An improved chromosome-level haplotype-resolved genome assembly and annotation of pitaya

The aim of this study was to sequence, assemble, and annotate the genome of pitaya to obtain comprehensive genomic information and explore its genetic diversity and biological characteristics, providing strong support for genetic improvement and conservation of pitaya. Using PacBio long reads, nanopore ultra-long reads, and high-throughput chromosome conformation capture (Hi-C) data, we assembled the data using the hifiasm2 software, resulting in a chromosome-level high-quality monoploid resolution genome assembly for pitaya. The two haplotypes had sizes of approximately 1.47 Gb and 1.44 Gb, respectively, and included 22 centromeres and 21 telomeres, reaching the T2T level, with N50 values of 133.4 Mb and 132.6 Mb, respectively. Subsequent gene prediction and annotation identified a total of 34,673 genes, covering most regions of the pitaya genome. Through functional annotation and analysis of the pitaya genome, we discovered numerous genes related to its biological characteristics and agronomic traits, including fruit color, texture, quality, and disease resistance.