Reference Genome of an Irruptive Migrant, the Pine Siskin (Spinus pinus)

Pine siskins (Spinus pinus) are irruptive migratory songbirds of biological interest in studies of endocrine regulation, immune function, and behavioral flexibility. Here, we present a chromosome-level reference genome from a female pine siskin, assembled de novo using long-read sequencing and scaffolded with a reference-guided approach. Synteny analyses also showed that our assembly can reliably reveal genomic rearrangements relative to other finches. Using reference-based annotation, we identified thousands of protein-coding genes, including loci relevant to metabolism and immune function that demonstrate the utility of this assembly for downstream studies. We also found evidence of gene duplications and pseudogenization in immune loci, showing the utility of our assembly for immunogenetic studies. Our analysis provides the first genome-wide view of transposable element (TE) activity in Spinus, revealing multiple bursts of long terminal repeat (LTR) retrotransposon expansion, including a recent one that coincides with the estimated diversification of North and South American siskins approximately 2.7 million years ago. We also detected putative lineage-specific LTR sequences, suggesting recent or ongoing TE diversification. This assembly fills a critical gap in passerine genomic resources and provides a resource for comparative, transcriptomic, and population-level studies across species with diverse migratory strategies.