Distinct extremely abundant siRNAs associated with cosuppression in petunia (2009)
De Paoli, Emanuele, Dorantes-Acosta, Ana, Zhai, Jixian, Accerbi, Monica, Jeong, Dong-Hoon, Park, Sunhee, ...
Cosuppression is a classical form of eukaryotic post-transcriptional gene silencing. It was first reported in transgenic petunia, where a sense transgene meant to overexpress the host Chalcone...
Iandolino, Alberto, Nobuta, Kan, Da Silva, Francisco, Cook, Douglas R, Meyers, Blake C
Abstract Background Vitis vinifera ( V. vinifera ) is the primary grape species cultivated for wine production, with an industry valued annually in the billions of dollars worldwide. In order to...
Deep Sequencing of Chicken microRNAs (2008)
Burnside, Joan, Ouyang, Ming, Anderson, Amy, Bernberg, Erin, Lu, Cheng, Meyers, Blake C, ...
Abstract Background The use of new, deep sequencing technologies has greatly accelerated microRNA discovery. We have applied this approach to the identification of chicken microRNAs and to the...
A spatial dissection of the Arabidopsis floral transcriptome by MPSS (2008)
Peiffer, Jason A, Kaushik, Shail, Sakai, Hajime, Arteaga-Vazquez, Mario, Sanchez-Leon, Nidia, Ghazal, Hassan, ...
Abstract Background We have further characterized floral organ-localized gene expression in the inflorescence of Arabidopsis thaliana by comparison of massively parallel signature sequencing (MPSS)...
Characterization of paralogous protein families in rice (2008)
Lin, Haining, Ouyang, Shu, Egan, Amy, Nobuta, Kan, Haas, Brian J, Zhu, Wei, ...
Abstract Background High gene numbers in plant genomes reflect polyploidy and major gene duplication events. Oryza sativa , cultivated rice, is a diploid monocotyledonous species with a ~390 Mb...
Chen, Junfeng, Agrawal, Vikas, Rattray, Magnus, West, Marilyn AL, St Clair, Dina A, Michelmore, Richard W, ...
Abstract Background Several high-throughput technologies can measure in parallel the abundance of many mRNA transcripts within a sample. These include the widely-used microarray as well as the more...
Tan, Xiaoping, Meyers, Blake C, Kozik, Alexander, West, Marilyn AL, Morgante, Michele, St Clair, Dina A, ...
Abstract Background Nucleotide binding site-leucine rich repeat (NBS-LRR)-encoding genes comprise the largest class of plant disease resistance genes. The 149 NBS-LRR-encoding genes and the 58...
Gowda, Malali, Venu, RC, Raghupathy, Mohan B, Nobuta, Kan, Li, Huameng, Wing, Rod, ...
Abstract Background Rice blast, caused by the fungal pathogen Magnaporthe grisea , is a devastating disease causing tremendous yield loss in rice production. The public availability of the complete...
Lu, Cheng, Kulkarni, Karthik, Souret, Frédéric F., MuthuValliappan, Ramesh, Tej, Shivakundan Singh, Poethig, R. Scott, ...
The Arabidopsis genome contains a highly complex and abundant population of small RNAs, and many of the endogenous siRNAs are dependent on RNA-Dependent RNA Polymerase 2 (RDR2) for their biogenesis....
Lu, Cheng, Kulkarni, Karthik, Souret, Frédéric F., MuthuValliappan, Ramesh, Tej, Shivakundan Singh, Poethig, R. Scott, ...
The Arabidopsis genome contains a highly complex and abundant population of small RNAs, and many of the endogenous siRNAs are dependent on RNA-Dependent RNA Polymerase 2 (RDR2) for their biogenesis....
Nakano, Mayumi, Nobuta, Kan, Vemaraju, Kalyan, Tej, Shivakundan Singh, Skogen, Jeremy W., Meyers, Blake C.
MPSS (massively parallel signature sequencing) is a sequencing-based technology that uses a unique method to quantify gene expression level, generating millions of short sequence tags per library. We...
Pseudomonas versus Arabidopsis: Models for Genomic Research into Plant Disease Resistance (2005)
The interaction between plants and their pathogens is complex. Plant pathogens have evolved a broad set of proteins that enable a stealthy entry into the plant cell and facilitate the evasion of host...
