Contribution of NAC Transcription Factors to Plant Adaptation to Land

Xu, Bo; Ohtani, Misato; Yamaguchi, Masatoshi; Toyooka, Kiminori; Wakazaki, Mayumi; Sato, Mayuko; Kubo, Minoru; Nakano, Yoshimi; Sano, Ryosuke; Hiwatashi, Yuji; Murata, Takashi; Kurata, Takeshi; Yoneda, Arata; Kato, Ko; Hasebe, Mitsuyasu; Demura, Taku

doi:10.1126/science.1248417

Cited by 212 publications

(185 citation statements)

References 42 publications

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“…Although unexpected, considering the well-documented mRNA transfer that occurs between parasitic plants and their hosts (31), we hypothesize that compared with mRNA, transfers of genomic fragments will more often result in functional transfers because genomic regions can contain intact promoters that may be recognized by the recipient plant species. Cross-species promoter recognition is common in experimental transformation studies (61,62), even among very distantly related plant species (63).…”

Section: Resultsmentioning

confidence: 99%

Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation

Yang

Zhang

Wafula

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Horizontal gene transfer (HGT) is the transfer of genetic material across species boundaries and has been a driving force in prokaryotic evolution. HGT involving eukaryotes appears to be much less frequent, and the functional implications of HGT in eukaryotes are poorly understood. We test the hypothesis that parasitic plants, because of their intimate feeding contacts with host plant tissues, are especially prone to horizontal gene acquisition. We sought evidence of HGTs in transcriptomes of three parasitic members of Orobanchaceae, a plant family containing species spanning the full spectrum of parasitic capabilities, plus the free-living Lindenbergia. Following initial phylogenetic detection and an extensive validation procedure, 52 highconfidence horizontal transfer events were detected, often from lineages of known host plants and with an increasing number of HGT events in species with the greatest parasitic dependence. Analyses of intron sequences in putative donor and recipient lineages provide evidence for integration of genomic fragments far more often than retro-processed RNA sequences. Purifying selection predominates in functionally transferred sequences, with a small fraction of adaptively evolving sites. HGT-acquired genes are preferentially expressed in the haustorium-the organ of parasitic plants-and are strongly biased in predicted gene functions, suggesting that expression products of horizontally acquired genes are contributing to the unique adaptive feeding structure of parasitic plants.

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Section: Resultsmentioning

confidence: 99%

Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation

Yang

Zhang

Wafula

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…The NAC gene family maintained high expression (P > 5%) until T030. NAC TFs modulate stress response, meristem boundary formation (38), auxin signaling (39), and xylem development (40). The HSF gene family showed high expression from T000 to T018 and at T066, suggesting involvement in other functions in addition to heat stress response (41).…”

Section: Expression Dynamics Of Tf Gene Families During Germination Andmentioning

confidence: 99%

Transcriptome dynamics of developing maize leaves and genomewide prediction ofciselements and their cognate transcription factors

Chen²,

Chang³

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Maize is a major crop and a model plant for studying C4 photosynthesis and leaf development. However, a genomewide regulatory network of leaf development is not yet available. This knowledge is useful for developing C3 crops to perform C4 photosynthesis for enhanced yields. Here, using 22 transcriptomes of developing maize leaves from dry seeds to 192 h post imbibition, we studied gene up-and down-regulation and functional transition during leaf development and inferred sets of strongly coexpressed genes. More significantly, we developed a method to predict transcription factor binding sites (TFBSs) and their cognate transcription factors (TFs) using genomic sequence and transcriptomic data. The method requires not only evolutionary conservation of candidate TFBSs and sets of strongly coexpressed genes but also that the genes in a gene set share the same Gene Ontology term so that they are involved in the same biological function. In addition, we developed another method to predict maize TF-TFBS pairs using known TF-TFBS pairs in Arabidopsis or rice. From these efforts, we predicted 1,340 novel TFBSs and 253 new TF-TFBS pairs in the maize genome, far exceeding the 30 TF-TFBS pairs currently known in maize. In most cases studied by both methods, the two methods gave similar predictions. In vitro tests of 12 predicted TF-TFBS interactions showed that our methods perform well. Our study has significantly expanded our knowledge on the regulatory network involved in maize leaf development. maize transcriptomes | coexpressed genes | cis binding site M aize (Zea mays) is a major crop and a model plant for studying C4 photosynthesis and leaf development. However, the regulatory network that controls maize leaf development is still not well understood. In fact, the number of known maize transcription factor (TF)-binding sites (TFBSs) is far smaller than that for Arabidopsis thaliana (1-3).To understand better the regulation of maize leaf development, several recent studies used next-generation sequencing (NGS) technologies to survey transcriptomic differences among maize leaf cell types and developmental stages. The first large-scale study was by Li et al. (7) investigated the transcriptomes of Kranz (i.e., the foliar leaf blade) and non-Kranz (the husk leaf sheath) maize leaves to identify cohorts of genes associated with procambium initiation and vascular patterning. Recently, Wang et al. (8) conducted comparative transcriptomic and metabolomic analyses of developing leaves in maize and rice and identified putative structural and regulatory components important for C4 and C3 photosynthesis. These studies provided insights into the regulatory mechanisms underlying the development of Kranz leaf anatomy in maize.In the present study, we obtained nine transcriptomes of the second leaf from 84-192 h post imbibition at 12-h (6:00 AM and 6:00 PM) or 24-h (6:00 PM only) intervals. Together with the 13 SignificanceMaize is a major crop and a model plant for studying C4 leaf development. However, its regulatory network of leaf ...

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“…Interestingly, the gene regulation system including NAC transcription factors which are responsible for the formation of water-conducting cells can be found in vascular and nonvascular plants, but operating in the sporophytic (Yamaguchi et al 2011) or in the gametophytic generation (Xu et al 2014), respectively.…”

Section: Several Regulatory Pathways Evolved In the Common Ancestor Omentioning

confidence: 99%

Can mosses serve as model organisms for forest research?

Müller

Gütle

Jacquot

et al. 2016

Annals of Forest Science

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& Key message Based on their impact on many ecosystems, we review the relevance of mosses in research regarding stress tolerance, metabolism, and cell biology. We introduce the potential use of mosses as complementary model systems in molecular forest research, with an emphasis on the most developed model moss Physcomitrella patens. & Context and aims Mosses are important components of several ecosystems. The moss P. patens is a well-established nonvascular model plant with a high amenability to molecular biology techniques and was designated as a JGI plant flagship genome. In this review, we will provide an introduction to moss research and highlight the characteristics of P. patens and other mosses as a potential complementary model system for forest research. & Methods Starting with an introduction into general moss biology, we summarize the knowledge about moss physiology and differences to seed plants. We provide an overview of the current research areas utilizing mosses, pinpointing potential links to tree biology. To complement literature review, we discuss moss advantages and available resources regarding molecular biology techniques. & Results and conclusion During the last decade, many fundamental processes and cell mechanisms have been studied in mosses and seed plants, increasing our knowledge of plant evolution. Additionally, moss-specific mechanisms of stress tolerance are under investigation to understand their resilience in ecosystems. Thus, using the advantages of model mosses such as P. patens is of high interest for various research approaches, including stress tolerance, organelle biology, cell polarity, and secondary metabolism.

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Contribution of NAC Transcription Factors to Plant Adaptation to Land

Cited by 212 publications

References 42 publications

Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation

Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation

Transcriptome dynamics of developing maize leaves and genomewide prediction ofciselements and their cognate transcription factors

Can mosses serve as model organisms for forest research?

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