Cryptobranchus alleganiensis shotgun sequencing

Salamanders have the largest genome among tetrapod vertebrates. Our previous results indicated that LTR retrotransposons contribute to the genomic gigantism of Plethodontid salamanders, however, it is elusive if this is the primarily mechanism underlying genomic expansion at the base of the salamander clade. To answer this question, hellbender, one salamander species from the family of Cryptobranchus, which is phylogenetically distantly related to Plethodontid, was employed in this study to explore its repeat landscape. High-throughput sequencing was used to generate shotgun reads for the hellbender genome, and its repeat content was explored using a pipeline specialized for low-coverage shotgun reads. Results indicated that over 75% of hellbender genome was made up of repetitive sequences, and the vast majority of them were derived from known transposable elements (TEs). Gypsy/Ty3 is the most abundant TE superfamily in hellbender, and compared with other vertebrates, there are much higher level of LTR retrotransposons in hellbender genome, suggesting that the proliferation of LTR elements also contributes to the genomic expansion of Cryptobranchus salamander. When comparing the TE landscape of Cryptobranchus with that of Plethodontid, we found that these two taxa of salamanders harbor similar amount of LTR and DNA elements. In contrast, there was much higher level of non-LTR retrotransposons in Cryptobranchus than in Plethodontid. More specifically, there was an increased proliferation of L1 and Penelope retrotransposons in Cryptobranchus. Taken together, our results indicated that salamanders harbor much higher level of LTR retrotransposon, especially Gypsy/Ty3 elements, in their genome than in other vertebrates, which is the primarily mechanism underlying genomic expansion at the base of the salamander clade. In addition, there is differential TE activity among salamanders. Thus, our results indicate that the balance between TE proliferation and host silencing differs dramatically not only between salamander and other vertebrates but also across salamanders.