazine in non-target watersheds, the debate has centered on the consequences of this contamination. The purpose of this study was to determine if atrazine is genotoxic to developing anurans. Anurans are one of the groups that have the highest potential for being affected by watershed contamination. In initial studies, larvae from two anuran species were exposed to known genotoxic agents. Upon flow cytometric analysis, those organisms exposed to the genotoxic agents resulted in a statistically significant increase in nuclear heterogeneity. Having demonstrated that flow cytometric analysis could be used to detect genotoxicity in anuran larvae, the larvae of the two species were exposed to different levels of atrazine for various durations. The concentrations and lengths of exposure were consistent (albeit on the higher side) with conditions found in the Midwestern US. In neither species was an increase in nuclear heterogeneity observed. Thus, atrazine at levels and time of exposure representing conditions found contaminating Midwestern watersheds does not appear to be genotoxic to developing anurans.

Errors in microdensitometry

Microdensitometric errors can originate in the instrument, in the specimen or in the human operator. Instrumental sources of systematic error mostly reduce the apparent integrated absorbance, especially of relatively small and highly absorbing objects. They can be assessed, minimized or eliminated by available techniques, but with modern apparatus are in general important only if results of high accuracy are required. Instrument errors include: (a) distributional error, due to the use of too large a measuring spot or the specimen being out of focus; (b) glare (stray light), due mainly to multiple reflections in the microscope objective; (c) monochromator error (the use of insufficiently pure light); (d) calibration errors; and (e) errors resulting from lack of photometric linearity, or the specimen absorbance exceeding the measuring range of the instrument. Specimen errors, including the problems of specificity and stoichiometry, are now the most important obstacles to a wider use of microdensitometry. The following selected topics are briefly discussed: fading; rate of staining; Beer's law deviations and the microdensitometry of opaque particles. Human errors include faulty logic, and failing to attempt an investigation because of anticipated difficulties which are in fact exaggerated or imaginary. The significance of microdensitometric results should, in general, be assessed by biological criteria rather than merely statistically; the use is urged of appropriate internal biological controls and standards wherever possible.

Isolation and separation of toad bladder epithelial cells

The epithelium of the urinary bladder of Bufo marinus is composed of 5 cell types, i.e., granular (Gr), mitochondria-rich (MR) and goblet (G) cells which face the urinary lumen, microfilament-rich (MFR) and undifferentiated cells (Un) located basally. The epithelium was dissociated by collagenase and EGTA treatment. Fractionation of dispersed cells by isopycnic centrifugation on dense serum albumin solutions yielded 4 fractions: (i) a very light fraction (p approximately equal to 1.025) enriched in MR and MFR cells; (ii) a light fraction (p approximately equal to 1.045) enriched in vacuolated Gr cells; (iii) a heavy fraction (p approximately equal to 1.065) composed essentially of aggregated Gr cells, and (iv) a pellet (p approximately equal to 1.085) enriched in G and undifferentiated cells. Recoveries were based on cell counts and DNA measurements. DNA content per cell was 13.2 pg +/- 0.9 (n = 37). From 1 g fresh tissue, 62 +/- 5 x 10(6) (n = 10) cells were recovered before isopycnic centrifugation of which about 70% excluded Trypan blue. After centrifugation, 90 to 95% of the cells excluded the vital dye and approximately 3(9) x 10(6) cells were recovered from the gradient. Cell metabolism in each fraction was estimated by oxygen consumption measurements in absence or presence of ouabain, acetazolamide, and dinitrophenol. The consumption measurements in absence or presence of ouabain, acetazolamide, and dinitrophenol. The consumption was threefold higher in the very light and light fractions when compared to the heavy and pellet fractions. Ouabain sensitive oxygen consumption (QO2) represented 12 to 35% of the total O2 consumption depending on the cell fraction, and acetazolamide sensitive QO2 varied from -0.8% in the heavy fractions to 20% in the lighter fractions. DNP increased QO2 in all fractions by 20 to 50%. Finally, the cells were able to reaggregate and form junctional complexes upon addition of calcium to the medium.

Replication of DNA in the chromosomes of eukaryotes

The evidence that each chromatid of a eukaryotic organism contains only one DNA double helix comes from a variety of observations. It begins with the autoradiographic demonstration by J. H. Taylor that tritiated thymidine, incorporated into chromosomes during one round of DNA synthesis, is present in both chromatids at the first division after labelling, but in only one chromatid after a further round of DNA synthesis accomplished in the absence of label. Further evidence comes from those experiments which demonstrate that when two sister chromatids break and fuse one with the other, each chromatid behaves as though it contained two chains of opposite polarity, fusion between chains being restricted to those of like polarity. J. G. Gall’s study of the kinetics of digestion of lampbrush chromosomes by pancreatic DNase also supports the view that each chromatid contains only two polynucleotide chains which are cleaved by this enzyme independently of one another; while O. L. Miller’s observations on the dimensions of the fibres remaining after lampbrush chromosomes have been digested by trypsin only allow for there being two polynucleotide chains per chromatid. By means of the technique of DNA fibre autoradiography devised by J. A. Huberman and A. D. Riggs, the units involved in replicating the chromosomal DNA of somatic cells ofXenopushave been compared with those ofTriturus. Both these organisms have initiation points for DNA replication that are arranged in tandem, and from each initiation point replication proceeds in opposite directions at divergent forks. The intervals between initiation points inXenopusrange from about 20 to 125µm apart, whereas those ofTriturusare much more widely separated. At 25 °C replication of DNA inXenopussomatic cells proceeds at 9µm per hour one-way at each fork, whereas the corresponding rate inTriturusis 20µm per hour.Triturussomatic cells take about 4 times longer than comparable cells ofXenopusto replicate their DNA. TheTriturusgenome contains about 10 times as much DNA as theXenopusgenome, and comparison of the replication process in these two organisms indirectly adds weight to the view that theTriturusgenome is 10 timeslongerthan that ofXenopus, rather than that it contains 10 times as many DNA double helices per chromatid. DNA fibre autoradiography has also been used to study replication inTriturusspermato-cytes. The round of DNA synthesis just before meiosis inTriturusis an exceptionally long-drawn-out process, taking 9 to 10 days for completion at 16 °C. This lengthy S-phase is not occasioned by abnormally slow replication, the rate being 12µm per hour one-way at 18 °C, nor is it the result of an exceptional staggering of replication starts. Instead it appears to be correlated with a gross reduction in the number of initiation points for replication. i.e. with an increase in the lengths of the replicating units. A rough calculation suggests that each meiotic chromomere may correspond to a unit of replication during the pre-meiotic S-phase.