Skip to main content


Plant genomics

Guest Editors: Mario Caccamo and Erich Grotewold

In this issue of Genome Biology, we present a special collection of Research, Method, Review, Opinion, Research highlight and Editorial pieces focusing on the topic of plant genomics. This issue provides many new insights into crop breeding, plant-pathogen interactions, and plant responses to the environment. A Research article from Philip Wigge and colleagues is celebrated as the winner of the Plant Biology, Environmental Biology and Ecology category of the BioMed Central Annual Research Awards.

  1. Review

    From pathogen genomes to host plant processes: the power of plant parasitic oomycetes

    Recent pathogenomic research on plant parasitic oomycete effector function and plant host responses has resulted in major conceptual advances in plant pathology, which has been possible thanks to the availabil...

    Marina Pais, Joe Win, Kentaro Yoshida, Graham J Etherington, Liliana M Cano, Sylvain Raffaele, Mark J Banfield, Alex Jones, Sophien Kamoun and Diane GO Saunders

    Genome Biology 2013 14:211

    Published on: 28 June 2013

  2. Research highlight

    A conifer genome spruces up plant phylogenomics

    The Norway spruce genome provides key insights into the evolution of plant genomes, leading to testable new hypotheses about conifer, gymnosperm, and vascular plant evolution.

    Pamela S Soltis and Douglas E Soltis

    Genome Biology 2013 14:122

    Published on: 27 June 2013

  3. Meeting report

    Plant genomics: from weed to wheat

    A report on the first 'Plant Genomics Congress' meeting, held in London, UK, 12-13 May 2013.

    Kerstin Kaufmann and Wolfgang Busch

    Genome Biology 2013 14:308

    Published on: 27 June 2013

  4. Research

    Mapping gene activity of Arabidopsis root hairs

    Quantitative information on gene activity at single cell-type resolution is essential for the understanding of how cells work and interact. Root hairs, or trichoblasts, tubular-shaped outgrowths of specialized...

    Ping Lan, Wenfeng Li, Wen-Dar Lin, Simonetta Santi and Wolfgang Schmidt

    Genome Biology 2013 14:R67

    Published on: 25 June 2013

  5. Research

    Phytophthora capsici-tomato interaction features dramatic shifts in gene expression associated with a hemi-biotrophic lifestyle

    Plant-microbe interactions feature complex signal interplay between pathogens and their hosts. Phytophthora species comprise a destructive group of fungus-like plant pathogens, collectively affecting a wide range...

    Julietta Jupe, Remco Stam, Andrew JM Howden, Jenny A Morris, Runxuan Zhang, Pete E Hedley and Edgar Huitema

    Genome Biology 2013 14:R63

    Published on: 25 June 2013

  6. Review

    The plant microbiome

    Plant genomes contribute to the structure and function of the plant microbiome, a key determinant of plant health and productivity. High-throughput technologies are revealing interactions between these complex...

    Thomas R Turner, Euan K James and Philip S Poole

    Genome Biology 2013 14:209

    Published on: 25 June 2013

  7. Research

    Separating homeologs by phasing in the tetraploid wheat transcriptome

    The high level of identity among duplicated homoeologous genomes in tetraploid pasta wheat presents substantial challenges for de novo transcriptome assembly. To solve this problem, we develop a specialized bioin...

    Ksenia V Krasileva, Vince Buffalo, Paul Bailey, Stephen Pearce, Sarah Ayling, Facundo Tabbita, Marcelo Soria, Shichen Wang, Eduard Akhunov, Cristobal Uauy and Jorge Dubcovsky

    Genome Biology 2013 14:R66

    Published on: 25 June 2013

  8. Research

    A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat

    As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repet...

    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…

    Genome Biology 2013 14:R64

    Published on: 25 June 2013

  9. Review

    The promise of genomics in the study of plant-pollinator interactions

    Flowers exist in exceedingly complex fitness landscapes, in which subtle variation in each trait can affect the pollinators, herbivores and pleiotropically linked traits in other plant tissues. A whole-genome ...

    Elizabeth L Clare, Florian P Schiestl, Andrew R Leitch and Lars Chittka

    Genome Biology 2013 14:207

    Published on: 24 June 2013

  10. Opinion

    Open access to tree genomes: the path to a better forest

    An open-access culture and a well-developed comparative-genomics infrastructure must be developed in forest trees to derive the full potential of genome sequencing in this diverse group of plants that are the ...

