The first telomere-to-telomere genome assembly of the soybean male-sterile germplasm 88-428BY by massive parallel sequencing

Soybean ( Glycine max (L.) Merr.) is a key source of plant protein and oil, yet genomic resources for male-sterile germplasms remain scarce. This study addresses this gap by presenting the first telomere-to-telomere (T2T) genome assembly of the landrace soybean 88-428BY, a Chinese photoperiod-sensitive genic male sterility (PGMS) germplasm with photoperiod-dependent fertility. Using a hybrid strategy combining PacBio HiFi, Oxford Nanopore ultra-long reads, and Hi-C scaffolding, we generated a high-quality reference genome of 1.01 Gb (N50 = 52.05 Mb), achieving 99.88% BUSCO completeness and assembling telomeres at both ends of 80% of the chromosomes. Annotation revealed 55,292 protein-coding genes and a high repetitive content (63.03%), which was dominated by LTR retrotransposons. Comparative genomics identified 35,236 structural variations (SVs), with hotspot regions harboring genes showing suppressed expression. Transcriptomic analysis under long-day and short-day conditions uncovered co-expression modules enriched in flavonoid biosynthesis and protease inhibitors, alongside key transcription factors (e.g., NAC25 , ERF113 ) potentially associated with fertility regulation. This T2T genome provides a critical resource for elucidating the molecular basis of photoperiod-sensitive male sterility and advancing functional genomics and molecular breeding in soybean. • First T2T genome assembly of the soybean PGMS line 88-428BY with photoperiod-sensitive male sterility. • Assembly size of 1.01 Gb with an N50 of 52.05 Mb, 99.88% BUSCO completeness, and telomeres assembled at both ends of 80% of chromosomes. • Repetitive elements account for 63.03% of the genome, the highest among T2T soybean assemblies, highlighting lineage-specific genome plasticity. • Identification of 35,236 SVs, with 522 SV hotspots harboring 11,730 genes exhibiting significantly suppressed expression, implicating SVs in global transcriptional regulation. • WGCNA identifies two photoperiod-responsive modules: darkmagenta and brown4 , linking metabolic pathways to fertility switching. • SV-associated TFs ( NAC25 , ERF113 ) and a frameshift mutation in AMT1 emerge as candidate regulators of photoperiod-sensitive male sterility.