TY  - JOUR
TI  - Simultaneous Transcriptomic Analysis of Both Host and Symbiont in Insect–Fungus Interactions
AU  - Laws, McKeon 
AU  - Burns, Ellie S.
AU  -  Kasson, Matthew T
AU  - Kijimoto, Teiya 
AU  - Stajich, Jason E.
VL  - 16
IS  - 13
PY  - 2026
DA  - 2026/07/05
SP  - e5739
C1  - Bio-protocol 2026;16:e5739
DO  - 10.21769/BioProtoc.5739
UR  - https://doi.org/10.21769/BioProtoc.5739
AB  - In the last two decades, the field of molecular entomology has seen a shift toward next-generation sequencing techniques as a means of uncovering genetic and developmental processes. However, the standardization of methods is not well-established, and studies for insect–fungus consortia lack established protocols for advanced molecular techniques and downstream analysis compared to approaches applied in model systems involving insect–bacteria interactions. To investigate insect–microbe interactions, RNA sequencing and analysis is often used to identify genes involved in the symbiosis. But such protocols do not often consider insect–fungus systems, which vary significantly in community member abundance and/or fail to describe the details of the process from collection to data processing. This paper will introduce a comprehensive approach for RNA sequencing using two non-model insect–fungus consortia, which lack established, published protocols seen in model systems: the ambrosia beetle mutualism and cicada Massospora parasitism. The protocol includes a detailed TRIzol RNA extraction and quantification, RNA sequencing, and data processing using Nextflow pipeline software. Validation of a range of symbiotic interactions from mutualistic to parasitic is considered to justify this procedure to be utilized in a range of insect–fungus interactions with varied abundances and host interactions.
KW  - Ambrosia beetle
KW  - Ambrosia Symbiosis
KW  - Euwallacea
KW  - Fusarium
KW  - Massospora
KW  - Cicada
KW  - RNA Extraction
KW  - RNA Seq
KW  - Nextflow
JF  - Bio-protocol
SN  - 2331-8325
PB  - Bio-protocol LLC.
BIO101  - False