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We wanted to compare the six genomes of Schistocerca to get insights on gene evolution and relationships regarding their numbers, content, function and location. In order to achieve this, we need to identify groups of orthologous genes among our species of interest, considering at least one outgroup.
Orthologs are genes from different species that originated from a single ancestral gene and evolved through speciation events. However since genes can be lost or duplicated during evolution, some genes may not have exactly one orthologue in the genome of another species. Here we will separate the 1:1 orthologs to the the concept of orthogroups. Orthogroups can contain 1:1 orthologs but also several several orthologs from different species, including paralogs and one-to-many orthologs. Paralogs are genes within the same species that have originated from a shared ancestral genes but have diverged over time following gene duplication events.
IMPORTANT. We used OrthoFinder to identify the orthogroups using amino acid sequences from the longest isoform of each gene. For this part, refers to the pipeline FormicidaeMolecularEvolution by Megan Barkdull. We describe below the modifications made.
Using the create file “input-XXX.txt” we downloaded the coding sequence, protein sequence, GFF annotation data for each of our six Schistocerca species and one termites outgroup Csec.
./scripts/DataDownload ./scripts/input-XXX.txt…WRITING/FORMATTING ONGOING
If you use this script, please cite:
Emms D.M. & Kelly S. (2019), Genome Biology 20:238
If you use the species tree in your work then please also cite:
Emms D.M. & Kelly S. (2017), MBE 34(12): 3267-3278 Emms D.M. & Kelly S. (2018), bioRxiv https://doi.org/10.1101/267914
sessionInfo()R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.1.2
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
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time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] workflowr_1.7.1
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[13] git2r_0.33.0 htmltools_0.5.7 httpuv_1.6.13 ps_1.7.5
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[29] fs_1.6.3 pkgconfig_2.0.3 Rcpp_1.0.12 rstudioapi_0.15.0
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