Improved maize reference genome with single molecule technologies

Jiao, Yinping; Peluso, Paul; Shi, Jinghua; Liang, Tiffany Y.; Stitzer, Michelle C.; Wang, Bo; Campbell, Michael S.; Stein, Joshua C.; Wei, Xuehong; Chin, Chen-Shan; Guill, Katherine E.; Regulski, Michael; Kumari, Sunita; Olson, Andrew; Gent, Jonathan I.; Schneider, Kevin; Wolfgruber, Thomas; May, Michael R.; Springer, Nathan M.; Antoniou, Eric; McCombie, Richard W.; Presting, Gernot G.; McMullen, Michael D.; Ross‐Ibarra, Jeffrey; Dawe, R. Kelly; Hastie, Alex; Rank, David R.; Ware, Doreen

doi:10.1101/079004

Cited by 113 publications

(176 citation statements)

References 53 publications

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“…The 2,300 Mb of maize genome includes ~32,000 genes with large intergenic regions and ~84% repeats (Jiao et al ., ). On average, every 72 kb contains a gene.…”

Section: Discussionmentioning

confidence: 97%

The genetic architecture of amylose biosynthesis in maize kernel

Huang

Rui-dong

et al. 2017

Plant Biotechnology Journal

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SummaryStarch is the most abundant storage carbohydrate in maize kernel. The content of amylose and amylopectin confers unique properties in food processing and industrial application. Thus, the resurgent interest has been switched to the study of individual amylose or amylopectin rather than total starch, whereas the enzymatic machinery for amylose synthesis remains elusive. We took advantage of the phenotype of amylose content and the genotype of 9,007,194 single nucleotide polymorphisms from 464 inbred maize lines. The genome‐wide association study identified 27 associated loci involving 39 candidate genes that were linked to amylose content including transcription factors, glycosyltransferases, glycosidases, as well as hydrolases. Except the waxy gene that encodes the granule‐bound starch synthase, the remaining candidate genes were located in the upstream pathway of amylose synthesis, while the downstream members were already known from prior studies. The linked candidate genes could be transferred to manipulate amylose content and thus add value to maize kernel in the breeding programme.

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“…The 2,300 Mb of maize genome includes ~32,000 genes with large intergenic regions and ~84% repeats (Jiao et al ., ). On average, every 72 kb contains a gene.…”

Section: Discussionmentioning

confidence: 97%

The genetic architecture of amylose biosynthesis in maize kernel

Huang

Rui-dong

et al. 2017

Plant Biotechnology Journal

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“…Higher quality assemblies could probably be obtained, at higher cost, using higher long read coverage, and possibly by also incorporating physical map technology, e.g. [40, 41], but Alpaca provides a lower-coverage option for genome assembly.…”

Section: Discussionmentioning

confidence: 99%

Hybrid assembly with long and short reads improves discovery of gene family expansions

et al. 2017

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BackgroundLong-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation.MethodsWe developed a hybrid assembly pipeline called “Alpaca” that can operate on 20X long-read coverage plus about 50X short-insert and 50X long-insert short-read coverage. To preclude collapse of tandem repeats, Alpaca relies on base-call-corrected long reads for contig formation.ResultsCompared to two other assembly protocols, Alpaca demonstrated the most reference agreement and repeat capture on the rice genome. On three accessions of the model legume Medicago truncatula, Alpaca generated the most agreement to a conspecific reference and predicted tandemly repeated genes absent from the other assemblies.ConclusionOur results suggest Alpaca is a useful tool for investigating structural and copy number variation within de novo assemblies of sampled populations.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3927-8) contains supplementary material, which is available to authorized users.

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“…In brief, the sequenced reads were pre‐processed for adapter clipping using Cutadapt 1.2.1 (Martin, ) and then trimmed on low sequence quality bases and filtered from rRNA contaminant reads with ERNE‐FILTER 1.2 (Del Fabbro, Scalabrin, Morgante, & Giorgi, ). High quality reads (Supplemental Data S1) were mapped against the maize B73 reference genome (RefGen ZmB73 Assembly AGPv4 and Zea_mays.AGPv4.34.gtf Gramene transcript annotation; Jiao et al, ) with Tophat 2.0.13 (Kim et al, ).…”

Section: Methodsmentioning

confidence: 99%

Epigenetic signatures of stress adaptation and flowering regulation in response to extended drought and recovery in Zea mays

Forestan

Farinati

Zambelli

et al. 2019

Plant Cell & Environment

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During their lifespan, plants respond to a multitude of stressful factors. Dynamic changes in chromatin and concomitant transcriptional variations control stress response and adaptation, with epigenetic memory mechanisms integrating environmental conditions and appropriate developmental programs over the time. Here we analyzed transcriptome and genome‐wide histone modifications of maize plants subjected to a mild and prolonged drought stress just before the flowering transition. Stress was followed by a complete recovery period to evaluate drought memory mechanisms. Three categories of stress‐memory genes were identified: i) “transcriptional memory” genes, with stable transcriptional changes persisting after the recovery; ii) “epigenetic memory candidate” genes in which stress‐induced chromatin changes persist longer than the stimulus, in absence of transcriptional changes; iii) “delayed memory” genes, not immediately affected by the stress, but perceiving and storing stress signal for a delayed response. This last memory mechanism is described for the first time in drought response. In addition, applied drought stress altered floral patterning, possibly by affecting expression and chromatin of flowering regulatory genes. Altogether, we provided a genome‐wide map of the coordination between genes and chromatin marks utilized by plants to adapt to a stressful environment, describing how this serves as a backbone for setting stress memory.

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Improved maize reference genome with single molecule technologies

Cited by 113 publications

References 53 publications

The genetic architecture of amylose biosynthesis in maize kernel

The genetic architecture of amylose biosynthesis in maize kernel

Hybrid assembly with long and short reads improves discovery of gene family expansions

Epigenetic signatures of stress adaptation and flowering regulation in response to extended drought and recovery in Zea mays

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