title: Proteogenomics of rare taxonomic phyla: A prospective treasure trove of protein coding genes.
abstract: Sustainable innovations in sequencing technologies have resulted in a torrent of microbial genome sequencing projects. However, the prokaryotic genomes sequenced so far are unequally distributed along their phylogenetic tree; few phyla contain the majority, the rest only a few representatives. Accurate genome annotation lags far behind genome sequencing. While automated computational prediction, aided by comparative genomics, remains a popular choice for genome annotation, substantial fraction of these annotations are erroneous. Proteogenomics utilizes protein level experimental observations to annotate protein coding genes on a genome wide scale. Benefits of proteogenomics include discovery and correction of gene annotations regardless of their phylogenetic conservation. This not only allows detection of common, conserved proteins but also the discovery of protein products of rare genes that may be horizontally transferred or taxonomy specific. Chances of encountering such genes are more in rare phyla that comprise a small number of complete genome sequences. We collated all bacterial and archaeal proteogenomic studies carried out to date and reviewed them in the context of genome sequencing projects. Here, we present a comprehensive list of microbial proteogenomic studies, their taxonomic distribution, and also urge for targeted proteogenomics of underexplored taxa to build an extensive reference of protein coding genes.
authors.affiliation: G. N. Ramachandran Knowledge Center of Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Delhi, India.
authors.forename: Dhirendra
authors.initials: D
authors.lastname: Kumar
authors.affiliation: G. N. Ramachandran Knowledge Center of Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Delhi, India.
authors.forename: Anupam Kumar
authors.initials: AK
authors.lastname: Mondal
authors.affiliation: G. N. Ramachandran Knowledge Center of Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Delhi, India.
authors.forename: Rintu
authors.initials: R
authors.lastname: Kutum
authors.affiliation: G. N. Ramachandran Knowledge Center of Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Delhi, India.
authors.forename: Debasis
authors.initials: D
authors.lastname: Dash
mesh_terms: D019843:Archaeal Proteins / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics*; D022761:Gene Transfer, Horizontal; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D006801:Humans; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D010802:Phylogeny; D020543:Proteome / Q000235:genetics*; D040901:Proteomics
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D020543:Proteome
keywords: Archaea; Bacteria; Gene prediction; Genome annotation; Microbiology; Phylogeny