Transcriptome analysis of gonads from male and female Nibea coibor

The Chu's croaker (Nibea coibor) is an important marine aquaculture species in China. To study the molecular basis of its gonadal development, we conducted histological and comparative transcriptomic analyses of testes and ovaries. The clean reads were aligned to a ribosome RNA (rRNA) database using Bowtie2 (version 2.2.8) , and rRNA-mapped reads were removed. The remaining reads were aligned to the N. coibor reference genome (GenBank ID: CM041792.1) using HISAT2 (v2.1.0) with default parameters Transcript assembly and quantification of expression levels were performed using StringTie (v1.3.1) in a reference-based approach (Pertea et al., 2016). Gene expression abundance was calculated as fragments per kilobase of transcript per million mapped reads (FPKM) using RSEM.