Comment
doi: 10.1038/s41467-021-24129-1.
Reply to: "Re-evaluating the evidence for a universal genetic boundary among microbial species"
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- PMID: 34234115
- PMCID: PMC8263725
- DOI: 10.1038/s41467-021-24129-1
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Reply to: "Re-evaluating the evidence for a universal genetic boundary among microbial species"
Nat Commun.
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No abstract available
Conflict of interest statement
The authors declare no competing interests.
Figures
This figure showcases the result of processing a Blastn search of metagenomic short reads (each matching read is represented by a dot in main panel 1) against a reference MAG sequence recovered from the same metagenome (x-axis). 1 Main panel representing the reads recruited (mapped), placed by location (x-axis) and identity (y-axis) across the reference sequence. 2 Sequencing depth (or coverage) across the reference, i.e., how many reads map at each base pair position, in logarithmic scale. Bars lower than the average represent regions with fewer mapped reads, which denote gene content differences. 3 Identity histogram of mapped reads per unit of identity (light gray) and smoothed spline (black), in logarithmic scale. 4 Sequencing depth histogram. Peaks based on the sequencing depth revealed in panel 2 are automatically identified as skewed normal distributions (in red). The background of panels 1 and 3, and the line colors in panels 2 and 4, correspond to matches with identity above (dark blue) and below (light blue) a user-defined cutoff. By default, the identity cutoff is set to 95%. Note the area of sequence discontinuity denoted by a decrease, by more than one order of magnitude (x-axis, panel 3), in the number of reads mapping around 95% identity (red arrow) relative to reads mapping at >98% identity. ANIr is estimated based on reads in the dark blue area only and represents the average nucleotide identity of reads to the reference sequence. The MAG represents an uncultivated member of the Actinobacteria phylum that shows about 45% average amino acid (AAI) to Ilumatobacter coccineus, its closest related named species with available genome representative(s). The metagenome was obtained from a planktonic sample from 1000 m in the Gulf of Mexico.
A reference genome representing the thaumarchaeotal population at 4000-m depth in the Pacific Ocean was queried against the previously described metagenomes from six different depths of the Pacific Ocean and the Gulf of Mexico (our unpublished data). A Range in nucleotide identities between the metagenomic read sequences and the genome, represented as letter-value plots, and their vertical line the median (x axis), plotted against the depth that the metagenomic sequences were recovered from (y axis). B Read recruitment representation for selected comparisons performed [the uppermost box-plot in the panel A represents the distribution of sequence identity values of the reads against the reference genome shown in the leftmost plot in the panel B. The plots in panel B are similar to the low, left panel of Fig. 1 but the data points (representing mapped reads) have been binned into a positional, hexagonal heatmap for demonstration purposes. Note that Thaumarchaeota are genetically distinct between different depths of the same water column (A) but genetically more similar across similar depths in geographically distant locations (B), and that if representative genomes or whole-populations from all depths are compared, they will show a range of ANI values between 89 and ~100% among themselves. Note also that the use of short Illumina reads tends to overestimate nucleotide identity (and thus ANIr values) compared to longer Sanger reads or whole/partial genomes used in our previous publications, especially for moderately identical sequences (e.g., in the range of 80–95% nucleotide identity), mostly due to inability of current read mapping algorithms to align such short sequences. Further, the mapping of metagenomic reads to the reference genome was performed with MegaBLAST, in contrast to Blastn in Fig. 1, and MegaBLAST is even less sensitive (but much faster) in finding reads of intermediate identity (e.g., in the range of 70–90% nucleotide identity) compared to Blastn. Therefore, the ANIr values shown are higher than our previous estimates for similar samples (or even Blastn-derived estimates based on the same metagenomic reads) due to this technical limitation, but the diversity patterns across depths remain similar.
Comment on
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High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries.Nat Commun. 2018 Nov 30;9(1):5114. doi: 10.1038/s41467-018-07641-9. Nat Commun. 2018. PMID: 30504855 Free PMC article.
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Re-evaluating the evidence for a universal genetic boundary among microbial species.Nat Commun. 2021 Jul 7;12(1):4059. doi: 10.1038/s41467-021-24128-2. Nat Commun. 2021. PMID: 34234129 Free PMC article. No abstract available.
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