The Wolbachia Holy Grail: loci behind CI

This obscure alpha-proteobacterium, named Wolbachia, was first discovered because of the weird ways in which it messed with insect reproduction - everything from parthenogenesis induction to male killing to the most common of effects, so-called "cytoplasmic incompatibility." In this case, Wolbachia somehow prevents uninfected females and infected males from mating. Ever since it was first described by Hertig and Wolbach back in 1924, folks have been trying to figure out the how of CI.  At the Wolbachia 2016 meetings, it seems like someone(s) has finally cracked that nut.  <DISCLAIMER: I am actually sitting on my ass in my home office and not at the #Wolb2016 meetings as they are in Australia and I'm allergic to traveling to Australia. However, I heard on the twitter that> Seth Bordenstein + Daniel LePage and John Beckman presented data on two loci - WD0631 and WD0632 - which  may be behind CI. It seems like these loci, when co-expressed in an uninfected male background, cause CI-like phenotype (not sure how much like CI - if this is just embryonic death or fecundity decrease) when crossed to an uninfected female.  Interestingly, though, this is rescued by crossing the same male (expressing the two transgenes) in an infected female (again, I don't know the extent or the phenotype in the embryos).

Now, Wolbachia is known to rescue some developmental abnormalities (see interactions between Wolbachia and sex lethal here) but this is the first time that transgenic expression of a Wolbachia gene(s) has been shown to induce a CI-like phenotype. Those folks that think lots about the mathematical models that may explain the patterns of CI across Wolbachia (the "lock and key" or "mod and rescue" models of Wolbachia CI induction) would be thinking about these loci as maybe the lock or the mod component. Immediately I started to think about some hypotheses you might have if these are in fact CI-related.

1) You should find homologs in all sequenced genomes of variants that cause CI
2) You should not find these homologs in genomes where the Wolbachia do not cause CI (that is debatable*)
3) The extent of expression of these genes should correlate with the extent of CI (stronger driven transgene, for example, should result in fewer progeny)
4) Homologs from incompatible Wolbachia should not rescue each other (if you express the strain A homolog, it should not be rescued by strain B, for example).
*maybe these homologs are behind other reproductive phenotypes as well and host genotype modulates this

Given that I am just sitting on my tuckus, and just wanted to shoot the proverbial shit for a while about this neat result, I will instead tackle the assumptions #1 and #2 above.

We (read: Danny W. Rice in my group) generated a database of orthologous groups using the publicly available Wolbachia genomes and reciprocal blast.  Here's a phylogeny, generated from a concatenated alignment of orthologs across these genomes:

Clearly the arthropod Wolbachia are more heavily represented than the others.  When I look for homologs to WD0631 and WD0632 in this dataset, here's what we find:

Table 1. Genes that are homologous to WD0631, a predicted CI-inducing gene, across Wolbachia genomes.

Genome	Locus
wVitA-gwv	gwv_142
wPipPel	WP_RS01410
wRi	WRI_RS02675
wSim (629 contigs)	WwSim0304
wHa	WHA_RS01435
wPip-JHB (21 contigs)	C1A_1302
wMel	WD_RS02835
wMelPop (80 contigs)	WMELPOP_03523
wGmm (201 contigs)	WGMM_RS02015
wBol1-b (144 contigs)	WBOL1_RS02195

Table 2. Genes that are homologous to WD0632, a predicted CI-inducing gene, across Wolbachia genomes.  

Genome	Locus
wVitA-gwv	gwv_141
wPipPel	WP_RS01415
wHa	WHA_RS01430
wPip-JHB (21 contigs)	C1A_1299
wMel	WD_RS02840
wMelPop (80 contigs)	WMELPOP_03528
wBol1-b (144 contigs)	WBOL1_RS02190
valsugana (110 contigs)	ON35_RS04655

So, when you look at these tables some trends seem to emerge that might, at first glance, seem to address our assumptions 1 and 2.  For example, both of these homologs are not found across all CI inducing strains - where are wRi and wSim's WD0632 homologs? Also, not all of these strains cause CI exclusively - check out wBol1, the male-killing Wolbachia from Hypolimnas bolina.  You could also include wBm's Wbm0463 in the WD0632 homolog list, although it is a more distant homolog as well.  I haven't had the chance yet to dig into the meat of this dataset but there are some interesting results so far.  For those Wolbachia researchers reading this, comments below welcomed.

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Thoughts after back-and-forths on the twitter-sphere:
1st - I would definitely agree that this discovery in no way claims to be the only mechanism behind CI and there could be many others, variations on this theme or highly divergent
2nd - Your definition of "homolog" most assuredly would change this list - I have posted stringent orthologs from a reciprocal blast search - removing paralogs within genomes (of which there are plenty).
3nd - Thanks to Greg Hurst for clarifying that wBol1 causes CI as well as male-killing (altered in text now).