Exploring bycatch diversity of organisms in whole genome sequencing of Erebidae moths (Lepidoptera)

Hamid Reza Ghanavi,Victoria G Twort,Anne Duplouy

doi:10.1038/s41598-021-03327-3

Hamid Reza Ghanavi, Victoria G Twort + Show 1 more

Open Access

https://doi.org/10.1038/s41598-021-03327-3

Copy DOI

Abstract

Models estimate that up to 80% of all butterfly and moth species host vertically transmitted endosymbiotic microorganisms, which can affect the host fitness, metabolism, reproduction, population dynamics, and genetic diversity, among others. The supporting empirical data are however currently highly biased towards the generally more colourful butterflies, and include less information about moths. Additionally, studies of symbiotic partners of Lepidoptera predominantly focus on the common bacterium Wolbachia pipientis, while infections by other inherited microbial partners have more rarely been investigated. Here, we mine the whole genome sequence data of 47 species of Erebidae moths, with the aims to both inform on the diversity of symbionts potentially associated with this Lepidoptera group, and discuss the potential of metagenomic approaches to inform on host associated microbiome diversity. Based on the result of Kraken2 and MetaPhlAn2 analyses, we found clear evidence of the presence of Wolbachia in four species. Our result also suggests the presence of three other bacterial symbionts (Burkholderia spp., Sodalis spp. and Arsenophonus spp.) in three other moth species. Additionally, we recovered genomic material from bracovirus in about half of our samples. The detection of the latter, usually found in mutualistic association to braconid parasitoid wasps, may inform on host-parasite interactions that take place in the natural habitat of the Erebidae moths, suggesting either contamination with material from species of the host community network, or horizontal transfer of members of the microbiome between interacting species.

Highlights

A growing scientific community sees each organism as a community of interacting species rather than as an independent entity
We mine the data produced from whole genome sequencing of 47 moth species from the hyper-diverse family Erebidae (24,000 species) to (1) explore the potential diversity of symbionts associated to this megadiverse Lepidoptera family; and (2) to evaluate the exploratory power of recovering information on natural hostsymbiont associations from the low coverage genome sequencing approaches
We identified the species Idia aemula, Luceria striata, Acantholipes circumdata and Oraesia excavata (RZ271, RZ42, RZ248, and RZ337) as infected by Wolbachia, and Wolbachia-associated phage WO (Table 1), with between 66,978 and 208,044 of the reads identified as belonging to the symbiont

Summary

Introduction

A growing scientific community sees each organism as a community of interacting species rather than as an independent entity. The effects of symbionts on their insect hosts are potentially as diverse as their taxonomy, ranging from pathogenic to obligate mutualists, and all the intermediate possible relationships[2]. This diversity has recently attracted the growing interest of the scientific community, but gaps and biases remain. Sequencing material from a particular study organism, either entirely or partially, may results in a mix of primary host specific DNA and DNA from other sources These other sources can include ecto/endosymbionts, food, opportunistic parasites and pathogens, among others. We mine the data produced from whole genome sequencing of 47 moth species from the hyper-diverse family Erebidae (24,000 species) to (1) explore the potential diversity of symbionts associated to this megadiverse Lepidoptera family; and (2) to evaluate the exploratory power of recovering information on natural hostsymbiont associations from the low coverage genome sequencing approaches

Methods

Results

Discussion

Conclusion