Recent Posts

Genomic variation in 3,010 diverse accessions of Asian cultivated rice (Nature)

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…

Genome-wide excision repair in Arabidopsis is coupled to transcription and reflects circadian gene expression patterns (Nature Comms)

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…

Recognizing featured Plant Cell first authors: André N. Müller

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…

Commentary. 10KP: A phylodiverse genome sequencing plan (GigaScience)

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…

Transcriptome landscape of a bacterial pathogen under plant immunity (PNAS)

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…

Initiation of meiotic recombination is regulated by epigenetic marks and chromatin structure (Genome Res.)

Meiotic recombination is an important source of genetic diversity by allowing the reshuffling of parental alleles during meiosis. It requires the generation of DNA double-strand breaks (DSBs) initiated by the activity of the SPO11 protein complex. In plants, the impact of chromatin structure and DNA…

Trust but Verify: A Lesson in Technology Limitations and Error Propagation

Unlike molecular biology techniques that are routinely used in individual investigator labs, the high cost of infrastructure historically has resulted in genome sequencing being performed at genome centers in which quality control and quality assessments are a mainstay, and it is the rare exception that…

The subgenomes of polyploid plants evolve at different rates (Plant Cell)

Polyploidy can result either through genome doubling followed by intraspecific crosses, or when two genomes from independent species hybridize, leading to autopolyploidy, or allopolyploidy, respectively. Polyploidy is an important evolutionary tool; the resultant redundancy from the duplication of genes…

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell (Nature Comms)

Every now and then a technology arrives on the scene that suddenly makes everything easier. When I was a student, PCR was developed. More recently, CRISPR/Cas9 applications were developed, and now the hot tool is nanopore flow cell sequencing. The crucial advancement in this method is that rather than…