Searching for GS Orthologs

Orthologs from crop in model plants and vice versa

Let’s imagine you are a beginner in the field of plant science, and glutamine synthetase (GS) is on the focus of your interest. You have been dealing with the literature and you have come across with a paper that awaken your interest: “Atomic Structure of Plant Glutamine Synthetase. A Key Enzyme for Plant Productivity” (J. Biol. Chem 29: 29287-29296).

In this paper, the authors reports the crystal structure of maize GS. However, as the author acknowledge, higher plants have several isoenzymes of GS differing in heat stability and catalytic properties. The author refer to the isoenzyme they are characterizing as GS1a, being Ile-161 a key residue responsible for the heat stability of this protein. Your aim is to find, if they exist, orthologs of this maize protein in the model plant Arabidopsis thaliana. You may be a beginner, but you don’t ignore that both maize and arabidopsis genomes have been shown to contain six GS genes each one.

GS isoforms from maize and arabidopsis found at Uniprot.

At first you’re slightly bewildered: none of the corn isoforms is called GS1a! But, everybody knows that GS1 implies a cytosolic form of the enzyme (while GS2 refer to the chloroplastic one), so our protein should be one of the five cytosolic isoenzymes present in maize. Taking into consideration that isoleucine should be present at position 161 and other information related to the sequence that is provided in the above mentioned paper, we conclude that GS1a match with GS1-4 from UniProt (or Zm_GS1b_4 using the phylo identifier of orthGS).

As a side note, point that the choice of GS1a to name this maize isoform was somewhat unfortunate. Indeed, among researcher in the gymnosperm field, GS1a is a term used to describe a set of evolutionary close cytosolic proteins whose expression and function is related to photosynthesis and photorespiration, reminiscent of GS2 in angiosperms.

In any case, we have already identified in maize the protein of interest (Zm_GS1b_4). Now, we have to look for orthologs in arabidopsis. Of course, the quickest and easiest way to do that is with the R package orthGS, but let’s pretend for a moment that we don’t know this resource. Thus, we are going to download all the arabidopsis and maize sequences, align them and build a phylogenetic tree, to see it this approach suggests something to us.

The function subsetGS() takes as argument the species of interest and return a dataframe with the sequences and information regarding the GS isoforms found in these species.

maize_ara <- subsetGS(c("Zea mays", "Arabidopsis thaliana"))

Afterward, we can proceed with the alignment and phylogenetic tree construction. Ensure the ‘muscle’ package is installed. If necessary, uncomment the following lines of code.

