[DOI] 10.5524/102221
[Title] Supporting data for "A chromosome-level genome assembly and annotation of a maize elite breeding line Dan340"
[Release Date] 2022-05-09
[Citation] Zhao, Y; Wang, Y; Ma, D; Feng, G; Huo, Y; Liu, Z; Zhou, L; Zhang, Y; Xu, L; Wang, L; Zhao, H; Zhao, J; Wang, F (2022): Supporting data for "A chromosome-level genome assembly and annotation of a maize elite breeding line Dan340" GigaScience Database. http://dx.doi.org/10.5524/102221
[Data Type] Genomic,Epigenomic
[Dataset Summary] 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.
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".
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 of intraspecific genome diversity in maize, but also provides a novel resource for maize breeding improvement.
[File Location] https://ftp.cngb.org/pub/gigadb/pub/10.5524/102001_103000/102221/
[File name] - [File Description]
BUSCO_short_summary.txt - BUSCO output of Zea mays Dan340. Genome Assembly - Short summary output
D340_all_repeat_without_trf.gff3.gz - Repeat sequence Annotation of Zea mays Dan340 (GFF format) without transcription factors
D340_all_repeat.gff3.gz - Repeat sequence Annotation of Zea mays Dan340 (GFF format)
D340_CDS.fasta.gz - Coding sequence of Zea mays Dan340 (FASTA format)
D340_genefam_hcluster.hcluster - Functional annotation of Zea mays Dan340 - output file from OrthoMCL (Hcluster format)
D340_genome_annotation.gff.gz - Annotation of Zea mays Dan340 (GFF format)
D340_genome.fasta.gz - Genome assembly of of Zea mays Dan340 (FASTA format)
D340_miRNA.gff3.gz - Annotation of Zea mays Dan340 (GFF format) - miRNA
D340_PBSV_SV_filt.vcf.gz - Stuctural variants of Zea mays Dan340 - output file from PBSV (VCF format)
BUSCO_full_table.tsv - BUSCO output of Zea mays Dan340. Genome Assembly - Full table output
D340_PEP.fasta.gz - Protein sequence of Zea mays Dan340 (FASTA format)
D340_rRNA.gff3.gz - Annotation of Zea mays Dan340 (GFF format) - rRNA
D340_tRNA.gff3.gz - Annotation of Zea mays Dan340 (GFF format) - tRNA
D340_genefam_hcluster_stat.stat - Functional annotation of Zea mays Dan340 - output file from OrthoMCL (Stat format)
D340_snRNA.gff3.gz - Annotation of Zea mays Dan340 (GFF format) - snRNA
BUSCO_missing_busco_list.tsv - BUSCO output of Zea mays Dan340. Genome Assembly - Missing BUSCO output
readme_102221.txt - None
Genetic_variation_analysis_description_PBSV.txt - Description of PBSV genetic variation analysis description
D340_Nucmer_SyRI_SV_filt.vcf.tar.gz - Structural variants from MUMmer analysis of genetic and structural variations between Dan340 and other maize inbred line
[License]
All files and data are distributed under the Creative Commons Attribution-CC0 License unless specifically stated otherwise, see http://gigadb.org/site/term for more details.
[Comments]
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