Reviving the transcriptome studies: an insight into the emergence of single-molecule transcriptome sequencing

B Wang, V Kumar, A Olson, D Ware - Frontiers in genetics, 2019 - frontiersin.org
Advances in transcriptomics have provided an exceptional opportunity to study functional
implications of the genetic variability. Technologies such as RNA-Seq have emerged as …

Genome-wide analysis of RNA secondary structure

PC Bevilacqua, LE Ritchey, Z Su… - Annual review of …, 2016 - annualreviews.org
Single-stranded RNA molecules fold into extraordinarily complicated secondary and tertiary
structures as a result of intramolecular base pairing. In vivo, these RNA structures are not …

A survey of the sorghum transcriptome using single-molecule long reads

SE Abdel-Ghany, M Hamilton, JL Jacobi… - Nature …, 2016 - nature.com
Alternative splicing and alternative polyadenylation (APA) of pre-mRNAs greatly contribute
to transcriptome diversity, coding capacity of a genome and gene regulatory mechanisms in …

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

Y Ding, Y Tang, CK Kwok, Y Zhang, PC Bevilacqua… - Nature, 2014 - nature.com
RNA structure has critical roles in processes ranging from ligand sensing to the regulation of
translation, polyadenylation and splicing,,,. However, a lack of genome-wide in vivo RNA …

Abiotic and biotic stresses induce a core transcriptome response in rice

SP Cohen, JE Leach - Scientific reports, 2019 - nature.com
Environmental stresses greatly limit crop yield. With the increase in extreme weather events
due to climate change and the constant pressure of diseases and pests, there is an urgent …

A global survey of alternative splicing in allopolyploid cotton: landscape, complexity and regulation

M Wang, P Wang, F Liang, Z Ye, J Li, C Shen… - New …, 2018 - Wiley Online Library
Alternative splicing (AS) is a crucial regulatory mechanism in eukaryotes, which acts by
greatly increasing transcriptome diversity. The extent and complexity of AS has been …

Transcript‐level expression control of plant NLR genes

Y Lai, T Eulgem - Molecular plant pathology, 2018 - Wiley Online Library
Plant NLR genes encode sensitive immune receptors that can mediate the specific
recognition of pathogen avirulence effectors and activate a strong defence response, termed …

A decade of pollen transcriptomics

N Rutley, D Twell - Plant reproduction, 2015 - Springer
Key message Overview of pollen transcriptome studies. Pollen development is driven by
gene expression, and knowledge of the molecular events underlying this process has …

A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing

B Wang, M Regulski, E Tseng, A Olson… - Genome …, 2018 - genome.cshlp.org
Maize and sorghum are both important crops with similar overall plant architectures, but they
have key differences, especially in regard to their inflorescences. To better understand these …

Improved Reference Genome Annotation of Brassica rapa by Pacific Biosciences RNA Sequencing

Z Zhang, J Guo, X Cai, Y Li, X **, R Lin… - Frontiers in plant …, 2022 - frontiersin.org
The species Brassica rapa includes several important vegetable crops. The draft reference
genome of B. rapa ssp. pekinensis was completed in 2011, and it has since been updated …