Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

Zhang, Gengyun; Liu, Xin; Quan, Zhiwu; Cheng, Shifeng; Xu, Xun; Pan, Shengkai; Xie, Min; Zeng, Peng; Yue, Zhen; Wang, Wenliang; Tao, Ye; Bian, Chao; Han, Changlei; Xia, Qiuju; Peng, Xiaohua; Cao, Rui; Yang, Xinhua; Zhan, Dongliang; Hu, Jingchu; Zhang, Yinxin; Li, Henan; Li, Hua; Li, Ning; Wang, Junyi; Wang, Chanchan; Wang, Renyi; Guo, Tao; Cai, Yanjie; Qin, Xianhui; Xiang, Haitao; Shi, Qiuxiang; Huang, Ping; Chen, Qingchun; Li, Yingrui; Jun, Wang; Zhao, Zhihai; Wang, Jian

doi:10.1038/nbt.2195

Cited by 617 publications

(532 citation statements)

References 80 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 'correlated molecular clock' and 'JC69' models were used. Published times for sorghum-rice (<55 million years ago, >35 million years ago) [109][110][111] , tomato-potato (<4 million years ago, >2 million years ago) 112 , and grape-rice (<130 million years ago, >240 million years ago) 113 divergence were used to calibrate divergence time.…”

Section: (Ref 105) (Supplementary Tables 19 and 62)mentioning

confidence: 99%

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

et al. 2016

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5 7Carrot (Daucus carota subsp. carota L.; 2n = 2x = 18) is a globally important root crop whose production has quadrupled between 1976 and 2013 (FAO Statistics; see URLs), outpacing the overall rate of increase in vegetable production and world population growth (FAO Statistics; see URLs) through development of high-value products for fresh consumption, juices, and natural pigments and cultivars adapted to warmer production regions 1 .The first documented colors for domesticated carrot root were yellow and purple in Central Asia approximately 1,100 years ago 2,3 , with orange carrots not reliably reported until the sixteenth century in Europe 4,5 . The popularity of orange carrots is fortuitous for modern consumers because the orange pigmentation results from high quantities of alpha-and beta-carotene, making carrots the richest source of provitamin A in the US diet 6 . Carrot breeding has substantially increased nutritional value, with a 50% average increase in carotene content in the United States as compared to 40 years ago 6 . Lycopene and lutein in red and yellow carrots, respectively, are also nutritionally important carotenoids, making carrot a model system to study storage root development and carotenoid accumulation.Carrot is the most important crop in the Apiaceae family, which includes numerous other vegetables, herbs, spices, and medicinal plants that enhance the epicurean experience 7 , including celery, parsnip, arracacha, parsley, fennel, coriander, and cumin. The Apiaceae family belongs to the euasterid II clade, which includes important crops such as lettuce and sunflower 8 . Genome sequences of euasterid I species have been reported, but only two genomes 9,10 have been published among the other euasterid II species.Here we report a high-quality genome assembly of a doubledhaploid orange carrot, characterization of the mechanism controlling carotenoid accumulation in storage roots, and the resequencing of 35 accessions spanning the genetic diversity of the Daucus genus. Our comprehensive genomic analyses provide insights into the evolution of the asterids and several gene families. These results will facilitate biological discovery and crop improvement in carrot and other crops.A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution We report a high-quality chromosome-scale assembly and analysis of the carrot (Daucus carota) genome, the first sequenced genome to include a comparative evolutionary analysis among members of the euasterid II clade. We characterized two new polyploidization events, both occurring after the divergence of carrot from members of the Asterales order, clarifying the evolutionary scenario before and after radiation of the two main asterid clades. Large- and small-scale lineage-specific duplications have contributed to the expansion of gene families, including those with roles in flowering time, defense response, flavor, and pigment accumulation. We identified a candidate gene, DCAR_032551, that conditions caro...

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“…The Solanaceae nTNL genes formed 55 monophyletic lineages with nTNL genes from S. indicum (two RNL lineages The phylogenetic relationship was constructed according to the APG III system (Bremer et al, 2009). The divergence times at different nodes of angiosperms were combined from previous studies (Lavin et al, 2005;Stefanovic et al, 2009;D'Hont et al, 2012;Zhang et al, 2012;Peng et al, 2013;Yang et al, 2013;Kim et al, 2014;Wang et al, 2014;Zeng et al, 2014). The total number of NBS genes and their classification in each species are shown.…”

Section: Phylogenetic Analysis Of Nbs Genes In Major Angiosperm Cladesmentioning

confidence: 99%

“…Because the divergence of these angiosperm families occurred in the Paleogene and the divergence of their higher level taxonomies all occurred in the Cretaceous ( Fig. 1; Lavin et al, 2005;Stefanovic et al, 2009;D'Hont et al, 2012;Zhang et al, 2012;Peng et al, 2013;Yang et al, 2013;Kim et al, 2014;Wang et al, 2014;Zeng et al, 2014), the observed intensive expansion of NBS genes in angiosperms more likely coincided with the CretaceousPaleogene (K-P) boundary (;66 MYA). This finding suggests that different lineages of angiosperms either underwent a process to reinforce resistance or experienced increased selective pressure from environmental pathogens during this period.…”

Section: Differential Expansion During Angiosperm Evolution Shaped Tnmentioning

confidence: 99%

Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns

et al. 2016

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Nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes make up the largest plant disease resistance gene family (R genes), with hundreds of copies occurring in individual angiosperm genomes. However, the expansion history of NBS-LRR genes during angiosperm evolution is largely unknown. By identifying more than 6,000 NBS-LRR genes in 22 representative angiosperms and reconstructing their phylogenies, we present a potential framework of NBS-LRR gene evolution in the angiosperm. Three anciently diverged NBS-LRR classes (TNLs, CNLs, and RNLs) were distinguished with unique exon-intron structures and DNA motif sequences. A total of seven ancient TNL, 14 CNL, and two RNL lineages were discovered in the ancestral angiosperm, from which all current NBS-LRR gene repertoires were evolved. A pattern of gradual expansion during the first 100 million years of evolution of the angiosperm clade was observed for CNLs. TNL numbers remained stable during this period but were eventually deleted in three divergent angiosperm lineages. We inferred that an intense expansion of both TNL and CNL genes started from the Cretaceous-Paleogene boundary. Because dramatic environmental changes and an explosion in fungal diversity occurred during this period, the observed expansions of R genes probably reflect convergent adaptive responses of various angiosperm families. An ancient whole-genome duplication event that occurred in an angiosperm ancestor resulted in two RNL lineages, which were conservatively evolved and acted as scaffold proteins for defense signal transduction. Overall, the reconstructed framework of angiosperm NBS-LRR gene evolution in this study may serve as a fundamental reference for better understanding angiosperm NBS-LRR genes.

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Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

Cited by 617 publications

References 80 publications

Foxtail Mosaic Virus-Induced Gene Silencing in Monocot Plants

Foxtail Mosaic Virus-Induced Gene Silencing in Monocot Plants

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns

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