Wright, Stephen I., Yau, C. B. Kenneth, Looseley, Mark, Meyers, Blake C.
We analyzed the complete genome sequence of Arabidopsis thaliana and sequence data from 83 genes in the outcrossing A. lyrata, to better understand the role of gene expression on the strength of...
The Use of MPSS for Whole-Genome Transcriptional Analysis in Arabidopsis (2004)
Meyers, Blake C., Tej, Shivakundan Singh, Vu, Tam H., Haudenschild, Christian D., Agrawal, Vikas, Edberg, Steve B., ...
We have generated 36,991,173 17-base sequence “signatures” representing transcripts from the model plant Arabidopsis. These data were derived by massively parallel signature sequencing (MPSS)...
Wright, Stephen I., Yau, C. B. Kenneth, Looseley, Mark, Meyers, Blake C.
We analyzed the complete genome sequence of Arabidopsis thaliana and sequence data from 83 genes in the outcrossing A. lyrata, to better understand the role of gene expression on the strength of...
Wright, Stephen I., Yau, C. B. Kenneth, Looseley, Mark, Meyers, Blake C.
We analyzed the complete genome sequence of Arabidopsis thaliana and sequence data from 83 genes in the outcrossing A. lyrata, to better understand the role of gene expression on the strength of...
Patterns of Positive Selection in the Complete NBS-LRR Gene Family of Arabidopsis thaliana (2002)
Mondragón-Palomino, Mariana, Meyers, Blake C., Michelmore, Richard W., Gaut, Brandon S.
Genome-Wide Analysis of NBS-LRR–Encoding Genes in ArabidopsisW⃞
Meyers, Blake C., Kozik, Alexander, Griego, Alyssa, Kuang, Hanhui, Michelmore, Richard W.
The Arabidopsis genome contains ∼200 genes that encode proteins with similarity to the nucleotide binding site and other domains characteristic of plant resistance proteins. Through a reiterative...
Patterns of Positive Selection in the Complete NBS-LRR Gene Family of Arabidopsis thaliana
Mondragón-Palomino, Mariana, Meyers, Blake C., Michelmore, Richard W., Gaut, Brandon S.
Plant disease resistance genes have been shown to be subject to positive selection, particularly in the leucine rich repeat (LRR) region that may determine resistance specificity. We performed a...
Abundance, Distribution, and Transcriptional Activity of Repetitive Elements in the Maize Genome
Meyers, Blake C., Tingey, Scott V., Morgante, Michele
Long terminal repeat (LTR) retrotransposons have been shown to make up much of the maize genome. Although these elements are known to be prevalent in plant genomes of a middle-to-large size, little...
The Use of MPSS for Whole-Genome Transcriptional Analysis in Arabidopsis
Meyers, Blake C., Tej, Shivakundan Singh, Vu, Tam H., Haudenschild, Christian D., Agrawal, Vikas, Edberg, Steve B., ...
We have generated 36,991,173 17-base sequence “signatures” representing transcripts from the model plant Arabidopsis. These data were derived by massively parallel signature sequencing (MPSS)...
Methods for Transcriptional Profiling in Plants. Be Fruitful and Replicate
Meyers, Blake C., Galbraith, David W., Nelson, Timothy, Agrawal, Vikas
Rudd, Stephen, Frisch, Matthias, Grote, Korbinian, Meyers, Blake C., Mayer, Klaus, Werner, Thomas
We carried out a genome-wide prediction of scaffold/matrix attachment regions (S/MARs) in Arabidopsis. Results indicate no uneven distribution on the chromosomal level but a clear underrepresentation...
Arabidopsis MPSS. An Online Resource for Quantitative Expression Analysis1[w]
Meyers, Blake C., Lee, David K., Vu, Tam H., Tej, Shivakundan Singh, Edberg, Steve B., Matvienko, Marta, ...
Haberer, Georg, Hindemitt, Tobias, Meyers, Blake C., Mayer, Klaus F.X.
In plants, duplication of individual genes, long chromosomal regions, and complete genomes provides a major source for evolutionary innovation. We investigated two different types of duplications,...
Kuang, Hanhui, Woo, Sung-Sick, Meyers, Blake C., Nevo, Eviatar, Michelmore, Richard W.
