Reference genome sequence of the model plant Setaria

Bennetzen, Jeffrey L.; Schmutz, Jeremy; Wang, Hao; Percifield, Ryan; Hawkins, Jennifer; Pontaroli, Ana Clara; Estep, Matt C.; Feng, Liang; Vaughn, Justin N.; Grimwood, Jane; Jenkins, Jerry; Barry, Kerrie; Lindquist, Erika; Hellsten, Uffe; Deshpande, Shweta; Wang, Xuewen; Wu, Xiaomei; Mitros, Therese; Triplett, Jimmy K.; Yang, Xiaohan; Ye, Chu-Yu; Mauro-Herrera, Margarita; Wang, Lin; Li, Pinghua; Sharma, Manoj K.; Sharma, Rita; Ronald, Pamela C.; Panaud, Olivier; Kellogg, Elizabeth A.; Brutnell, Thomas P.; Doust, Andrew N.; Tuskan, Gerald A.; Rokhsar, Daniel S.; Devos, Katrien M.

doi:10.1038/nbt.2196

Cited by 792 publications

(811 citation statements)

References 76 publications

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“…Measurements were repeated three times, respectively. The error bar indicates SE. millet has been published (Bennetzen et al, 2012;Zhang et al, 2012). Therefore this first report of an efficient VIGS system based on pFoMV-sg provides a timely toolbox for high-throughput assays of gene functions in foxtail millet and many other economically important monocot crops.…”

Section: Discussionmentioning

confidence: 99%

Foxtail Mosaic Virus-Induced Gene Silencing in Monocot Plants

et al. 2016

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Section: Discussionmentioning

confidence: 99%

Foxtail Mosaic Virus-Induced Gene Silencing in Monocot Plants

et al. 2016

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“…The panicoid grass lineage is about 26 million years old (Bennetzen et al, 2012), and includes such important crops as maize (Zea mays), sorghum (Sorghum bicolor), sugarcane (Saccharum spp.) and pearl millet (Pennisetum glaucum).…”

Section: Introductionmentioning

confidence: 99%

The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution

2013

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Sample sequence analysis was employed to investigate the repetitive DNAs that were most responsible for the evolved variation in genome content across seven panicoid grasses with 45-fold variation in genome size and different histories of polyploidy. In all cases, the most abundant repeats were LTR retrotransposons, but the particular families that had become dominant were found to be different in the Pennisetum, Saccharum, Sorghum and Zea lineages. One element family, Huck, has been very active in all of the studied species over the last few million years. This suggests the transmittal of an active or quiescent autonomous set of Huck elements to this lineage at the founding of the panicoids. Similarly, independent recent activity of Ji and Opie elements in Zea and of Leviathan elements in Sorghum and Saccharum species suggests that members of these families with exceptional activation potential were present in the genome(s) of the founders of these lineages. In a detailed analysis of the Zea lineage, the combined action of several families of LTR retrotransposons were observed to have approximately doubled the genome size of Zea luxurians relative to Zea mays and Zea diploperennis in just the last few million years. One of the LTR retrotransposon amplification bursts in Zea may have been initiated by polyploidy, but the great majority of transposable element activations are not. Instead, the results suggest random activation of a few or many LTR retrotransposons families in particular lineages over evolutionary time, with some families especially prone to future activation and hyper-amplification.

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“…Oropetium has the smallest known genome among the grasses 17 at 90%, 60%, 50%, 30% and 10% the size of Brachypodium 10 , rice 4 , Setaria 18 , Sorghum 5 and maize 7 , respectively. We found that Oropetium has a solo:intact LTR ratio >1, which is similar to small grass genomes like rice and Brachypodium, where proliferating LTRs are removed by illegitimate recombination, whereas large grass genomes like Sorghum and maize have solo:intact LTR ratios <1 (ref.…”

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confidence: 99%

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

VanBuren

Bryant

Edger

et al. 2015

Nature

288

271

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Plant genomes, and eukaryotic genomes in general, are typically repetitive, polyploid and heterozygous, which complicates genome assembly 1 . The short read lengths of early Sanger and current next-generation sequencing platforms hinder assembly through complex repeat regions, and many draft and reference genomes are fragmented, lacking skewed GC and repetitive intergenic sequences, which are gaining importance due to projects like the Encyclopedia of DNA Elements (ENCODE) 2 . Here we report the whole-genome sequencing and assembly of the desiccationtolerant grass Oropetium thomaeum. Using only single-molecule real-time sequencing, which generates long (>16 kilobases) reads with random errors, we assembled 99% (244 megabases) of the Oropetium genome into 625 contigs with an N50 length of 2.4 megabases. Oropetium is an example of a 'near-complete' draft genome which includes gapless coverage over gene space as well as intergenic sequences such as centromeres, telomeres, transposable elements and rRNA clusters that are typically unassembled in draft genomes. Oropetium has 28,466 protein-coding genes and 43% repeat sequences, yet with 30% more compact euchromatic regions it is the smallest known grass genome. The Oropetium genome demonstrates the utility of single-molecule real-time sequencing for assembling high-quality plant and other eukaryotic genomes, and serves as a valuable resource for the plant comparative genomics community.The genomes of Arabidopsis 3 , rice 4 , poplar, grape and Sorghum 5 were first sequenced using high-quality and reiterative Sanger-based approaches producing a series of 'gold standard' reference genomes. The advent of next-generation sequencing (NGS) technologies reduced costs of sequencing substantially, which has enabled sequencing of over 100 plant genomes 1 . The quality of plant genome assemblies depends on genome size, ploidy, heterozygosity and sequence coverage, but most NGS-based genomes have on the order of tens of thousands of short contigs distributed in thousands of scaffolds. The short read lengths of NGS, inherent biases and non-random sequencing errors have resulted in highly fragmented draft genome assemblies that are not complete, which means they are missing biologically meaningful sequences including entire genes, regulatory regions, transposable elements, centromeres, telomeres and haplotype-specific structural variations. It is becoming clear from ENCODE projects that complete genomes are needed to better understand the importance of the non-coding regions of genomes 2 .More than 40% of calories consumed by humans are derived from grasses, and the grass family (Poaceae) is arguably the most important plant family with regard to global food security 6 . The size and complexity of most grass genomes has challenged progress in gene discovery and comparative genomics, although draft genomes are now available for most agriculturally important grasses 1 . The largest genome assemblies, such as maize (2,300 megabases (Mb)) 7 , barley (5,100 Mb) 8 and wheat (hexaploid, 1...

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Reference genome sequence of the model plant Setaria

Cited by 792 publications

References 76 publications

Foxtail Mosaic Virus-Induced Gene Silencing in Monocot Plants

Foxtail Mosaic Virus-Induced Gene Silencing in Monocot Plants

The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

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