Reference transcriptome and associated annotations for Chaetoceros decipiens (UNC1416). A culture was grown into late exponential phase for filtration. Total RNA was extracted using the RNAqueous-4PCR Total RNA Isolation Kit (Ambion, Foster City, CA, USA) according to the manufacturer’s protocol with an initial bead beating step to disrupt cells. RNA libraries were created with either the Illumina TruSeq Stranded mRNA Library Preparation Kit. The library was sequenced on an Illumina MiSeq (300 bp, paired-end reads) and an Illumina HiSeq 2500 with one lane in high output mode (100 bp, paired-end reads) and another lane in rapid run mode (150 bp, paired-end reads). Raw reads were trimmed for quality with Trimmomatic v0.36 then assembled de novo with Trinity v2.5.1 with the default parameters for paired-reads and a minimum contig length of 90 bp. Contigs were clustered based on 99% similarity using CD-HIT-EST v4.7 and then protein sequences were predicted with GeneMark S-T. Protein sequences were annotated by best-homology (lowest E-value) with the KEGG (Release 86.0), UniProt (Release 2018_03), and PhyloDB (v1.076) databases via BLASTP v2.7.1 (E-value ≤ 10-5) and with Pfam 31.0 via HMMER v3.1b2 (Dataset S2). KEGG Ortholog (KO) annotations were assigned from the top hit with a KO annotation from the top 10 hits (https://github.com/ctberthiaume/keggannot). Provided here are predicted proteins as nucleotides and peptides. Raw reads are deposited in SRA (SRP234548).