# if (!require("BiocManager", quietly = TRUE))
#     install.packages("BiocManager")
# 
# BiocManager::install("muscle")

aln <- msa(sequences = maize_ara$prot, ids = maize_ara$phylo_id, inhouse = FALSE)
#> 
#> MUSCLE v3.8.31 by Robert C. Edgar
#> 
#> http://www.drive5.com/muscle
#> This software is donated to the public domain.
#> Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.
#> 
#> file163b3f3ff6e8 12 seqs, max length 430, avg  length 369
#> 1164 MB(7%)00:00:00                Iter   1    1.28%  K-mer dist pass 11164 MB(7%)00:00:00                Iter   1  100.00%  K-mer dist pass 1
#> 1164 MB(7%)00:00:00                Iter   1    1.28%  K-mer dist pass 21164 MB(7%)00:00:00                Iter   1  100.00%  K-mer dist pass 2
#> 1164 MB(7%)00:00:00                Iter   1    9.09%  Align node       1164 MB(7%)00:00:00                Iter   1   18.18%  Align node1164 MB(7%)00:00:00                Iter   1   27.27%  Align node1164 MB(7%)00:00:00                Iter   1   36.36%  Align node1164 MB(7%)00:00:00                Iter   1   45.45%  Align node1164 MB(7%)00:00:00                Iter   1   54.55%  Align node1164 MB(7%)00:00:00                Iter   1   63.64%  Align node1164 MB(7%)00:00:00                Iter   1   72.73%  Align node1164 MB(7%)00:00:00                Iter   1   81.82%  Align node1164 MB(7%)00:00:00                Iter   1   90.91%  Align node1164 MB(7%)00:00:00                Iter   1  100.00%  Align node1164 MB(7%)00:00:00                Iter   1  100.00%  Align node
#> 1164 MB(7%)00:00:00                Iter   1    8.33%  Root alignment1164 MB(7%)00:00:00                Iter   1   16.67%  Root alignment1164 MB(7%)00:00:00                Iter   1   25.00%  Root alignment1164 MB(7%)00:00:00                Iter   1   33.33%  Root alignment1164 MB(7%)00:00:00                Iter   1   41.67%  Root alignment1164 MB(7%)00:00:00                Iter   1   50.00%  Root alignment1164 MB(7%)00:00:00                Iter   1   58.33%  Root alignment1164 MB(7%)00:00:00                Iter   1   66.67%  Root alignment1164 MB(7%)00:00:00                Iter   1   75.00%  Root alignment1164 MB(7%)00:00:00                Iter   1   83.33%  Root alignment1164 MB(7%)00:00:00                Iter   1   91.67%  Root alignment1164 MB(7%)00:00:00                Iter   1  100.00%  Root alignment1164 MB(7%)00:00:00                Iter   1  100.00%  Root alignment
#> 1164 MB(7%)00:00:00                Iter   2   10.00%  Refine tree   1164 MB(7%)00:00:00                Iter   2   20.00%  Refine tree1164 MB(7%)00:00:00                Iter   2   30.00%  Refine tree1164 MB(7%)00:00:00                Iter   2   40.00%  Refine tree1164 MB(7%)00:00:00                Iter   2   50.00%  Refine tree1164 MB(7%)00:00:00                Iter   2   60.00%  Refine tree1164 MB(7%)00:00:00                Iter   2  100.00%  Refine tree
#> 1164 MB(7%)00:00:00                Iter   2    8.33%  Root alignment1164 MB(7%)00:00:00                Iter   2   16.67%  Root alignment1164 MB(7%)00:00:00                Iter   2   25.00%  Root alignment1164 MB(7%)00:00:00                Iter   2   33.33%  Root alignment1164 MB(7%)00:00:00                Iter   2   41.67%  Root alignment1164 MB(7%)00:00:00                Iter   2   50.00%  Root alignment1164 MB(7%)00:00:00                Iter   2   58.33%  Root alignment1164 MB(7%)00:00:00                Iter   2   66.67%  Root alignment1164 MB(7%)00:00:00                Iter   2   75.00%  Root alignment1164 MB(7%)00:00:00                Iter   2   83.33%  Root alignment1164 MB(7%)00:00:00                Iter   2   91.67%  Root alignment1164 MB(7%)00:00:00                Iter   2  100.00%  Root alignment1164 MB(7%)00:00:00                Iter   2  100.00%  Root alignment
#> 1164 MB(7%)00:00:00                Iter   2  100.00%  Root alignment
