Genome Biology | Volume 14 Issue 6

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	Volume 14 Issue 6
	Comment
	Editorial Turning over a new leaf in plant genomics Mario Caccamo, Erich Grotewold Genome Biology 2013, 14:403 (27 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Mario Caccamo and Erich Grotewold, Guest Editors of Genome Biology's special issue, discuss why plant genomics is such a hot topic
	Editorial Plant genomics: sowing the seeds of success Gemma D Bilsborough Genome Biology 2013, 14:404 (28 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genome Biology's Special Issue Editor, Gemma Bilsborough, gives an overview of our plant genomics issue
	Comment The DNA60IFX contest Michael C Schatz, James Taylor, Sven-Eric Schelhorn Genome Biology 2013, 14:124 (28 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The curators and winner of Genome Biology's DNA60IFX challenge offer their thoughts on code cracking and crowd bioinformatics - includes full solutions
	Research highlight Plastic, fantastic! Phenotypic variance in the transcriptional landscape of the grape berry Alisdair R Fernie, Takayuki Tohge Genome Biology 2013, 14:119 (7 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight covering Mario Pezzotti's research article analyzing the plasticity of grape berrys in response to environmental changes
	Research highlight A conifer genome spruces up plant phylogenomics Pamela S Soltis, Douglas E Soltis Genome Biology 2013, 14:122 (27 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Pam and Doug Soltis highlight the sequencing of the Norway Spruce genome, and how this has shed light on gymnosperm evolution
	Review
	Review Genomics reveals new landscapes for crop improvement Michael W Bevan, Cristobal Uauy Genome Biology 2013, 14:206 (24 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Mike Bevan reviews how genomic approaches are being used to accelerate and improve crop breeding
	Review The promise of genomics in the study of plant-pollinator interactions Elizabeth L Clare, Florian P Schiestl, Andrew R Leitch, Lars Chittka Genome Biology 2013, 14:207 (24 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Lars Chittka and colleagues review current advances in understanding the genetic basis of plant-pollinator interactions
	Review The circadian clock goes genomic Dorothee Staiger, Jieun Shin, Mikael Johansson, Seth J Davis Genome Biology 2013, 14:208 (24 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Seth Davis and colleagues review how comparative genomics approaches have advanced our understanding of regulation of the circadian clock in plants
	Review The plant microbiome Thomas R Turner, Euan K James, Philip S Poole Genome Biology 2013, 14:209 (25 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Philip Poole and colleagues discuss how genomics approaches are unraveling the complex interactions between plant hosts and microbiome communities
	Review Biofuel and energy crops: high-yield Saccharinae take center stage in the post-genomics era Savio de Siqueira Ferreira, Milton Nishiyama, Andrew H Paterson, Glaucia Souza Genome Biology 2013, 14:210 (27 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Review of developments in our ability to improve desirable traits in biofuel and energy crops
	Review From pathogen genomes to host plant processes: the power of plant parasitic oomycetes Marina Pais, Joe Win, Kentaro Yoshida, Graham J Etherington, Liliana M Cano, Sylvain Raffaele, Mark J Banfield, Alex Jones, Sophien Kamoun, Diane GO Saunders Genome Biology 2013, 14:211 (28 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Saunders, Kamoun & co review recent genomics insights into plant parasitic oomycete effector function and plant host responses
	Opinion Open access to tree genomes: the path to a better forest David B Neale, Charles H Langley, Steven L Salzberg, Jill L Wegrzyn Genome Biology 2013, 14:120 (24 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary David Neale, Steven Salzberg and colleagues share their view on the need for a better open access infrastructure in tree genomics
	Opinion Interactions of beneficial and detrimental root-colonizing filamentous microbes with plant hosts Thomas Rey, Sebastian Schornack Genome Biology 2013, 14:121 (25 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An Opinion describing the similarities and differences in how plants respond to symbiotic and parasitic microbes
	Opinion Gene regulatory networks in plants: learning causality from time and perturbation Gabriel Krouk, Jesse Lingeman, Amy Colon, Gloria Coruzzi, Dennis Shasha Genome Biology 2013, 14:123 (27 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Opinion: how are systems biology approaches being utilized to model causality in gene regulatory networks?
