Florida Scrub-Jay genome assembly and annotation

Scripts for de novo genome assembly of the Florida Scrub-Jay (Aphelocoma coerulescens) genome.

Find the genome assembly under NCBI accession GCA_041296385.1 (UR_Acoe_1.0). Raw sequence reads are available on NCBI under BioProjects PRJNA1076903 and PRJNA1097984. The genome annotation, repeat library and repeat annotation, and sex-averaged and sex-specific linkage maps are available on Figshare at figshare(.)com/projects/Florida_Scrub-Jay_genome_assembly/220939.

If you use any data associated with this project, please cite:

Faye G. Romero, Felix E.G. Beaudry, Eyvind Hovmand Warner, Tram N. Nguyen, John W. Fitzpatrick, Nancy Chen. A new high-quality genome assembly and annotation for the threatened Florida Scrub-Jay (Aphelocoma coerulescens). bioRxiv 2024.04.05.588142. DOI: 10.1101/2024.04.05.588142.

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Input data for basic genome assembly and annotation:

• PacBio HiFi raw reads
• Illumina paired-end reads of parents of the reference individual
• Hi-C reads
• linkage map
• RNA-seq reads

Input data for sex-linked scaffold identification pipeline:

• Paired-end whole-genome Illumina reads for at least 1 male and 1 female individual (here, I use 25 male and 25 female)

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Data in this repository (found in data/) include:

• TE_lengths_v123_July2024.Rdata: repeat element classifications and lengths for 3 versions of the Florida Scrub-Jay genome (v1 = Feng et al. 2020, Nature; v2 = Driscoll & Beaudry et al. 2024, Genetics; v3 = Romero et al. 2024, bioRxiv)
• TE_counts_v23_July2024.Rdata: repeat element classifications and counts for 2 versions of the Florida Scrub-Jay genome (v2 = Driscoll & Beaudry et al. 2024, Genetics; v3 = Romero et al. 2024, bioRxiv)
• FSJgenome_July2024_FINAl_*.fasta.tbl: RepeatMasker table summaries
• AllSamples_AvgCov_Wunloc3_AllPos_1kbwin.Rdata: average read depth for 50 jays, in 1 kb windows, across the chimeric ZW contig
• Indiv_Cov_Per_Scaf.Rdata: average read depth for 50 jays across all scaffolds in the genome
• unmasked_seq_pos_FSJgenome_July2024_FINAL.bed: positions of unmasked (i.e., uppercase) sequence in the genome (generated with the script sex-linked-scaffold-id/extract_unmasked_seq_pos.py)

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Please direct any questions about this project to Faye Romero ([email protected]).