#> 1164 MB(7%)00:00:00                Iter   3    9.52%  Refine biparts1164 MB(7%)00:00:00                Iter   3   14.29%  Refine biparts1164 MB(7%)00:00:00                Iter   3   19.05%  Refine biparts1164 MB(7%)00:00:00                Iter   3   23.81%  Refine biparts1164 MB(7%)00:00:00                Iter   3   28.57%  Refine biparts1164 MB(7%)00:00:00                Iter   3   33.33%  Refine biparts1164 MB(7%)00:00:00                Iter   3   38.10%  Refine biparts1164 MB(7%)00:00:00                Iter   3   42.86%  Refine biparts1164 MB(7%)00:00:00                Iter   3   47.62%  Refine biparts1164 MB(7%)00:00:00                Iter   3   52.38%  Refine biparts1164 MB(7%)00:00:00                Iter   3   57.14%  Refine biparts1164 MB(7%)00:00:00                Iter   3   61.90%  Refine biparts1164 MB(7%)00:00:00                Iter   3   66.67%  Refine biparts1164 MB(7%)00:00:00                Iter   3   71.43%  Refine biparts1164 MB(7%)00:00:00                Iter   3   76.19%  Refine biparts1164 MB(7%)00:00:00                Iter   3   80.95%  Refine biparts1164 MB(7%)00:00:00                Iter   3   85.71%  Refine biparts1164 MB(7%)00:00:00                Iter   3   90.48%  Refine biparts1164 MB(7%)00:00:00                Iter   3   95.24%  Refine biparts1164 MB(7%)00:00:00                Iter   3  100.00%  Refine biparts1164 MB(7%)00:00:00                Iter   3  104.76%  Refine biparts1164 MB(7%)00:00:00                Iter   3  100.00%  Refine biparts
#> 1164 MB(7%)00:00:00                Iter   4    9.52%  Refine biparts1164 MB(7%)00:00:00                Iter   4   14.29%  Refine biparts1164 MB(7%)00:00:00                Iter   4   19.05%  Refine biparts1164 MB(7%)00:00:00                Iter   4   23.81%  Refine biparts1164 MB(7%)00:00:00                Iter   4   28.57%  Refine biparts1164 MB(7%)00:00:00                Iter   4   33.33%  Refine biparts1164 MB(7%)00:00:00                Iter   4   38.10%  Refine biparts1164 MB(7%)00:00:00                Iter   4   42.86%  Refine biparts1164 MB(7%)00:00:00                Iter   4   47.62%  Refine biparts1164 MB(7%)00:00:00                Iter   4   52.38%  Refine biparts1164 MB(7%)00:00:00                Iter   4   57.14%  Refine biparts1164 MB(7%)00:00:00                Iter   4   61.90%  Refine biparts1164 MB(7%)00:00:00                Iter   4   66.67%  Refine biparts1164 MB(7%)00:00:00                Iter   4   71.43%  Refine biparts1164 MB(7%)00:00:00                Iter   4   76.19%  Refine biparts1164 MB(7%)00:00:00                Iter   4   80.95%  Refine biparts1164 MB(7%)00:00:00                Iter   4   85.71%  Refine biparts1164 MB(7%)00:00:00                Iter   4   90.48%  Refine biparts1164 MB(7%)00:00:00                Iter   4   95.24%  Refine biparts1164 MB(7%)00:00:00                Iter   4  100.00%  Refine biparts1164 MB(7%)00:00:00                Iter   4  104.76%  Refine biparts1164 MB(7%)00:00:00                Iter   4  100.00%  Refine biparts
#> 1164 MB(7%)00:00:00                Iter   5    9.52%  Refine biparts1164 MB(7%)00:00:00                Iter   5   14.29%  Refine biparts1164 MB(7%)00:00:00                Iter   5   19.05%  Refine biparts1164 MB(7%)00:00:00                Iter   5   23.81%  Refine biparts1164 MB(7%)00:00:00                Iter   5   28.57%  Refine biparts1164 MB(7%)00:00:00                Iter   5   33.33%  Refine biparts1164 MB(7%)00:00:00                Iter   5   38.10%  Refine biparts1164 MB(7%)00:00:00                Iter   5   42.86%  Refine biparts1164 MB(7%)00:00:00                Iter   5   47.62%  Refine biparts1164 MB(7%)00:00:00                Iter   5   52.38%  Refine biparts1164 MB(7%)00:00:00                Iter   5   57.14%  Refine biparts1164 MB(7%)00:00:00                Iter   5   61.90%  Refine biparts1164 MB(7%)00:00:00                Iter   5   66.67%  Refine biparts1164 MB(7%)00:00:00                Iter   5   71.43%  Refine biparts1164 MB(7%)00:00:00                Iter   5   76.19%  Refine biparts1164 MB(7%)00:00:00                Iter   5   80.95%  Refine biparts1164 MB(7%)00:00:00                Iter   5   85.71%  Refine biparts1164 MB(7%)00:00:00                Iter   5   90.48%  Refine biparts1164 MB(7%)00:00:00                Iter   5   95.24%  Refine biparts1164 MB(7%)00:00:00                Iter   5  100.00%  Refine biparts1164 MB(7%)00:00:00                Iter   5  104.76%  Refine biparts1164 MB(7%)00:00:00                Iter   5  100.00%  Refine biparts
