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Rapid identification and interpretation of gene–environment associations using the new R.SamBada landscape genomics pipeline
Author(s) -
Duruz Solange,
Sevane Natalia,
Selmoni Oliver,
Vajana Elia,
Leempoel Kevin,
Stucki Sylvie,
OrozcoterWengel Pablo,
Rochat Estelle,
Dunner Susana,
Bruford Michael W.,
Joost Stéphane
Publication year - 2019
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.13044
Subject(s) - ensembl , local adaptation , pipeline (software) , biology , annotation , identification (biology) , genomics , adaptation (eye) , population genomics , gene annotation , population , computational biology , genome , gene , bioinformatics , computer science , genetics , ecology , demography , neuroscience , sociology , programming language
sam β ada is a genome–environment association software, designed to search for signatures of local adaptation. However, pre‐ and postprocessing of data can be labour‐intensive, preventing wider uptake of the method. We have now developed R.SamBada, an r ‐package providing a pipeline for landscape genomic analysis based on sam β ada , spanning from the retrieval of environmental conditions at sampling locations to gene annotation using the Ensembl genome browser. As a result, R.SamBada standardizes the landscape genomics pipeline and eases the search for candidate genes of local adaptation, enhancing reproducibility of landscape genomic studies. The efficiency and power of the pipeline is illustrated using two examples: sheep populations from Morocco with no evident population structure and Lidia cattle from Spain displaying population substructuring. In both cases, R.SamBada enabled rapid identification and interpretation of candidate genes, which are further discussed in the light of local adaptation. The package is available in the r CRAN package repository and on GitHub (github.com/SolangeD/R.SamBada).