bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/414433

artMAP: a user-friendly tool for mapping EMS-induced mutations in Arabidopsis

Javorka, P.·Raxwal, V. K.·Najvarek, J.·Riha, K.
View original source ↗Export metadata ↓

Abstract

Mapping-by-sequencing is a rapid method for identifying both natural as well as induced variations in the genome. However, it requires extensive bioinformatics expertise along with the computational infrastructure to analyze the sequencing data and these requirements have limited its widespread adoption. In the current study, we develop an easy to use tool, artMAP, to discover ethyl methanesulfonate (EMS) induced mutations in the Arabidopsis genome. The artMAP pipeline consists of well-established tools including TrimGalore, BWA, BEDTools, SAMtools, and SnpEff which were integrated in a Docker container. artMAP provides a graphical user interface and can be run on a regular laptop and desktop, thereby limiting the bioinformatics expertise required. artMAP can process input sequencing files generated from single or paired-end sequencing. The results of the analysis are presented in interactive graphs which display the annotation details of each mutation. Due to its ease of use, artMAP made the identification of EMS-induced mutations in Arabidopsis possible with only a few mouse click. The source code of artMAP is available on Github (https://github.com/RihaLab/artMAP).

Source connections

Explore related subjects

plant biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Javorka, P., Raxwal, V. K., Najvarek, J., Riha, K.. 2018-09-12. artMAP: a user-friendly tool for mapping EMS-induced mutations in Arabidopsis. https://doi.org/10.1101/414433

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Anionic lipids stabilize etioplast prolamellar bodies and facilitate thylakoid biogenesis during etioplast-to-chloroplast differentiation

Etioplasts of dark-grown angiosperm seedlings contain prolamellar bodies (PLBs), lattice-like membranes that are quickly transformed into thylakoids upon illumination. Phosphatidylglycerol (PG) and sulfoquinovosyldiacylglycerol (SQDG) are major anionic lipids in these membranes, but their roles in etioplast-to-chloroplast differentiation remain unclear. We analyzed Arabidopsis thaliana mutants with reduced PG biosynthesis (pgp1-1), complete SQDG deficiency (sqd1), and the pgp1-1 sqd1 double mutant. Although pgp1-1 etioplasts showed a loosened PLB lattice when fixed under white light, they retained regular, wild-type-like lattices when fixed under infrared light, suggesting that their PLBs were more susceptible to light-induced disassembly. The rapid PLB disassembly in pgp1-1 upon illumination was accompanied by rapid conversion of dark-accumulated protochlorophyllide to chlorophyll and lamellar membrane formation, suggesting a link between membrane remodeling and chlorophyll formation. However, subsequent chlorophyll accumulation through de novo biosynthesis was retarded in illuminated pgp1-1 seedlings, whereas photosynthetic electron transport was quickly activated. Although sqd1 showed no obvious defects, pgp1-1 sqd1 exhibited more severe defects than pgp1-1, particularly in internal membrane formation, chlorophyll accumulation, photosynthetic activation, and photosynthetic gene expression. These findings suggest that PG is crucial for membrane-associated processes during etioplast-to-chloroplast differentiation, while SQDG may help maintain chloroplast development when PG availability is limited.

plant biology↗
bioRxiv2026

PHYRE, a Translated uORF, is Required for Phytochrome B Translation and Photomorphogenesis in Arabidopsis

Translational control allows cells to adjust protein output independently of transcription, yet the mRNA-encoded mechanisms that govern this regulatory layer remain poorly understood. Upstream open reading frames (uORFs) are among the most prevalent translational regulatory elements in eukaryotic genomes; however, characterised examples of activating uORFs that promote rather than inhibit downstream translation are exceedingly rare. Here we show that efficient expression of phytochrome B (phyB), the master red-light photoreceptor of Arabidopsis thaliana, requires translation of a short uORF in its own 5'UTR, which we name PHYTOCHROME REGULATOR (PHYRE). Loss of PHYRE function phenocopies phyB null mutants across germination, hypocotyl growth, leaf development, and flowering time. PHYRE activity depends on its encoded peptide sequence, and the spacing between PHYRE and the PHYB start codon is a critical determinant of downstream translation efficiency, consistent with a position-dependent reinitiation mechanism. PHYRE-like elements are conserved across eudicots, establishing uORF-mediated translational gating as a broadly maintained regulatory layer controlling a master photoreceptor.

plant biology↗
bioRxiv2026

The chloroplast-localised transporter RETICULATA controls palisade mesophyll cell division and expansion

Plant leaves contain extensive intercellular air spaces, which contribute to photosynthetic capacity and water use efficiency in different environments. Despite this importance, the developmental mechanisms that control leaf air space patterning are poorly understood. For over 20 years it has been known that plants with disrupted chloroplast biogenesis and metabolism have increased intercellular air spaces, but the underlying molecular mechanism is unknown. Here, we characterise leaf air space morphogenesis in mutants of the chloroplast amino acid transporter RETICULATA (RE), which has enlarged air spaces. We show that the reticulata-6 (re-6) loss of function mutant exhibits increased air space expansion specifically in the palisade, and not the spongy, mesophyll. We also show that RE does not regulate air space patterning via programmed cell death, via a change in stomatal density or a change in cell identity of the mesophyll tissue. Instead, we quantify mesophyll cell morphology and division rates to show that RE acts by promoting early palisade cell division and suppressing later cell expansion. Overall, we show that RE specifically regulated palisade mesophyll morphogenesis and air space patterning and hypothesise that chloroplasts may act to regulate air space patterning in the palisade mesophyll in response to light.

plant biology↗