Bias in RNA‐seq library preparation: current challenges and solutions

H Shi, Y Zhou, E Jia, M Pan, Y Bai… - BioMed research …, 2021 - Wiley Online Library
Although RNA sequencing (RNA‐seq) has become the most advanced technology for
transcriptome analysis, it also confronts various challenges. As we all know, the workflow of …

The transcriptional landscape of Arabidopsis thaliana pattern-triggered immunity

M Bjornson, P Pimprikar, T Nürnberger, C Zipfel - Nature plants, 2021 - nature.com
Plants tailor their metabolism to environmental conditions, in part through the recognition of
a wide array of self and non-self molecules. In particular, the perception of microbial or plant …

Identification and application of exogenous dsRNA confers plant protection against Sclerotinia sclerotiorum and Botrytis cinerea

AG McLoughlin, N Wytinck, PL Walker, IJ Girard… - Scientific reports, 2018 - nature.com
Sclerotinia sclerotiorum, the causal agent of white stem rot, is responsible for significant
losses in crop yields around the globe. While our understanding of S. sclerotiorum infection …

Current and future methods for mRNA analysis: a drive toward single molecule sequencing

A Bayega, S Fahiminiya, S Oikonomopoulos… - … Analysis: Methods and …, 2018 - Springer
The transcriptome encompasses a range of species including messenger RNA, and other
noncoding RNA such as rRNA, tRNA, and short and long noncoding RNAs. Due to the huge …

Histone modification dynamics at H3K27 are associated with altered transcription of in planta induced genes in Magnaporthe oryzae

W Zhang, J Huang, DE Cook - PLoS genetics, 2021 - journals.plos.org
Transcriptional dynamic in response to environmental and developmental cues are
fundamental to biology, yet many mechanistic aspects are poorly understood. One such …

A modern ampelography: a genetic basis for leaf shape and venation patterning in grape

DH Chitwood, A Ranjan, CC Martinez… - Plant …, 2014 - academic.oup.com
Terroir, the unique interaction between genotype, environment, and culture, is highly refined
in domesticated grape (Vitis vinifera). Toward cultivating terroir, the science of …

A quantitative genetic basis for leaf morphology in a set of precisely defined tomato introgression lines

DH Chitwood, R Kumar, LR Headland, A Ranjan… - The Plant …, 2013 - academic.oup.com
Introgression lines (ILs), in which genetic material from wild tomato species is introgressed
into a domesticated background, have been used extensively in tomato (Solanum …

Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape

Y Ichihashi, JA Aguilar-Martínez… - Proceedings of the …, 2014 - National Acad Sciences
Despite a long-standing interest in the genetic basis of morphological diversity, the
molecular mechanisms that give rise to developmental variation are incompletely …

Integrative analysis from the epigenome to translatome uncovers patterns of dominant nuclear regulation during transient stress

TA Lee, J Bailey-Serres - The Plant Cell, 2019 - academic.oup.com
Gene regulation is a dynamic process involving changes ranging from the remodeling of
chromatin to preferential translation. To understand integrated nuclear and cytoplasmic …

De novo assembly and characterization of the transcriptome of the parasitic weed dodder identifies genes associated with plant parasitism

A Ranjan, Y Ichihashi, M Farhi, K Zumstein… - Plant …, 2014 - academic.oup.com
Parasitic flowering plants are one of the most destructive agricultural pests and have major
impact on crop yields throughout the world. Being dependent on finding a host plant for …