#> 1164 MB(7%)00:00:00                Iter   6    9.52%  Refine biparts1164 MB(7%)00:00:00                Iter   6   14.29%  Refine biparts1164 MB(7%)00:00:00                Iter   6   19.05%  Refine biparts1164 MB(7%)00:00:00                Iter   6   23.81%  Refine biparts1164 MB(7%)00:00:00                Iter   6   28.57%  Refine biparts1164 MB(7%)00:00:00                Iter   6   33.33%  Refine biparts1164 MB(7%)00:00:00                Iter   6   38.10%  Refine biparts1164 MB(7%)00:00:00                Iter   6   42.86%  Refine biparts1164 MB(7%)00:00:00                Iter   6   47.62%  Refine biparts1164 MB(7%)00:00:00                Iter   6   52.38%  Refine biparts1164 MB(7%)00:00:00                Iter   6   57.14%  Refine biparts1164 MB(7%)00:00:00                Iter   6   61.90%  Refine biparts1164 MB(7%)00:00:00                Iter   6   66.67%  Refine biparts1164 MB(7%)00:00:00                Iter   6   71.43%  Refine biparts1164 MB(7%)00:00:00                Iter   6   76.19%  Refine biparts1164 MB(7%)00:00:00                Iter   6   80.95%  Refine biparts1164 MB(7%)00:00:00                Iter   6   85.71%  Refine biparts1164 MB(7%)00:00:00                Iter   6   90.48%  Refine biparts1164 MB(7%)00:00:00                Iter   6   95.24%  Refine biparts1164 MB(7%)00:00:00                Iter   6  100.00%  Refine biparts1164 MB(7%)00:00:00                Iter   6  104.76%  Refine biparts1164 MB(7%)00:00:00                Iter   6  100.00%  Refine biparts
#> 1164 MB(7%)00:00:00                Iter   7    9.52%  Refine biparts1164 MB(7%)00:00:00                Iter   7   14.29%  Refine biparts1164 MB(7%)00:00:00                Iter   7   19.05%  Refine biparts1164 MB(7%)00:00:00                Iter   7   23.81%  Refine biparts1164 MB(7%)00:00:00                Iter   7   28.57%  Refine biparts1164 MB(7%)00:00:00                Iter   7   33.33%  Refine biparts1164 MB(7%)00:00:00                Iter   7   38.10%  Refine biparts1164 MB(7%)00:00:00                Iter   7   42.86%  Refine biparts1164 MB(7%)00:00:00                Iter   7   47.62%  Refine biparts1164 MB(7%)00:00:00                Iter   7   52.38%  Refine biparts1164 MB(7%)00:00:00                Iter   7   57.14%  Refine biparts1164 MB(7%)00:00:00                Iter   7   61.90%  Refine biparts1164 MB(7%)00:00:00                Iter   7   66.67%  Refine biparts1164 MB(7%)00:00:00                Iter   7   71.43%  Refine biparts1164 MB(7%)00:00:00                Iter   7   76.19%  Refine biparts1164 MB(7%)00:00:00                Iter   7   80.95%  Refine biparts1164 MB(7%)00:00:00                Iter   7   85.71%  Refine biparts1164 MB(7%)00:00:00                Iter   7   90.48%  Refine biparts1164 MB(7%)00:00:00                Iter   7   95.24%  Refine biparts1164 MB(7%)00:00:00                Iter   7  100.00%  Refine biparts1164 MB(7%)00:00:00                Iter   7  104.76%  Refine biparts1164 MB(7%)00:00:00                Iter   7  100.00%  Refine biparts
#> 1164 MB(7%)00:00:00                Iter   8    9.52%  Refine biparts1164 MB(7%)00:00:00                Iter   8   14.29%  Refine biparts1164 MB(7%)00:00:00                Iter   8   19.05%  Refine biparts1164 MB(7%)00:00:00                Iter   8   23.81%  Refine biparts1164 MB(7%)00:00:00                Iter   8   28.57%  Refine biparts1164 MB(7%)00:00:00                Iter   8   33.33%  Refine biparts1164 MB(7%)00:00:00                Iter   8   38.10%  Refine biparts1164 MB(7%)00:00:00                Iter   8   42.86%  Refine biparts1164 MB(7%)00:00:00                Iter   8   47.62%  Refine biparts1164 MB(7%)00:00:00                Iter   8   52.38%  Refine biparts1164 MB(7%)00:00:00                Iter   8   57.14%  Refine biparts1164 MB(7%)00:00:00                Iter   8   61.90%  Refine biparts1164 MB(7%)00:00:00                Iter   8   66.67%  Refine biparts1164 MB(7%)00:00:00                Iter   8   71.43%  Refine biparts1164 MB(7%)00:00:00                Iter   8   76.19%  Refine biparts1164 MB(7%)00:00:00                Iter   8   80.95%  Refine biparts1164 MB(7%)00:00:00                Iter   8   85.71%  Refine biparts1164 MB(7%)00:00:00                Iter   8   90.48%  Refine biparts1164 MB(7%)00:00:00                Iter   8   95.24%  Refine biparts1164 MB(7%)00:00:00                Iter   8  100.00%  Refine biparts1164 MB(7%)00:00:00                Iter   8  104.76%  Refine biparts1164 MB(7%)00:00:00                Iter   8  100.00%  Refine biparts
