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

Zhao, Yikun; Wang, Yuancong; Ma, De; Feng, Guang; Huo, Yongxue; Liu, Zhihao; Zhou, Ling; Zhang, Yunlong; Xu, Li‐Wen; Wang, Liang; Zhao, Han; Zhao, Jiuran; Wang, Fengge

doi:10.46471/gigabyte.63

Cited by 6 publications

(2 citation statements)

References 55 publications

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“…2, Table 1). The highest copy number, 5,947, was found in the genome of Zea mays (genome assembly id GCA_024505845 (Zhao et al, 2022)). Also, many Metazoa possessed several copies (Table 1), with the insect Clusia tigrina having the highest number with 4,691 copies (genome assembly id GCA_920105625 (Crowley et al, 2023)).…”

Section: Resultsmentioning

confidence: 99%

The Ribosomal Operon Database (ROD): A full-length rDNA operon database derived from genome assemblies

Krabberød,

Stokke,

Thoen

et al. 2024

Preprint

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Current rDNA reference sequence databases are tailored towards shorter DNA markers, such as parts of the 16/18S marker or the ITS region. However, due to advances in long-read DNA sequencing technologies, longer stretches of the rDNA operon are increasingly used in environmental sequencing studies to increase the phylogenetic resolution. There is, therefore, a growing need for longer rDNA reference sequences. Here, we present the Ribosomal Operon Database (ROD), which includes eukaryotic full-length rDNA operons fished from publicly available genome assemblies. Full-length operons were detected in 34.1% of the 34,701 examined eukaryotic genome assemblies from NCBI. In most cases (53.1%), more than one operon variant was detected, which can be due to intragenomic operon copy variability, allelic variation in non-haploid genomes, or technical errors from the sequencing and assembly process. The highest copy number found was 5,947 in Zea mays. In total, 453,697 unique operons were detected, with 69,480 operon clusters remaining after intragenomic clustering at 99% sequence identity. The operon length varied extensively across eukaryotes, ranging from 4,136 to 16,463 bp, which will lead to considerable PCR bias during PCR amplification of the entire operon. Clustering the full-length operons revealed that the different parts (i.e., 18S, 28S, the hypervariable region V4 of 18S, and ITS) provide divergent taxonomic resolution, with 18S and the V4 region being the most conserved. The Ribosomal Operon Database (ROD) will be updated regularly to provide an increasing number of full-length rDNA operons to the scientific community.

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Section: Resultsmentioning

confidence: 99%

The Ribosomal Operon Database (ROD): A full-length rDNA operon database derived from genome assemblies

Krabberød,

Stokke,

Thoen

et al. 2024

Preprint

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“…We generated a total of ~118.0 Gb HiFi reads (N50 ~16.1 kb) from 6 SMRT cells, which covered approximately 27x of each haploid maize genome (Table S2 and Fig. S1), according to the experience from maize, human and other representative species [15][16][17] that approximately 25x to 30x of the HiFi long reads was sufficient for assembling a high-quality reference genome. Subsequently, we tested three popular assemblers, Hifiasm [12], HiCanu [18] and Verkko [19], and found that Hifiasm generated the assemblies with the overall best contiguity, completeness and accuracy (Table S3).…”

Section: Chromosome-scale Well-phased Assemblies Of Highly Heterozygo...mentioning

confidence: 99%

Bi-parental graph strategy to represent and analyze hybrid plant genomes

Kong,

Jiang,

Wang

et al. 2023

Preprint

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Hybrid plants are universally existed in wild and often exhibit greater performance of complex traits compared with their parents and other selfing plants. This phenomenon, known as heterosis, has been extensively applied in plant breeding for decades. However, the process of decoding hybrid plant genomes has seriously lagged due to the challenges in their genome assembling and the lack of proper methods to further represent and analyze them. Here we report the assembly and analysis of two hybrids: an intraspecific hybrid between two maize inbred lines and an interspecific hybrid between maize and its wild relative teosinte, based on the combination of PacBio High Fidelity (HiFi) sequencing and chromatin conformation capture sequencing data. The haplotypic assemblies are well-phased at chromosomal scale, successfully resolving the complex loci with extensive parental structural variations (SVs). By integrating into a bi-parental genome graph, the haplotypic assemblies can facilitate downstream short-reads based SV calling and allele-specific gene expression analysis, demonstrating outstanding advantages over one single linear genome. Our work provides an entire workflow which hopefully can promote the deciphering of the large numbers of hybrid plant genomes, especially those whose parents are unknown or unavailable and help to understand genome evolution and heterosis.

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Genome assembly of KA105, a new resource for maize molecular breeding and genomic research

Li,

Xu,

Zhao

et al. 2023

The Crop Journal

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

Cited by 6 publications

References 55 publications

The Ribosomal Operon Database (ROD): A full-length rDNA operon database derived from genome assemblies

The Ribosomal Operon Database (ROD): A full-length rDNA operon database derived from genome assemblies

Bi-parental graph strategy to represent and analyze hybrid plant genomes

Genome assembly of KA105, a new resource for maize molecular breeding and genomic research

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