Metatranscriptomic and metagenomic analyses of cotton aphids (Aphis gossypii) collected from cotton fields in Alabama, USA

Authors: Zhao, Chaoyang; ESCALANTE, CESAR - Auburn University; JACOBSON, ALANA - Auburn University; Balkcom, Kipling; CONNER, KASSIE - Auburn University; MARTIN, KATHLEEN - Auburn University

Submitted to: Frontiers in Insect Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/7/2025
Publication Date: 2/26/2025
Citation: Zhao, C., Escalante, C., Jacobson, A.L., Balkcom, K.S., Conner, K.N., Martin, K.M. 2025. Metatranscriptomic and metagenomic analyses of cotton aphids (Aphis gossypii) collected from cotton fields in Alabama, USA. Frontiers in Insect Science. 5:1461588. https://doi.org/10.3389/finsc.2025.1461588.
DOI: https://doi.org/10.3389/finsc.2025.1461588

Interpretive Summary: The cotton aphid is a globally distributed agricultural pest that can feed on at least 700 plant species from numerous families. It is a major insect pest of cotton and the sole known vector responsible for transmitting the cotton leafroll dwarf virus (CLRDV), a relatively new pathogen infecting cotton crops in the United States. ARS scientists in Auburn, AL, and collaborators from Auburn University sequenced aphid samples collected from cotton fields in South Alabama. They analyzed both RNA and DNA datasets and discovered microbial sequences corresponding to various putative beneficial symbionts, plant pathogens, and insect pathogens, as well as plant sequences likely derived from the aphids' gut contents. Although no CLRDV sequences were detected, this study provides valuable insights into the investigation of aphid-transmitted cotton diseases in Alabama. Additionally, it sheds light on the discovery of insect pathogens that could potentially be developed as aphid biocontrol agents.

Technical Abstract: The cotton aphid, Aphis gossypii, is a highly polyphagous insect pest that can feed on a wide range of host plants including many economically important crops. It can also transmit numerous plant pathogens such as cotton leafroll dwarf virus (CLRDV). In addition to phytopathogens, A. gossypii may harbor beneficial microsymbionts and entomopathogens. To examine the microbial community of A. gossypii in Alabama, a primary cotton-growing state in the USA, we sequenced RNA and DNA from alataes collected during 2020-2021 from cotton fields in South Alabama. Two de novo assemblies, a metatranscriptome and a metagenome, were generated using the non-host sequence reads that were not mapped to the aphid genome. While no CLRDV sequences were found in either assembly, taxonomic annotation using the DIAMOND+MEGAN approach on the assembled contigs revealed a variety of microbes including bacteria, fungi, and viruses that may be involved in complex interactions with A. gossypii. Moreover, some plant sequences were detected, reflecting the polyphagous feeding behavior of the insects. These datasets provide genetic information that may be used to investigate plant diseases transmitted by A. gossypii and identify insect pathogens that could be developed for aphid biocontrol.