Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins

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Figure 2.
Figure 2.

Large scale-identification of species-specific orphan genes (SSOGs) in the human gut microbiome. (A) The main steps of the computational workflow of similarity searches. (B) Distribution of the SSOG proportion in a given species’ pangenome. The red dashed line denotes the distribution mean. (C) SSOG number strongly correlates with the number of genomes available for a given species. (D) Distribution of percentage of genomes in which a gene is present for SSOGs and conserved genes. Only species with at least 10 genomes are included (n = 1369). The inset plot shows the same data but as relative proportion in each bin. (E) Distribution (60 bins) of the average pairwise omega (dN/dS) per family for SSOGs (solid black line), intraspecific alignments of conserved genes (orange), and three negative controls (for details, see Methods). The red line marks dN/dS = 1, which corresponds to neutral evolution.

This Article

  1. Published in Advance July 8, 2024, doi: 10.1101/gr.278977.124 Genome Res. 34: 888-903

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