#> 1164 MB(7%)00:00:00                Iter   9    9.52%  Refine biparts1164 MB(7%)00:00:00                Iter   9   14.29%  Refine biparts1164 MB(7%)00:00:00                Iter   9   19.05%  Refine biparts1164 MB(7%)00:00:00                Iter   9   23.81%  Refine biparts1164 MB(7%)00:00:00                Iter   9   28.57%  Refine biparts1164 MB(7%)00:00:00                Iter   9   33.33%  Refine biparts1164 MB(7%)00:00:00                Iter   9   38.10%  Refine biparts1164 MB(7%)00:00:00                Iter   9   42.86%  Refine biparts1164 MB(7%)00:00:00                Iter   9   47.62%  Refine biparts1164 MB(7%)00:00:00                Iter   9   52.38%  Refine biparts1164 MB(7%)00:00:00                Iter   9   57.14%  Refine biparts1164 MB(7%)00:00:00                Iter   9   61.90%  Refine biparts1164 MB(7%)00:00:00                Iter   9   66.67%  Refine biparts1164 MB(7%)00:00:00                Iter   9   71.43%  Refine biparts1164 MB(7%)00:00:00                Iter   9   76.19%  Refine biparts1164 MB(7%)00:00:00                Iter   9   80.95%  Refine biparts1164 MB(7%)00:00:00                Iter   9   85.71%  Refine biparts1164 MB(7%)00:00:00                Iter   9   90.48%  Refine biparts1164 MB(7%)00:00:00                Iter   9   95.24%  Refine biparts1164 MB(7%)00:00:00                Iter   9  100.00%  Refine biparts1164 MB(7%)00:00:00                Iter   9  104.76%  Refine biparts1164 MB(7%)00:00:00                Iter   9  100.00%  Refine biparts
#> 1164 MB(7%)00:00:00                Iter  10    9.52%  Refine biparts1164 MB(7%)00:00:00                Iter  10   14.29%  Refine biparts1164 MB(7%)00:00:00                Iter  10   19.05%  Refine biparts1164 MB(7%)00:00:00                Iter  10   23.81%  Refine biparts1164 MB(7%)00:00:00                Iter  10   28.57%  Refine biparts1164 MB(7%)00:00:00                Iter  10   33.33%  Refine biparts1164 MB(7%)00:00:00                Iter  10   38.10%  Refine biparts1164 MB(7%)00:00:00                Iter  10   42.86%  Refine biparts1164 MB(7%)00:00:00                Iter  10   47.62%  Refine biparts1164 MB(7%)00:00:00                Iter  10   52.38%  Refine biparts1164 MB(7%)00:00:00                Iter  10   57.14%  Refine biparts1164 MB(7%)00:00:00                Iter  10   61.90%  Refine biparts1164 MB(7%)00:00:00                Iter  10   66.67%  Refine biparts1164 MB(7%)00:00:00                Iter  10   71.43%  Refine biparts1164 MB(7%)00:00:00                Iter  10   76.19%  Refine biparts1164 MB(7%)00:00:00                Iter  10   80.95%  Refine biparts1164 MB(7%)00:00:00                Iter  10   85.71%  Refine biparts1164 MB(7%)00:00:00                Iter  10   90.48%  Refine biparts1164 MB(7%)00:00:00                Iter  10   95.24%  Refine biparts1164 MB(7%)00:00:00                Iter  10  100.00%  Refine biparts1164 MB(7%)00:00:00                Iter  10  104.76%  Refine biparts1164 MB(7%)00:00:00                Iter  10  100.00%  Refine biparts
#> 1164 MB(7%)00:00:00                Iter  11    9.52%  Refine biparts1164 MB(7%)00:00:00                Iter  11   14.29%  Refine biparts1164 MB(7%)00:00:00                Iter  11   19.05%  Refine biparts1164 MB(7%)00:00:00                Iter  11   23.81%  Refine biparts1164 MB(7%)00:00:00                Iter  11   28.57%  Refine biparts1164 MB(7%)00:00:00                Iter  11   33.33%  Refine biparts1164 MB(7%)00:00:00                Iter  11   38.10%  Refine biparts1164 MB(7%)00:00:00                Iter  11   42.86%  Refine biparts1164 MB(7%)00:00:00                Iter  11   47.62%  Refine biparts1164 MB(7%)00:00:00                Iter  11   52.38%  Refine biparts1164 MB(7%)00:00:00                Iter  11   57.14%  Refine biparts1164 MB(7%)00:00:00                Iter  11   61.90%  Refine biparts1164 MB(7%)00:00:00                Iter  11   66.67%  Refine biparts1164 MB(7%)00:00:00                Iter  11   71.43%  Refine biparts1164 MB(7%)00:00:00                Iter  11   76.19%  Refine biparts1164 MB(7%)00:00:00                Iter  11   80.95%  Refine biparts1164 MB(7%)00:00:00                Iter  11   85.71%  Refine biparts1164 MB(7%)00:00:00                Iter  11   90.48%  Refine biparts1164 MB(7%)00:00:00                Iter  11   95.24%  Refine biparts1164 MB(7%)00:00:00                Iter  11  100.00%  Refine biparts1164 MB(7%)00:00:00                Iter  11  104.76%  Refine biparts1164 MB(7%)00:00:00                Iter  11  100.00%  Refine biparts
