Multigene phylogeny using single-copy core orthogroups

[maggimars]

True, most of them are on par with the transcriptomes in the other study- the P. cordata and P. jahnii transcriptomes are the two with the lowest proportion of genes in core orthogroups (but similar absolute number of genes in the core groups). I sequenced these two transcriptomes and the sequencing depth was much higher than the MMETSP sequencing and I used 100bp rather than 50bp sequencing. I think this is why there are more "genes" in these two transcriptomes than the others. I also sequenced the P.globosa 1528 transcriptome, but less aggressively.

This makes a lot of sense! Probably just need to incorporate that into your ultimate interpretation. It might make sense (now that we are talking about it) to include estimated BUSCO completeness for all the transcriptomes. It can be used to inform our interpretation.

The multigene phylogeny sounds like a great idea. Especially if we can compare it to some sort of 18S type tree (not sure what the standard protocol is with Phaeo land).

Re: half-baked, poorly articulated idea: I was thinking that for the upset plot instead of plotting the number of genes in the group potentially looking at the relative abundance in metaT / metaG space of each of the groupings (or perhaps normalized abundance for # of genes) for a given site. As in, sum the counts from the various genes into the groupings based on the figure in #2.

Originally posted by @halexand in https://github.com/maggimars/Tara-Phaeo/issues/7#issuecomment-756376370

[maggimars]

[maggimars]

• [x] get CDS sequences for E. hux (need outgroup for tree)
• [x] rerun orthofinder with E. hux (get SCGs for Phaeo+Ehux)
• [x] extract SCG sequences
• [x] do an alignment for each SCG
• [x] trim alignments + concatenate alignments
• [x] make tree

[maggimars]

lol... that was a lot of work for the topology to be exactly the same as the 18S tree

(based on 61 single-copy-orthologues present in all (including ehux))