	Report
	Meeting report Plant genomics: from weed to wheat Kerstin Kaufmann, Wolfgang Busch Genome Biology 2013, 14:308 (27 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the first 'Plant Genomics Congress' meeting, held in London, UK, 12-13 May 2013.
	Research
	Research The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color Juan C Motamayor, Keithanne Mockaitis, Jeremy Schmutz, Niina Haiminen, Donald Livingstone, Omar Cornejo, Seth D Findley, Ping Zheng, Filippo Utro, Stefan Royaert, Christopher Saski, Jerry Jenkins, Ram Podicheti, Meixia Zhao, Brian E Scheffler, Joseph C Stack, Frank A Feltus, Guiliana M Mustiga, Freddy Amores, Wilbert Phillips, Jean Philippe Marelli, Gregory D May, Howard Shapiro, Jianxin Ma, Carlos D Bustamante, Raymond J Schnell, Dorrie Main, Don Gilbert, Laxmi Parida, David N Kuhn et al. Genome Biology 2013, 14:R53 (3 June 2013) Abstract \| Provisional PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome sequence of Theobroma cacao Matina 1-6 allows the identification of a gene associated with pod color
	Research The plasticity of the grapevine berry transcriptome Silvia Dal Santo, Giovanni Tornielli, Sara Zenoni, Marianna Fasoli, Lorenzo Farina, Andrea Anesi, Flavia Guzzo, Massimo Delledonne, Mario Pezzotti Genome Biology 2013, 14:r54 (7 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A transcriptomic and metabolomic analysis of the plasticity of grapevine berry gene expression in response to development and the environment
	Research Comprehensive genotyping of the USA national maize inbred seed bank Maria C Romay, Mark J Millard, Jeffrey C Glaubitz, Jason A Peiffer, Kelly L Swarts, Terry M Casstevens, Robert J Elshire, Charlotte B Acharya, Sharon E Mitchell, Sherry A Flint-Garcia, Michael D McMullen, James B Holland, Edward S Buckler, Candice A Gardner Genome Biology 2013, 14:R55 (11 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genotyping-by-Sequencing analysis of maize inbred accessions, identifying candidate genes for kernel color, sweet corn, and flowering time
	Research Identification of pathways directly regulated by SHORT VEGETATIVE PHASE during vegetative and reproductive development in Arabidopsis Veronica Gregis, Fernando Andrés, Alice Sessa, Rosalinda F Guerra, Sara Simonini, Julieta L Mateos, Stefano Torti, Federico Zambelli, Gian Prazzoli, Katrine N Bjerkan, Paul E Grini, Giulio Pavesi, Lucia Colombo, George Coupland, Martin M Kater Genome Biology 2013, 14:R56 (11 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of SVP-regulated pathways that control vegetative and floral meristem development
	Research Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids Guangming He, Beibei Chen, Xuncheng Wang, Xueyong Li, Jigang Li, Hang He, Mei Yang, Lu Lu, Yijun Qi, Xiping Wang, Xing Wang Deng Genome Biology 2013, 14:R57 (12 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the effect of genotype and tissue type on transcriptional and epigenetic changes in maize inbred lines and hybrids
	Research Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome María Muñoz-Amatriaín, Steven R Eichten, Thomas Wicker, Todd A Richmond, Martin Mascher, Burkhard Steuernagel, Uwe Scholz, Ruvini Ariyadasa, Manuel Spannagl, Thomas Nussbaumer, Klaus FX Mayer, Stefan Taudien, Matthias Platzer, Jeffrey A Jeddeloh, Nathan M Springer, Gary J Muehlbauer, Nils Stein Genome Biology 2013, 14:R58 (12 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of copy number variations in 14 barley genomes shows that DNA repair and template slippage may have caused variations
	Research Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome Emanuela Sani, Pawel Herzyk, Giorgio Perrella, Vincent Colot, Anna Amtmann Genome Biology 2013, 14:R59 (14 June 2013) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary Exposure of young seedlings to salt stress causes histone modifications and transcriptional changes, enhancing stress tolerance in mature plants
	Research Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis Nicolas Sierro, James ND Battey, Sonia Ouadi, Lucien Bovet, Simon Goepfert, Nicolas Bakaher, Manuel C Peitsch, Nikolai V Ivanov Genome Biology 2013, 14:R60 (17 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genome sequencing and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis show that differences in alkaloid production may regulate insect resistance
