Easymap: A User-Friendly Software Package for Rapid Mapping-by-Sequencing of Point Mutations and Large Insertions

Abstract

Mapping-by-sequencing strategies combine next-generation sequencing (NGS) with classical linkage analysis, allowing rapid identification of the causal mutations of the phenotypes exhibited by mutants isolated in a genetic screen. Computer programs that analyze NGS data obtained from a mapping population of individuals derived from a mutant of interest to identify a causal mutation are available; however, the installation and usage of such programs requires bioinformatic skills, modifying or combining pieces of existing software, or purchasing licenses. To ease this process, we developed Easymap, an open-source program that simplifies the data analysis workflows from raw NGS reads to candidate mutations. Easymap can perform bulked segregant mapping of point mutations induced by ethyl methanesulfonate (EMS) with DNA-seq or RNA-seq datasets, as well as tagged-sequence mapping for large insertions, such as transposons or T-DNAs. The mapping analyses implemented in Easymap have been validated with experimental and simulated datasets from different plant and animal model species. Easymap was designed to be accessible to all users regardless of their bioinformatics skills by implementing a user-friendly graphical interface, a simple universal installation script, and detailed mapping reports, including informative images and complementary data for assessment of the mapping results. Easymap is available at http://genetics.edu.umh.es/resources/easymap; its Quickstart Installation Guide details the recommended procedure for installation.

Inactivation of the entire Arabidopsis group II GH3s confers tolerance to salinity and water deficit

“…A total of 47 million 150-bp-long reads were obtained, reaching a 599 genome depth. Trimmed FASTQ files were used to map the different insertions using EASYMAP software (Lup et al, 2021). Raw reads were deposited in the short read archive (SRA) with the code SRX8771538.…”

Short-interval traffic lines: versatile tools for genetic analysis in Arabidopsis thaliana

“…Next-generation sequencing has revealed that many induced mutations are associated with linked second-site mutations ( Schneeberger et al 2009 ; Enders et al 2015 ; Thole and Strader 2015 ; Lup et al 2021 ). Determining whether the phenotype of these lines is attributable to one or more of these linked mutations can be problematic if the mutations are so tightly linked that they do not readily segregate from each other.…”

Versatile mapping-by-sequencing with Easymap v.2

“…Specifically, for mutation mapping, few tools implement workflows that use raw reads to generate a list of candidate mutations in a user-friendly manner, and most of these tools lack versatility. The first version of Easymap was designed to ease mutation mapping by linkage analysis and to map large DNA insertions, making it quite useful for identifying transgenes and characterizing insertional lines of any type ( Lup et al., 2021 ). In Easymap v.2, we implemented additional workflows for other common mapping strategies.…”

“…Easymap was developed as a user-friendly software package to facilitate conventional mapping-by-sequencing of point mutations and tagged-sequence mapping of large insertions, both using NGS datasets ( Lup et al., 2021 ; Lup et al., 2022 ). Easymap implements mapping workflows for diverse types of datasets, including DNA whole-genome resequencing and transcriptome sequencing (RNA-seq) data, mapping populations obtained by backcrossing, outcrossing or selfing of a mutant, and control samples consisting of the whole-genome sequences of any parental line of the mapping population or a pool of phenotypically wild-type siblings of the mapping population.…”