2026-10-14T05:49:49Z https://api.figshare.com/v2/oai

oai:figshare.com:article/32098903 2026-10-08T18:37:55Z category_24037 item_type_3 month_year_10_2026

Supporting data and scripts for transcriptome-derived SNP analysis of genomic differentiation among <i>Chamaecyparis hodginsii</i> provenances Zou yuhong (23790754) Tree improvement (incl. selection and breeding) Chamaecyparis hodginsii <p dir="ltr">This dataset provides supporting data, analysis results, and custom scripts associated with the revised manuscript entitled <b>“Transcriptome-derived SNPs reveal genomic differentiation among Chamaecyparis hodginsii provenances with contrasting wood-property profiles.”</b></p><p dir="ltr">The study reanalyzed 26 previously generated RNA-seq libraries representing 13 geographic provenances of <i>Chamaecyparis hodginsii</i>, with two biological replicates per provenance. The dataset includes provenance-level phenotypic measurements, coverage-aware transcriptome-derived SNP data, population-structure and genetic-differentiation analysis results, XP-CLR results, SIFT4G functional annotations, and related analysis outputs and scripts.</p><p dir="ltr">The provenance labels L1–L13 used in the manuscript correspond respectively to the original dataset codes <b>L1, L14, L15, L4, L18, L19, L7, L8, L9, L22, L11, L23, and L13</b>.</p><p dir="ltr">Based on principal component analysis (PCA) and SNP-based maximum-likelihood clustering, L6, L11, and L12 were designated as Pop1, whereas the remaining ten provenances were designated as Pop2. These groups were defined according to SNP-based clustering patterns rather than wood-property classifications. XP-CLR was used as an exploratory analysis to identify genomic regions showing elevated differentiation between Pop1 and Pop2, rather than to establish direct associations between genetic variants and wood-property traits.</p><p dir="ltr">All files in this repository correspond to the current revised version of the manuscript. Detailed descriptions of individual files, data processing procedures, analytical methods, and relevant supplementary information are provided in the accompanying <b>README.txt</b>.</p><p dir="ltr">The chromosome-level <i>C. hodginsii</i> reference genome and corresponding annotation are available separately at <a href="https://doi.org/10.6084/m9.figshare.26064412.v1" target="_blank">https://doi.org/10.6084/m9.figshare.26064412.v1</a>.</p> 2026-04-26T02:40:42Z Dataset Dataset 10.6084/m9.figshare.32098903.v10 https://figshare.com/articles/dataset/_b_The_Genetic_Basis_of_Wood_Property_Variation_in_b_b_i_Chamaecyparis_hodginsii_i_b_b_b_b_and_the_Identification_of_Candidate_Genes_b_/32098903 CC BY 4.0