The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)

Peng, Zhenhua; Lu, Ying; Li, Lubin; Zhao, Qiang; Feng, Qi; Gao, Zhimin; Lu, Hengyun; Hu, Tao; Yao, Na; Liu, Kunyan; Li, Yan; Fan, Danlin; Guo, Yunli; Li, Wenjun; Lu, Yiqi; Weng, Qijun; Zhou, Congcong; Zhang, Lei; Huang, Tao; Zhao, Yan; Zhu, Chuanrang; Liu, Xinge; Yang, Xuewen; Wang, T.; Miao, Kun; Caiyun, Zhuang; Cao, Xiaolu; Tang, Wenli; Liu, Guanshui; Liu, Yingli; Chen, Jie; Liu, Zhenjing; Yuan, Licai; Liu, Zhenhua; Huang, Xuehui; Lu, Tingting; Fei, Benhua; Ning, Zemin; Han, Bin; Jiang, Zehui

doi:10.1038/ng.2569

Cited by 480 publications

(518 citation statements)

References 57 publications

(52 reference statements)

Supporting

Mentioning

474

Contrasting

Unclassified

Order By: Relevance

“…The reconstructed monocot nTNL phylogeny (Supplemental Fig. S1) revealed that nTNL genes from the six Poaceae species formed 456 monophyletic lineages, indicating the presence of at least 456 ancestral nTNL genes in the Poaceae common ancestor (;62 million years ago [MYA]; Peng et al, 2013. These Poaceae nTNL genes formed 57 monophyletic lineages when grouped with M. acuminata nTNL genes (one RNL lineage designated as Mo-R1, and 56 CNL lineages identified as Mo-C1 to Mo-C56), suggesting that nTNL genes from the seven monocot genomes were actually derived from 57 ancestral Mo-NBS genes ;110 MYA ( Fig.…”

Section: Phylogenetic Analysis Of Nbs Genes In Major Angiosperm Cladesmentioning

confidence: 99%

“…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%

“…Files of Amborella trichopoda, Capsicum annuum, Sesamum indicum, Phyllostachys heterocycla, and Musa acuminata were downloaded from the Pepper Genome Database (http://peppersequence. genomics.cn/page/species/index.jsp; Qin et al, 2014), Sinbase (http://ocrigenomics.org/Sinbase/manual.htm; Wang et al, 2014), BambooGDB (http:// www.bamboogdb.org/page/download.jsp; Peng et al, 2013), Banana Genome Hub (http://banana-genome.cirad.fr; D 'Hont et al, 2012), and the Amborella genome database (http://www.amborella.org; Amborella-Genome-Project, 2013), respectively.…”

Section: Databasementioning

confidence: 99%

See 3 more Smart Citations

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

et al. 2016

View full text Add to dashboard Cite

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.

show abstract

Section: Phylogenetic Analysis Of Nbs Genes In Major Angiosperm Cladesmentioning

confidence: 99%

Section: Phylogenetic Analysis Of Nbs Genes In Major Angiosperm Cladesmentioning

confidence: 99%

Section: Differential Expansion During Angiosperm Evolution Shaped Tnmentioning

confidence: 99%

Section: Databasementioning

confidence: 99%

See 2 more Smart Citations

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

et al. 2016

View full text Add to dashboard Cite

show abstract

“…Many plants (Arabidopsis, Phyllostachys heterocycla, Mimulus guttatus, etc.) accelerate flowering to complete life cycle under drought conditions (Peng et al, 2013;Wolfe and Tonsor, 2014;Kooyers et al, 2015), a phenomenon referred to as drought escape (DE). Because drought triggers phytohormone abscisic acid (ABA) biosynthesis and signal transduction, it has been proposed that ABA mediates DE response.…”

mentioning

confidence: 99%

A Drought-Inducible Transcription Factor Delays Reproductive Timing in Rice

Zhang

Zhao

et al. 2016

Plant Physiol.

View full text Add to dashboard Cite

The molecular mechanisms underlying photoperiod or temperature control of flowering time have been recently elucidated, but how plants regulate flowering time in response to other external factors, such as water availability, remains poorly understood. Using a large-scale Hybrid Transcription Factor approach, we identified a bZIP transcriptional factor, O. sativa ABA responsive element binding factor 1 (OsABF1), which acts as a suppressor of floral transition in a photoperiod-independent manner. Simultaneous knockdown of both OsABF1 and its closest homologous gene, OsbZIP40, in rice (Oryza sativa) by RNA interference results in a significantly earlier flowering phenotype. Molecular and genetic analyses demonstrate that a drought regime enhances expression of the OsABF1 gene, which indirectly suppresses expression of the Early heading date 1 (Ehd1) gene that encodes a key activator of rice flowering. Furthermore, we identified a drought-inducible gene named OsWRKY104 that is under the direct regulation of OsABF1. Overexpression of OsWRKY104 can suppress Ehd1 expression and confers a later flowering phenotype in rice. Together, these findings reveal a novel pathway by which rice modulates heading date in response to the change of ambient water availability.Flowering time (or heading date) and drought resistance are two major yield traits in crops, especially rice (Oryza sativa). As global climatic change looms, drought has become the biggest abiotic stress to limit crop yields. Breeders have capitalized on naturally occurring genetic variations to improve or maintain crop yield in times or areas of drought by different strategies (Eisenstein, 2013). Manipulation of floral transition has been a promising way to maximize crop yield during dry periods. This strategy has been successful due to extensive identification of genetic loci and elucidation of molecular mechanisms that control flowering time under diverse or unpredictable environments.Heading date in rice is influenced by many environmental cues such as day length (photoperiod), temperature, nutrition, and water availability. Molecular mechanisms that underlie photoperiod regulation of flowering time have already been characterized, probably because day length is more predictable than other environmental factors during seasonal changes. Rice is a facultative short-day plant that flowers earlier in short days (SDs) than in long days (LDs). Heading date 3a (Hd3a) and RICE FLOWERING LOCUS T1 (RFT1) are two paralogous genes in rice encoding "florigen" molecules expressed in the phloem of leaves and transported to the shoot apical meristem to promote flowering (Tamaki et al., 2007;

show abstract

Grass Sequencing Projects

Gaines

2019

Grasses

View full text Add to dashboard Cite

The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)

Cited by 480 publications

References 57 publications

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

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

A Drought-Inducible Transcription Factor Delays Reproductive Timing in Rice

Grass Sequencing Projects

Contact Info

Product

Resources

About