Chromosome-level genome assembly of a regenerable maize inbred line A188

Lin, Guifang, He, Cheng, Zheng, Jun, Koo, Dal-Hoe, Le, Ha, Zheng, Huakun, Tamang, Tej Man, Lin, Jinguang, Liu, Yan, Zhao, Mingxia, Hao, Yangfan, McFraland, Frank, Wang, Bo, Qin, Yang, Tang, Haibao, McCarty, Donald R, Wei, Hairong, Cho, Myeong-Je, Park, Sunghun, Kaeppler, Heidi, Kaeppler, Shawn M, Liu, Yunjun, Springer, Nathan, Schnable, Patrick S, Wang, Guoying, White, Frank F, Liu, Sanzhen (June 2021) Chromosome-level genome assembly of a regenerable maize inbred line A188. Genome biology, 22 (1). p. 175. ISSN 1474-760X

[thumbnail of 2021.Lin.Maize.pdf] PDF
2021.Lin.Maize.pdf
Available under License Creative Commons Attribution.

Download (6MB)
DOI: 10.1186/s13059-021-02396-x

Abstract

BACKGROUND The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies. RESULTS Here, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus. CONCLUSIONS The A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues.

Item Type: Paper
Subjects: bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA methylation
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
organism description > plant > maize
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosome
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosomes, structure and function > chromosome
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosomes, structure and function
organs, tissues, organelles, cell types and functions > tissues types and functions > endosperm
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
organs, tissues, organelles, cell types and functions
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > plant proteins
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types
organs, tissues, organelles, cell types and functions > tissues types and functions
CSHL Authors:
Communities: CSHL labs > Jackson lab
Depositing User: Sasha Luks-Morgan
Date: 9 June 2021
Date Deposited: 24 Jun 2021 13:59
Last Modified: 25 Jan 2024 14:56
PMCID: PMC8188678
Related URLs:
URI: https://repository.cshl.edu/id/eprint/40226

Actions (login required)

Administrator's edit/view item Administrator's edit/view item
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving