Abstract
Nucleotide composition (GC content) varies across bacteria species, genome regions, and specific genes. In Xylella fastidiosa, a vector-borne fastidious plant pathogen infecting multiple crops, GC content ranges between ∼51-52%; however, these values were gathered using limited genomic data. We evaluated GC content variations across X. fastidiosa subspecies fastidiosa (N = 194), subsp. pauca (N = 107), and subsp. multiplex (N = 39). Genomes were classified based on plant host and geographic origin; individual genes within each genome were classified based on gene function, strand, length, ortholog group, core vs accessory, and recombinant vs non-recombinant. GC content was calculated for each gene within each evaluated genome. The effects of genome and gene-level variables were evaluated with a mixed effect ANOVA, and the marginal-GC content was calculated for each gene. Also, the correlation between gene-specific GC content vs natural selection (dN/dS) and recombination/mutation (r/m) was estimated. Our analyses show that intra-genomic changes in nucleotide composition in X. fastidiosa are small and influenced by multiple variables. Higher AT-richness is observed in genes involved in replication and translation, and genes in the leading strand. In addition, we observed a negative correlation between high-AT and dN/dS in subsp. pauca. The relationship between recombination and GC content varied between core and accessory genes. We hypothesize that distinct evolutionary forces and energetic constraints both drive and limit these small variations in nucleotide composition.
Highlights
GC content variations are more readily observed within the accessory genome Core and accessory genome sizes varied within X. fastidiosa subspecies and in the other phytopathogens examined (Table 1)
It should be noted that the shell genome has the widest range in relation to the percentage of strains sharing a given gene (15–95%). It can potentially cover a wider range of gene presence/absence variations compared with the soft-core and the cloud genomes
Our results indicate that GC content has dropped in X. fastidiosa compared with its closest relative
Summary
The relevance of nucleotide composition (GC content) in genome evolution has been well established from a genomics (Arndt et al 2005; Amit et al 2012; Smarda et al 2014; Mugal et al 2015; Almpanis et al 2018), ecological (Bolhuis et al 2006; Smarda et al 2014; Luo et al 2015), and biological perspective (Mann and Chen 2010; Udaondo et al 2016; Bohlin et al 2017; Du et al 2018; Castillo et al 2019a). One mechanism is GC-biased gene conversion (gBGC), which refers to a repair bias favoring GC over AT alleles during recombination (Galtier et al 2001) This mechanism describes how highly recombinant genome regions, or organisms where recombination is more frequent, tend to be more GC-rich (Lassalle et al 2015; Romiguier and Roux 2017). The GC content of substituted bases (sbGC) has been found to be GC biased compared with the GC content of the core genome in most microbial genomes (except for those highly GC-rich) This trend has been proposed to be linked to natural selection countering the C/G to T/A transitional bias universally observed in microbial genomes (Bohlin et al 2018)
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