using a de novo approach 17), data from different experiments that use different restriction enzymes cannot be directly compared without being aligned to the reference genome. Whilst population genomic analyses of CRB’s RAD-Seq data have been done in a reference-free manner (i.e. Until recently, however, absence of a reference genome assembly for CRB’s nuclear and mitochondrial genomes have prevented the direct comparison and collation of different datasets. Over the last few years, next-generation sequencing (NGS) experiments have been done for different CBR collections, accumulating data from the reduced-representation sequencing (Restriction site-Associated DNA sequencing, RAD-Seq Genotyping-by-Sequencing, GBS) 7, 9, as well as RNA sequencing (RNA-Seq) 10, 11, 12, 13 and Whole Genome Sequencing (WGS) 14, 15, 16. The power to resolve alternative hypotheses within this framework depends on the ability to grow the reference dataset for CRB populations and OrNV isolates, with spatial and temporal collections spanning native and invasive range. Population genomics and phylogenetics provide a good framework for testing different hypotheses around CRB invasions, including interactions with its biocontrol agent (OrNV), through the analyses of genetic patterns of both biological systems in space and time.
Understanding the mechanisms behind the breakdown of a formerly-successful biocontrol strategy is critical for re-establishing effective suppression of this pest and for preventing its future invasions.
However, new data show that OrNV infections are common in the CRB-G lineage 7, 8, and some evidence supports the hypothesis of an emergent OrNV strain that is less-virulent 8. rhinoceros, one being beetle’s increased tolerance to the OrNV’s pathogenicity, associated with a particular mitochondrial lineage (known as the “CRB-G” biotype) that is common in the newly-invaded regions 6. Different hypotheses have been proposed to explain the resurgence of O.
#Coconut rhinoceros beetle babies free#
rhinoceros were recorded in territories that were previously free of this pest, from Guam, Hawai’i and Solomon Islands 3, 4 to Vanuatu and New Caledonia 5. In recent years, however, incursions of O. Invasive CRB populations across the South Pacific islands were suppressed for decades with a largely non-chemical toolbox that included the use of an entomopathogenic virus, Oryctes rhinoceros nudivirus (OrNV) 2. The coconut rhinoceros beetle (CRB), Oryctes rhinoceros, has been responsible for major yield losses of coconut and oil palms across its native and invasive range 1. With these genomic resources, new data can be analysed without re-processing the published samples and then integrated to expand the reference datasets. SNP data provide high resolution for determining the geographic origin of invasive CRB. I also provide reference-based datasets for the CRB’s mitochondrial variants and for variants of its viral biocontrol agent Oryctes rhinoceros nudivirus. 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). 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. 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.
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