Mapping-by-Sequencing of Point and Insertional Mutations with Easymap

Lup, Samuel Daniel; Wilson-Sánchez, David; Micol, José Luis

doi:10.1007/978-1-0716-2253-7_23

Cited by 4 publications

(3 citation statements)

References 9 publications

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“…Subsequently, the complete genomes of sea4-1 and sea4-2 were sequenced by BGI (Shenzhen, China) using the BGISEQ platform. The raw data were analyzed using Easymap v.2 (Lup et al, 2021; Lup et al, 2022; Lup et al, 2023). Reads were aligned to the L er genome (Zapata et al, 2016); the options used were based on the facts that the mutations under study were present in the reference genetic background, the mapping population resulted from a backcross, and the control sample was the parental line of the mutant strain.…”

Section: Methodsmentioning

confidence: 99%

Postembryonic developmental roles of the ArabidopsisKEULEgene

Ruiz-Bayón,

Cara-Rodríguez,

Sarmiento-Mañús

et al. 2024

Preprint

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Cytokinesis in plant cells begins with the fusion of vesicles that transport cell wall materials at the center of the cell division plane, where the cell plate forms and expands radially until it fuses with the parental cell wall at the preprophase band. Vesicle fusion is facilitated bytrans-SNARE complexes, with assistance from Sec1/Munc18 (SM) proteins. The SNARE protein KNOLLE and the SM protein KEULE are required for membrane fusion at the cell plate. Due to the crucial function of KEULE, all Arabidopsis (Arabidopsis thaliana)keulemutants identified to date are seedling lethal. Here, we identified the Arabidopsisserrata4-1(sea4-1) andsea4-2mutants, which carry recessive, hypomorphic alleles ofKEULE. Homozygoussea4-1andsea4-2plants are viable and fertile but exhibit smaller rosettes and fewer leaves at bolting than the wild type. Their leaves are serrated, small, and undulated, with a complex venation pattern, develop necrotic patches, and undergo premature senescence. We established a likely relationship between these phenotypes and their defects in cytokinesis through reduced cell wall integrity and increased unfolded protein response. These findings shed light on the roles of KEULE in postembryonic development, particularly in the patterning of rosette leaves and leaf margins.

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Section: Methodsmentioning

confidence: 99%

Postembryonic developmental roles of the ArabidopsisKEULEgene

Ruiz-Bayón,

Cara-Rodríguez,

Sarmiento-Mañús

et al. 2024

Preprint

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“…Subsequently, the complete genomes of sea4-1 and sea4-2 were sequenced by BGI (BGI, Shenzhen, China) using the BGISEQ platform. The raw data were analyzed using Easymap v.2 [ 55 , 56 , 57 ]. Reads were aligned to the L er genome [ 58 ]; the options used were based on the assumptions that the mutations under study were present in the reference genetic background, the mapping population resulted from a backcross, and the control sample was the parental line of the mutant strain.…”

Section: Methodsmentioning

confidence: 99%

Roles of the Arabidopsis KEULE Gene in Postembryonic Development

Ruiz-Bayón,

Cara-Rodríguez,

Sarmiento-Mañús

et al. 2024

IJMS

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Cytokinesis in plant cells begins with the fusion of vesicles that transport cell wall materials to the center of the cell division plane, where the cell plate forms and expands radially until it fuses with the parental cell wall. Vesicle fusion is facilitated by trans-SNARE complexes, with assistance from Sec1/Munc18 (SM) proteins. The SNARE protein KNOLLE and the SM protein KEULE are required for membrane fusion at the cell plate. Due to the crucial function of KEULE, all Arabidopsis (Arabidopsis thaliana) keule mutants identified to date are seedling lethal. Here, we identified the Arabidopsis serrata4-1 (sea4-1) and sea4-2 mutants, which carry recessive, hypomorphic alleles of KEULE. Homozygous sea4-1 and sea4-2 plants are viable and fertile but have smaller rosettes and fewer leaves at bolting than the wild type. Their leaves are serrated, small, and wavy, with a complex venation pattern. The mutant leaves also develop necrotic patches and undergo premature senescence. RNA-seq revealed transcriptome changes likely leading to reduced cell wall integrity and an increase in the unfolded protein response. These findings shed light on the roles of KEULE in postembryonic development, particularly in the patterning of rosette leaves and leaf margins.

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“…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.…”

Section: Introductionmentioning

confidence: 99%

Versatile mapping-by-sequencing with Easymap v.2

2023

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Mapping-by-sequencing combines Next Generation Sequencing (NGS) with classical genetic mapping by linkage analysis to establish gene-to-phenotype relationships. Although numerous tools have been developed to analyze NGS datasets, only a few are available for mapping-by-sequencing. One such tool is Easymap, a versatile, easy-to-use package that performs automated mapping of point mutations and large DNA insertions. Here, we describe Easymap v.2, which also maps small insertion/deletions (InDels), and includes workflows to perform QTL-seq and variant density mapping analyses. Each mapping workflow can accommodate different experimental designs, including outcrossing and backcrossing, F2, M2, and M3 mapping populations, chemically induced mutation and natural variant mapping, input files containing single-end or paired-end reads of genomic or complementary DNA sequences, and alternative control sample files in FASTQ and VCF formats. Easymap v.2 can also be used as a variant analyzer in the absence of a mapping algorithm and includes a multi-threading option.

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Mapping-by-Sequencing of Point and Insertional Mutations with Easymap

Cited by 4 publications

References 9 publications

Postembryonic developmental roles of the ArabidopsisKEULEgene

Postembryonic developmental roles of the ArabidopsisKEULEgene

Roles of the Arabidopsis KEULE Gene in Postembryonic Development

Versatile mapping-by-sequencing with Easymap v.2

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