	Research Analyzing the soybean transcriptome during autoregulation of mycorrhization identifies the transcription factors GmNF-YA1a/b as positive regulators of arbuscular mycorrhization Sara Schaarschmidt, Peter M Gresshoff, Bettina Hause Genome Biology 2013, 14:R62 (18 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A transcriptomic analysis of changes in soybean gene expression in response to mycorrhization identifies GmNF-YA1a/b as positive regulators of arbuscular mycorrhization
	Research Phytophthora capsici-tomato interaction features dramatic shifts in gene expression associated with a hemi-biotrophic lifestyle Julietta Jupe, Remco Stam, Andrew JM Howden, Jenny A Morris, Runxuan Zhang, Pete E Hedley, Edgar Huitema Genome Biology 2013, 14:R63 (25 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of tomato and Phytophthora transcriptomes during infection identifies gene expression changes associated with biotrophy and the switch to necrotrophy
	Research A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat Romain Philippe, Etienne Paux, Isabelle Bertin, Pierre Sourdille, Fréderic Choulet, Christel Laugier, Hana Šimková, Jan Šafář, Arnaud Bellec, Sonia Vautrin, Zeev Frenkel, Federica Cattonaro, Federica Magni, Simone Scalabrin, Mihaela M Martis, Klaus FX Mayer, Abraham Korol, Hélène Bergès, Jaroslav Doležel, Catherine Feuillet Genome Biology 2013, 14:R64 (25 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The physical map of wheat chromosome 1BL allows analysis of grass gene evolution and will aid wheat breeding
	Research Thermal stress effects on grain yield in Brachypodium distachyon occur via H2A.Z-nucleosomes Scott A Boden, Monika Kavanová, E Finnegan, Philip A Wigge Genome Biology 2013, 14:R65 (25 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Repressing H2A.Z-nucleosome deposition phenocopies stress effects of higher temperatures on Brachypodium distachyon grain development
	Research Separating homeologs by phasing in the tetraploid wheat transcriptome Ksenia V Krasileva, Vince Buffalo, Paul Bailey, Stephen Pearce, Sarah Ayling, Facundo Tabbita, Marcelo Soria, Shichen Wang, Iwgs Consortium, Eduard Akhunov, Cristobal Uauy, Jorge Dubcovsky Genome Biology 2013, 14:R66 (25 June 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A novel transcriptome assembly pipeline that separates merged homeologs allows assembly of the tetraploid wheat transcriptome
	Research Mapping gene activity of Arabidopsis root hairs Ping Lan, Wenfeng Li, Wen-Dar Lin, Simonetta Santi, Wolfgang Schmidt Genome Biology 2013, 14:R67 (25 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of gene and protein expression in protoplasts derived from root hairs or non-root hair cells in Arabidopsis
	Research Retrospective genomic analysis of sorghum adaptation to temperate-zone grain production Carrie S Thurber, Justin M Ma, Race H Higgins, Patrick J Brown Genome Biology 2013, 14:R68 (26 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comprehensive marker coverage of sorghum conversion lines and their progenitors allows identification of candidate loci regulating agronomic traits of interest
	Method User guide for mapping-by-sequencing in Arabidopsis Geo James, Vipul Patel, Karl JV Nordström, Jonas R Klasen, Patrice A Salomé, Detlef Weigel, Korbinian Schneeberger Genome Biology 2013, 14:R61 (17 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Method for mapping-by-sequencing in Arabidopsis, using the Pop-seq software, and application to barley and rice as well
	Correspondence
	Correspondence The advantages of SMRT sequencing Richard J Roberts, Mauricio O Carneiro, Michael C Schatz Genome Biology 2013, 14:405 (3 July 2013) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Rich Roberts, Mauricio Carneiro and Michael Schatz argue for a greater uptake of the impressive PacBio SMRT sequencing platform

	Volume 14 Issue 6
	Comment
	Editorial Turning over a new leaf in plant genomics Mario Caccamo, Erich Grotewold Genome Biology 2013, 14:403 (27 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Mario Caccamo and Erich Grotewold, Guest Editors of Genome Biology's special issue, discuss why plant genomics is such a hot topic
