Upcoming progress of transcriptomics studies on plants: An overview

P Tyagi, D Singh, S Mathur, A Singh… - Frontiers in Plant …, 2022 - frontiersin.org
Transcriptome sequencing or RNA-Sequencing is a high-resolution, sensitive and high-
throughput next-generation sequencing (NGS) approach used to study non-model plants …

Alternative splicing control of abiotic stress responses

T Laloum, G Martín, P Duque - Trends in plant science, 2018 - cell.com
Alternative splicing, which generates multiple transcripts from the same gene, is an
important modulator of gene expression that can increase proteome diversity and regulate …

A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA‐seq profiling

AV Klepikova, AS Kasianov, ES Gerasimov… - The Plant …, 2016 - Wiley Online Library
Arabidopsis thaliana is a long established model species for plant molecular biology,
genetics and genomics, and studies of A. thaliana gene function provide the basis for …

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 …

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

S Liu, Y Liu, X Yang, C Tong, D Edwards… - Nature …, 2014 - nature.com
Polyploidization has provided much genetic variation for plant adaptive evolution, but the
mechanisms by which the molecular evolution of polyploid genomes establishes genetic …

Analysis of RNA-Seq data using TopHat and Cufflinks

S Ghosh, CKK Chan - Plant Bioinformatics: Methods and Protocols, 2016 - Springer
The recent advances in high throughput RNA sequencing (RNA-Seq) have generated huge
amounts of data in a very short span of time for a single sample. These data have required …

Alternative splicing of TaHSFA6e modulates heat shock protein–mediated translational regulation in response to heat stress in wheat

J Wen, Z Qin, L Sun, Y Zhang, D Wang, H Peng… - New …, 2023 - Wiley Online Library
Heat stress greatly threatens crop production. Plants have evolved multiple adaptive
mechanisms, including alternative splicing, that allow them to withstand this stress …

Splicing regulation by long noncoding RNAs

N Romero-Barrios, MF Legascue… - Nucleic acids …, 2018 - academic.oup.com
Massive high-throughput sequencing techniques allowed the identification of thousands of
noncoding RNAs (ncRNAs) and a plethora of different mRNA processing events occurring in …

Complexity of the alternative splicing landscape in plants

ASN Reddy, Y Marquez, M Kalyna, A Barta - The Plant Cell, 2013 - academic.oup.com
Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows
organisms to increase their coding potential and regulate gene expression through multiple …

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

P Lamesch, TZ Berardini, D Li, D Swarbreck… - Nucleic acids …, 2012 - academic.oup.com
Abstract The Arabidopsis Information Resource (TAIR, http://arabidopsis. org) is a genome
database for Arabidopsis thaliana, an important reference organism for many fundamental …