Metagenomic shotgun sequencing reveals host species as an important driver of virome composition in mosquitoes

Abstract

High-throughput nucleic acid sequencing has greatly accelerated the discovery of viruses in the environment. Mosquitoes, because of their public health importance, are among those organisms whose viromes are being intensively characterized. Despite the deluge of sequence information, our understanding of the major drivers influencing the ecology of mosquito viromes remains limited. Using methods to increase the relative proportion of microbial RNA coupled with RNA-seq we characterize RNA viruses and other symbionts of three mosquito species collected along a rural to urban habitat gradient in Thailand. The full factorial study design allows us to explicitly investigate the relative importance of host species and habitat in structuring viral communities. We found that the pattern of virus presence was defined primarily by host species rather than by geographic locations or habitats. Our result suggests that insect-associated viruses display relatively narrow host ranges but are capable of spreading through a mosquito population at the geographical scale of our study. We also detected various single-celled and multicellular microorganisms such as bacteria, alveolates, fungi, and nematodes. Our study emphasizes the importance of including ecological information in viromic studies in order to gain further insights into viral ecology in systems where host specificity is driving both viral ecology and evolution.

Transcriptomics Reveal Several Novel Viruses from Canegrubs (Coleoptera: Scarabaeidae) in Central Queensland, Australia

“…These unclassified sobemo-like viruses have been identified through metagenomic studies in many mosquitos, such as Aedes albopictus from southern Switzerland [ 66 ], Ae. vexans nipponii from the Republic of Korea [ 67 ], and Armigeres subalbatus from Thailand [ 68 ]. They are also among the dominated virome of termites, and five sobemo-like viruses have been reported from various Australian termite species [ 69 ].…”

Decoding rRNA sequences for improved metagenomics of sylvatic mosquito species

“…In library preparations of mosquito samples for RNAseq, the most common methods for depleting rRNA are commercial kits optimized for human or mice samples (19–24) or probe hybridization followed by ribonuclease digestion where the probes are 80-100 base pair antisense oligos. In cases where the reference rRNA sequence of the target species is not known, oligos would be designed based on the rRNA sequence of the closest related species (25, this study). These methods should be able to produce acceptable rRNA depletion efficiencies due to the assumption that rRNA sequences have high degrees of homology across taxa.…”

Genetic and microbial diversity of the invasive mosquito vector speciesCulex tritaeniorhynchusacross its extensive inter-continental geographic range

“…Apibacter is a genus of bacteria classified within the Family Weeksellaceae which have been relatively recently first isolated and classified in 2016 from various bee species (148,149), as well as a strain being reported from house flies in 2019 (150) and one report in 2021 which found bacterial reads related to Apibacter in Cx. fuscocephala mosquitoes from Thailand (151). These bacteria are thought to be beneficial endosymbionts with characteristics of adaptation to the gut environment and a degree of host-specificity (152).…”