Format

Send to

Choose Destination
Microb Genom. 2020 Mar 3. doi: 10.1099/mgen.0.000341. [Epub ahead of print]

An assessment of genome annotation coverage across the bacterial tree of life.

Author information

1
Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada.
2
Department of Biology, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON, Canada.

Abstract

Although gene-finding in bacterial genomes is relatively straightforward, the automated assignment of gene function is still challenging, resulting in a vast quantity of hypothetical sequences of unknown function. But how prevalent are hypothetical sequences across bacteria, what proportion of genes in different bacterial genomes remain unannotated, and what factors affect annotation completeness? To address these questions, we surveyed over 27 000 bacterial genomes from the Genome Taxonomy Database, and measured genome annotation completeness as a function of annotation method, taxonomy, genome size, 'research bias' and publication date. Our analysis revealed that 52 and 79 % of the average bacterial proteome could be functionally annotated based on protein and domain-based homology searches, respectively. Annotation coverage using protein homology search varied significantly from as low as 14 % in some species to as high as 98 % in others. We found that taxonomy is a major factor influencing annotation completeness, with distinct trends observed across the microbial tree (e.g. the lowest level of completeness was found in the Patescibacteria lineage). Most lineages showed a significant association between genome size and annotation incompleteness, likely reflecting a greater degree of uncharacterized sequences in 'accessory' proteomes than in 'core' proteomes. Finally, research bias, as measured by publication volume, was also an important factor influencing genome annotation completeness, with early model organisms showing high completeness levels relative to other genomes in their own taxonomic lineages. Our work highlights the disparity in annotation coverage across the bacterial tree of life and emphasizes a need for more experimental characterization of accessory proteomes as well as understudied lineages.

KEYWORDS:

bacterial genomics; functional annotation; gene function prediction; genome annotation; phylogenomics; tree of life

PMID:
32124724
DOI:
10.1099/mgen.0.000341
Free full text

Supplemental Content

Full text links

Icon for Ingenta plc
Loading ...
Support Center