	Editorial Plant genomics: sowing the seeds of success Gemma D Bilsborough Genome Biology 2013, 14:404 (28 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genome Biology's Special Issue Editor, Gemma Bilsborough, gives an overview of our plant genomics issue
	Comment The DNA60IFX contest Michael C Schatz, James Taylor, Sven-Eric Schelhorn Genome Biology 2013, 14:124 (28 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The curators and winner of Genome Biology's DNA60IFX challenge offer their thoughts on code cracking and crowd bioinformatics - includes full solutions
	Research highlight Plastic, fantastic! Phenotypic variance in the transcriptional landscape of the grape berry Alisdair R Fernie, Takayuki Tohge Genome Biology 2013, 14:119 (7 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight covering Mario Pezzotti's research article analyzing the plasticity of grape berrys in response to environmental changes
	Research highlight A conifer genome spruces up plant phylogenomics Pamela S Soltis, Douglas E Soltis Genome Biology 2013, 14:122 (27 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Pam and Doug Soltis highlight the sequencing of the Norway Spruce genome, and how this has shed light on gymnosperm evolution
	Review
	Review Genomics reveals new landscapes for crop improvement Michael W Bevan, Cristobal Uauy Genome Biology 2013, 14:206 (24 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Mike Bevan reviews how genomic approaches are being used to accelerate and improve crop breeding
	Review The promise of genomics in the study of plant-pollinator interactions Elizabeth L Clare, Florian P Schiestl, Andrew R Leitch, Lars Chittka Genome Biology 2013, 14:207 (24 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Lars Chittka and colleagues review current advances in understanding the genetic basis of plant-pollinator interactions
	Review The circadian clock goes genomic Dorothee Staiger, Jieun Shin, Mikael Johansson, Seth J Davis Genome Biology 2013, 14:208 (24 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Seth Davis and colleagues review how comparative genomics approaches have advanced our understanding of regulation of the circadian clock in plants
	Review The plant microbiome Thomas R Turner, Euan K James, Philip S Poole Genome Biology 2013, 14:209 (25 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Philip Poole and colleagues discuss how genomics approaches are unraveling the complex interactions between plant hosts and microbiome communities
	Review Biofuel and energy crops: high-yield Saccharinae take center stage in the post-genomics era Savio de Siqueira Ferreira, Milton Nishiyama, Andrew H Paterson, Glaucia Souza Genome Biology 2013, 14:210 (27 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Review of developments in our ability to improve desirable traits in biofuel and energy crops
	Review From pathogen genomes to host plant processes: the power of plant parasitic oomycetes Marina Pais, Joe Win, Kentaro Yoshida, Graham J Etherington, Liliana M Cano, Sylvain Raffaele, Mark J Banfield, Alex Jones, Sophien Kamoun, Diane GO Saunders Genome Biology 2013, 14:211 (28 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Saunders, Kamoun & co review recent genomics insights into plant parasitic oomycete effector function and plant host responses
	Opinion Open access to tree genomes: the path to a better forest David B Neale, Charles H Langley, Steven L Salzberg, Jill L Wegrzyn Genome Biology 2013, 14:120 (24 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary David Neale, Steven Salzberg and colleagues share their view on the need for a better open access infrastructure in tree genomics
	Opinion Interactions of beneficial and detrimental root-colonizing filamentous microbes with plant hosts Thomas Rey, Sebastian Schornack Genome Biology 2013, 14:121 (25 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An Opinion describing the similarities and differences in how plants respond to symbiotic and parasitic microbes
	Opinion Gene regulatory networks in plants: learning causality from time and perturbation Gabriel Krouk, Jesse Lingeman, Amy Colon, Gloria Coruzzi, Dennis Shasha Genome Biology 2013, 14:123 (27 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Opinion: how are systems biology approaches being utilized to model causality in gene regulatory networks?
