include MAG in Orthogroups analysis

maggimars / Tara-Phaeo

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include MAG in Orthogroups analysis #5

Open maggimars opened 3 years ago

maggimars commented 3 years ago

See /vortexfs1/omics/alexander/share/formaggi for the genomic contigs, predicted coding sequences, and amino acid sequences :)

Originally posted by @halexand in https://github.com/maggimars/Tara-Phaeo/issues/2#issuecomment-754043352

maggimars commented 3 years ago

When TOPAZ_SAD1_E044 was added the orthofinder run, there were only 17 single-copy-core genes. A fasttree based on the 17 genes placed the mag between P. globosa and P. antarctica (the rest of the tree topology stayed the same as when the tree was based on 61 single-copy-core genes): phaeo_fasttree_wMAG nwk

maggimars commented 3 years ago

To Do:

[x] Single-gene trees for the tree above (17 sccg's) - is there one gene that is causing the MAG to pop out of the P. antarctica branch?
[ ] run orthofinder with the other good phaeo mags and rebuild the tree - TOPAZ_SAS3_E008 (31.37% BUSCO), and TOPAZ_SOD1_E001 (28.24%BUSCO)

maggimars commented 3 years ago

Well .... this one is probably a problem:

OG0009310_fasttree nwk

However, most of the other trees do place this MAG between Antarctica and globosa, and some trees have it in the globosa clade. Maybe if there were more strains included the Antarctica branch would be fuller and this MAG would sit in it instead of just above it. Or maybe there is a big of chimera action going on? Probably not enough data to speculate?

maggimars commented 3 years ago

As expected, making a tree with 16 sccgs instead of 17 and excluding that one really wonky gene did not make a big difference on the concatenated gene tree: phaeo_fasttree_nobadMAGgene nwk

Moving on to making a tree including all 3 mags

maggimars commented 3 years ago

AHHH NO single-copy core genes when I include all three MAGs in the orthofinder run .... @halexand do you recommend trying to include one mag at a time for the two additional mags?