    David B Neale, Charles H Langley, Steven L Salzberg and Jill L Wegrzyn

    Genome Biology 2013 14:120

    Published on: 24 June 2013

  11. Review

    The circadian clock goes genomic

    Large-scale biology among plant species, as well as comparative genomics of circadian clock architecture and clock-regulated output processes, have greatly advanced our understanding of the endogenous timing s...

    Dorothee Staiger, Jieun Shin, Mikael Johansson and Seth J Davis

    Genome Biology 2013 14:208

    Published on: 24 June 2013

  12. Review

    Genomics reveals new landscapes for crop improvement

    The sequencing of large and complex genomes of crop species, facilitated by new sequencing technologies and bioinformatic approaches, has provided new opportunities for crop improvement. Current challenges inc...

    Michael W Bevan and Cristobal Uauy

    Genome Biology 2013 14:206

    Published on: 24 June 2013

  13. Research

    Analyzing the soybean transcriptome during autoregulation of mycorrhization identifies the transcription factors GmNF-YA1a/b as positive regulators of arbuscular mycorrhization

    Similarly to the legume-rhizobia symbiosis, the arbuscular mycorrhiza interaction is controlled by autoregulation representing a feedback inhibition involving the CLAVATA1-like receptor kinase NARK in shoots. ...

    Sara Schaarschmidt, Peter M Gresshoff and Bettina Hause

    Genome Biology 2013 14:R62

    Published on: 18 June 2013

  14. Research

    Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis

    Nicotiana sylvestris and Nicotiana tomentosiformis are members of the Solanaceae family that includes tomato, potato, eggplant and pepper. These two Nicotiana species originate from South America and exhibit diff...

    Nicolas Sierro, James ND Battey, Sonia Ouadi, Lucien Bovet, Simon Goepfert, Nicolas Bakaher, Manuel C Peitsch and Nikolai V Ivanov

    Genome Biology 2013 14:R60

    Published on: 17 June 2013

  15. Research

    Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome

    In arid and semi-arid environments, drought and soil salinity usually occur at the beginning and end of a plant's life cycle, offering a natural opportunity for the priming of young plants to enhance stress to...

    Emanuela Sani, Pawel Herzyk, Giorgio Perrella, Vincent Colot and Anna Amtmann

    Genome Biology 2013 14:R59

    Published on: 14 June 2013

  16. Research

    Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids

    Recent genome-wide studies suggested that in addition to genetic variations, epigenetic variations may also be associated with differential gene expression and growth vigor in plant hybrids. Maize is an ideal ...

    Guangming He, Beibei Chen, Xuncheng Wang, Xueyong Li, Jigang Li, Hang He, Mei Yang, Lu Lu, Yijun Qi, Xiping Wang and Xing Wang Deng

    Genome Biology 2013 14:R57

    Published on: 12 June 2013

  17. Research

    Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome

    There is growing evidence for the prevalence of copy number variation (CNV) and its role in phenotypic variation in many eukaryotic species. Here we use array comparative genomic hybridization to explore the e...

    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…

    Genome Biology 2013 14:R58

    Published on: 12 June 2013

  18. Research

    Comprehensive genotyping of the USA national maize inbred seed bank

    Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The colle...

    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 and Candice A Gardner

    Genome Biology 2013 14:R55

    Published on: 11 June 2013

  19. Research

    Identification of pathways directly regulated by SHORT VEGETATIVE PHASE during vegetative and reproductive development in Arabidopsis

    MADS-domain transcription factors play important roles during plant development. The Arabidopsis MADS-box gene SHORT VEGETATIVE PHASE (SVP) is a key regulator of two developmental phases. It functions as a repres...

    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 and Martin M Kater

    Genome Biology 2013 14:R56

    Published on: 11 June 2013

  20. Research

    The plasticity of the grapevine berry transcriptome

    Phenotypic plasticity refers to the range of phenotypes a single genotype can express as a function of its environment. These phenotypic variations are attributable to the effect of the environment on the expr...

    Silvia Dal Santo, Giovanni Battista Tornielli, Sara Zenoni, Marianna Fasoli, Lorenzo Farina, Andrea Anesi, Flavia Guzzo, Massimo Delledonne and Mario Pezzotti

    Genome Biology 2013 14:r54

    Published on: 7 June 2013