DOI: 10.5061/dryad.xsj3tx9tc
title: Reference genome of an irruptive migrant, the pine siskin (<em>Spinus pinus</em>)

description: 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.
description: To generate scaffolded assemblies, we used RagTag v2.1.0 to order
 and orient contigs against the Azores Bullfinch (<em>Pyrrhula
 murina</em>) reference genome (bPyrMur1.1, NCBI). This process
 produced AGP files documenting contig placement and orientation
 (<code>ragtag.scaffold.Hap1.agp</code>,
 <code>ragtag.scaffold.Hap2.agp</code>). For
 repeat annotation, we ran RepeatModeler2 v2.0.6, which identified and
 classified de novo repeat families
 (<code>pisiRepeats-families.fa</code>). Curated repeat
 libraries were then generated using MCHelper v1.1.7, producing redundant
 (<code>curated_sequences_R.fa</code>) and nonredundant
 (<code>curated_sequences_NR.fa</code>) sequence sets for
 downstream analyses. Unscaffolded haplotype assemblies
 (<code>pisiContigs_hap1.fasta</code>,
 <code>pisiContigs_hap2.fasta</code>) correspond to the
 scaffolded genomes deposited in NCBI under BioProject accessions
 PRJNA1281197 (primary) and PRJNA1281196 (alternate).
description: # 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:** 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:** 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.agp **Description:** Scaffold path file produced by
 RagTag v2.1.0 showing the order and orientation of contigs for the primary
 haplotype relative to the *Pyrrhula murina* (bPyrMur1.1) reference genome.
 #### File: ragtag.scaffold.Hap2.agp **Description:** Scaffold path file
 produced by RagTag v2.1.0 showing the order and orientation of contigs for
 the alternate haplotype relative to the *Pyrrhula murina* (bPyrMur1.1)
 reference genome. #### File: pisiRepeats-families.fa **Description:** Raw
 *de novo* repeat family predictions generated by RepeatModeler2 v2.0.6
 from the pine siskin genome assemblies. #### File: curated_sequences_R.fa
 **Description:** Curated repeat library generated with MCHelper v1.1.7,
 containing redundant sequences from raw repeat predictions. #### File:
 curated_sequences_NR.fa **Description:** Curated repeat library generated
 with MCHelper v1.1.7, containing nonredundant sequences from raw repeat
 predictions.