	Report
	Meeting report Plant genomics: from weed to wheat Kerstin Kaufmann, Wolfgang Busch Genome Biology 2013, 14:308 (27 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the first 'Plant Genomics Congress' meeting, held in London, UK, 12-13 May 2013.
	Research
	Research The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color Juan C Motamayor, Keithanne Mockaitis, Jeremy Schmutz, Niina Haiminen, Donald Livingstone, Omar Cornejo, Seth D Findley, Ping Zheng, Filippo Utro, Stefan Royaert, Christopher Saski, Jerry Jenkins, Ram Podicheti, Meixia Zhao, Brian E Scheffler, Joseph C Stack, Frank A Feltus, Guiliana M Mustiga, Freddy Amores, Wilbert Phillips, Jean Philippe Marelli, Gregory D May, Howard Shapiro, Jianxin Ma, Carlos D Bustamante, Raymond J Schnell, Dorrie Main, Don Gilbert, Laxmi Parida, David N Kuhn et al. Genome Biology 2013, 14:R53 (3 June 2013) Abstract \| Provisional PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome sequence of Theobroma cacao Matina 1-6 allows the identification of a gene associated with pod color
	Research The plasticity of the grapevine berry transcriptome Silvia Dal Santo, Giovanni Tornielli, Sara Zenoni, Marianna Fasoli, Lorenzo Farina, Andrea Anesi, Flavia Guzzo, Massimo Delledonne, Mario Pezzotti Genome Biology 2013, 14:r54 (7 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A transcriptomic and metabolomic analysis of the plasticity of grapevine berry gene expression in response to development and the environment
	Research Comprehensive genotyping of the USA national maize inbred seed bank Maria C Romay, Mark J Millard, Jeffrey C Glaubitz, Jason A Peiffer, Kelly L Swarts, Terry M Casstevens, Robert J Elshire, Charlotte B Acharya, Sharon E Mitchell, Sherry A Flint-Garcia, Michael D McMullen, James B Holland, Edward S Buckler, Candice A Gardner Genome Biology 2013, 14:R55 (11 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genotyping-by-Sequencing analysis of maize inbred accessions, identifying candidate genes for kernel color, sweet corn, and flowering time
	Research Identification of pathways directly regulated by SHORT VEGETATIVE PHASE during vegetative and reproductive development in Arabidopsis Veronica Gregis, Fernando Andrés, Alice Sessa, Rosalinda F Guerra, Sara Simonini, Julieta L Mateos, Stefano Torti, Federico Zambelli, Gian Prazzoli, Katrine N Bjerkan, Paul E Grini, Giulio Pavesi, Lucia Colombo, George Coupland, Martin M Kater Genome Biology 2013, 14:R56 (11 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of SVP-regulated pathways that control vegetative and floral meristem development
	Research Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids Guangming He, Beibei Chen, Xuncheng Wang, Xueyong Li, Jigang Li, Hang He, Mei Yang, Lu Lu, Yijun Qi, Xiping Wang, Xing Wang Deng Genome Biology 2013, 14:R57 (12 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the effect of genotype and tissue type on transcriptional and epigenetic changes in maize inbred lines and hybrids
	Research Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome María Muñoz-Amatriaín, Steven R Eichten, Thomas Wicker, Todd A Richmond, Martin Mascher, Burkhard Steuernagel, Uwe Scholz, Ruvini Ariyadasa, Manuel Spannagl, Thomas Nussbaumer, Klaus FX Mayer, Stefan Taudien, Matthias Platzer, Jeffrey A Jeddeloh, Nathan M Springer, Gary J Muehlbauer, Nils Stein Genome Biology 2013, 14:R58 (12 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of copy number variations in 14 barley genomes shows that DNA repair and template slippage may have caused variations
	Research Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome Emanuela Sani, Pawel Herzyk, Giorgio Perrella, Vincent Colot, Anna Amtmann Genome Biology 2013, 14:R59 (14 June 2013) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary Exposure of young seedlings to salt stress causes histone modifications and transcriptional changes, enhancing stress tolerance in mature plants
	Research Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis Nicolas Sierro, James ND Battey, Sonia Ouadi, Lucien Bovet, Simon Goepfert, Nicolas Bakaher, Manuel C Peitsch, Nikolai V Ivanov Genome Biology 2013, 14:R60 (17 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genome sequencing and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis show that differences in alkaloid production may regulate insect resistance
