Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress.

BMC Genomics
Caitlin M A SimopoulosElizabeth A Weretilnyk

Abstract

The severity and frequency of drought has increased around the globe, creating challenges in ensuring food security for a growing world population. As a consequence, improving water use efficiency by crops has become an important objective for crop improvement. Some wild crop relatives have adapted to extreme osmotic stresses and can provide valuable insights into traits and genetic signatures that can guide efforts to improve crop tolerance to water deficits. Eutrema salsugineum, a close relative of many cruciferous crops, is a halophytic plant and extremophyte model for abiotic stress research. Using comparative transcriptomics, we show that two E. salsugineum ecotypes display significantly different transcriptional responses towards a two-stage drought treatment. Even before visibly wilting, water deficit led to the differential expression of almost 1,100 genes for an ecotype from the semi-arid, sub-arctic Yukon, Canada, but only 63 genes for an ecotype from the semi-tropical, monsoonal, Shandong, China. After recovery and a second drought treatment, about 5,000 differentially expressed genes were detected in Shandong plants versus 1,900 genes in Yukon plants. Only 13 genes displayed similar drought-responsive patterns for b...Continue Reading

References

Apr 5, 2007·Plant, Cell & Environment·Marilyn GriffithBarbara Moffatt
Jul 24, 2007·Nature Genetics·José Manuel Franco-ZorrillaJavier Paz-Ares
Oct 29, 1982·Science·J S Boyer
May 27, 2008·Plant Physiology·Ayako NishizawaShigeru Shigeoka
Dec 31, 2008·BMC Bioinformatics·Peter Langfelder, Steve Horvath
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
Jul 27, 2011·PloS One·Fran SupekTomislav Šmuc
Aug 16, 2011·The Plant Journal : for Cell and Molecular Biology·Yun KangMichael Udvardi
Nov 24, 2011·Nucleic Acids Research·David M GoodsteinDaniel S Rokhsar
Mar 15, 2012·Nature Communications·Yong DingZoya Avramova
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Jan 1, 2014·BMC Plant Biology·Yong DingZoya Avramova
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Jul 30, 2014·Developmental Cell·Florian BardouMartin Crespi
Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders
Feb 19, 2015·Nature Biotechnology·Mihaela PerteaSteven L Salzberg
Jul 25, 2015·Molecular Plant·Peng Cui, Liming Xiong
May 16, 2017·Frontiers in Plant Science·Dawei XueZhong-Hua Chen
May 4, 2018·BMC Genomics·Caitlin M A SimopoulosG Brian Golding
Jun 5, 2018·Molecular Ecology·Xiao-Juan WangJian-Quan Liu
Jun 17, 2018·Plant Science : an International Journal of Experimental Plant Biology·Michael L NuccioSean R Cutler
Apr 8, 2019·The New Phytologist·Nora Marín-de la RosaPascal Falter-Braun
Jul 1, 2016·Functional Plant Biology : FPB·Yang Ping LeeDirk K Hincha

❮ Previous
Next ❯

Citations


❮ Previous
Next ❯

Methods Mentioned

BETA
RNA-Seq
PCA
RNASeq
transgenic
chips
Hi-Seq
PCR

Software Mentioned

DESeq2 Bioconductor
Revigo webserver
CREMA
Phytozome
REVIGO
custom
gffcompare
DESeq2
STAR
WCGNA

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.