Reproducible analysis scripts for phenotypic and genomic divergence in Camellia sect. Tuberculata from the Chishui River Valley

Tuberculata from the Chishui River Valley. The archive includes workflows for whole-genome resequencing quality control and read mapping, SNP calling and filtering, population structure analysis, principal component analysis, nuclear phylogenomic reconstruction, genome-wide genetic differentiation and nucleotide diversity scans, identification of candidate differentiated regions, GO and KEGG enrichment analyses, TreeMix migration analysis, ABBA–BABA tests, PSMC demographic inference, plastome assembly and phylogenetic analyses, and multidimensional morphological analyses.

The newly generated whole-genome resequencing data have been deposited in the National Genomics Data Center (NGDC) under BioProject PRJCA067429. The Camellia sinensis outgroup data were obtained from BioProject PRJCA001158, experiment accession CRX091206. This dataset is intended to facilitate reproducibility, validation, and further comparative analyses related to the associated study.