Regeneration tissue
The Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic) tool was used to remove low-quality reads, adapter sequences, and contaminant sequences.  The read quality and coverage were improved using SeqPrep (https://github.com/jstjohn/SeqPrep). Clean reads were mapped to the reference genome of S. paramamosain (NGDC; BioProject: PRJCA001790; Accession No.: GWHALOH00000000) using HISAT2 tool (https://daehwankimlab.github.io/hisat2/). RSEM (RNA-Seq by Expectation-Maximization) software was used to estimate gene and isoform expression levels from RNA sequencing data. The differential expression analysis was performed using EdgeR (http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html).