Macauba genome, CDS, Proteins and GFFs

Acrocomia aculeata (macaúba) is an emerging oil-producing palm with high potential for sustainable bioenergy and agricultural systems in tropical regions. Here, we present the first chromosome-scale, haplotype-resolved (phased) genome assembly of the species and the first genomic reference for the genus, generated using Oxford Nanopore, PacBio HiFi, and Hi-C sequencing technologies. The final assembly comprises a highly contiguous 1.94 Gbp genome organized into 15 pseudochromosomes (N50 = 143.43 Mbp; QV = 76.4), alongside two fully phased haplotypes (Hap1: 1.93 Gbp; Hap2: 1.92 Gbp), each resolved at chromosome scale. Genome completeness was high, with 98.9% complete BUSCOs for predicted proteins and k-mer completeness exceeding 90%. Repetitive elements account for ~73-77% of the genome, with long terminal repeat (LTR) retrotransposons representing ~55%. The LTR Assembly Index (LAI = 25.11) supports a gold-standard reference genome, with consistently high values across both haplotypes. A total of 28,367 protein-coding genes were predicted using transcriptome-supported annotation, showing structural consistency across haplotypes and similarity to other palm genomes. Comparative analyses revealed strong chromosomal collinearity with closely related species. This high-quality phased genome provides a comprehensive resource for evolutionary genomics, conservation, and molecular breeding of macaúba.