#> 1164 MB(7%)00:00:00                Iter  12    9.52%  Refine biparts1164 MB(7%)00:00:00                Iter  12   14.29%  Refine biparts1164 MB(7%)00:00:00                Iter  12   19.05%  Refine biparts1164 MB(7%)00:00:00                Iter  12   23.81%  Refine biparts1164 MB(7%)00:00:00                Iter  12   28.57%  Refine biparts1164 MB(7%)00:00:00                Iter  12   33.33%  Refine biparts1164 MB(7%)00:00:00                Iter  12   38.10%  Refine biparts1164 MB(7%)00:00:00                Iter  12   42.86%  Refine biparts1164 MB(7%)00:00:00                Iter  12   47.62%  Refine biparts1164 MB(7%)00:00:00                Iter  12   52.38%  Refine biparts1164 MB(7%)00:00:00                Iter  12   57.14%  Refine biparts1164 MB(7%)00:00:00                Iter  12   61.90%  Refine biparts1164 MB(7%)00:00:00                Iter  12   66.67%  Refine biparts1164 MB(7%)00:00:00                Iter  12   71.43%  Refine biparts1164 MB(7%)00:00:00                Iter  12   76.19%  Refine biparts1164 MB(7%)00:00:00                Iter  12   80.95%  Refine biparts1164 MB(7%)00:00:00                Iter  12   85.71%  Refine biparts1164 MB(7%)00:00:00                Iter  12   90.48%  Refine biparts1164 MB(7%)00:00:00                Iter  12   95.24%  Refine biparts1164 MB(7%)00:00:00                Iter  12  100.00%  Refine biparts1164 MB(7%)00:00:00                Iter  12  104.76%  Refine biparts1164 MB(7%)00:00:00                Iter  12  100.00%  Refine biparts
#> 1164 MB(7%)00:00:00                Iter  13    9.52%  Refine biparts1164 MB(7%)00:00:00                Iter  13   14.29%  Refine biparts1164 MB(7%)00:00:00                Iter  13   19.05%  Refine biparts1164 MB(7%)00:00:00                Iter  13   23.81%  Refine biparts1164 MB(7%)00:00:00                Iter  13   28.57%  Refine biparts1164 MB(7%)00:00:00                Iter  13   33.33%  Refine biparts1164 MB(7%)00:00:00                Iter  13   38.10%  Refine biparts1164 MB(7%)00:00:00                Iter  13   42.86%  Refine biparts1164 MB(7%)00:00:00                Iter  13   47.62%  Refine biparts1164 MB(7%)00:00:00                Iter  13   52.38%  Refine biparts1164 MB(7%)00:00:00                Iter  13   57.14%  Refine biparts1164 MB(7%)00:00:00                Iter  13   61.90%  Refine biparts1164 MB(7%)00:00:00                Iter  13   66.67%  Refine biparts1164 MB(7%)00:00:00                Iter  13   71.43%  Refine biparts1164 MB(7%)00:00:00                Iter  13   76.19%  Refine biparts1164 MB(7%)00:00:00                Iter  13   80.95%  Refine biparts1164 MB(7%)00:00:00                Iter  13   85.71%  Refine biparts1164 MB(7%)00:00:00                Iter  13   90.48%  Refine biparts1164 MB(7%)00:00:00                Iter  13   95.24%  Refine biparts1164 MB(7%)00:00:00                Iter  13  100.00%  Refine biparts1164 MB(7%)00:00:00                Iter  13  104.76%  Refine biparts1164 MB(7%)00:00:00                Iter  13  100.00%  Refine biparts
#> 1164 MB(7%)00:00:00                Iter  14    9.52%  Refine biparts1164 MB(7%)00:00:00                Iter  14   14.29%  Refine biparts1164 MB(7%)00:00:00                Iter  14   19.05%  Refine biparts1164 MB(7%)00:00:00                Iter  14   23.81%  Refine biparts1164 MB(7%)00:00:00                Iter  14   28.57%  Refine biparts1164 MB(7%)00:00:00                Iter  14   33.33%  Refine biparts1164 MB(7%)00:00:00                Iter  14   38.10%  Refine biparts1164 MB(7%)00:00:00                Iter  14   42.86%  Refine biparts1164 MB(7%)00:00:00                Iter  14   47.62%  Refine biparts1164 MB(7%)00:00:00                Iter  14   52.38%  Refine biparts1164 MB(7%)00:00:00                Iter  14   57.14%  Refine biparts1164 MB(7%)00:00:00                Iter  14   61.90%  Refine biparts1164 MB(7%)00:00:00                Iter  14   66.67%  Refine biparts1164 MB(7%)00:00:00                Iter  14   71.43%  Refine biparts1164 MB(7%)00:00:00                Iter  14   76.19%  Refine biparts1164 MB(7%)00:00:00                Iter  14   80.95%  Refine biparts1164 MB(7%)00:00:00                Iter  14   85.71%  Refine biparts1164 MB(7%)00:00:00                Iter  14   90.48%  Refine biparts1164 MB(7%)00:00:00                Iter  14   95.24%  Refine biparts1164 MB(7%)00:00:00                Iter  14  100.00%  Refine biparts1164 MB(7%)00:00:00                Iter  14  104.76%  Refine biparts1164 MB(7%)00:00:00                Iter  14  100.00%  Refine biparts
a <- aln$ali
rownames(a) <-  maize_ara$phylo_id
tr <- mltree(a)$tree
#> optimize edge weights:  -3293.606 --> -3027.366 
#> optimize edge weights:  -3027.366 --> -3027.366 
#> optimize edge weights:  -3027.366 --> -3027.366
plot(phangorn::midpoint(tr), cex = 0.7)

