RNA-Seq of Chlamydomonas reinhardtii subjected to black phosphorous
The quality of raw reads was evaluated using FastQC (v0.11.9) and MultiQC (v1.9). Trimming low-quality bases and clipping adaptor sequences was carried out using cutadapt (v2.6). The trimmed reads were aligned to the Chlamydomonas reinhardtii (v5.5) reference sequence using bowtie2 (v2.3.5.1). Unmapped reads were extracted (bedtools v2.27.1), merged and assembled using SPAdes genome assembler v3.13.1 in RNA mode. Contigs over 300bp were used to identify candidate coding regions (TransDecoder v5.5.0). Predicted transcripts were annotated based on the UniProt Reference Clusters (UniRef) using BLAST (v2.2.31+). The contigs annotated like known genes from Chlamydomonas reinhardtii were filtered out.