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 makes 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).

ARTIN Brno Czech Republic

CEITEC Masaryk University Brno Czech Republic

Zobrazit více v PubMed

Allen, R. S. , Nakasugi, K. , Doran, R. L. , Millar, A. A. , & Waterhouse, P. M. (2013). Facile mutant identification via a single parental backcross method and application of whole genome sequencing based mapping pipelines. Frontiers in Plant Science, 4, 362 http://journal.frontiersin.org/article/10.3389/fpls.2013.00362/abstract PubMed DOI PMC

Austin, R. S. , Vidaurre, D. , Stamatiou, G. , Breit, R. , Provart, N. J. , Bonetta, D. , … Guttman, D. S. (2011). Next‐generation mapping of Arabidopsis genes. The Plant Journal, 67, 715–725. 10.1111/j.1365-313X.2011.04619.x PubMed DOI

Berardini, T. Z. , Reiser, L. , Li, D. , Mezheritsky, Y. , Muller, R. , Strait, E. , & Huala, E. (2015). The arabidopsis information resource: Making and mining the “gold standard” annotated reference plant genome. Genesis, 53, 474–485. 10.1002/dvg.22877 PubMed DOI PMC

Candela, H. , & Hake, S. (2008). The art and design of genetic screens: Maize. Nature Reviews Genetics, 9, 192–203. 10.1038/nrg2291 PubMed DOI

Casselton, L. , & Zolan, M. (2002). The art and design of genetic screens: Filamentous fungi. Nature Reviews Genetics, 3, 683–697. 10.1038/nrg889 PubMed DOI

Cingolani, P. , Platts, A. , Wang, L. L. , Coon, M. , Nguyen, T. , Wang, L. , … Ruden, D. M. (2012). A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso‐2; iso‐3. Fly (Austin), 6, 80–92. 10.4161/fly.19695 PubMed DOI PMC

Clouse, S. D. , Langford, M. , & McMorris, T. C. (1996). A brassinosteroid‐insensitive mutant in Arabidopsis Thaliana exhibits multiple defects in growth and development. Plant Physiology, 111, 671–678. 10.1104/pp.111.3.671 PubMed DOI PMC

Forsburg, S. L. (2001). The art and design of genetic screens: Yeast. Nature Reviews Genetics, 2, 659–668. 10.1038/35088500 PubMed DOI

Grimm, S. (2004). The art and design of genetic screens: Mammalian culture cells. Nature Reviews Genetics, 5, 179–189. 10.1038/nrg1291 PubMed DOI

Hartwig, B. , James, G. V. , Konrad, K. , Schneeberger, K. , & Turck, F. (2012). Fast isogenic mapping‐by‐sequencing of ethyl methanesulfonate‐induced mutant bulks. Plant Physiology, 160, 591–600. 10.1104/pp.112.200311 PubMed DOI PMC

James, G. V. , Patel, V. , Nordström, K. J. V. , Klasen, J. R. , Salomé, P. A. , Weigel, D. , & Schneeberger, K. (2013). User guide for mapping‐by‐sequencing in Arabidopsis. Genome Biology, 14, R61. PubMed PMC

Jorgensen, E. M. , & Mango, S. E. (2002). The art and design of genetic screens: Caenorhabditis elegans. Nature Reviews Genetics, 3, 356–369. 10.1038/nrg794 PubMed DOI

Kile, B. T. , & Hilton, D. J. (2005). The art and design of genetic screens: Mouse. Nature Reviews Genetics, 6, 557–567. 10.1038/nrg1636 PubMed DOI

Li, H. , & Durbin, R. (2009). Fast and accurate short read alignment with Burrows‐Wheeler transform. Bioinformatics, 25, 1754–1760. 10.1093/bioinformatics/btp324 PubMed DOI PMC

Li, H. , Handsaker, B. , Wysoker, A. , Fennell, T. , Ruan, J. , Homer, N. , … Durbin, R. (2009). The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078–2079. 10.1093/bioinformatics/btp352 PubMed DOI PMC

Lindner, H. , Raissig, M. T. , Sailer, C. , Shimosato‐Asano, H. , Bruggmann, R. , & Grossniklaus, U. (2012). SNP‐ratio mapping (SRM): Identifying lethal alleles and mutations in complex genetic backgrounds by next‐generation sequencing. Genetics, 191, 1381–1386. 10.1534/genetics.112.141341 PubMed DOI PMC

Manavella, P. A. , Hagmann, J. , Ott, F. , Laubinger, S. , Franz, M. , MacEk, B. , & Weigel, D. (2012). Fast‐forward genetics identifies plant CPL phosphatases as regulators of miRNA processing factor HYL1. Cell, 151, 859–870. 10.1016/j.cell.2012.09.039 PubMed DOI

Minevich, G. , Park, D. S. , Blankenberg, D. , Poole, R. J. , & Hobert, O. (2012). CloudMap: A cloud‐based pipeline for analysis of mutant genome sequences. Genetics, 192, 1249–1269. 10.1534/genetics.112.144204 PubMed DOI PMC

Page, D. R. , & Grossniklaus, U. (2002). The art and design of genetic screens: Arabidopsis thaliana. Nature Reviews Genetics, 3, 124–136. 10.1038/nrg730 PubMed DOI

Patton, E. E. , & Zon, L. I. (2001). The art and design of genetic screens: Zebrafish. Nature Reviews Genetics, 2, 956–966. Available at:http://www.ncbi.nlm.nih.gov/pubmed/11733748. PubMed

Quinlan, A. R. , & Hall, I. M. (2010). BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841–842. 10.1093/bioinformatics/btq033 PubMed DOI PMC

Robinson, J. T. , Thorvaldsdóttir, H. , Winckler, W. , Guttman, M. , Lander, E. S. , Getz, G. , & Mesirov, J. P. (2011). Integrative genomics viewer. Nature Biotechnology, 29, 24–26. 10.1038/nbt.1754 PubMed DOI PMC

Schneeberger, K. , Ossowski, S. , Lanz, C. , Juul, T. , Petersen, A. H. , Nielsen, K. L. , … Andersen, S. U. (2009). SHOREmap: Simultaneous mapping and mutation identification by deep sequencing. Nature Methods, 6, 550–551. 10.1038/nmeth0809-550 PubMed DOI

Shuman, H. , & Silvahy, T. (2003). The art and design of genetic screens: Escherichia coli. Nature Reviews Genetics, 3, 176–188. Available at:http://www.ncbi.nlm.nih.gov/pubmed/11972155. PubMed

St Johnston, D. (2002). The art and design of genetic screens: Drosophila melanogaster. Nature Reviews Genetics, 3, 176–188. 10.1038/nrg751 PubMed DOI

Wachsman, G. , Modliszewski, J. L. , Valdes, M. , & Benfey, P. N. (2017). A SIMPLE pipeline for mapping point mutations. Plant Physiology, 174, 1307–1313. 10.1104/pp.17.00415 PubMed DOI PMC

Yin, Y. , Wang, Z. Y. , Mora‐Garcia, S. , Li, J. , Yoshida, S. , Asami, T. , & Chory, J. (2002). BES1 accumulates in the nucleus in response to brassinosteroids to regulate gene expression and promote stem elongation. Cell, 109, 181–191. 10.1016/S0092-8674(02)00721-3 PubMed DOI

A complex role of Arabidopsis CDKD;3 in meiotic progression and cytokinesis

A CENH3 mutation promotes meiotic exit and restores fertility in SMG7-deficient Arabidopsis

Arabidopsis Flippases Cooperate with ARF GTPase Exchange Factors to Regulate the Trafficking and Polarity of PIN Auxin Transporters