If we want to be rigorous, and of course we want, in view of these results there is little, if anything, to conclude with respect to orthology relationships between maize and arabidopsis GS proteins. So, it’s time to switch to a more suitable approach. Firstly, we will use the function orthG(), which takes as argument the set of species to be included in the analysis and return an orthology graph: two nodes (two GS proteins) are connected if and only if they are orthologs (also an adjacency matrix is provided if wished).

orthG(c("Zea mays", "Arabidopsis thaliana"))

Arabidopsis and maize don’t share GS orthologs: the 12 proteins are paralogs between them

Let’s now include the rice in the set of species to be analyzed:

orthG(c("Zea mays", "Arabidopsis thaliana", "Oryza sativa"))

As you can appreciate, the enzyme Osa_GS1b_1 is orthologous to the maize Zm_GS1b_4. Furthermore, rice and maize share a few orthologs, but arabidopsis has no orthologs neither in rice nor maize.

A function slightly different from the one we have just used, which you might find useful on occasion is orthP(). Let’s see it in action:

x <- orthP(phylo_id = "Zm_GS1b_4", set = "all")
plot(x[[1]], tip.color = x[[2]], cex = 0.7)

In red, the GS protein whose ortholgs we are searching for. In blue, the proteins detected as ortholgs in other plant species.

While Zm_GS1b_4 is orthologous of any GS1b from gymnosperms, among the angiosperms we only find three orthologs: Atr_GS1b_2, Sly_GS1b2 and Osa_GS1b_1. To decode which species are Atr, Sly and Osa, we proceed as follows:

speciesGS(c("Atr", "Sly", "Osa"))
#>   input               output
#> 1   Atr Amborella trichopoda
#> 2   Sly Solanum lycopersicum
#> 3   Osa         Oryza sativa

- Orthologs from crop in model plants and vice versa