Abstract
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.
Highlights
The sex determination system (XX-XY or ZZ-ZW) is known to change often during evolution of organisms, and the systems in amphibians and fishes have changed at a higher rate than that in mammals and birds (Bachtrog et al, 2014)
A research project aimed at complete genome sequencing of G. rugosa, including an advanced assembly, gene annotations, and chromosomal attributions, is still underway, but the present study focused on the analysis of speciesspecific genomic characteristics and searched for possible structures involved in sex chromosomes
We found Mb-level large CpG islands on frog genomes by comparative genomics using seven species (G. rugosa, P. adspersus, Rhinella marina, Spea multiplicata, Leptobrachium leishanense, X. laevis, and Xenopus tropicalis) and showed that G. rugosa had genome characteristics with a high CG frequency
Summary
The sex determination system (XX-XY or ZZ-ZW) is known to change often during evolution of organisms, and the systems in amphibians and fishes have changed at a higher rate than that in mammals and birds (Bachtrog et al, 2014). To clarify its genome characteristics, we have decoded the genome sequence of G. rugosa which is a diploid species, but whose assembled genome size (7.08 Gb) is larger than that of the tetraploid Xenopus laevis (2.7 Gb; Session et al, 2016; Li et al, 2019) and ~4.5 times larger than that of the evolutionarily related diploid Pyxicephalus adspersus (1.56 Gb; Denton et al, 2018 Preprint). A research project aimed at complete genome sequencing of G. rugosa, including an advanced assembly, gene annotations, and chromosomal attributions, is still underway, but the present study focused on the analysis of speciesspecific genomic characteristics and searched for possible structures involved in sex chromosomes
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