DOI: 10.5061/dryad.6hdr7sqwd
title: Comparative transcriptomics reveals the molecular genetic basis of pigmentation loss in Sinocyclocheilus cavefishes

description: 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
 DEGs (including GNAQ, PKA, NRAS, and p38) are downregulated in cavefish
 species. They are involved in key signaling pathways of pigment synthesis,
 such as the melanogenesis, Wnt, and MAPK pathways. This trend of
 downregulation was confirmed through qPCR experiments. This study will
 deepen our understanding of the formation of troglomorphic traits in
 cavefishes.
description: 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.
description: # 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 tianlinensis data set, Sinocyclocheilus brevibarbatus data set, and Sinocyclocheilus data set. The third dataset of maculatus is the dataset numbered 3 (R) and the entire dataset of Sinocyclocheilus oxycephalus. ## Sharing/Access information Data was derived from the following sources: n/a ##