A complete telomere-to-telomere assembly of the maize genome

Jian Chen; Zijian Wang; Kaiwen Tan; Wei Huang; Junpeng Shi; Tong Li; Jiang Hu; Kai Wang; Chao Wang; Beibei Xin; Haiming Zhao; Weibin Song; Matthew B Hufford; James C Schnable; Weiwei Jin; Jinsheng Lai

doi:10.1038/s41588-023-01419-6

A complete telomere-to-telomere assembly of the maize genome

Nat Genet. 2023 Jul;55(7):1221-1231. doi: 10.1038/s41588-023-01419-6. Epub 2023 Jun 15.

Authors

Jian Chen^#¹, Zijian Wang^#¹, Kaiwen Tan¹, Wei Huang¹, Junpeng Shi¹, Tong Li¹, Jiang Hu², Kai Wang², Chao Wang², Beibei Xin¹, Haiming Zhao¹, Weibin Song¹, Matthew B Hufford³, James C Schnable⁴, Weiwei Jin¹, Jinsheng Lai^{5

6

7

8}

Affiliations

¹ State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China.
² Grandomics Biosciences, Wuhan, P. R. China.
³ Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
⁴ Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA.
⁵ State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China. jlai@cau.edu.cn.
⁶ Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, P. R. China. jlai@cau.edu.cn.
⁷ Sanya Institute of China Agricultural University, Sanya, P. R. China. jlai@cau.edu.cn.
⁸ Hainan Yazhou Bay Seed Laboratory, Sanya, P. R. China. jlai@cau.edu.cn.

^# Contributed equally.

Abstract

A complete telomere-to-telomere (T2T) finished genome has been the long pursuit of genomic research. Through generating deep coverage ultralong Oxford Nanopore Technology (ONT) and PacBio HiFi reads, we report here a complete genome assembly of maize with each chromosome entirely traversed in a single contig. The 2,178.6 Mb T2T Mo17 genome with a base accuracy of over 99.99% unveiled the structural features of all repetitive regions of the genome. There were several super-long simple-sequence-repeat arrays having consecutive thymine-adenine-guanine (TAG) tri-nucleotide repeats up to 235 kb. The assembly of the entire nucleolar organizer region of the 26.8 Mb array with 2,974 45S rDNA copies revealed the enormously complex patterns of rDNA duplications and transposon insertions. Additionally, complete assemblies of all ten centromeres enabled us to precisely dissect the repeat compositions of both CentC-rich and CentC-poor centromeres. The complete Mo17 genome represents a major step forward in understanding the complexity of the highly recalcitrant repetitive regions of higher plant genomes.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genome, Plant
Genomics*
High-Throughput Nucleotide Sequencing
Repetitive Sequences, Nucleic Acid / genetics
Sequence Analysis, DNA
Telomere / genetics
Zea mays* / genetics