Small but with a huge genome: the challenge of sequencing the Apennine yellow-bellied toad (part 2 of 4) 20.07.2020

Genome complexity can vary a lot across different species in terms of genome size, chromosome number, amount of repetitive regions, and fraction of regions coding for proteins. The knowledge of the genomic characteristic of the target species is a fundamental piece of the puzzle, as it provides cues for the optimization of the genotyping protocols, from library preparation to downstream data analysis.
The broad variety of new genotyping technique can thus be combined according to the genetic feature of the target species. Endemixit project is a good example of the flexibility required to obtain good results from species with so different genomic architectures, sizes and complexities.

This rather small toad has a genome size three times larger than human’s (Ph. Daniele Canestrelli)

The Apennine yellow-bellied toad, of the five species that will be studied in the project, is one to be treated carefully. Indeed, its genome has been estimated at a size of more than 10 gigabases (10 billions of nucleotides, or 10.55 picograms according to Feulgen densitometry), which is four to 20 times bigger than the genomes of the other species studied in the project. The number of chromosomes is though relatively low (2n=24), which can ease the genotyping task thanks to a technique that we will describe later on.
Population genetic characteristics must be also taken in consideration, as they can shape genome-wide diversity and guide the selection of the best individual to be used for genome assembly. Bombina pachypus can be subdivided into two main genetic clusters: a southern one, which has been a glacial refugia for the species; and a northern population, generated by post-glacial range expansion. This is a typical scenario, also called ‘southern richness and northern purity’ (Hewitt 2000). Directly related to this demographic history is the fact that the southern population is genetically richer and more variable (a so called intra-specific hot-spot of biodiversity). Moreover, the southern group can be further split in two sub-groups separated by historical barriers to gene flow.

(a) Geographical range of Bombina pachypus and localities sampled in Canestrelli et al (2006). (b) Minimum spanning network for 13 mitochondrial haplotypes. The higher variability in southern populations can be appreciated from the higher number of haplotypes in the south (Figure from Canestrelli et al. 2006).

References
– Canestrelli, D., Cimmaruta, R., Costantini, V., & Nascetti, G. (2006). Genetic diversity and phylogeography of the Apennine yellow‐bellied toad Bombina pachypus, with implications for conservation. Molecular Ecology, 15(12), 3741-3754.
– Hewitt GM (2000) The genetic legacy of the Quaternary ice ages. Nature, 405, 907–913

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