Re-annotation and unified nomenclature of the MADS-box gene family in the chromosome-scale genome of rubber tree (Hevea brasiliensis)

Re-annotation and unified nomenclature of the MADS-box gene family in the chromosome-scale GT1 genome of rubber tree (Hevea brasiliensis), together with a public RNA-seq expression atlas and a comparison against the haplotype-resolved 7-33-97 T2T assembly. The bundle contains: the identification pipeline (PF00319 inclusion / PF01486 K-box discriminator), reciprocal-best-hit authority tables and MD5-pinned NCBI runtime inputs; the 71-member HbMADS01-HbMADS71 unified naming table with genomic coordinates, domain assignments, K-box criteria and previous-name reconciliation; full-family, type II and domain-anchored type I phylogenies (IQ-TREE2), MEME K-box motifs, Ka/Ks and duplication dating, MCScanX collinearity and cross-haplotype anchors; 17 MADS-box genes recovered from unannotated GT1 intergenic loci by miniprot and re-scanned with pyhmmer (including FLC, FLC/MAF and SVP/AGL24), local-structure verdicts resolving the apparent FLC relocation to a 52,234 bp annotation gap, and 13 cross-assembly multicopy naming groups; an expression atlas for 33 public RNA-seq libraries (tapping latex, a female flower bud plantation-site contrast and a tetrad-stage male fertility contrast), with count/TPM matrices and Welch t plus genome-wide BH-FDR tables; a companion gametophyte validation plan with qPCR primers; and the manuscript v7.1 (docx), the six main and ten supplementary figures (300 dpi PNG), the supplementary tables, and an MD5-verified manifest (MANIFEST_md5.txt) covering every archived file. What is new in v7.1: the manuscript is updated to v7.1 (Tropical Plants format, 49 references, six main figures); the supplementary tables are renumbered into first-citation order (Table S1 unified naming; Table S2 gametophytic-data search log; Table S3 the 17 recovered genes; Table S4 cross-assembly multicopy groups; Table S5 the RNA-seq quantification and differential-expression workbook; Table S6 the 5-extended gene models), and all figure and table files now match the manuscript; the archive is a single zip (69,016,654 bytes) with MANIFEST_md5.txt inside, replacing the split-part format of v5.3.x; the scientific results are unchanged relative to v5.3.1. The data availability statement cites only the concept DOI 10.5281/zenodo.23410860, which always resolves to the latest release.