With the rise of next-generation sequencing technologies,restriction-site associated DNA sequencing (RAD-seq) has become a mainstream method for quickly obtaining high-density single nucleotide polymorphisms (SNPs) in organisms due to its independence from reference genomes. However, few studies have scrutinized the impact of comparing the use of closely related species as the reference genome versus the species itself as the reference genome.
In a study published in Plant Science, researchers from Xishuangbanna Tropical Botanical Garden (XTBG) evaluated the merits and limitations of both reference-based approaches, namely, employing a closely related species as the reference genome versus the species itself as the reference genome.
Using the bioinformatics software STACKS, the researchers explored the impact of using different reference genomes on SNP calling. They utilized RAD-seq data from 242 individuals of Engelhardia roxburghiana, a tropical tree of the walnut family (Juglandaceae). They focused on two different reference genomes: using a closely related species (i.e., Pterocarya stenoptera) as the reference genome, and using the species itself (i.e., Engelhardia roxburghiana) as the reference genome.

They found found a significant difference in the number of SNPs obtained between using the species itself as the reference genome and using a closely related species as the reference genome, with the former producing significantly more SNPs than the latter.

"This result indicates that choosing the species itself as the reference genome is the optimal solution for SNP calling,” said LI Jie of XTBG.

The researchers suggested that a closely related species' reference genome when the species itself reference is not available. It is recommended to avoid using species with a distant phylogenetic relationship.

"Our study contributes to enrich the understanding of the impact of SNP acquisition when utilizing different reference genomes," said MENG Honghu.

Contact
LI Jie Ph.D Principal Investigator
Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
E-mail:jieli@xtbg.ac.cn
First published: 3 May 2024