First chromosome scale genome of Acrocomia aculeata.

Acrocomia aculeata (macaúba) is an oil-producing palm with high potential for sustainable bioenergy in tropical regions. We present the first chromosome-scale, haplotype-resolved genome assembly for the species and the genus, generated with Oxford Nanopore, PacBio HiFi, and Hi-C sequencing. The assembly spans 1.94 Gbp organized into 15 pseudochromosomes (N50 = 143.43 Mbp; QV = 76.4), with two fully phased haplotypes (Hap1: 1.93 Gbp; Hap2: 1.92 Gbp) resolved at chromosome scale. Genome completeness reached 98.9% complete BUSCOs for predicted proteins and > 90% k-mer completeness. Repetitive elements comprise 73-77% of the genome, with LTR retrotransposons accounting for ~55%. The LTR Assembly Index (LAI = 25.11) confirms gold-standard quality, sustained across both haplotypes. Annotation predicted 28,367 protein-coding genes with structural consistency across haplotypes and similarity to other palm genomes. Comparative analyses revealed strong chromosomal collinearity with closely related species. This reference genome supports evolutionary genomics, conservation, and molecular breeding of macaúba.