RNA-Seq of C. siamense
Short reads generated on the Illumina NOvaseq 6000 platform were checked for low quality bases and adapter content using FastQC. Adapter decontamination and removal of low-quality bases was done using bbduk from the BBMap package (v38.96). Trinity (v2.9.1) was used to assemble the reads into transcripts. Assembled transcripts were annotated using eggNOGmapper (v2.1). Transcript estimate and abundance were performed on the clean reads and the assembly to find the TPM value by using salmon. Transcripts with TPM > 1 were considered for Gene Ontology and Pathway analysis using the R package clusterProfiler (v4.4.2). CDS prediction was performed by TransDecoder (v5.3.0) to identify protein coding regions. COG analysis is a method for functional annotation of genes by identifying orthologous groups of proteins that share similar functions.