The<i>Setaria viridis</i>genome and diversity panel enables discovery of a novel domestication gene

Mamidi, Sujan; Healey, Adam; Huang, Pu; Grimwood, Jane; Jenkins, Jerry; Barry, Kerrie; Sreedasyam, Avinash; Shu, Shengqiang; Lovell, John T.; Feldman, Max; Wu, Jinxia; Yu, Yunqing; Chen, Cindy; Johnson, Jenifer; Sakakibara, Hitoshi; Kiba, Takatoshi; Sakurai, Tetsuya; Tavares, Rachel; Nusinow, Dmitri A.; Baxter, Ivan; Schmutz, Jeremy; Brutnell, Thomas P.; Kellogg, Elizabeth A.

doi:10.1101/744557

Cited by 17 publications

(19 citation statements)

References 105 publications

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“…The repeat content of sorghum and maize was 62.7% and 80.8%, 355respectively(Table S5). These results are consistent with the pattern that millets have 356 less repetitive sequence than the nuclear genomes of other grasses(Haberer et al Zhang et al 2012;Huang et al 2019). We observed that 365 gene density was highest near the ends of chromosomes and generally replete in 366…”

supporting

confidence: 88%

Reference genome for the highly transformableSetaria viridiscultivar ME034V

Thielen

Pendleton²,

Player

et al. 2020

Preprint

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24Setaria viridis (green foxtail) is an important model system for improving cereal crops 25 due to its diploid genome, ease of cultivation, and use of C4 photosynthesis. The S. 26 viridis cultivar ME034V is exceptionally transformable, but the lack of a sequenced 27 genome for this cultivar has limited its utility. We present a 397 Mb highly contiguous de 28 novo assembly of ME034V using ultra-long nanopore sequencing technology (read 29 N50=41kb). We estimate that this genome is largely complete based on our updated k-30 mer based genome size estimate of 401 Mb for S. viridis. Genome annotation identified 31 37,908 protein-coding genes and >300k repetitive elements comprising 46% of the 32 genome. We compared the ME034V assembly with two other previously sequenced 33Setaria genomes as well as to a diversity panel of 235 S. viridis cultivars. We found the 34 genome assemblies to be largely syntenic, but numerous unique polymorphic structural 35 variants were discovered. Several ME034V deletions may be associated with recent 36 retrotransposition of copia and gypsy LTR repeat families, as evidenced by their low 37 genotype frequencies in the sampled population. Lastly, we performed a phylogenomic 38 analysis to identify gene families that have expanded in Setaria, including those 39 involved in specialized metabolism and plant defense response. The high continuity of 40 the ME034V genome assembly validates the utility of ultra-long DNA sequencing to 41 improve genetic resources for emerging model organisms. Structural variation present 42 in Setaria illustrates the importance of obtaining the proper genome reference for 43 genetic experiments. Thus, we anticipate that the ME034V genome will be of significant 44 utility for the Setaria research community. 45 47 Grasses of the genus Setaria represent diverse species, with phenotypes ranging from 48 the domesticated food crop foxtail millet, S. italica, to its weedy ancestral progenitor, 49 green foxtail, S. viridis (Li and Brutnell 2011). Simple growth requirements, small 50 stature, and short lifecycle make Setaria a tractable monocot model system for studying 51 C4 photosynthesis (Brutnell et al. 2010; Li and Brutnell 2011; Van Eck and Swartwood 52 2015). Furthermore, close phylogenetic relationships with agriculturally important crops 53 such as maize and sorghum promise to inform genetic and cell biology knowledge of 54 other food crops of global importance. Current genome resources for Setaria include a 55 reference genome for S. italica (Bennetzen et al. 2012; Zhang et al. 2012) based on the 56 cultivar Yugu1, a variety of foxtail millet widely grown as a food crop in China. 57 Additionally, a de novo assembly of S. viridis cultivar A10.1 (hereafter referred to as 58 A10) was recently made available alongside low coverage resequencing of more than 59 600 Setaria ecotypes (Huang et al. 2019). 60 61 Efficient genetic modification is a primary requirement for development of any model 62 organism. Approaches for Setaria protoplasting, particle bombardment, and 63...

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confidence: 88%

Reference genome for the highly transformableSetaria viridiscultivar ME034V

Thielen

Pendleton²,

Player

et al. 2020

Preprint

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“…After the 24-hour incubation, seeds were sterilized with 50% bleach for 10 minutes, followed by 5 water rinses and planted on germination media (0.5X MS, 0.5% sucrose, 0.4% PhytaGel, pH 5.7). Seedlings were transplanted to soil six days after germination and grown at 26°C/22°C (day/night) with a photoperiod of 16h/8h (day/night), under 30% relative humidity, a modified protocol from (Huang et al ., 2019).…”

