DOI: 10.6084/m9.figshare.16885255
title: Dataset and R code for: High functional allelic diversity and copy number in both MHC classes in the common buzzard

description: This data includes the genomic PacBio HiFi raw reads (fastq), Flye contigs (fasta) and phasebook generated haplotype-aware contigs (fasta), and Hi-C chromosome 29 sequence of the MHC class I and class II region (96,746 bp; fasta) in a zip folder. Sample information including amplicon ID, amplicon and allele depth, and MHC genotype, is included as well as data for 81 samples used for RNA sequencing, including ID, date sampled, MHC RNA transcipts, MHC genotypes (when available) and a key to identify MHC allele names with preliminary IDs. The data also includes R code and data necessary to reproduce Figure 1, 2, 3, 4, S2, S4, and S6-11. The code has been written by Jamie Winternitz, who can be contacted at jcwinternitz-at-gmail-dot-com. <br> Genomic data in zipped folder "Genomic Buteo buteo MHC data.zip": Pacbio HiFi raw reads: "raw_HiFi.zip": "hi48toc29b.fq" "hi64toc29b.fq" "hi263toc29b.fq" "hi326toc29b.fq" Flye contigs: "7 Flye contigs from Buteo buteo genome MHC region.fasta" Phasebook haplotype-aware contigs: "haplotype-aware_contigs_phasebook.zip": "hi48toc29b_contigs_phasebook.fa" "hi64toc29b_contigs_phasebook.fa" "hi263toc29b_contigs_phasebook.fa" "hi326toc29b_contigs_phasebook.fa" Hi-C consensus from 3 individuals of MHC region of chromosome 29: "HiC_scaffold_33-Ch29 MHC region (96746 bp).fasta" <br> Sample information for MHC-I and II genotypes as well as RNA transcript sampling data: "individual_allele_report_MHCI_genbank_names.csv" "individual_allele_report_MHCII_genbank_names.csv" "Samples with MHC-Iex3 and IIBex2 RNA transcripts and amplicon genotypes.xlsx" "MHC_1ex2&2Aexon2_transcripts_exact_match_transcriptomes_2018_9.xlsx" <br> The R code required to reproduce Figure 1, S2 and S4 is "MHC allele freq and expression.R". The data required to reproduce Figure 1 is the following: "Pop_allele_freq_RNAseq_data.csv" "CRC_MHC_allele_per_indiv.csv" <br> The R code required to reproduce Figure 2 and S6 is "multiple sequence alignment figures.R". The data required to reproduce Figure 2 and S6 is the following: "Buteo buteo MHC1 and HLA-A and Haal-UA exon 3 translation alignment character vectors.csv" "PBS_MHC-I_exon3.csv" "Buteo buteo MHC2 and HLA-DRB and Buga-DRB translation alignment character vectors.csv" "PBS_DRB1_exon2.csv" "Buteo buteo MHC2 recomb segments removed and HLA-DRB and Buga-DRB translation alignment character vectors.csv" "PBS_DRB1_exon2_no_recomb_segments.csv" "Buteo buteo MHC-I exon 2 and human and chicken translation alignment character vectors.csv" "PBS_MHC-I_exon2.csv" "Buteo buteo MHCIIA exon 2 with chicken alignment character vectors.csv" "PBS_MHC-IIA_exon2.csv" <br> The R code required to reproduce Figure 3, S7-S10 is "Phylogenetic figures.R". The data required to reproduce Figure 3, S7-S10 is the following: "MHC1 FastTree.newick" "MHC1 IQ-TREE.newick" "MHC1 FastTree 110 sequences.csv" "Common species dataset MHC1 and MHC2.csv" "MHC2 FastTree.newick" "MHC2 IQ-TREE.newick" "MHC2 FastTree 65 sequences.csv" "10speciesBirdTree.nex" "hawk.png" "owl.png" "grouse.png" "vulture.png" <br> The R code required to reproduce Figure 4 and S11 is "phylogeny for MHC-Iex2 and MHC-IIAex2.R" The data required to reproduce Figure 4 and S11 is the following: "MHC-I exon 2 FastTree.newick" "MHC1ex2 IQ-TREE.newick" "Sequences used for Real tree MHC-I exon 2.csv" "MHC-IIA exon 2 FastTree.newick" "MHC2A IQ-TREE.newick" "Sequences used for Real tree MHC-IIA exon 2.csv" "5speciesBirdTree.nex" <br>