Maize ABS4 reference genome assembly and annotation

We created a reference genome assembly of the maize ABS4 line used for synthetic centromeres. The original ABS4 heterozygous line in a Hi-II background (Dawe et al. 2023 https://doi.org/10.1038/s41477-023-01370-8, Zhang et al. 2012 https://doi.org/10.1111/j.1365-313X.2011.04867.x) was selfed five times, and a sequencing library was prepared using a SMARTbell Express Template Prep Kit 3.0. Sequencing was conducted on a PacBio Revio system with a Revio Sequencing Plate in CCS mode. Raw PacBio reads in fastq format are available under NCBI Bioproject PRJNA874319, SRA accession SRR31749818. File AbsGenomePBHIFI_version_1.fa is the complete reference sequence in fasta format including 10 chromosomes and unplaced primary contigs. It was generated using primary contigs with hifiasm v0.19.4. Ragtag v2.1.0 was used to scaffold the contigs based on the maize A188 reference genome (Lin et al. 2021 https://doi.org/10.1186/s13059-021-02396-x). Heterozygous and misassembled contigs were processed through manual curation and RagTag v2.1.0 'correct' command. File AbsGenomePBHIFI_version_1.fa.mod.EDTA.intact.gff3 is a TE annotation file generated by EDTA v2.1.0. File AbsGenomePBHIFI_version_1_liftoffA188.gff3 is a gene annotation file generated using Liftoff v1.6.3 based on the A188 reference and gene annotation, version 1.0 (Zm-A188-REFERENCE-KSU-1.0).