Genome Biology | Tags

Submit a manuscript Register Contact us Follow us on Twitter

Explore Genome Biology

Advertisement

Articles

Search plants on BioMed Central

#plants

42 items(s) found

Display/download options Articles per page: 25 | 50 | 100

Display options

Editor's summary Citation

Download options

Send
To

	All
	1.	Review The circadian clock goes genomic Dorothee Staiger, Jieung Shin, Mikael Johansson, Seth J Davis Genome Biology 2013, 14:208 ($dateTool.format('d MMMMM yyyy', $article.publicationDate)) Abstract \| Provisional PDF \| Editor’s summary Seth Davis and colleagues review how comparative genomics approaches have advanced our understanding of regulation of the circadian clock in plants
	2.	Review The promise of genomics in the study of plant-pollinator interactions Elizabeth L Clare, Florian P Schiestl, Andrew R Leitch, Lars Chittka Genome Biology 2013, 14:207 ($dateTool.format('d MMMMM yyyy', $article.publicationDate)) Abstract \| Provisional PDF \| Editor’s summary Lars Chittka and colleagues review current advances in understanding the genetic basis of plant-pollinator interactions
	3.	Review Genomics reveals new landscapes for crop improvement Michael Bevan, Cristobal Uauy Genome Biology 2013, 14:206 ($dateTool.format('d MMMMM yyyy', $article.publicationDate)) Abstract \| Provisional PDF \| Editor’s summary Mike Bevan reviews how genomic approaches are being used to accelerate and improve crop breeding
	4.	Opinion Interactions of beneficial and detrimental root-colonizing filamentous microbes with plant hosts Thomas Rey, Sebastian Schornack Genome Biology 2013, 14:121 ($dateTool.format('d MMMMM yyyy', $article.publicationDate)) Abstract \| Provisional PDF \| Editor’s summary An Opinion describing the similarities and differences in how plants respond to symbiotic and parasitic microbes
	5.	Opinion Open access to tree genomes: the path to a better forest David B Neale, Charles H Langley, Steven L Salzberg, Jill L Wegrzyn Genome Biology 2013, 14:120 ($dateTool.format('d MMMMM yyyy', $article.publicationDate)) Abstract \| Provisional PDF \| Editor’s summary David Neale, Steven Salzberg and colleagues share their view on the need for a better open access infrastructure in tree genomics
	6.	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 \| Provisional PDF \| 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
	7.	Method User guide for mapping-by-sequencing in Arabidopsis Geo Velikkakam James, Vipul Patel, Karl JV Nordstrom, Jonas R Klasen, Patrice A Salome, Detlef Weigel, Korbinian Schneeberger Genome Biology 2013, 14:R61 (17 June 2013) Abstract \| Provisional PDF \| Editor’s summary Method for mapping-by-sequencing in Arabidopsis, using the Pop-seq software, and application to barley and rice as well
	8.	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 \| Provisional PDF \| Editor’s summary Genome sequencing and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis show that differences in alkaloid production may regulate insect resistance
	9.	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 \| Provisional PDF \| Editor’s summary Exposure of young seedlings to salt stress causes histone modifications and transcriptional changes, enhancing stress tolerance in mature plants
	10.	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 \| Provisional PDF \| PubMed \| Editor’s summary An analysis of copy number variations in 14 barley genomes shows that DNA repair and template slippage may have caused variations
	11.	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 \| Provisional PDF \| PubMed \| Editor’s summary An analysis of the effect of genotype and tissue type on transcriptional and epigenetic changes in maize inbred lines and hybrids
	12.	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 Marco 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 \| Provisional PDF \| PubMed \| Editor’s summary An analysis of SVP-regulated pathways that control vegetative and floral meristem development
	13.	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 \| Provisional PDF \| PubMed \| Editor’s summary Genotyping-by-Sequencing analysis of maize inbred accessions, identifying candidate genes for kernel color, sweet corn, and flowering time
	14.	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
	15.	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 \| Provisional PDF \| PubMed \| Editor’s summary A transcriptomic and metabolomic analysis of the plasticity of grapevine berry gene expression in response to development and the environment
	16.	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 Genome Biology 2013, 14:R53 (3 June 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The genome sequence of Theobroma cacao Matina 1-6 allows the identification of a gene associated with pod color