Section: Methodsmentioning

confidence: 99%

“…S. viridis has many features that make it an attractive model system including a short life cycle, compact stature, reproduction via self-pollination and the ability to generate a high number of seeds (Defelice, 2002; Brutnell et al ., 2010). Furthermore, the expanding genetic and genomic resources, including diverse germplasm accessions, chemically induced mutant populations, high quality reference genome of the A10.1 variety and the resequenced genomes from more than 600 wild accessions, make it possible to conduct large-scale gene discovery and functional genomics in S. viridis (Bennetzen et al ., 2012; Zhu, Yang and Shyu, 2017; Huang et al ., 2019). Lastly, as another key factor for a successful model plant system, an efficient agrobacterium-mediated transformation method has been reported in S. viridis indicating it is amenable to genetic engineering techniques (Van Eck, 2018; Huang et al ., 2019; Nguyen et al ., 2020).…”

Section: Introductionmentioning

confidence: 99%

“…Although one example of the CRISPR/Cas9 mediated gene knockouts has been described in S. viridis, a highly efficient, multiplexed gene editing system has yet to be reported (Huang et al ., 2019). In this study, we developed a protoplast-based transient assay for rapidly testing and optimizing the multiplexed CRISPR/Cas9 system in S. viridis.…”

Section: Introductionmentioning

confidence: 99%

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Optimization of multiplexed CRISPR/Cas9 system for highly efficient genome editing inSetaria viridis

Weiss

Wang

Kang

et al. 2020

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In recent years, Setaria viridis has been developed as a model plant to better understand the C4 photosynthetic pathway in major crops. With the increasing availability of genomic resources for S. viridis research, highly efficient genome editing technologies are needed to create genetic variation resources for functional genomics. Here, we developed a protoplast assay to rapidly optimize the multiplexed CRISPR/Cas9 system in S. viridis. Targeted mutagenesis efficiency was further improved by an average of 1.4-fold with the exonuclease, Trex2. Distinctive mutation profiles were found in the Cas9_Trex2 samples with 94% of deletions larger than 10bp, and less than 1% of mutations being insertions. Further analyses indicated that 52.2% of deletions induced by Cas9_Trex2, as opposed to 3.5% by Cas9 alone, were repaired through microhomology-mediated end joining (MMEJ) rather than the canonical NHEJ DNA repair pathway. Combined with the robust agrobacterium-mediated transformation method with more than 90% efficiency, the multiplex CRISPR/Cas9_Trex2 system was demonstrated to induce targeted mutations in two tightly linked genes, svDrm1a and svDrm1b, at the frequency ranging from 73% to 100% in T0 plants. These mutations were transmitted to at least 60% of the transgene-free T1 plants with 33% of them containing bi-allelic or homozygous mutations in both genes. This highly efficient multiplex CRISPR/Cas9_Trex2 system makes it possible to create a large mutant resource for S. viridis in a rapid and high throughput manner, and has the potential to be widely applicable in achieving more predictable MMEJ-mediated mutations in many plant species.

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“…Current genome resources for Setaria include a reference genome for S. italica (Bennetzen et al 2012;Zhang et al 2012) based on the Yugu1, a variety of foxtail millet widely grown as a food crop in China. Additionally, a de novo assembly of S. viridis accession A10.1 (hereafter referred to as A10) was recently made available alongside low coverage resequencing of more than 600 Setaria ecotypes (Huang et al 2019).…”

Section: Introductionmentioning

confidence: 99%

Reference Genome for the Highly TransformableSetaria viridisME034V

Thielen

Pendleton

Player

et al. 2020

G3 Genes|Genomes|Genetics

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Setaria viridis (green foxtail) is an important model system for improving cereal crops due to its diploid genome, ease of cultivation, and use of C4 photosynthesis. The S. viridis accession ME034V is exceptionally transformable, but the lack of a sequenced genome for this accession has limited its utility. We present a 397 Mb highly contiguous de novo assembly of ME034V using ultra-long nanopore sequencing technology (read N50=41kb). We estimate that this genome is largely complete based on our updated k-mer based genome size estimate of 401 Mb for S. viridis. Genome annotation identified 37,908 protein-coding genes and >300k repetitive elements comprising 46% of the genome. We compared the ME034V assembly with two other previously sequenced Setaria genomes as well as to a diversity panel of 235 S. viridis accessions. We found the genome assemblies to be largely syntenic, but numerous unique polymorphic structural variants were discovered. Several ME034V deletions may be associated with recent retrotransposition of copia and gypsy LTR repeat families, as evidenced by their low genotype frequencies in the sampled population. Lastly, we performed a phylogenomic analysis to identify gene families that have expanded in Setaria, including those involved in specialized metabolism and plant defense response. The high continuity of the ME034V genome assembly validates the utility of ultra-long DNA sequencing to improve genetic resources for emerging model organisms. Structural variation present in Setaria illustrates the importance of obtaining the proper genome reference for genetic experiments. Thus, we anticipate that the ME034V genome will be of significant utility for the Setaria research community.

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TheSetaria viridisgenome and diversity panel enables discovery of a novel domestication gene

Cited by 17 publications

References 105 publications

Reference genome for the highly transformableSetaria viridiscultivar ME034V

Reference genome for the highly transformableSetaria viridiscultivar ME034V

Optimization of multiplexed CRISPR/Cas9 system for highly efficient genome editing inSetaria viridis

Reference Genome for the Highly TransformableSetaria viridisME034V

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