Micromonas comparison

[maggimars]

SO far we have downloaded available micromonas transcriptomes and genomes and mapped the small-size fraction (0.8-5µm)Tara metaG and metaT reads to those references. We see different results from metaT v. metaG read mapping, but does not follow the same pattern as in Phaeo (i.e., metaT mapping to transcriptomes and metaG mapping to genomes). @rondorice please add these figures in a comment.

To do:

• [ ] get metaT and metaG salmon mapping rates and plot these overall rates on the world map for comparison with the species breakdown
• [ ] Check out the ratio of micromonas mapping rates to phaeo mapping rates for metaT v. metaG data
• [ ] Run BUSCO analysis on micromonas references - how complete is each reference? does the completeness
• [x] Run Orthofinder for micromonas references - look at species tree, how many shared orthologues between references?
• [x] run FastANI for micromonas (and phaeo) - what is the average nucleotide identity between references?

[rondorice]

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[maggimars]

which map is metaT and which is metaG?

[maggimars]

Based on 1,641 single-copy core genes:

[rondorice]

the top one (red prominent) is MetaG and bottom is metaT

[halexand]

Interesting. So, not to terribly closely related yet popping up between metaT and metaG variably.

[halexand]

This paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6299001/ might help provide some context. They also look at v9 abundance for these species. There isn't a 1:1 sort of graph, but it might be worth looking at the SI data to see if they have total abundances per station that we can compare against.

[rondorice]

[rondorice]

ANI heatmap^