SuperSAGE: The Most Advanced Transcriptome Technology for Functional Genomics

Terauchi, Ryohei; Matsumura, Hideo; Krüger, Detlev H.; Kahl, Günter

doi:10.1002/9783527622542.ch3

Cited by 7 publications

(9 citation statements)

References 37 publications

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“…The leaf sheaths were incubated at 258C under dark conditions for 40 h. Super-SAGE library was made from total RNA of the leaf sheaths as described (Matsumura et al, 2003;Terauchi et al, 2008). Di-tag fragments were sequenced by the 454 FLX sequencer (454 Life Sciences).…”

Section: Supersage Of M Oryzae Strain Ina168-infected Rice Leavesmentioning

confidence: 99%

Association Genetics Reveals Three Novel Avirulence Genes from the Rice Blast Fungal Pathogen Magnaporthe oryzae

et al. 2009

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To subvert rice (Oryza sativa) host defenses, the devastating ascomycete fungus pathogen Magnaporthe oryzae produces a battery of effector molecules, including some with avirulence (AVR) activity, which are recognized by host resistance (R) proteins resulting in rapid and effective activation of innate immunity. To isolate novel avirulence genes from M. oryzae, we examined DNA polymorphisms of secreted protein genes predicted from the genome sequence of isolate 70-15 and looked for an association with AVR activity. This large-scale study found significantly more presence/absence polymorphisms than nucleotide polymorphisms among 1032 putative secreted protein genes. Nucleotide diversity of M. oryzae among 46 isolates of a worldwide collection was extremely low (u = 8.2 3 10 25 ), suggestive of recent pathogen dispersal. However, no association between DNA polymorphism and AVR was identified. Therefore, we used genome resequencing of Ina168, an M. oryzae isolate that contains nine AVR genes. Remarkably, a total of 1.68 Mb regions, comprising 316 candidate effector genes, were present in Ina168 but absent in the assembled sequence of isolate 70-15. Association analyses of these 316 genes revealed three novel AVR genes, AVR-Pia, AVR-Pii, and AVR-Pik/km/kp, corresponding to five previously known AVR genes, whose products are recognized inside rice cells possessing the cognate R genes. AVR-Pia and AVR-Pii have evolved by gene gain/loss processes, whereas AVR-Pik/km/kp has evolved by nucleotide substitutions and gene gain/loss.

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Section: Supersage Of M Oryzae Strain Ina168-infected Rice Leavesmentioning

confidence: 99%

Association Genetics Reveals Three Novel Avirulence Genes from the Rice Blast Fungal Pathogen Magnaporthe oryzae

et al. 2009

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“…To obtain the SuperSAGE libraries, we followed the original SuperSAGE protocol described by Matsumura and colleagues (Matsumura et al, 2003;Terauchi et al, 2008) with some modification. Total RNA was isolated from the third to sixth leaves of Ws and the ppi2-1 mutant using RNAiso reagent (TaKaRa).…”

Section: Supersage Library Construction and Tag Sequencingmentioning

confidence: 99%

Coordination of Plastid Protein Import and Nuclear Gene Expression by Plastid-to-Nucleus Retrograde Signaling

et al. 2009

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Expression of nuclear-encoded plastid proteins and import of those proteins into plastids are indispensable for plastid biogenesis. One possible cellular mechanism that coordinates these two essential processes is retrograde signaling from plastids to the nucleus. However, the molecular details of how this signaling occurs remain elusive. Using the plastid protein import2 mutant of Arabidopsis (Arabidopsis thaliana), which lacks the atToc159 protein import receptor, we demonstrate that the expression of photosynthesis-related nuclear genes is tightly coordinated with their import into plastids. Down-regulation of photosynthesis-related nuclear genes is also observed in mutants lacking other components of the plastid protein import apparatus. Genetic studies indicate that the coordination of plastid protein import and nuclear gene expression is independent of proposed plastid signaling pathways such as the accumulation of Mg-protoporphyrin IX and the activity of ABA INSENSITIVE4 (ABI4). Instead, it may involve GUN1 and the transcription factor AtGLK. The expression level of AtGLK1 is tightly correlated with the expression of photosynthesis-related nuclear genes in mutants defective in plastid protein import. Furthermore, the activity of GUN1 appears to down-regulate the expression of AtGLK1 when plastids are dysfunctional. Based on these data, we suggest that defects in plastid protein import generate a signal that represses photosynthesis-related nuclear genes through repression of AtGLK1 expression but not through activation of ABI4.Plastids are a diverse group of organelles that perform essential metabolic and signaling functions within all plant cells. It is generally believed that plastids originated from a unicellular photosynthetic bacterium that was taken up by a eukaryotic host cell (Dyall et al., 2004). During evolution, most of the genes encoded by the bacterial ancestor have been transferred to the host nuclear genome; for example, the plastid genome of Arabidopsis (Arabidopsis thaliana) encodes fewer than 100 open reading frames (Martin et al., 1998). Consequently, plastid biogenesis is dependent on the import of nuclear-encoded plastid proteins (Keegstra and Cline, 1999;Soll and Schleiff, 2004;Kessler and Schnell, 2006;Inaba and Schnell, 2008;Jarvis, 2008), the genes for which must be expressed at an appropriate level. For example, many of the photosynthesis-related nuclear genes that are required for chloroplast biogenesis are induced via photoreceptors, such as phytochrome, in response to light quality and quantity (Terzaghi and Cashmore, 1995), so that the photosynthesis-related proteins will be available for import into the developing chloroplasts. Other types of plastids, according to their specific metabolic functions, need other sets of nuclear-encoded proteins. Therefore, the expression of specific sets of nuclear genes and the import of their translation products are indispensable for plastid differentiation.After they have been imported into plastids, nuclear-encoded plastid proteins combi...

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“…By recent new sequencing techniques, such as the emulsion-PCR-coupled pyrosequencing procedure (454 Life sciences, Branford, CT) and SOLiD sequencing technology (Applied Biosystems, Carlsbad, CA), sequencing will become cheaper. 13 In forensic pathology, SuperSAGE would thus be a promising method for gene expression analysis and biomarker detection.…”

Section: Discussionmentioning

confidence: 99%

“…For tag extractions, sequence data were analyzed with programs for SuperSAGE. 13 The proportion in normal and hypothermic libraries was compared by c 2 analysis, 17 and P values of 0.05 or less were considered statistically significant. For annotations of SuperSAGE tags, sequence files were analyzed by resources of National Center for Biotechnology SAGE Web page (http://www.ncbi.nlm.nih.gov/ SAGE).…”

Section: Supersagementioning

confidence: 99%