Octopod Hox genes and cephalopod plesiomorphies

2 assembled transcriptomes and the respective raw reads

“Ovu1”: mRNA of almost hatched individuals (stage XX)

“Ovu2”: pooled mRNA of developmental stages VIII, XI, XV, XVIII

RNA-seq libraries were constructed with a Lexogen SENSE mRNA-Seq Library Prep Kit V2 and sequenced with an Illumina Hi-Seq 2500 generating paired-end, stranded 125 bp libraries resulting in 53,523,481 (ovu1) and 63,328,653 (ovu2) paired end reads. The overall transcriptome assembly follows the procedure performed by De Oliveira et al. (2016) [42]. The short‐read libraries were preprocessed using Trimmomatic v. 0.36 (ref. [43]) to remove known specific Illumina adapters from the paired‐end libraries (Illumina universal adapter). Filtering by quality and length was performed with a SLIDINGWINDOW:4:15 MINLEN:36. First and last nucleotides from reads with low quality score were clipped and the library file was converted into FASTA format using fq2fa from SeqKit version 0.11.0 (ref. [44]). Quality of the initial and filtered library was assessed with the software FastQC v.0.11.8 (ref. [45]) considering quality score of the bases, GC‐content, and read length. 13.33% (ovu1) and 16,23% (ovu2) of reads were excluded during the preprocessing procedure resulting in a total of 46,386,109 (ovu1) and 53,052,713 (ovu2) reads. The assemblies and all downstream analyses were conducted with a high‐quality and clean library. The filtered transcriptome was assembled into contiguous cDNA sequences with IDBA_tran v1.1.3 software (ref. [46]) using the default settings (except: −mink20 −maxk 80 −step5). The resulting assembly was assessed using the tool QUAST (available at: http://quast.bioinf.spbau.ru [47]). The number of contigs was 16,723 sequences (ovu1) and 18,551 (ovu2).

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