Genomic resources for population analyses of an invasive insect pest Oryctes rhinoceros

Abstract

Over the last few years, various types of NGS data have been accumulating for the coconut rhinoceros beetle (CRB, Oryctes rhinoceros), reflecting the growing interest in curtailing this invasive pest of palm trees. Whilst reference-free analyses of RNA-seq and RAD-seq datasets have been done for different CRB collections, recent availability of the CRB’s genome assembly provides an opportunity to collate diverse data and create a reference-based population dataset. Here, I release such a dataset containing 6,725,935 SNPs and genotypes called across 393 individual samples from 16 populations, using the previously published raw sequences generated in 9 different experiments (RAD-Seq, RNA-Seq, WGS). I also provide reference-based datasets for the CRB’s mitochondrial variants and for variants of its viral biocontrol agent Oryctes rhinoceros nudivirus. SNP data provide high resolution for determining the geographic origin of invasive CRB. With these genomic resources, new data can be analysed without re-processing the published samples and then integrated to expand the reference datasets.

Finding divergent sequences of homomorphic sex chromosomes via diploidized nanopore-based assembly from a single male

“…The total number of analysed individuals was 59 (28 females and 31 males). Data processing, sequence mapping and realignment, and genotype calling were done following the steps outlined by Igor Filipović (Filipović 2023). The final number of SNP loci was 1,921 for HDR, and 4,052 for the autosomes (chromosomes 2 and 3), which had ≤15% missingness per individual.…”