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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.

  2. 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...

    Authors: 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
    Citation: Genome Biology 2013 14:211
    Content type: Review Published on:

  6. The Saccharinae, especially sugarcane, Miscanthus and sorghum, present remarkable characteristics for bioenergy production. Biotechnology of these plants will be important for a sustainable feedstock supply. Here...

    Authors: Savio de Siqueira Ferreira, Milton Yutaka Nishiyama Jr, Andrew H Paterson and Glaucia Mendes Souza
    Citation: Genome Biology 2013 14:210
    Content type: Review Published on:

  8. 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.

    Authors: Pamela S Soltis and Douglas E Soltis
    Citation: Genome Biology 2013 14:122
    Content type: Research highlight Published on:

  10. 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...

    Authors: Thomas R Turner, Euan K James and Philip S Poole
    Citation: Genome Biology 2013 14:209
    Content type: Review Published on:

  12. 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...

    Authors: Ping Lan, Wenfeng Li, Wen-Dar Lin, Simonetta Santi and Wolfgang Schmidt
    Citation: Genome Biology 2013 14:R67
    Content type: Research Published on:

  13. 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...

    Authors: Ksenia V Krasileva, Vince Buffalo, Paul Bailey, Stephen Pearce, Sarah Ayling, Facundo Tabbita, Marcelo Soria, Shichen Wang, Eduard Akhunov, Cristobal Uauy and Jorge Dubcovsky
    Citation: Genome Biology 2013 14:R66
    Content type: Research Published on:

  15. 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...

    Authors: 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…
    Citation: Genome Biology 2013 14:R64
    Content type: Research Published on:

  16. 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...

    Authors: Julietta Jupe, Remco Stam, Andrew JM Howden, Jenny A Morris, Runxuan Zhang, Pete E Hedley and Edgar Huitema
    Citation: Genome Biology 2013 14:R63
    Content type: Research Published on:

  17. 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...

    Authors: Dorothee Staiger, Jieun Shin, Mikael Johansson and Seth J Davis
    Citation: Genome Biology 2013 14:208
    Content type: Review Published on:

  19. 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...

    Authors: Michael W Bevan and Cristobal Uauy
    Citation: Genome Biology 2013 14:206
    Content type: Review Published on:

  20. 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 ...

    Authors: David B Neale, Charles H Langley, Steven L Salzberg and Jill L Wegrzyn
    Citation: Genome Biology 2013 14:120
    Content type: Opinion Published on:

  21. 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. ...

    Authors: Sara Schaarschmidt, Peter M Gresshoff and Bettina Hause
    Citation: Genome Biology 2013 14:R62
    Content type: Research Published on:

  22. 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...

    Authors: Nicolas Sierro, James ND Battey, Sonia Ouadi, Lucien Bovet, Simon Goepfert, Nicolas Bakaher, Manuel C Peitsch and Nikolai V Ivanov
    Citation: Genome Biology 2013 14:R60
    Content type: Research Published on:

  23. 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...

    Authors: Emanuela Sani, Pawel Herzyk, Giorgio Perrella, Vincent Colot and Anna Amtmann
    Citation: Genome Biology 2013 14:R59
    Content type: Research Published on:

  24. 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...

    Authors: 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…
    Citation: Genome Biology 2013 14:R58
    Content type: Research Published on:

  25. 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 ...

    Authors: Guangming He, Beibei Chen, Xuncheng Wang, Xueyong Li, Jigang Li, Hang He, Mei Yang, Lu Lu, Yijun Qi, Xiping Wang and Xing Wang Deng
    Citation: Genome Biology 2013 14:R57
    Content type: Research Published on:

  26. 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...

    Authors: 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
    Citation: Genome Biology 2013 14:R56
    Content type: Research Published on:

  27. 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...

    Authors: 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
    Citation: Genome Biology 2013 14:R55
    Content type: Research Published on:

  29. 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...

    Authors: Silvia Dal Santo, Giovanni Battista Tornielli, Sara Zenoni, Marianna Fasoli, Lorenzo Farina, Andrea Anesi, Flavia Guzzo, Massimo Delledonne and Mario Pezzotti
    Citation: Genome Biology 2013 14:r54
    Content type: Research Published on: