Entries by Saima Shahid

On UPF Proteins, Baking Cookies, and the Many Targets of Nonsense-Mediated RNA Decay

When we cut out cookies from rolled-out dough, we often end up with unwanted dough scraps, and sometimes the dough sticks to the cookie-cutter, resulting in misshapen cookies. Just like these misshapen cookies, faulty or aberrant RNAs can arise in cells due to mistakes during transcription, RNA processing, or frameshift mutations. Nonsense-mediated decay (NMD) is […]

To Be or Not To Be Pathogenic: Transcriptional Reprogramming Dictates a Fungal Pathogen’s Response to Different Hosts

The fungal pathogen Fusarium virguliforme invades a wide spectrum of host plants, ranging from eudicots to monocots. Interestingly, fungal root colonization results in disease-producing phenotypes only in certain eudicot hosts (Kolander et al., 2012). For instance, F. virguliforme causes sudden death syndrome, one of the most destructive diseases in soybean. Diseased soybean plants exhibit an […]

Dramatic changes in repeat element content and gene family sizes underlie the high-altitude adaptation of rock-cress  (PNAS)

The ability to grow on the ‘roof of the world’ – the Qinghai-Tibet Plateau, makes Crucihimalaya himalaica (Rock-cress) an important model for studying adaptive evolution. A draft genome sequence of C. himalaica reported by Zhang et al. now provides clues to its speciation and ecological adaptation. About 45% of C. himalaica genome consists of transposable […]

Review: Copy Number Variations shaping plant domestication (Trends Plant Sci)

Human-associated plant domestication is a co-evolutionary process that began at least 12,000 years ago. However, the genetic variations underlying many domestication traits are still unknown. In this review, Lye and Purugganan discuss how copy number variations (CNVs) have played an important role in plant and animal domestication. CNVs are deletions, duplications or amplifications (usually at […]

Century-old museum specimens predict a timeline for declines in monarch butterflies and their host milkweed (PNAS)

Milkweeds are often found in agriculture fields, and are susceptible to herbicides sprayed in such fields. A decline in milkweeds, which provide food for monarch butterflies, has been historically linked to the wide cultivation of herbicide-resistant genetically modified (GM) crops. Boyle et al. attempt to reconstruct a timeline of monarch and milkweed abundance based on […]

A rich evolutionary history of transposable element families in the maize genome (bioRxiv)

Transposable elements (TEs) make up nearly ~85% of the maize genome. Stitzer et al. report a comprehensive analysis of diverse TE families in maize based on the improved annotation of the updated B73 genome assembly. The authors found all of the known plant TE superfamilies in the maize genome, with Long Terminal Repeats (LTRs) occupying […]

The volatile indole primes rice defense against caterpillar attack (Plant Cell)

Herbivore-induced volatiles have been shown to prime plant defense response in multiple species. A new study by Ye et al. unveils some of the early signaling events in volatile-mediated defense priming in rice. The authors show that rice plants release increased amounts of the volatile indole when attacked by fall armyworm caterpillars. Indole pre-exposure induces […]

Tapping into the genetic diversity of wild crops for engineering disease resistance (Nature Biotech)

Lack of sequence information makes harnessing the diversity of disease resistance (R) genes in wild crops highly challenging. Arora and Steuernagel et al. report AgRenSeq, a reference genome-free technique, for rapid cloning of nucleotide binding/Leucine-rich repeat (NLR) resistance genes from wild crops. Using R gene enrichment sequencing, the authors captured thousands of NLR-specific contigs from 151 […]