	17.	Research Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) Ray Ming, Robert VanBuren, Yanling Liu, Mei Yang, Yuepeng Han, Lei-Ting Li, Qiong Zhang, Min-Jeong Kim, Michael C Schatz, Michael Campbell, Jingping Li, John E Bowers, Haibao Tang, Eric Lyons, Ann A Ferguson, Giuseppe Narzisi, David R Nelson, Crysten E Blaby-Haas, Andrea R Gschwend, Yuannian Jiao, Joshua P Der, Fanchang Zeng, Jennifer Han, Xiang Jia Min, Karen A Hudson, Ratnesh Singh, Aleel K Grennan, Steven J Karpowicz, Jennifer R Watling, Kikukatsu Ito et al. Genome Biology 2013, 14:R41 (10 May 2013) Abstract \| Provisional PDF \| PubMed \| F1000 Biology \| Editor’s summary The genome of the long-living, slowly evolving sacred lotus reveals the genetic mechanisms underlying its adaptation to limited nutrient availability
	18.	Meeting report Food for thought from plant and animal genomes Emily Abrash Genome Biology 2013, 14:302 (27 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Plant and Animal Genome XXI meeting, held in San Diego, USA, January 12-16, 2013.
	19.	Research *Natural variation of H3K27me3 distribution between two Arabidopsis* accessions and its association with flanking transposable elements** Xue Dong, Julia Reimer, Ulrike Göbel, Julia Engelhorn, Fei He, Heiko Schoof, Franziska Turck Genome Biology 2012, 13:R117 (19 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of natural variation of H3K27me3 in 2 Arabidopsis thaliana accessions and in their F1 hybrids
	20.	Meeting report International plant molecular biology: a bright future for green science Sibum Sung, Enamul Huq, Z Jeffrey Chen Genome Biology 2012, 13:323 (19 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 10th International Congress of Plant Molecular Biology, Jeju, South Korea, October 21-26, 2012.
	21.	Meeting report Strategies towards sequencing complex crop genomes James C Abbott, Sarah A Butcher Genome Biology 2012, 13:322 (19 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Strategies for de novo assemblies of complex crop genomes workshop held at The Genome Analysis Centre, Norwich, UK, 8-10 October 2012.
	22.	Research Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis Lidija Berke, Gabino F Sanchez-Perez, Berend Snel Genome Biology 2012, 13:R94 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary H3K27me3 is linked to lower expression divergence yet higher coding sequence divergence following Arabidopsis thaliana's recent whole genome duplication
	23.	Opinion The tomato genome: implications for plant breeding, genomics and evolution Aashish Ranjan, Yasunori Ichihashi, Neelima R Sinha Genome Biology 2012, 13:167 (30 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The importance of the tomato genome for plant breeding and the future of crop research
	24.	Research highlight Genomes of extremophile crucifers: new platforms for comparative genomics and beyond Simon M Dittami, Thierry Tonon Genome Biology 2012, 13:166 (16 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Research Highlight: the genome sequences of extremophile crucifers provide valuable insights into the underlying mechanisms of stress tolerance in plants
	25.	Research Apple miRNAs and tasiRNAs with novel regulatory networks Rui Xia, Hong Zhu, Yong-qiang An, Eric P Beers, Zongrang Liu Genome Biology 2012, 13:R47 (15 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive analysis of short regulatory RNAs including, miRNAs, siRNAs and tasiRNAs in the apple tree Malus domestica Golden Delicious
	26.	Review *Current challenges in de novo* plant genome sequencing and assembly** Michael C Schatz, Jan Witkowski, W Richard McCombie Genome Biology 2012, 13:243 (27 April 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Michael Schatz and colleagues assess challenges in de novo plant genome assembly and review the best practices for the plant community
	27.	Research highlight *The Arabidopsis* clock: time for an about-face?** David E Somers Genome Biology 2012, 13:153 (27 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary David Somers highlights three recent papers that arrive at a surprising conclusion about how TOC1 functions in the plant circadian clock
	28.	Research Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function Xiaoming Zhang, Jing Xia, Yifan E Lii, Blanca E Barrera-Figueroa, Xuefeng Zhou, Shang Gao, Lu Lu, Dongdong Niu, Zheng Chen, Christy Leung, Timothy Wong, Huiming Zhang, Jianhua Guo, Yi Li, Renyi Liu, Wanqi Liang, Jian-Kang Zhu, Weixiong Zhang, Hailing Jin Genome Biology 2012, 13:R20 (22 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In Arabidopsis and rice, natural antisense transcripts are processed into siRNAs by DCL1 and DCL3
	29.	Review Life at the extreme: lessons from the genome Dong-Ha Oh, Maheshi Dassanayake, Hans J Bohnert, John M Cheeseman Genome Biology 2012, 13:241 (6 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary High-throughput studies are providing insights into how extremophile plants adapt to life in places where most plant species cannot survive
