Chromosome-level genome assembly of an endangered bird Java Sparrow (Padda oryzivora)

The Java sparrow (Padda oryzivora) is an endangered passerine bird native to the Indonesian islands of Java, Bali, and Bawean that has experienced substantial population decline in the wild due to habitat loss and overexploitation, despite being widely introduced and bred as a cage bird. However, this species still lacks a high-quality genome, which would provide important genetic resources for its conservation. Here, we present a chromosome-level genome assembly for P. oryzivora generated using an integrated sequencing strategy combining long-read sequencing, short-read sequencing, transcriptome sequencing, and chromosome conformation capture technologies. The final assembly spans ~1.20 Gb with a contig N50 of ~36.16 Mb, scaffold N50 of ~75.01 Mb, and a BUSCO completeness of 98.8%. A total of 21,199 protein-coding genes were predicted, of which 19,422 were functionally annotated. This high-quality reference genome provides an important genetic resource for the conservation of this species.