Resistance Gene Candidate2 (RGC2) genes belong to a large, highly duplicated family of nucleotide binding site–leucine rich repeat (NBS-LRR) encoding disease resistance genes located at a single...
Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA
Nakano, Mayumi, Nobuta, Kan, Vemaraju, Kalyan, Tej, Shivakundan Singh, Skogen, Jeremy W., Meyers, Blake C.
MPSS (massively parallel signature sequencing) is a sequencing-based technology that uses a unique method to quantify gene expression level, generating millions of short sequence tags per library. We...
Tetko, Igor V, Haberer, Georg, Rudd, Stephen, Meyers, Blake C, Mewes, Hans-Werner, Mayer, Klaus F. X
Genome-Wide Analysis of NBS-LRR–Encoding Genes in ArabidopsisW⃞
Meyers, Blake C., Kozik, Alexander, Griego, Alyssa, Kuang, Hanhui, Michelmore, Richard W.
The Arabidopsis genome contains ∼200 genes that encode proteins with similarity to the nucleotide binding site and other domains characteristic of plant resistance proteins. Through a reiterative...
Patterns of Positive Selection in the Complete NBS-LRR Gene Family of Arabidopsis thaliana
Mondragón-Palomino, Mariana, Meyers, Blake C., Michelmore, Richard W., Gaut, Brandon S.
Plant disease resistance genes have been shown to be subject to positive selection, particularly in the leucine rich repeat (LRR) region that may determine resistance specificity. We performed a...
Abundance, Distribution, and Transcriptional Activity of Repetitive Elements in the Maize Genome
Meyers, Blake C., Tingey, Scott V., Morgante, Michele
Long terminal repeat (LTR) retrotransposons have been shown to make up much of the maize genome. Although these elements are known to be prevalent in plant genomes of a middle-to-large size, little...
The Use of MPSS for Whole-Genome Transcriptional Analysis in Arabidopsis
Meyers, Blake C., Tej, Shivakundan Singh, Vu, Tam H., Haudenschild, Christian D., Agrawal, Vikas, Edberg, Steve B., ...
We have generated 36,991,173 17-base sequence “signatures” representing transcripts from the model plant Arabidopsis. These data were derived by massively parallel signature sequencing (MPSS)...
Methods for Transcriptional Profiling in Plants. Be Fruitful and Replicate
Meyers, Blake C., Galbraith, David W., Nelson, Timothy, Agrawal, Vikas
Rudd, Stephen, Frisch, Matthias, Grote, Korbinian, Meyers, Blake C., Mayer, Klaus, Werner, Thomas
We carried out a genome-wide prediction of scaffold/matrix attachment regions (S/MARs) in Arabidopsis. Results indicate no uneven distribution on the chromosomal level but a clear underrepresentation...
Arabidopsis MPSS. An Online Resource for Quantitative Expression Analysis1[w]
Meyers, Blake C., Lee, David K., Vu, Tam H., Tej, Shivakundan Singh, Edberg, Steve B., Matvienko, Marta, ...
Haberer, Georg, Hindemitt, Tobias, Meyers, Blake C., Mayer, Klaus F.X.
In plants, duplication of individual genes, long chromosomal regions, and complete genomes provides a major source for evolutionary innovation. We investigated two different types of duplications,...
Kuang, Hanhui, Woo, Sung-Sick, Meyers, Blake C., Nevo, Eviatar, Michelmore, Richard W.
Resistance Gene Candidate2 (RGC2) genes belong to a large, highly duplicated family of nucleotide binding site–leucine rich repeat (NBS-LRR) encoding disease resistance genes located at a single...
Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA
Nakano, Mayumi, Nobuta, Kan, Vemaraju, Kalyan, Tej, Shivakundan Singh, Skogen, Jeremy W., Meyers, Blake C.
MPSS (massively parallel signature sequencing) is a sequencing-based technology that uses a unique method to quantify gene expression level, generating millions of short sequence tags per library. We...
Tetko, Igor V, Haberer, Georg, Rudd, Stephen, Meyers, Blake C, Mewes, Hans-Werner, Mayer, Klaus F. X
Marek's Disease Virus Encodes MicroRNAs That Map to meq and the Latency-Associated Transcript†
Burnside, Joan, Bernberg, Erin, Anderson, Amy, Lu, Cheng, Meyers, Blake C., Green, Pamela J., ...
