A chromosome-level genome assembly and annotation of a maize elite breeding line Dan340

Background Maize is not only one of the most important crops grown worldwide for food, forage, and biofuel, but also an important model organism for fundamental research in genetics and genomics. Owing to its importance in crop science, genetics and genomics, several reference genomes of common maize inbred line (genetic material) have been released, but some genomes of important genetic germplasm resources in maize breeding research are still lacking. The maize cultivar Dan340 is an excellent backbone inbred line of the Luda Red Cob Group with several desirable characteristics, such as disease resistance, lodging resistance, high combining ability, and wide adaptability. Findings In this study, we constructed a high-quality chromosome-level reference genome for Dan340 by combining PacBio long HiFi sequencing reads, Illumina short reads and chromosomal conformational capture (Hi-C) sequencing reads. The final assembly of the Dan340 genome was 2,348.72 Mb, including 2,738 contigs and 2,315 scaffolds with N50 of 41.49 Mb and 215.35 Mb, respectively. Repeat sequences accounted for 73.40% of the genome size and 39,733 protein-coding genes were annotated. Analysis of genes in the Dan340 genome, together with those from B73, Mo17 and SK, were clustered into 27,654 gene families. There were 1,806 genes from 359 gene families that were specific to Dan340, of which many had functional gene ontology annotations relating to “porphyrin-containing compound metabolic process”, “tetrapyrrole biosynthetic process”, and “tetrapyrrole metabolic process”. Conclusions The completeness and continuity of the genome were comparable to those of other important maize inbred lines. The assembly and annotation of this genome not only facilitates our understanding about of intraspecific genome diversity in maize, but also provides a novel resource for maize breeding improvement. Research Areas Genetics and Genomics; Agriculture, Plant Genetics ### Competing Interest Statement The authors have declared no competing interest. * BUSCO : Benchmarking Universal Single-Copy Orthologs Hi-C : chromosomal conformation capture CCS : circular consensus sequencing HiFi : long high-fidelity CEGMA : Core Eukaryotic Genes Mapping Approach LTR : long-terminal repeat LAI : long-terminal repeat assembly index TEs : transposable elements TRF : Tandem Repeats Finder EVM : EVidenceModeler KEGG : Kyoto Encyclopedia of Genes and Genomes GO : Gene Ontology MCL : Markov clustering NCBI : National Center for Biotechnology Information PacBio : Pacific Biosciences tRNA : Transfer RNA rRNAs : Ribosomal RNAs miRNA : microRNA snRNA : small nuclear RNA