R. bonasus and L. erinacea embryo fin transcriptomes

Using bycatch of commercial fisheries, samples from embryos undergoing paired fin development were collected from a wild population of cownose rays (Rhinoptera bonasus; Rbo) in Chesapeake Bay. RNA extractions were made from various fin domains and sequenced on an Illumina HiSeq4000 and Illumina MiSeq. Adapters and low quality sequences from cownose ray data were trimmed from fastq files using the TrimGalore wrapper for Cutadapt and FastQC. Overlapping reads were combined with Flash prior to assembly and orphaned reads were retained. To reduce the impact of genetic variability, data from fin domains of only three individuals were used in the assembly, including: two regions of a stage one embryo (broad anterior pectoral fin region and mid-anterior pectoral fin), one region of a stage seven embryo (clasper) and eight regions of stage three embryos (cephalic lobe, anterior pectoral fin, mid-anterior pectoral fin, mid-pectoral fin, mid-posterior pectoral fin, posterior pectoral fin, zipper region, and pelvic fin). Sequencing with both HiSeq (stage 3 samples, 100bp PE reads) and MiSeq (stage 1 and stage 7 samples, 300 bp PE reads) was conducted to help generate full length transcripts. Abyss was used to assemble contiguous sequences (contigs) from the paired end (PE) and orphaned sequence data with 10 kmer sizes ranging from 25-70 nucleotides. Contigs of 500 nucleotides or greater were summarized according to similarity (e-value Using iterative BLAST searches and pairwise alignments, contig sequences with strong e-values (Leucoraja erinacea; Ler) using publicly available stage 31 L. erinacea 100bp PE RNA-seq data (SRA, PRJNA288370)