MicroRNAs (miRNAs) are a class of small (∼22-nucleotide) regulatory molecules that block translation or induce degradation of target mRNAs. These have been identified in a wide range of organisms,...
MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant
Lu, Cheng, Kulkarni, Karthik, Souret, Frédéric F., MuthuValliappan, Ramesh, Tej, Shivakundan Singh, Poethig, R. Scott, ...
The Arabidopsis genome contains a highly complex and abundant population of small RNAs, and many of the endogenous siRNAs are dependent on RNA-Dependent RNA Polymerase 2 (RDR2) for their biogenesis....
Yan, Huihuang, Ito, Hidetaka, Nobuta, Kan, Ouyang, Shu, Jin, Weiwei, Tian, Shulan, ...
The centromere is the chromosomal site for assembly of the kinetochore where spindle fibers attach during cell division. In most multicellular eukaryotes, centromeres are composed of long tracts of...
Tan, Xiaoping, Meyers, Blake C, Kozik, Alexander, West, Marilyn AL, Morgante, Michele, St Clair, Dina A, ...
A comparison of microarray and MPSS technology platforms for expression analysis of Arabidopsis
Chen, Junfeng, Agrawal, Vikas, Rattray, Magnus, West, Marilyn AL, St Clair, Dina A, Michelmore, Richard W, ...
Characterization of paralogous protein families in rice
Lin, Haining, Ouyang, Shu, Egan, Amy, Nobuta, Kan, Haas, Brian J, Zhu, Wei, ...
Small RNA-Directed Epigenetic Natural Variation in Arabidopsis thaliana
Zhai, Jixian, Liu, Jun, Liu, Bin, Li, Pingchuan, Meyers, Blake C., Chen, Xuemei, ...
Progress in epigenetics has revealed mechanisms that can heritably regulate gene function independent of genetic alterations. Nevertheless, little is known about the role of epigenetics in evolution....
A spatial dissection of the Arabidopsis floral transcriptome by MPSS
Peiffer, Jason A, Kaushik, Shail, Sakai, Hajime, Arteaga-Vazquez, Mario, Sanchez-Leon, Nidia, Ghazal, Hassan, ...
Deep Sequencing of Chicken microRNAs
Burnside, Joan, Ouyang, Ming, Anderson, Amy, Bernberg, Erin, Lu, Cheng, Meyers, Blake C, ...
Lu, Cheng, Jeong, Dong-Hoon, Kulkarni, Karthik, Pillay, Manoj, Nobuta, Kan, German, Rana, ...
Small RNAs (21–24 nt) are involved in gene regulation through translation inhibition, mRNA cleavage, or directing chromatin modifications. In rice, currently ≈240 microRNAs (miRNAs) have been...
Nobuta, Kan, Lu, Cheng, Shrivastava, Roli, Pillay, Manoj, De Paoli, Emanuele, Accerbi, Monica, ...
Small RNAs from plants are known to be highly complex and abundant, with this complexity proportional to genome size. Most endogenous siRNAs in Arabidopsis are dependent on RNA-DEPENDENT RNA...
Sequence Conservation and Differential Expression of Marek's Disease Virus MicroRNAs▿
Morgan, Robin, Anderson, Amy, Bernberg, Erin, Kamboj, Sachin, Huang, Emily, Lagasse, Grace, ...
Marek's disease virus (MDV), a herpesvirus that causes a lymphoproliferative disorder in chickens, encodes a number of microRNAs derived primarily from two locations in the MDV genome. One cluster of...
Distinct extremely abundant siRNAs associated with cosuppression in petunia
De Paoli, Emanuele, Dorantes-Acosta, Ana, Zhai, Jixian, Accerbi, Monica, Jeong, Dong-Hoon, Park, Sunhee, ...
Cosuppression is a classical form of eukaryotic post-transcriptional gene silencing. It was first reported in transgenic petunia, where a sense transgene meant to overexpress the host Chalcone...
Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome
Wei, Fusheng, Stein, Joshua C., Liang, Chengzhi, Zhang, Jianwei, Fulton, Robert S., Baucom, Regina S., ...
Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete...