Genomic Traces of the Fruit Fly Anastrepha obliqua Associated with Its Polyphagous Nature

Abstract

Anastrepha obliqua (Macquart) (Diptera: Tephritidae) is an important pest in the neotropical region. It is considered a polyphagous insect, meaning it infests plants of different taxonomic families and readily colonizes new host plants. The change to new hosts can lead to diversification and the formation of host races. Previous studies investigating the effect of host plants on population structure and selection in Anastrepha obliqua have focused on the use of data from the mitochondrial DNA sequence and microsatellite markers of nuclear DNA, and there are no analyses at the genomic level. To better understand this issue, we used a pooled restriction site-associated DNA sequencing (pooled RAD-seq) approach to assess genomic differentiation and population structure across sympatric populations of Anastrepha obliqua that infest three host plants—Spondias purpurea (red mombin), Mangifera indica (mango) of the family Anacardiaceae and Averrhoa carambola (carambola) of the family Oxalidaceae—in sympatric populations of the species Anastrepha obliqua of Inter-Andean Valley of the Cauca River in southwestern Colombia. Our results show genomic differentiation of populations from carambola compared to mango and red mombin populations, but the genetic structure was mainly established by geography rather than by the host plant. On the other hand, we identified 54 SNPs in 23 sequences significantly associated with the use of the host plant. Of these 23 sequences, we identified 17 candidate genes and nine protein families, of which four protein families are involved in the nutrition of these flies. Future studies should investigate the adaptive processes undergone by phytophagous insects in the Neotropics, using fruit flies as a model and state-of-the-art molecular tools.

An omics evolutionary perspective on phytophagous insect–host plant interactions in Anastrepha obliqua: a review

“…In both studies, the main differences were found in flies infesting carambola, which could be related to the chemical composition of these fruits and their recent introduction to the American continent (Velasco-Cuervo et al, 2021). Aguirre-Ramirez et al (2021) found similar results at the genomic level. Populations of A. obliqua infesting carambola have a greater genomic difference [based on restriction-site associated DNA sequencing (RAD-seq; Box 2] compared to populations infesting red mombin and mango.…”

“…Populations of A. obliqua infesting carambola have a greater genomic difference [based on restriction‐site associated DNA sequencing (RAD‐seq; Box 2] compared to populations infesting red mombin and mango. Additionally, 54 single nucleotide polymorphisms (SNPs) were found to be associated with host plant use, some of which in protein families that could be annotated in pathways related to nutrition (Aguirre‐Ramirez et al, 2021).…”

“…This methodology produces thousands of SNPs throughout the entire genome. RAD‐seq has been used to characterize genomic variation in populations with gene flow and to identify genomic markers of differentiation or selection associated with different environmental parameters in non‐model organisms within Lepidoptera (Nadeau et al, 2014) and fruit flies (Egan et al, 2015; Aguirre‐Ramirez et al, 2021) (for more information on the family of RAD‐seq methodologies, see Andrews et al, 2016). On the other hand, WGS has two widely used approaches: de novo sequencing and re‐sequencing (WGR).…”

Whole metagenome sequencing reveals host plant influences microbial community associated with larvae ofAnastrepha obliqua

“…In Rhagoletis cerasi (L.), the dynamics of Wolbachia infection can vary depending on the host plant, as in the process of ecological specialization, the vertical transmission of these bacteria is affected, as well as their gene flow. According to Aguirre‐Ramirez et al (2021), the populations of A. obliqua in southwestern Colombia could be in an incipient stage of specialization; therefore, we suggest that another factor responsible for the observed differences between metabarcoding and WMS is the possible divergence between populations of A. obliqua depending on the host plant.…”

Nuclear genetic diversity and structure of Anastrepha ludens wild populations evidenced by microsatellite markers

“…Where each management unit could be colonized by sterile specimens derived from the same unit. This would also require developing strains compatible with each local population, by utilizing genomics differentiation in A. ludens populations and associations with different host plants and predicting the geographic and environmental ranges and relative abundances of invasive species using ecological niche modeling to give policies on a scientific basis (Santos et al, 2020;Aguirre-Ramirez et al, 2021;Gutierrez et al, 2021).…”