![]() ![]() Codon frequency for selected amino acids in the GyrB proteins of E. Yet I stop right here because untangling these inversions/transpositions is beyond the scope of a blog post.įigure 2.2. ![]() It would be tricky but in principle possible to resolve the limited number of smaller inversions and transpositions along the evolutionary trajectory of the Nardonella quartet. This tentatively inferred branching order is also seen in a monogenic phylogenetic tree based on a single protein (see Figure 2.3 below). Already from such a 'quick 'n dirty' analysis of genome dotplots it is possible to infer that the ancestor of these four Nardonella isolates had at least two rRNA operons (free-living enterobacteria usually have ~5), while genomic inversions in two separate lineages with subsequent loss of one rRNA operon ‒ in both cases 'the other one' ‒ led to the isolates studied by Anbutsu et al. The same recombination has occurred in the pair NARPIN1 and NAREPO1 that appear as mirror images when projected onto NARSGI1: after inversion of ~88% of the genome between the two oppositely oriented rRNA operons in NARPIN1 one rRNA operon was lost in NAREPO1, the smaller genome (see here). coli lab strains MG1655 and W3110 (see here). Genomic inversions between rRNA operons are not that uncommon, a well-known case is the inversion in the E. This inversion took place between the two rRNA operons in NARSGI1 that are transcribed in opposite direction to each other, and was followed by loss of one rRNA operon in NARFRE1, the smaller genome of these two (red arrows/dotted lines in Figure 2.1). Micro-rearrangements (<1 kb) are not visible at the low resolution of the dotplot but it is apparent that an inversion of ~83% of the chromosome occurred in NARFRE1 (Fig. The ten-or-so gaps in the NARGSI1 (0.23 Mb) × NARFRE1 (0.2 Mb) dotplot in Figure 2.1 add up, roughly, to the ~30 kb difference in chromosome size of both isolates. Frontispiece: transmission electron microscopic image of Nardonella cells in the larval bacteriocyte. The direction of transcription of rRNA operons is indicated by red arrowheads positions of rRNA operons are indicated by red dotted lines (± 1 kb). In the hetero-comparisons, inverted diagonals indicate inversions and horizontally offset diagonals/inverted diagonals indicate transpositions of homologous regions. Self‑comparison (upper left) results in a straight diagonal while offset diagonal stretches indicate duplications. NARSGI1 sequence ("discontiguous megablast" option). ![]() The DNA sequences of Nardonella isolates NARSGI1, NAREPO1, NARRFE1, and NARPIN1 were "blasted" ( NCBI BLASTn) against the Nardonella sp. Dot plot comparison of four Nardonella sp. If you then consider that these Nardonella strains co-evolved with their present weevil hosts, that is, 'survived' the speciation of the latter from their common ancestor, it is mind-blowing how stable these genomes are over millions of years of constant 'editing' despite ongoing genome reduction.įigure 2.1. This high degree of synteny makes it intuitively clear that the four Nardonellas are isolates ‒ or if you wish: strains ‒ of one single bacterial species irrespective of how you prefer to define a 'bacterial species' (see our post on ' bacterial species'). Figure 2.1 shows that today the four genomes are still almost completely syntenic, that is, have much the same gene order that is only interrupted by very few indels (=insertions/deletions), inversions and transpositions (see legend to Fig. A similar process of losing more than 90% of the genome of an enterobacterial ancestor was ‒ and probably still is ‒ underway in Nardonella. Earlier, Moran and Mira had partially reconstructed the ~4 Mb genome of a hypothetical enterobacterial ancestor of the small Buchnera genomes (0.45‒0.65 Mb) by what could be aptly called ' in silico molecular archaeology'. As said in part 1, the genomes are tiny (0.2‒0.23 Mb) and contain ~200 open reading frames. paper (Figure 1.2 in part 1, or here), is so stuffed with information about the weevils' Nardonella endosymbiont genomes that I better tear it apart a little to show you that it is actually possible to observe genome reduction 'at work'. Yet, do not take this as peer-reviewed scientific work, it's just a finger exercise.įigure 2 in the Anbutsu et al. Here now I give you a summary of what I read. When I was drafting part 1 of the weevil–Nardonella story, the symbiosis aspect, I could hardly wait to take a deeper look at the endosymbiont genomes, literally 'reading' the annotated genomes. ![]()
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