	30.	Meeting report Low-cost sequencing opens new insights into diverse plant genomes Kenneth D Birnbaum Genome Biology 2012, 13:311 (30 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 2011 ?Plant Genomes and Biotechnology: From Genes to Networks? meeting, held at Cold Spring Harbor Laboratory.
	31.	Research A genome triplication associated with early diversification of the core eudicots Yuannian Jiao, Jim Leebens-Mack, Saravanaraj Ayyampalayam, John E Bowers, Michael R McKain, Joel McNeal, Megan Rolf, Daniel R Ruzicka, Eric Wafula, Norman J Wickett, Xiaolei Wu, Yong Zhang, Jun Wang, Yeting Zhang, Eric J Carpenter, Michael K Deyholos, Toni M Kutchan, Andre S Chanderbali, Pamela S Soltis, Dennis W Stevenson, Richard McCombie, J Pires, Gane Wong, Douglas E Soltis, Claude W dePamphilis Genome Biology 2012, 13:R3 (26 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An investigation of when the gamma polyploidization event occurred in relation to speciation events in angiosperm history
	32.	Research *RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum* L.)** Caroline Pont, Florent Murat, Carole Confolent, Sandrine Balzergue, Jérôme Salse Genome Biology 2011, 12:R119 (2 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptomics reveals the evolutionary trajectory of polyploidization, with insights into gene networks and genome organization
	33.	Research *Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor)* Lei-Ying Zheng, Xiao-Sen Guo, Bing He, Lian-Jun Sun, Yao Peng, Shan-Shan Dong, Teng-Fei Liu, Shuye Jiang, Srinivasan Ramachandran, Chun-Ming Liu, Hai-Chun Jing Genome Biology 2011, 12:R114 (21 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genomes from three strains of Sorghum bicolor (one grain and two sweet) have been sequenced and compared with the reference genome
	34.	Review Genome-wide association studies in plants: the missing heritability is in the field Benjamin Brachi, Geoffrey P Morris, Justin O Borevitz Genome Biology 2011, 12:232 (28 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Justin Borevitz on how high-power association mapping is going back 'into the field' through the combination of genomics and population biology
	35.	Editorial How hemp got high Naomi Attar Genome Biology 2011, 12:409 (20 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Senior Assistant Editor Naomi Attar discusses the genome sequence of cannabis
	36.	Research The draft genome and transcriptome of Cannabis sativa Harm van Bakel, Jake M Stout, Atina G Cote, Carling M Tallon, Andrew G Sharpe, Timothy R Hughes, Jonathan E Page Genome Biology 2011, 12:R102 (20 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| F1000 Biology \| Editor’s summary The genome and transcriptome of marijuana, and comparative analysis with resequenced hemp, explains the genetic basis of psychoactivity
	37.	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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Capture tools for 3.5 Mb exon regions of allotetraploid wheat are developed and applied to identify coding differences in wild and cultivated wheat
	38.	Research highlight Repeated phenotypic changes highlight molecular targets of convergent evolution Maggie R Wagner, Thomas Mitchell-Olds Genome Biology 2011, 12:124 (23 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Maggie Wagner and Thomas Mitchell-Olds discuss how selection might preferentially target certain genes that have a strong phenotypic effect
	39.	Research Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa Li Wei, Long Yan, Tai Wang Genome Biology 2011, 12:R53 (16 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Deep sequencing reveals miRNAs expressed during rice pollen development
	40.	Research highlight A mystery unveiled Yves Van de Peer Genome Biology 2011, 12:113 (30 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A recent phylogenomic study has provided new evidence for two ancient whole genome duplications in plants, with potential importance for the evolution of seed and flowering plants
	41.	Research *A physical map for the Amborella trichopoda* genome sheds light on the evolution of angiosperm genome structure** Andrea Zuccolo, John E Bowers, James C Estill, Zhiyong Xiong, Meizhong Luo, Aswathy Sebastian, José Goicoechea, Kristi Collura, Yeisoo Yu, Yuannian Jiao, Jill Duarte, Haibao Tang, Saravanaraj Ayyampalayam, Steve Rounsley, Dave Kudrna, Andrew H Paterson, J Pires, Andre Chanderbali, Douglas E Soltis, Srikar Chamala, Brad Barbazuk, Pamela S Soltis, Victor A Albert, Hong Ma, Dina Mandoli, Jody Banks, John E Carlson, Jeffrey Tomkins, Claude W dePamphilis, Rod A Wing, Jim Leebens-Mack et al. Genome Biology 2011, 12:R48 (27 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Mapping an outlier helps reconstruct the polyploidy timeline in angiosperms
	42.	Review Silencing signals in plants: a long journey for small RNAs Attila Molnar, Charles Melnyk, David C Baulcombe Genome Biology 2011, 12:215 (11 January 2011) Abstract \| Full text \| PDF \| PubMed