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

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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.

Abstract

A complete telomere-to-telomere genome assembly of the maize Mo17 inbred line uncovers structural features of the highly complex maize genome.

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The Sequence Alignment/Map format and SAMtools

Heng Li, Bob Handsaker, Alec Wysoker … (2009)

Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk

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Fast gapped-read alignment with Bowtie 2.

Ben Langmead, Steven L Salzberg (2012)

As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.

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Fast and accurate short read alignment with Burrows–Wheeler transform

Heng Li, Richard Durbin (2009)

Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk

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Author and article information

Contributors

Jinsheng Lai:

ORCID: http://orcid.org/0000-0001-9202-9641

jlai@cau.edu.cn

Journal

Journal ID (nlm-ta): Nat Genet

Journal ID (iso-abbrev): Nat Genet

Title: Nature Genetics

Publisher: Nature Publishing Group US (New York )

ISSN (Print): 1061-4036

ISSN (Electronic): 1546-1718

Publication date (Electronic): 15 June 2023

Publication date PMC-release: 15 June 2023

Publication date (Print): 2023

Volume: 55

Issue: 7

Pages: 1221-1231

Affiliations

[1 ]GRID grid.22935.3f, ISNI 0000 0004 0530 8290, 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 ]GRID grid.34421.30, ISNI 0000 0004 1936 7312, Department of Ecology, Evolution, and Organismal Biology, , Iowa State University, ; Ames, IA USA

[4 ]GRID grid.24434.35, ISNI 0000 0004 1937 0060, Department of Agronomy and Horticulture, , University of Nebraska–Lincoln, ; Lincoln, NE USA

[5 ]GRID grid.22935.3f, ISNI 0000 0004 0530 8290, Center for Crop Functional Genomics and Molecular Breeding, , China Agricultural University, ; Beijing, P. R. China

[6 ]Sanya Institute of China Agricultural University, Sanya, P. R. China

[7 ]Hainan Yazhou Bay Seed Laboratory, Sanya, P. R. China

Author information

Kaiwen Tan http://orcid.org/0000-0001-8745-1047

Tong Li http://orcid.org/0000-0002-3568-9886

Matthew B. Hufford http://orcid.org/0000-0003-3945-1143

James C. Schnable http://orcid.org/0000-0001-6739-5527

Jinsheng Lai http://orcid.org/0000-0001-9202-9641

Article

Publisher ID: 1419

DOI: 10.1038/s41588-023-01419-6

PMC ID: 10335936

PubMed ID: 37322109

SO-VID: e4dcb8b0-f6db-4db7-bcb4-93ffae92da96

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 6 April 2022

Date accepted : 5 May 2023

Funding

Funded by: FundRef https://doi.org/10.13039/501100001809, National Natural Science Foundation of China (National Science Foundation of China);

Award ID: 62031003

Award Recipient : Jinsheng Lai

Funded by: This work was supported by grants from the National Key Research and Development Program of China (2021YFF1000500), the Hainan Yazhou Bay Seed Lab (B21HJ0509), the Henan Modern Seed Industry Co. LTD (2022010202-3), the Yazhou Bay Science and Technology City Administration (SYND-2022-03), the National Natural Science Foundation of China (62031003).

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ScienceOpen disciplines: Genetics

Keywords: plant genetics,genomics

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ScienceOpen disciplines: Genetics

Keywords: plant genetics, genomics

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

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Genome Integrity

Most cited references 118

The Sequence Alignment/Map format and SAMtools

Fast gapped-read alignment with Bowtie 2.

Fast and accurate short read alignment with Burrows–Wheeler transform

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Cited by 46

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