Research article  

Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers

Sukhjiwan Kaur, Luke W Pembleton, Noel OI Cogan, Keith W Savin, Tony Leonforte, Jeffrey Paull, Michael Materne, John W Forster BMC Genomics 2012, 13:104 (20 March 2012)

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Research article  

De novo assembly and characterization of a maternal and developmental transcriptome for the emerging model crustacean Parhyale hawaiensis

Victor Zeng, Karina E Villanueva, Ben S Ewen-Campen, Frederike Alwes, William E Browne, Cassandra G Extavour BMC Genomics 2011, 12:581 (25 November 2011)

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Research article  

RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus

Emilie Villar, Christophe Klopp, Céline Noirot, Evandro Novaes, Matias Kirst, Christophe Plomion, Jean-Marc Gion BMC Genomics 2011, 12:538 (2 November 2011)

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Research article  

Identification, utilisation and mapping of novel transcriptome-based markers from blackcurrant (Ribes nigrum)

Joanne R Russell, Micha Bayer, Clare Booth, Linda Cardle, Christine A Hackett, Pete E Hedley, Linzi Jorgensen, Jenny A Morris, Rex M Brennan BMC Plant Biology 2011, 11:147 (28 October 2011)

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Research article  

Transcriptomic analysis of the interaction between Helianthus annuus and its obligate parasite Plasmopara halstedii shows single nucleotide polymorphisms in CRN sequences

Falah As-sadi, Sébastien Carrere, Quentin Gascuel, Thibaut Hourlier, David Rengel, Marie-Christine Le Paslier, Amandine Bordat, Marie-Claude Boniface, Dominique Brunel, Jérôme Gouzy, Laurence Godiard, Patrick Vincourt BMC Genomics 2011, 12:498 (11 October 2011)

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Research article  

From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.)

Grit Haseneyer, Thomas Schmutzer, Michael Seidel, Ruonan Zhou, Martin Mascher, Chris-Carolin Schön, Stefan Taudien, Uwe Scholz, Nils Stein, Klaus FX Mayer, Eva Bauer BMC Plant Biology 2011, 11:131 (28 September 2011)

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Research article  

Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers

Wenliang Wei, Xiaoqiong Qi, Linhai Wang, Yanxin Zhang, Wei Hua, Donghua Li, Haixia Lv, Xiurong Zhang BMC Genomics 2011, 12:451 (19 September 2011)

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Research  

Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome

Cyrille Saintenac, Dayou Jiang, Eduard D Akhunov Genome Biology 2011, 12:R88 (14 September 2011)

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Invited speaker presentation  

The Eucalyptus grandis Genome Project: Genome and transcriptome resources for comparative analysis of woody plant biology

Alexander Myburg, Dario Grattapaglia, Gerald Tuskan, Jerry Jenkins, Jeremy Schmutz, Eshchar Mizrachi, Charles Hefer, Georgios Pappas, Lieven Sterck, Yves Van De Peer, Richard Hayes, Daniel Rokhsar BMC Proceedings 2011, 5(Suppl 7):I20 (13 September 2011)

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Oral presentation  

High-throughput targeted SNP discovery using Next Generation Sequencing (NGS) in few selected candidate genes in Eucalyptus camaldulensis

Prasad Hendre, Rathinam Kamalakannan, Rathinavelu Rajkumar, Mohan Varghese BMC Proceedings 2011, 5(Suppl 7):O17 (13 September 2011)

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Research article  

Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata)

Prabin Bajgain, Bryce A Richardson, Jared C Price, Richard C Cronn, Joshua A Udall BMC Genomics 2011, 12:370 (18 July 2011)

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Research article  

Gene discovery using next-generation pyrosequencing to develop ESTs for Phalaenopsis orchids

Yu-Yun Hsiao, Yun-Wen Chen, Shi-Ching Huang, Zhao-Jun Pan, Chih-Hsiung Fu, Wen-Huei Chen, Wen-Chieh Tsai, Hong-Hwa Chen BMC Genomics 2011, 12:360 (12 July 2011)

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Research article  

Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis

Yuanhong Han, Yun Kang, Ivone Torres-Jerez, Foo Cheung, Christopher D Town, Patrick X Zhao, Michael K Udvardi, Maria J Monteros BMC Genomics 2011, 12:350 (6 July 2011)

