Shark and ray genome size estimation: methodological optimization for inclusive and controllable biodiversity genomics

Abstract

Estimate of nuclear DNA content serves as an independent tool for validating the completeness of whole genome sequences and investigating the among-species variation of genome sizes, but for some species, the requirement of fresh cells makes this tool highly inaccessible. Here we focused on elasmobranch species (sharks and rays), and using flow cytometry or quantitative PCR (qPCR), estimated the nuclear DNA contents of brownbanded bamboo shark, white spotted bamboo shark, zebra shark, small-spotted catshark, sandbar shark, slendertail lanternshark, basking shark, megamouth shark, red stingray, and ocellate spot skate. Our results revealed their genome sizes spanning from 3.18 pg (for ocellate spot skate) to 13.34 pg (for slendertail lanternshark), reflecting the huge variation of genome sizes already documented for elasmobranchs. Our qPCR-based method ‘sQuantGenome’ enabled accurate genome size estimation without using live cells, which has been a severe limitation with elasmobranchs. These findings and our methodology are expected to contribute to better understanding of the diversity of genome sizes in elasmobranchs even including species with limited availability of fresh tissue materials. It will also help validate the completeness of already obtained or anticipated whole genome sequences.