Reference genome of an irruptive migrant, the pine siskin (<em>Spinus pinus</em>)

This dataset contains unscaffolded and supporting files associated with the chromosome-level genome assembly of the Pine Siskin (Spinus pinus). We provide two unscaffolded haplotype assemblies (pisiContigs_hap1.fasta and pisiContigs_hap2.fasta) that correspond to the scaffolded assemblies deposited in NCBI under BioProject accession numbers [PRJNA1281197] (primary haplotype) and [PRJNA1281196] (alternate haplotype). To document the scaffolding process, we include AGP files generated by RagTag (ragtag.scaffold.Hap1.agp and ragtag.scaffold.Hap2.agp), which specify the ordering and orientation of contigs into pseudochromosomes. To support repeat annotation and comparative analyses, we also provide both raw and curated repeat libraries. The raw library (pisiRepeats-families.fa) contains de novo repeat family predictions. Curated libraries were refined using MCHelper and are provided in redundant (curated_sequences_R.fa) and nonredundant (curated_sequences_NR.fa) formats. , To generate scaffolded assemblies, we used RagTag v2.1.0 to order and orient contigs against the Azores Bullfinch (Pyrrhula murina) reference genome (bPyrMur1.1, NCBI). This process produced AGP files documenting contig placement and orientation (ragtag.scaffold.Hap1.agp, ragtag.scaffold.Hap2.agp). For repeat annotation, we ran RepeatModeler2 v2.0.6, which identified and classified de novo repeat families (pisiRepeats-families.fa). Curated repeat libraries were then generated using MCHelper v1.1.7, producing redundant (curated_sequences_R.fa) and nonredundant (curated_sequences_NR.fa) sequence sets for downstream analyses. Unscaffolded haplotype assemblies (pisiContigs_hap1.fasta, pisiContigs_hap2.fasta) correspond to the scaffolded genomes deposited in NCBI under BioProject accessions PRJNA1281197 (primary) and PRJNA1281196 (alternate). , # Reference genome of an irruptive migrant, the pine siskin (*Spinus pinus*) Dataset DOI: [10.5061/dryad.xsj3tx9tc](10.5061/dryad.xsj3tx9tc) ## Description of the data and file structure These data were generated as part of an effort to produce a high-quality, chromosome-level genome assembly of the pine siskin (*Spinus pinus*). The assembly was designed to support research on avian genome evolution, comparative genomics, and studies of immune and ecological adaptation. ### Files and variables #### File: pisiContigs_hap1.fasta **Description:**Â Unscaffolded contig-level assembly of the pine siskin (*Spinus pinus*) primary haplotype. Corresponds to the scaffolded genome deposited under BioProject accession PRJNA1281197. #### File: pisiContigs_hap2.fasta **Description:**Â Unscaffolded contig-level assembly of the pine siskin (*Spinus pinus*) alternate haplotype. Corresponds to the scaffolded genome deposited under BioProject accession PRJNA1281196. #### File: ragtag.scaffold.Hap1.ag...,