This GARNet research Roundup includes a broad range of topics and contributing institutions. First is a study from TSL that investigates the molecular basis of Arabidopsis and Brassica responses to white rust disease. Second is work from Warwick that uses Arabidopsis as a tool to test genes involved in the evolution of Flax domestication.
The third paper is work from Cambridge that models the response of the circadian oscillator to nicotinamide whilst the fourth paper is a study from the University of Dundee that compares differential gene expression software in the analysis of RNAseq data from a complex organism. The penultimate paper includes a co-author from the University of Oxford and has generated an extended phylogeny of the Brassicaceae family. The final paper compares the growth and metabolite profiles of Arabidopsis and Eutrema salsugineum following drought stress.
Cevik V, Boutrot F, Apel W, Robert-Seilaniantz A, Furzer OJ, Redkar
A, Castel B, Kover PX, Prince DC, Holub EB, Jones JDG (2019) Transgressive segregation reveals mechanisms of Arabidopsis immunity to Brassica-infecting races of white rust (Albugo candida). Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1812911116
Volkan Cevik is the lead author on this international collaboration
that is led by Jonathan Jones at the Sainsbury Lab, Norwich. They have
taken advantage of Arabidopsis resistance to white rust (Albugo candida)
and used the Multiparent Advanced Generation InterCross (MAGIC) lines
to identity the genes responsible for this resistance. This is important
as related crop species Brassica juncea and Brassica oleracea
are sensitive to this economically important pathogen. They identified a
range of nucleotide-binding, leucine-rich repeat (NLR)-encoding genes
that were involved in resistance to the pathogen.
Gutaker RM, Zaidem M, Fu YB, Diederichsen A, Smith O, Ware R, Allaby RG (2019) Flax latitudinal adaptation at LuTFL1 altered architecture and promoted fiber production. Sci Rep. doi: 10.1038/s41598-018-37086-5
Rafal Gutaker is the lead author on this collaborative study between
the University of Warwick and colleagues in Germany, Canada and Denmark,
which investigated the route of domestication of the cultivated crop
Flax. At northern european latitudes flax evolved to become a fibre crop
rather than an oil crop by stem expansion and reduction of seed size.
The authors investigated the role in this adaptation of PEBP family
genes in the flax genome, LuTFL1 and LuTFL2. LuTFL1 was heterologously
expressed in Arabidopsis, demonstrating that it is able to perform roles
in flowering time and plant architecture. This research highlights the
importance of Arabidopsis as a tool for testing the function of genes
from less-easily transformed organisms.
Mombaerts L, Carignano A, Robertson FR, Hearn TJ, Junyang J, Hayden
D, Rutterford Z, Hotta CT, Hubbard KE, Maria MRC, Yuan Y, Hannah MA,
Goncalves J, Webb AAR (2019) Dynamical differential expression (DyDE) reveals the period control mechanisms of the Arabidopsis circadian oscillator. PLoS Comput Biol. doi: 10.1371/journal.pcbi.1006674
Laurents Mombarts is the first author in this collaboration between
the departments of Plant science and Engineering at the University of
Cambridge that looked at the mechanistic effect on nicotinamide on the
timing of the circadian oscillation. They developed a systematic and
practical modeling framework for the gene regulatory circuits that
respond to nicotinamide. They initially developed a mathematical model
and then experimentally confirmed their predictions to uncover a role
for blue light signalling in this response. Overall their approach could
be adapted to predict mechanisms of drug action in other complex
Froussios K, Schurch NJ, Mackinnon K, Gierlinski M, Duc C, Simpson GG, Barton GJ (2019) How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study in A. thaliana. Bioinformatics. doi: 10.1093/bioinformatics/btz089
Gordon Simpson and colleagues at the University of Dundee collaborate
with researchers in Clermont-Ferrand with Kimon Froussios as first
author. They use Arabidopsis as a model to test a set of Differential
Gene Expression (DGE) tools for the effective analysis of RNAseq data
generated with three or fewer biological replicates. They tested nine
widely used DGE tools and ultimately recommend the use of tools that are
based on the negative binomial distribution.
Nikolov LA, Shushkov P, Nevado B, Gan X, Al-Shehbaz IA, Filatov D, Bailey CD, Tsiantis M (2019) Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity. New Phytol. doi: 10.1111/nph.15732.
This German, US and UK collaboration is led by Lachezar Nikolov and includes Dmitry Filatov from the University of Oxford as a co-author. They generated a phylogeny of the Brassicaceae,
the family that contains Arabidopsis and a number of economically
important crops. They used a mixture of fresh tissue and herbarium
samples to perform the analysis on almost 80 species; enabling the
resolution of new relationships between family members. This work
represents an important tool for phylogenetic and comparative studies to
maximise future outputs.
Pinheiro C, Dickinson E, Marriott A, Ribeiro IC, Pintó-Marijuan M,
António C, Zarrouk O, Chaves MM, Dodd IC, Munné-Bosch S, Thomas-Oates
J, Wilson J (2019) Distinctive phytohormonal and metabolic profiles of Arabidopsis thaliana and Eutrema salsugineum under similar soil drying. Planta. doi: 10.1007/s00425-019-03095-5
This collaboration between the UK and Portugal is led by Carla Pinheiro and the corresponding author is Julie Wilson
from the University of York. Eutrema salsugineum is a stress-tolerance
relative of Arabidopsis and in this study the authors have compared the
response of these plants following growth on drying soils. Whereas
stomatal sensitivity was similar in both species there were significant
differences in metabolite profiles and water usage following drought
stress. This analysis allowed the authors to conclude that Arabidopsis
is indeed a good model for analysis of responses to commonly encountered
levels of drought stress.