Recent Posts

Orchidstra 2.0 – A transcriptomics resource for the orchid family ($)

There are more than 25,000 species in the Orchidaceae, the orchid family. Chao et al. have updated and restructured the Orchidstra database, which now houses more than half-a million protein-coding genes from 18 species (12 genera and five subfamilies). Access and explore it at http://orchidstra2.abrc.sinica.edu.tw.…

MarpoDB: An open registry for Marchantia polymorpha genetic parts

Marchantia polymorpha (a liverwort) is a living relative of the earliest terrestrial plants. As it has a simple genome and morphology and is readily transformable, it provides a good platform for synthetic biology (see https://www.openplant.org/marchantia/). Delmans et al. have designed an “engineering-oriented”…

How can genomics help neglected crops fight disease?

Guest post by Kelsey Wood (@klsywd) a PhD student researching the genetics and genomics of plant-pathogen interactions at the University of California, Davis. I recently attended a Plant Pathology symposium on “Genomics Strategies for Developing Sustainable Disease Resistance for Neglected Crops…

Protocol: Laser capture microdissection for woody tissues

Laser capture microdissection (LCM) was developed 20 years ago as a way to isolate single cells or clusters of cells for subsequent –omic analysis.  In LCM, thin sections are generated, the cells of interest cut out using a focused laser, and the isolated cells collected for subsequent studies. Several…

Uncovering hidden variation in polyploid wheat

One of the big challenges of working with wheat, as compared to rice, is that the wheat we eat is polyploid; bread wheat (Triticum aestivum) is hexaploid (six copies of each gene) and pasta wheat (Triticum turgidum) is tetraploid (four copies each). Polyploidy makes forward genetics difficult; knocking…

CATchUP: A web database providing information on spatiotemporal specific gene expression

Nakamura et al. have created a searchable database, CATchUP (http://plantomics.mind.meiji.ac.jp/CATchUP) that allows the user to explore the spatiotemporal expression of genes across eight plant species (monocots and dicots) using data from publically available databases of large-scale RNA-Seq data.…

Water deficit-induced changes in transcription factor expression in maize seedlings ($)

Understanding plant responses to water deficit is crucial for the development of drought-reliance, but complicated by the different ways plant researchers induce water deficit. Starting with the premise that transcription factors are important coordinators of water-deficit responses, Seeve et al. carried…

More than Window Dressing: Revealing 5-Methylcytocine Patterns that Decorate Arabidopsis RNA

IN BRIEF by Jennifer Lockhart jlockhart@aspb.org DNA is sculpted by several types of epigenetic modifications with profound effects on gene expression, development, and stress responses. Much less is known about the more than 100 chemical modifications shaping plant RNA, a topic explored in the newly…

Transcriptional response to microbial pattern conferred by three WRKY transcription factors ($)

Plants perceive microbial pathogens though cell-surface receptors that recognize conserved microbial patterns such as flagellin. Previous studies have identified the WRKY family of transcription factors as contributors to Microbial-Associated Molecular Pattern (MAMP)-Triggered Immunity (MTI). Birkenbihl…