Digital Gene Expression Profiling by 5′-End Sequencing of cDNAs during Reprogramming in the Moss Physcomitrella patens

Nishiyama, Tomoaki; Miyawaki, Kaori; Ohshima, Masumi; Thompson, Kari; Nagashima, Akitomo; Hasebe, Mitsuyasu; Kurata, Takeshi

doi:10.1371/journal.pone.0036471

Cited by 28 publications

(37 citation statements)

References 63 publications

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“…For research, moss tissue can easily be cultivated either on agar plates where gametophores are formed within few weeks or as protonema in liquid medium. Cells from a detached leaflet, a protoplast, or a wounded protonema filament undergo reprogramming to a meristematic protonema tip cell without the addition of exogenous hormones (Nishiyama et al 2012). Fig.…”

Section: Mosses Are Haploid Dominantmentioning

confidence: 99%

“…Scale bars: a 6 μm, b 50 μm, c 1 mm, d 500 μm, e 200 μm, f 100 μm This high regeneration capacity also supports the cultivation of moss tissue in liquid medium using weekly disruption cycles and the easy regeneration of plants from protoplasts. The molecular mechanisms underlying this pluripotency have been investigated and unraveled several key players including a basic helix loop helix transcription factor and two WUSCHEL-related homeobox 13-like genes (Busch et al 2013;Nishiyama et al 2012;Sakakibara et al 2014). …”

Section: Mosses Are Haploid Dominantmentioning

confidence: 99%

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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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Section: Mosses Are Haploid Dominantmentioning

confidence: 99%

Section: Mosses Are Haploid Dominantmentioning

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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“…Deep sequencing of small non-coding RNAs (sRNAs) from the wild type, the DICER-LIKE 3 (DCL3)-deficient DPpDCL3 and DPpDCL4 mutants, enlightened the origin and biogenesis of specific sRNA classes (Cho et al, 2008;Arif et al, 2012) and deep sequencing of 5' ends of uncapped mRNAs (degradome) revealed microRNA (miRNA) biogenesis and target cleavage at a genome-wide resolution (Addo-Quaye et al, 2009). Recently, deep sequencing of 5' mRNA ends was used for a quantitative genome-wide expression analysis to study changes in gene expression during the reprogramming of leaf cells upon phylloid excision (Nishiyama et al, 2012).…”

Section: Moss Transgenesis 555mentioning

confidence: 99%

The moss Physcomitrella patens: methods and tools from cultivation to targeted analysis of gene function

Strotbek¹,

Krinninger²,

Frank³

2013

Int. J. Dev. Biol.

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To comprehensively understand the major processes in plant biology, it is necessary to study a diverse set of species that represent the complexity of plants. This research will help to comprehend common conserved mechanisms and principles, as well as to elucidate those mechanisms that are specific to a particular plant clade. Thereby, we will gain knowledge about the invention and loss of mechanisms and their biological impact causing the distinct specifications throughout the plant kingdom. Since the establishment of transgenic plants, these studies concentrate on the elucidation of gene functions applying an increasing repertoire of molecular techniques. In the last two decades, the moss Physcomitrella patens joined the established set of plant models based on its evolutionary position bridging unicellular algae and vascular plants and a number of specific features alleviating gene function analysis. Here, we want to provide an overview of the specific features of P. patens making it an interesting model for many research fields in plant biology, to present the major achievements in P. patens genetic engineering, and to introduce common techniques to scientists who intend to use P. patens as a model in their research activities.

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“…It is more advantageous than previous microarrays technology which has several limitations, including the accuracy of low abundance expression measurements, the differences of hybridization properties, and limitation to known genes (Wheelan et al, 2008). This technique has been widely used in transcriptomic studies in various species, including Caenorhabditis elegans (Nesbitt et al, 2010), Physcomitrella patens (Nishiyama et al, 2012), Cucumis sativus (Qi et al, 2012), Microsporum canis , Bombyx mori (Zhang et al, 2014), and Mus musculus (Zhang et al, 2013). Aiming to elucidate the molecular mechanisms of thermal stress tolerance in C. hongkongensis, a DGE based gene expression analysis was performed with Hong Kong oysters.…”

Section: Introductionmentioning

confidence: 99%

Characterization and Identification of Differentially Expressed Genes Involved in Thermal Adaptation of the Hong Kong Oyster Crassostrea hongkongensis by Digital Gene Expression Profiling

Zhang

Mao

et al. 2017

Front. Mar. Sci.

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Thermal exposure of sessile marine animals inhabiting estuarine intertidal regions is a serious concern with respect to their physiological processes. Organisms living in this region can be exposed to high temperature (>40 • C) during the low tide, which may affect the survival of these organisms. The Hong Kong oyster, Crassostrea hongkongensis, distributed along the coast waters of the South China Sea, is one of the dominant sessile inhabitants of marine intertidal region which undergoes large seasonal temperature fluctuations (up to 10-20 • C during diurnal cycles) every year. To cope with acute thermal stress, it has developed several adaptation mechanisms, e.g., the firmly shut of the shells. However, the genetic basis of these mechanisms remain largely unclear. To better understand how acute thermal exposure affects the biology of the oyster, two cDNA libraries obtained from the gill of oysters exposed to 37 • C thermal stress and ambient temperature were sequenced using the Digital Gene Expression (DGE) tag profiling strategy. In total, 5.9 and 6.2 million reads were obtained from thermal stress and control libraries, respectively, with approximately 74.25 and 75.02% of the reads mapping to the Crassostrea hongkongensis reference sequence. A total of 605 differentially expressed transcripts could be detected in the thermal stress group as compared to the control group, of which 378 are up-regulated and 227 are down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that these Differentially Expressed Genes (DEGs) were enriched with a broad spectrum of biological processes and pathways, including those associated with chaperones, antioxidants, immunity, apoptosis and cytoskeletal reorganization. Among these significantly enriched pathways, protein processing in the endoplasmic reticulum was the most affected metabolic pathway, which plays an important role in the unfolded protein response (UPR) and ER-associated degradation (ERAD) processes. Our results demonstrate the complex multi-modal cellular response to thermal stress in C. hongkongensis.

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Digital Gene Expression Profiling by 5′-End Sequencing of cDNAs during Reprogramming in the Moss Physcomitrella patens

Cited by 28 publications

References 63 publications

Can mosses serve as model organisms for forest research?

Can mosses serve as model organisms for forest research?

The moss Physcomitrella patens: methods and tools from cultivation to targeted analysis of gene function

Characterization and Identification of Differentially Expressed Genes Involved in Thermal Adaptation of the Hong Kong Oyster Crassostrea hongkongensis by Digital Gene Expression Profiling

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