Patterns and drivers of genome-wide codon usage bias in the fungal order Sordariales

We present a study on amino acid composition, codon usage bias (CUB), and levels of selection driving codon usage in Sordariales fungi. We found that GC-ending codons are used more often than AT-ending codons in all Sordariales genomes, but the strength of CUB differs amongst families. The families Podosporaceae and Sordariaceae contain relatively low genome-wide levels of CUB, while the highest levels of CUB are found in Chaetomiaceae and the "BLLNS" group, a monophyletic group of 5 other Sordariales families. Based on genomic clustering, we show that Podosporaceae and Sordariaceae are more similar to each other than either of them are to any of the other groups. Comparatively, the Chaetomiaceae and BLLNS show increased natural selection driving use of specific codons, resulting in higher genome-wide CUB. We hypothesize that the higher levels of CUB in Chaetomiaceae genomes might have been caused by ecological niche specialization, versus the more generalist nature of many Sordariaceae and Podosporaceae species.