The Asian elephant (Elephas maximus), a keystone species with both ecological and cultural significance, is highly endangered and has disappeared from 95% of its historical range. In this study, we present a chromosome-level assembly and an annotation of the Asian elephant genome, providing a foundational resource for population genomics, conservation biology and evolutionary research.

The primary genome assembly spans 190 contigs, with an N50 of 87,987,108 bp and is scaffolded into 64 sequences, with an N50 of 127,432,672 bp. We also present two haplotype-resolved assemblies with contig N50s of 75,101,715 bp and 88,213,608 bp. The genome assemblies and annotated protein-coding models in the primary assembly are highly complete, with 98.2%, 98.2%, and 96.0% BUSCO single-copy orthologs identified in the primary and two haplotype genome assemblies, respectively, and 98.8% recovered in the protein-coding annotation. We showcase how this reference genome enables insights into functional and evolutionary genomics, including the transposable element landscape, demographic history, a comparison against an individual sequenced from another population, as well as an investigation into genomic regions with increased levels of heterozygosity that colocalise with multi-copy gene families associated with immune and sensory-responses.

The development of a high-quality genome assembly and annotation for E. maximus gives researchers a valuable resource to help understand the evolutionary history of this iconic species as well as guide conservation efforts. Here we have shown that highly contiguous, complete and accurate chromosome sequences help uncover regions with increased levels of homozygosity, indicative of inbreeding, and areas of increased heterozygosity, enriched for genes key to the immune response and other sensory mechanisms.