<i>De novo</i> assembly, annotation, and comparative analysis of 26 diverse maize genomes

Hufford, Matthew B.; Seetharam, Arun S.; Woodhouse, Margaret R.; Chougule, Kapeel; Ou, Shujun; Liu, Jianing; Ricci, William A.; Guo, Tingting; Olson, Andrew; Qiu, Yinjie; Coletta, Rafael Della; Tittes, Silas; Hudson, Asher I.; Marand, Alexandre P.; Wei, Sharon; Lu, Zhenyuan; Wang, Bo; Tello-Ruiz, Marcela K.; Piri, Rebecca D.; Wang, Na; Kim, Dong Won; Zeng, Yibing; O’Connor, Christine H.; Li, Xianran; Gilbert, Amanda M.; Baggs, Erin; Krasileva, Ksenia; Portwood, John L.; Cannon, Ethalinda K. S.; Andorf, Carson M.; Manchanda, Nancy; Snodgrass, Samantha J.; Hufnagel, David E.; Jiang, Qiuhan; Pedersen, Sarah; Syring, Michael; Kudrna, David; Llaca, Víctor; Fengler, Kevin; Schmitz, Robert J.; Ross‐Ibarra, Jeffrey; Yu, Jianming; Gent, Jonathan I.; Hirsch, Candice N.; Ware, Doreen; Dawe, R. Kelly

doi:10.1101/2021.01.14.426684

Cited by 29 publications

(48 citation statements)

References 166 publications

(127 reference statements)

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“…SNPs, small insertions, and deletions were identified as well. SyRI analyses using minimap2 alignments were also performed between A188Ref1 and each of the newly assembled genomes of NAM founders, including version 5 of B73Ref5 [18], as well as genome assemblies of Mo17 [10] and SK [11]. The parameter used for minimap2 alignments is "-ax asm10 -t 16 -K 800M -f 500 --eqx" [83].…”

Section: Comparative Genomic Analysis Via Syri and Cgrdmentioning

confidence: 99%

“…Since then, additional assemblies have been produced using so-called next-generation highthroughput sequencing, including both short-and long-read technologies [9][10][11][12][13][14][15]. Recently, long-read technologies were combined with optical DNA mapping to produce high-continuity maize assemblies, including Nested Association Mapping (NAM) founder lines [16][17][18]. Here, we used Nanopore long reads and optical DNA mapping to construct a chromosome-level maize genome of A188 for the discovery of structural variation as well as performed transcriptome and DNA methylome analyses of embryogenic callus.…”

Section: Introductionmentioning

confidence: 99%

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

Lin

Zheng

et al. 2021

Genome Biol

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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.

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Section: Comparative Genomic Analysis Via Syri and Cgrdmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Lin

Zheng

et al. 2021

Genome Biol

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“…Structural variants (SVs) for the stiff-stalk genomes were characterized as described previously (Hufford et al, 2021). Briefly, this SV-detection pipeline includes a combination of three different methods using three different data types mapped against the B73 v4 reference (Jiao et al, 2017).…”

Section: Structural Variationmentioning

confidence: 99%

Genomic variation within the maize stiff‐stalk heterotic germplasm pool

et al. 2021

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The stiff-stalk heterotic group in Maize (Zea mays L.) is an important source of inbreds used in U.S. commercial hybrid production. Founder inbreds B14, B37, B73, and, to a lesser extent, B84, are found in the pedigrees of a majority of commercial seed parent inbred lines. We created high-quality genome assemblies of B84 and four expired Plant Variety Protection (ex-PVP) lines LH145 representing B14, NKH8431 of mixed descent, PHB47 representing B37, and PHJ40, which is a Pioneer Hi-Bred International (PHI) early stiff-stalk type. Sequence was generated using long-read sequencing achieving highly contiguous assemblies of 2.13-2.18 Gbp with N50 scaffold lengths >200 Mbp. Inbred-specific gene annotations were generated using a

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“…Variants were categorized based on overlap with five annotated features: promoters (2,000bp upstream of the TSS), 5' UTRs, 3' UTRs, CDS, and introns. SNPs were categorized using the GenomicFeatures 54 package in R 55 , based on the Zm00001eb.1 annotation of B73 48 . Each combination of gene, feature, and inbred was given a binary classification for whether or not it contained a rare (MAF < 0.02) SNP allele.…”

Section: Effects Of Rare Variants On Protein Abundancementioning

confidence: 99%

Variation in upstream open reading frames contributes to allelic diversity in protein abundance

Mali

McLoughlin

et al. 2021

Preprint

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The 5' untranslated region (UTR) sequence of eukaryotic mRNAs may contain upstream open reading frames (uORFs), which can regulate translation of the main open reading frame (mORF). The current model of translational regulation by uORFs posits that when a ribosome scans an mRNA and encounters a uORF, translation of that uORF can prevent ribosomes from reaching the mORF and cause decreased mORF translation. In this study, we first observed that rare variants in the 5' UTR dysregulate protein abundance. Upon further investigation, we found that rare variants near the start codon of uORFs can repress or derepress mORF translation, causing allelic changes in protein abundance. This finding holds for common variants as well, and common variants that modify uORF start codons also contribute disproportionately to metabolic and whole-plant phenotypes, suggesting that translational regulation by uORFs serves an adaptive function. These results provide evidence for the mechanisms by which natural sequence variation modulates gene expression, and ultimately, phenotype.

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De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

Cited by 29 publications

References 166 publications

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

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

Genomic variation within the maize stiff‐stalk heterotic germplasm pool

Variation in upstream open reading frames contributes to allelic diversity in protein abundance

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