methods.md

A more detailed description of methods.

Agalma v2.0.0 (Dunn et al. 2023, Guang et al. 2021) was used to run QC, clean rRNA, and assemble a Trinity transcriptome Grabherr et al. 2011. Bowtie2 mapping rates were used to assess the assembly quality. Transdecoder was used for translation, and OrthoFinder2 was used to identify orthologous genes. Finally, trinotate Bryant et al. 2022 was used to annotate transcripts and genes.