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Research article  

Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing

Melissa ML Wong, Charles H Cannon, Ratnam Wickneswari BMC Genomics 2011, 12:342 (5 July 2011)

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Research article  

Comprehensive genetic dissection of wood properties in a widely-grown tropical tree: Eucalyptus

Jean-Marc Gion, Audrey Carouché, Sylvie Deweer, Franck Bedon, Frédérique Pichavant, Jean-Paul Charpentier, Henri Baillères, Philippe Rozenberg, Victor Carocha, Nina Ognouabi, Daniel Verhaegen, Jacqueline Grima-Pettenati, Philippe Vigneron, Christophe Plomion BMC Genomics 2011, 12:301 (8 June 2011)

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Research article  

Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate

Wiesław Babik, Michał Stuglik, Weihong Qi, Marzanna Kuenzli, Katarzyna Kuduk, Paweł Koteja, Jacek Radwan BMC Genomics 2010, 11:390 (21 June 2010)

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Research article  

SNP identification, verification, and utility for population genetics in a non-model genus

Larissa M Williams, Xin Ma, Adam R Boyko, Carlos D Bustamante, Marjorie F Oleksiak BMC Genetics 2010, 11:32 (30 April 2010)

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Research article  

Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery

Thomas L Parchman, Katherine S Geist, Johan A Grahnen, Craig W Benkman, C Alex Buerkle BMC Genomics 2010, 11:180 (16 March 2010)

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Research article  

Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella

Dietmar Schwarz, Hugh M Robertson, Jeffrey L Feder, Kranthi Varala, Matthew E Hudson, Gregory J Ragland, Daniel A Hahn, Stewart H Berlocher BMC Genomics 2009, 10:633 (27 December 2009)

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Research article  

Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library

Cecilia Sánchez, Timothy PL Smith, Ralph T Wiedmann, Roger L Vallejo, Mohamed Salem, Jianbo Yao, Caird E Rexroad BMC Genomics 2009, 10:559 (25 November 2009)

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Methodology article  

Combining next-generation pyrosequencing with microarray for large scale expression analysis in non-model species

Diana Bellin, Alberto Ferrarini, Antonio Chimento, Olaf Kaiser, Natasha Levenkova, Pascal Bouffard, Massimo Delledonne BMC Genomics 2009, 10:555 (24 November 2009)

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Research article  

Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development

Fiammetta Alagna, Nunzio D'Agostino, Laura Torchia, Maurizio Servili, Rosa Rao, Marco Pietrella, Giovanni Giuliano, Maria Chiusano, Luciana Baldoni, Gaetano Perrotta BMC Genomics 2009, 10:399 (26 August 2009)

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Research article  

Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing

Erik Kristiansson, Noomi Asker, Lars Förlin, DG Joakim Larsson BMC Genomics 2009, 10:345 (31 July 2009)

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Research article  

A set of EST-SNPs for map saturation and cultivar identification in melon

Wim Deleu, Cristina Esteras, Cristina Roig, Mireia González-To, Iria Fernández-Silva, Daniel Gonzalez-Ibeas, José Blanca, Miguel A Aranda, Pere Arús, Fernando Nuez, Antonio J Monforte, Maria Picó, Jordi Garcia-Mas BMC Plant Biology 2009, 9:90 (15 July 2009)

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Research article  

Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx

Eli Meyer, Galina V Aglyamova, Shi Wang, Jade Buchanan-Carter, David Abrego, John K Colbourne, Bette L Willis, Mikhail V Matz BMC Genomics 2009, 10:219 (12 May 2009)

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Research article  

Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery

Matthew C Hale, Cory R McCormick, James R Jackson, J Andrew DeWoody BMC Genomics 2009, 10:203 (29 April 2009)

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Research article  

A new genomic resource dedicated to wood formation in Eucalyptus

David Rengel, Hélène Clemente, Florence Servant, Nathalie Ladouce, Etienne Paux, Patrick Wincker, Arnaud Couloux, Pierre Sivadon, Jacqueline Grima-Pettenati BMC Plant Biology 2009, 9:36 (27 March 2009)

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