Microsatellite Variation in the Most Devastating Beetle Pests (Coleoptera: Curculionidae) of Agricultural and Forest Crops

Abstract

Weevils, classified in the family Curculionidae (true weevils), constitute a group of phytophagous insects of which many species are considered significant pests of crops. Within this family, the red palm weevil (RPW), Rhynchophorus ferrugineus, has an integral role in destroying crops and has invaded all countries of the Middle East and many in North Africa, Southern Europe, Southeast Asia, Oceania, and the Caribbean Islands. Simple sequence repeats (SSRs), also termed microsatellites, have become the DNA marker technology most applied to study population structure, evolution, and genetic diversity. Although these markers have been widely examined in many mammalian and plant species, and draft genome assemblies are available for many species of true weevils, very little is yet known about SSRs in weevil genomes. Here we carried out a comparative analysis examining and comparing the relative abundance, relative density, and GC content of SSRs in previously sequenced draft genomes of nine true weevils, with an emphasis on R. ferrugineus. We also used Illumina paired-end sequencing to generate draft sequence for adult female RPW and characterized it in terms of perfect SSRs with 1–6 bp nucleotide motifs. Among weevil genomes, mono- to trinucleotide SSRs were the most frequent, and mono-, di-, and hexanucleotide SSRs exhibited the highest GC content. In these draft genomes, SSR number and genome size were significantly correlated. This work will aid our understanding of the genome architecture and evolution of Curculionidae weevils and facilitate exploring SSR molecular marker development in these species.

Omics in the Red Palm Weevil Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae): A Bridge to the Pest

“…An additional draft genome of the RPW was reported by Manee et al [ 72 ], for which data were generated using Illumina paired-end sequencing. The DNA for this assembly were obtained from a single female adult RPW.…”

“…Interestingly, the sizes of available RPW genome assemblies vary greatly, from 589.40 to 1121.36 Mb [ 68 , 70 , 72 ]. Although this observation could indicate intraspecific variation in genome size [ 73 ], other explanations have been proposed.…”

“…The study of repeats in the RPW genome is in its infancy, but the use of genomics has greatly accelerated its progress. In the past year, two studies were published using short-read sequencing to characterize microsatellites and satDNAs in the RPW [ 72 , 87 ]. Manee et al [ 72 ] generated a new low-coverage draft genome of the adult female RPW to search for microsatellite content (1–6 bp long) and compare it to other beetles from the Curculionidae family, including the two publicly available draft genomes of the RPW [ 72 ].…”