	Research Analyzing the soybean transcriptome during autoregulation of mycorrhization identifies the transcription factors GmNF-YA1a/b as positive regulators of arbuscular mycorrhization Sara Schaarschmidt, Peter M Gresshoff, Bettina Hause Genome Biology 2013, 14:R62 (18 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A transcriptomic analysis of changes in soybean gene expression in response to mycorrhization identifies GmNF-YA1a/b as positive regulators of arbuscular mycorrhization
	Research Phytophthora capsici-tomato interaction features dramatic shifts in gene expression associated with a hemi-biotrophic lifestyle Julietta Jupe, Remco Stam, Andrew JM Howden, Jenny A Morris, Runxuan Zhang, Pete E Hedley, Edgar Huitema Genome Biology 2013, 14:R63 (25 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of tomato and Phytophthora transcriptomes during infection identifies gene expression changes associated with biotrophy and the switch to necrotrophy
	Research A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat Romain Philippe, Etienne Paux, Isabelle Bertin, Pierre Sourdille, Fréderic Choulet, Christel Laugier, Hana Šimková, Jan Šafář, Arnaud Bellec, Sonia Vautrin, Zeev Frenkel, Federica Cattonaro, Federica Magni, Simone Scalabrin, Mihaela M Martis, Klaus FX Mayer, Abraham Korol, Hélène Bergès, Jaroslav Doležel, Catherine Feuillet Genome Biology 2013, 14:R64 (25 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The physical map of wheat chromosome 1BL allows analysis of grass gene evolution and will aid wheat breeding
	Research Thermal stress effects on grain yield in Brachypodium distachyon occur via H2A.Z-nucleosomes Scott A Boden, Monika Kavanová, E Finnegan, Philip A Wigge Genome Biology 2013, 14:R65 (25 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Repressing H2A.Z-nucleosome deposition phenocopies stress effects of higher temperatures on Brachypodium distachyon grain development
	Research Separating homeologs by phasing in the tetraploid wheat transcriptome Ksenia V Krasileva, Vince Buffalo, Paul Bailey, Stephen Pearce, Sarah Ayling, Facundo Tabbita, Marcelo Soria, Shichen Wang, Iwgs Consortium, Eduard Akhunov, Cristobal Uauy, Jorge Dubcovsky Genome Biology 2013, 14:R66 (25 June 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A novel transcriptome assembly pipeline that separates merged homeologs allows assembly of the tetraploid wheat transcriptome
	Research Mapping gene activity of Arabidopsis root hairs Ping Lan, Wenfeng Li, Wen-Dar Lin, Simonetta Santi, Wolfgang Schmidt Genome Biology 2013, 14:R67 (25 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of gene and protein expression in protoplasts derived from root hairs or non-root hair cells in Arabidopsis
	Research Retrospective genomic analysis of sorghum adaptation to temperate-zone grain production Carrie S Thurber, Justin M Ma, Race H Higgins, Patrick J Brown Genome Biology 2013, 14:R68 (26 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comprehensive marker coverage of sorghum conversion lines and their progenitors allows identification of candidate loci regulating agronomic traits of interest
	Method User guide for mapping-by-sequencing in Arabidopsis Geo James, Vipul Patel, Karl JV Nordström, Jonas R Klasen, Patrice A Salomé, Detlef Weigel, Korbinian Schneeberger Genome Biology 2013, 14:R61 (17 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Method for mapping-by-sequencing in Arabidopsis, using the Pop-seq software, and application to barley and rice as well
	Correspondence
	Correspondence The advantages of SMRT sequencing Richard J Roberts, Mauricio O Carneiro, Michael C Schatz Genome Biology 2013, 14:405 (3 July 2013) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Rich Roberts, Mauricio Carneiro and Michael Schatz argue for a greater uptake of the impressive PacBio SMRT sequencing platform

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Volume 14 Issue 6

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Research

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