Noah SpencerJun 22, 2023

https://academic.oup.com/gbe/article/15/6/evad100/7189782

Living+evolving inside insect cells for millions of years can drive bacterial genomes to mind-boggling extremes. New paper in @GenomeBiolEvol asks what bacterial transcription looks like at the extremes of genome reduction (<200kb), genome fragmentation (40+ chromosomes/genomes!), and gene dosage imbalance (1:100+).

This is my first first-author paper and the first of my PhD w/ @mcsymbiont. I'm thrilled to have it finally out, + in one of my fav journals! Check it out!

No Transcriptional Compensation for Extreme Gene Dosage Imbalance in Fragmented Bacterial Endosymbionts of Cicadas

Abstract. Bacteria that form long-term intracellular associations with host cells lose many genes, a process that often results in tiny, gene-dense, and st

OUP Academic
Show threadMichael GemarJun 23, 2023
@noahspencer @ehud @GenomeBiolEvol @mcsymbiont So, if I’m understanding correctly, this bacteria species has essentially split into several independent “species” that each only carry a subset of the total needed genome? Wow — is this common to see in these sorts of symbionts?
Show threadJohn McCutcheonJun 23, 2023

@michaelgemar @noahspencer @ehud @GenomeBiolEvol

Yes, Michael, you've got it right (in the first paper describing this we called it "sympatric speciation" in the title). It's not common, although I would say it might just be a sampling bias at this point. I would be surprised if other symbionts don't do this, but so far none have.

There are other cases of genomes sort of blowing up into multiple chromosomes (some mitochondria do this) but these new chromosomes are not in new cells.

Show threadMichael GemarJun 23, 2023
@mcsymbiont @noahspencer @ehud @GenomeBiolEvol So this is the only known instance of this phenomenon? That’s fascinating (and presumably another asterisk on any straightforward definition of “species”).
Show threadJohn McCutcheonJun 23, 2023

@michaelgemar @noahspencer @ehud @GenomeBiolEvol

As far as I know, it's the only example in bacteria that has been proven so far (there is at least one other case with genome data suggesting its similar, but I am not sure about the cellular data).

It's mind bending, for sure. When we first found it, we really struggled with 'simple' labels (genome, lineage, species, population, etc.).

Show threadSmall Things ConsideredJun 27, 2023

@mcsymbiont @michaelgemar @noahspencer @ehud @GenomeBiolEvol

'lineage' is fine in this case imo.
would it not be pretty masochistic – not to say perverse – to enter into a hardcore debate of 'species' for Hodgkinia if this guy is on the road to perdition and maybe even gone before such a debate could be settled?

it's a beautiful work, noah & john et al., but so damn depressing to painstakingly document the demise of a symbiont rather than learning how it started.

Show threadMichael GemarJun 27, 2023
@STCmicrobeblog @mcsymbiont @noahspencer @ehud @GenomeBiolEvol I think the deeply interesting debate is not so much whether this lineage(s) of Hodgkinia is itself a species, but rather what it says about the species concept more generally.
Show threadNoah Spencer
@michaelgemar @STCmicrobeblog @mcsymbiont @ehud @GenomeBiolEvol The Hodgkinia case, while extreme, seems to me emblematic of a problem that's been growing for a long time, particularly in microbiology space. As Doolittle says, "the more we learn about genomes [...] the more unlikely it seems that any unifying species concept will be possible."
Jun 27, 2023 at 2:30pmWeb
Show threadMichael GemarJun 27, 2023
@noahspencer @STCmicrobeblog @mcsymbiont @ehud @GenomeBiolEvol Yep, which is why I find this so fascinating. The notion of species seems deeply embedded in our accounts of evolution, and genomes certainly seem to “clump” into groups of similar things, but the nature of that clumping sure seems more porous and stranger than a strictly orderly universe would provide. Biology is so delightfully “messy”.