Comparative transcriptomics reveals the molecular genetic basis of pigmentation loss in Sinocyclocheilus cavefishes

Cave-dwelling animals evolve distinct troglomorphic traits, such as loss of eyes, skin pigmentation, and augmentation of senses following long-term adaptation to the perpetual darkness. However, the molecular genetic mechanisms underlying these phenotypic variations remain unclear. In this study, we conducted comparative histology and comparative transcriptomics study of the skin of eight Sinocyclocheilus species (Cypriniformes: Cyprinidae) that included surface and cave-dwelling species. We analyzed four surface and four cavefish species by using next-generation sequencing, and a total of 802,798,907 clean reads were generated and assembled into 505,495,009 transcripts, which contributed to 1,037,334 unigenes. Bioinformatics comparisons of four different surface-cave fish groups revealed between 10,629 and 6442 significantly differentially expressed unigenes. Further, tens of differentially expressed genes (DEGs) potentially related to skin pigmentation were identified. Most of these D..., Raw data (raw reads) in the fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N, and low-quality reads from raw data. At the same time, Q20, Q30, GC-content, and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality, and then transcriptome assembly was conducted using Trinity (Grabherr et al., 2011), with min_kmer_cov set to 2 by default; all other parameters were set to default values., , # Comparative transcriptomics reveals the molecular genetic basis of pigmentation loss in Sinocyclocheilus cavefishes

[https://doi.org/10.5061/dryad.6hdr7sqwd](https://doi.org/10.5061/dryad.6hdr7sqwd)

**This data set is a corrected data set. After the article was published in 2020, the data was uploaded to the Dryad database. When it was referenced by others, it was found that there was an error in the data upload, so a new data set was created to correct the wrong data.**

## Description of the data and file structure

This dataset is the original data of the skin transcriptome of the samples of Sinomelus in the paper. Each sample has three biological replicates, and each replicate includes two replicates, which are represented by 1 (F), 1 (R), 2 (F), 2 (R), 3(F) and 3(R) respectively. Some errors occurred when uploading the dataset. Therefore, a new data set was established for correction. There were 19 data sets of Sinocyclocheilus that needed to be corrected: sinocyclocheilus tian...