MHC-IIB (fasta) We generated a high-quality genome assembly, using a combination of long-read, linked-read, and short-read sequencing, as well as optical mapping, of a single great reed warbler Acrocephalus arundinaceus (Aaru-DAB) for which the genomic and expressed MHC-I and -IIB gene diversities had been thoroughly characterized previously. We then annotated scaffolds containing the MHC and MHC-associated genes. We also partly annotated homologous regions in three additional species where long-read genomes were available; hooded crow Corvus cornix (Ccor-DAB) and jackdaw Coloeus monedula (Cmon-DAB) and zebra finch Taeniopygia guttata (Tgut-DAB). The following 127 full-length MHC-IIB genes in open reading frame were retrieved and have been manually edited and aligned. MHC-I (fasta) We generated a high-quality genome assembly, using a combination of long-read, linked-read, and short-read sequencing, as well as optical mapping, of a single great reed warbler Acrocephalus arundinaceus (Aaru-UA) for which the genomic and expressed MHC-I and -IIB gene diversities had been thoroughly characterized previously. We then annotated scaffolds containing the MHC and MHC-associated genes. We also partly annotated homologous regions in three additional species where long-read genomes were available; hooded crow Corvus cornix (Ccor-UA) and jackdaw Coloeus monedula (Cmon-UA) and zebra finch Taeniopygia guttata (Tgut-UA). The following 27 full-length MHC-I genes in open reading frame were retrieved and have been manually edited and aligned. Intragenic repeats (xls) We generated a high-quality genome assembly, using a combination of long-read, linked-read, and short-read sequencing, as well as optical mapping, of a single great reed warbler Acrocephalus arundinaceus for which the genomic and expressed MHC-I and -IIB gene diversities had been thoroughly characterized previously. We then annotated scaffolds containing the MHC and MHC-associated genes. We also partly annotated homologous regions in three additional species where long-read genomes were available; hooded crow Corvus cornix (Ccor-UA) and jackdaw Coloeus monedula (Cmon-UA) and zebra finch Taeniopygia guttata (Tgut-UA). The total gene size, the intragenic repeat length, and intragenic repeat length of long-terminal repeats (ltr) of MHC-I and MHC-IIB genes were assessed. Intergenic repeats (xls) We generated a high-quality genome assembly, using a combination of long-read, linked-read, and short-read sequencing, as well as optical mapping, of a single great reed warbler Acrocephalus arundinaceus for which the genomic and expressed MHC-I and -IIB gene diversities had been thoroughly characterized previously. We then annotated scaffolds containing the MHC and MHC-associated genes. We also partly annotated homologous regions in three additional species where long-read genomes were available; hooded crow Corvus cornix (Ccor-UA) and jackdaw Coloeus monedula (Cmon-UA) and zebra finch Taeniopygia guttata (Tgut-UA). The intergenic distance (<30kb, intergenic_region_length), total intergenic repeat length and intergenic repeat length of long-terminal repeats (ltr) of tandemly duplicated MHC-IIB genes were assessed. Annotationswebapollogrw_Annotated MHC and MHC-associated scaffolds in great reed warbler (gff) We generated a high-quality genome assembly, using a combination of long-read, linked-read, and short-read sequencing, as well as optical mapping, of a single great reed warbler Acrocephalus arundinaceus for which the genomic and expressed MHC-I and -IIB gene diversities had been thoroughly characterized previously. We then annotated protein-coding genes on the scaffolds containing MHC genes and MHC-associated genes (MHC-I genes (ha1f) and MHC-IIB genes (hb2l)). MUNGzfprimary_Annotated MHC contigs in zebra finch (gff) We annotated (protein-coding, contig positions given) genes on contigs (MUGN01000) containing MHC genes and MHC-associated genes in zebra finch Taeniopygia guttata (ZF), see gff file containing all augustus-predicted genes (not manually curated (AugPred_ZF) that show similarity to vertebrate swissprot proteins. ZFgenescoretap_Annotated MHC contigs in zebra finch (gff) We annotated (protein-coding, contig positions given) curated MHC-I and MHC-IIB genes (MHC_ZF) on contigs (MUGN01000) in zebra finch Taeniopygia guttata (ZF), see gff file containing curated MHC-I and MHC-IIB genes. genomeJD_Annotated MHC contigs in jackdaw (gff) We annotated (protein-coding, contig positions given) genes on contigs (00XXXXF) containing MHC genes and MHC-associated genes in jackdaw Coloeus monedula (JD), see gff file containing all augustus-predicted genes (not manually curated (AugPred_JD)) that show similarity to vertebrate swissprot proteins. JDgenescoretap_Annotated MHC contigs in jackdaw (gff) We annotated (protein-coding, contig positions given) curated MHC-I and MHC-IIB genes (MHC_JD) on contigs (00XXXXF) in jackdaw Coloeus monedula (JD), see gff file containing curated MHC-I and MHC-IIB genes. genomeHC_Annotated MHC contigs in hooded crow (gff) We annotated (protein-coding, contig positions given) genes on contigs (00XXXXF) containing MHC genes and MHC-associated genes in hooded crow Corvus cornix (HC), see gff file containing all augustus-predicted genes (not manually curated (AugPred_HD)) that show similarity to vertebrate swissprot proteins. HCgenescoretap_Annotated MHC contigs in hooded crow (gff) We annotated (protein-coding, contig positions given) curated MHC-I and MHC-IIB genes (MHC_HD) on contigs (00XXXXF) in hooded crow Corvus cornix (HC), see gff file containing curated MHC-I and MHC-IIB genes JDMHCregion Jackdaw Coloeus monedula (JD) MHC contigs (fasta) We annotated (protein-coding, contig positions given) genes on contigs (000195F 000214F 000245F 000261F 000277F 000327F 000330F 000334F 000370F 000380F 000397F 000414F 000520F 000558F 000715F 000846F 001669F 001718F 2283) containing MHC genes and MHC-associated genes in jackdaw Coloeus monedula (JD), see fasta file.