HL10: Evolution of genome structure: what statistics can tell us about the biology of chromosomes (ISMB 2009)

Aaron Darling

Yersinia alignment computed with Mauve. The blog length distribution is approximately geometric, in agreement with Nadeau and Taylor’s random breakage. However, he thinks there is a lot of structure in the process, even if we get a pattern that suggests uniform breakage. In order to transfer the alignment into phylogeny, you need to encode homologous segments as a signed gene-order matrix. They used the BADGER software, which uses Bayesian MCMC.

The resulting consensus network is a consensus of 30,000 sampled tree topologies.The Bayesian topology method says some things are unresolvable. May clades agree. Inversion branch lengths are very different to SNP branches. Seevolution is an interactive program that can visualise the process of evolution via inversion, etc.

Bacteria have bilateral genomic symmetry, if you want to call it that. Genes can be encoded on either the leading or lagging strand. Highly-transcribed genes are generally transcribed from the leading strand. There’s also polarized motifs that are short and non-palindromic, and therefore have a directionality. Some motifs (AIMS) function in cell segregation and they point towards the last part of the chromosome to be copied. If the inversion were to happen in these AIMS, it could be very bad. Inversion events in bacteria are generally scattered across the chromosome. A breakpoint can be re-used or created anew for each inversion. Breakpoints near the origin of the replication are 5-6x more frequent than at the terminus of replication. Is this configuration driven by natural selection? Does the caonoical OriDif exist in other bacteria?

Inversion lengths tend to be short, but there are some long ones. 46.3% of inversions act within a single replichore and don’t affect balance. By definition, within-replichore inversions ar expected to be shorter than the inter-replichore. Within-replichore inversions are really short. Combinatorial inversion theory enables better sampling.

Allyson’s thoughts: I’m afraid much of this was over my head, and so there may be some glaring errors.

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Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else’s. I’m happy to correct any errors you may spot – just let me know!

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