Tag: Genomics

Godfroy et al investigate basal cell fate determination in the brown alga Ectocarpus https://doi.org/10.1105/tpc.17.00440 BACKGROUND: Brown algae are multicellular photosynthetic marine organisms living on rocky shores across the globe and representing one of the most developmentally complex groups…

Zhao et al. demonstrate that duplicated genomes in maize and soybean followed distinct trajectories over millions of years https://doi.org/10.1105/tpc.17.00595 By Meixia Zhao, Biao Zhang, Damon Lisch, and Jianxin Ma Background: Over evolutionary time, many organisms, particularly plants, have periodically…

One of the hardest parts of any sequencing project is putting the pieces together. Physical sequence alignments can be cross checked against genetic linkage maps when they are available, but what about for species without genetic linkage data? Udall and Dawe describe the use of optical mapping, using…

Experiments using large germplasm collections are prone to contamination. With dropping sequencing costs, it becomes easier to validate the genotype using minimal sequencing coverage. Pisupati and colleagues developed an open-source python pipeline, called SNPmatch, allowing identification of 930 Arabidopsis…

Transposable elements are a major part of plant genomes. Long-terminal repeat retrotransposons (LTR (LTR-RTs) alone make up 78% of the maize genome (retrotransposons use a “copy and paste” transposition method meaning that a single source element can generate numerous clones of itself, leading to…

DNA methylation is instrumental in promoting transcriptional silencing at repetitive elements, inhibiting illegitimate recombination and establishing genomic imprinting. In plants, DNA methylation profiles are stably inherited over generations through the activities of cytosine DNA methyltransferases…

Cis-regulatory elements direct transcriptional output during cell differentiation and coordinate adaptive responses to environmental stress. DNA becomes open and accessible when nucleosomes are displaced by DNA-binding proteins, indicating a correlation between open chromatin regions and transcriptional…

Plants are highly plastic and can modulate their growth and development to better respond to abiotic and biotic surroundings. Among the molecules involved in the adaptation to the environment, a crucial role is played by small secreted peptides (SSPs). In their paper, integrating 144 transcriptomic experiments,…