Perpustakaan Digital ITB

The Annona species, members of the Annonaceae family, are well known for their distinct sweet-flavored fruit packed with nutrients and possess important biological activities which are widely used as traditional medicine. In Africa–the native range of many Annona species, both indigenous and introduced species, remain underexplored and inadequately represented at the genomic level, bringing the species into the category of orphan crops. Hence, this study aimed to explore the comparative genomics of three Annona species, namely A. senegalensis, A. reticulata, and A. muricata, to gain deeper insights into their genome structure and characteristics, gene content, and evolutionary relationships. High-quality whole-genome assemblies of A. senegalensis and A. reticulata were generated and compared with the existing A. muricata genome. The genome sizes ranged from 617.2–688.4 Mbp, consisting of 34% GC bases and more than 50% repetitive sequences, primarily long terminal repeats (LTRs). Gene prediction revealed 22,070–29,846 protein-coding genes, exhibiting distinct structural characteristics: A. muricata presented compact gene structures, A. reticulata showed fragmented genes and possible expansion, and A. senegalensis featured genes associated with defense and stress adaptation. Orthogroup analysis identified 9,803 shared gene families. Phylogenomic reconstruction and divergence time estimation placed A. reticulata and A. muricata in a closer clade, with A. senegalensis diverging earlier from A. muricata. Whole-genome duplication analysis revealed a shared ancient duplication event, along with an additional lineage-specific duplication. By providing new genomic resources for the Annona genus and expanding its representation in genomic databases, these findings will support future efforts in breeding, conservation, and crop improvement strategies.