Tag: Genomics

The ability to participate in nitrogen-fixing root nodule symbiosis shows an interesting phylogenetic pattern, with some families showing a large number of nodulating species interspersed with non-nodulating ones, and some families showing only a few nodulating species. A current model suggests that…

Every year, genome assembly gets faster and cheaper. Li and Harkness provide a practical guide to today’s methods, with caveats and precautions that need to be considered at each step, even questions to ask before embarking on a sequencing project.  Topics include how to estimate genome size and complexity,…

Xiao et al. used 1,033 rice accessions for GWAS to identify QTLs associated with cold tolerance.  In general, japonica-type varieties showed greater cold tolerance than indica types.  The authors identified many QTLs for cold tolerance at the seedling and booting (initiation of panicles) stages. They…

Wang et al. analyse data from the 3000 rice (Oryza sativa) genome (3K-RG) project, identifying “29 million single nucleotide polymorphisms, 2.4 million small indels and over 90,000 structural variations”. The data of course strongly support the two major rice types (Indica and Japonica), but also…

Exposure to ultraviolet radiation and numerous other factors can cause mispairing of the nucleotides in the DNA, compromising genome integrity. Luckily, plants employ excision repair systems to recognize and repair such DNA damage. Oztas et al. examined the dynamics of such a repair system by using excision…

André N. Müller, featured first author of The Biotrophic Development of Ustilago maydis Studied by RNA-Seq Analysis Current Position: Project Manager, GSK Vaccines GmbH, Marburg Education: PhD in Molecular Phytopathology, Department of Organismic Interactions, Max Planck Institute for Terrestrial…

Nobody doubts the great insights we have gained about plant diversity and evolution from genome sequencing, but the patchy nature of available genomes within the plant phylogeny remains a problem. Cheng et al. describe the 10KP (10,000 Plants) Genome Sequencing Project, which aims to sequence genomes…

Many studies have examined how plants respond transcriptionally to pathogen attack. This study investigates how a bacterial pathogen [Pseudomonas syringae pv. tomato DC3000 (Pto)] alters its transcriptome very early in the infection process. To accomplish this, Nobori et al. developed two methods to…