title: Overlapping genes: A significant genomic correlate of prokaryotic growth rates.
abstract: Elucidating the genomic features influencing prokaryotic growth rates has always been a study of interest. Previously, it was observed that overlapping genes (OGs) play a crucial role in the prokaryotic genome size reduction. This study is focused to explore whether OGs act as a potential correlate of prokaryotic growth rates. For this purpose, we compiled a dataset of 25 archaeal and 117 eubacterial genomes and analyzed the inter-correlation between the proportion of overlapping regions in these genomes with their growth rates. Here, we observed that the proportion of overlapping region holds a significant negative correlation with generation time in archaeal domain, whereas no correlation was observed in the eubacterial domain. However, after masking the effect of tRNA, rRNA multiplicity and environmental diversity, OGs show an independent effect over growth rates in the eubacterial domain as well as in the archaeal domain. Moreover, the influence of OGs on prokaryotic growth rates provides different delineations in archaeal and eubacterial domains. In archaea, both long overlap frequency (LOF) and short overlap frequency (SOF) influence the growth rates by increasing the degree of operonization. On the contrary, in the case of bacteria, neither SOF nor LOF plays any significant role in achieving faster growth rates.
authors: Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India. Electronic address: deeya@jcbose.ac.in.
authors: Deeya
authors: D
authors: Saha
authors: Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India. Electronic address: soumita@jcbose.ac.in.
authors: Soumita
authors: S
authors: Podder
authors: Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India. Electronic address: arup@jcbose.ac.in.
authors: Arup
authors: A
authors: Panda
authors: Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India. Electronic address: tapash@jcbose.ac.in.
authors: Tapash Chandra
authors: TC
authors: Ghosh
mesh_terms: D001105:Archaea / Q000235:genetics* / Q000254:growth & development*; D001419:Bacteria / Q000235:genetics* / Q000254:growth & development*; D005807:Genes, Overlapping; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D013997:Time Factors
keywords: Archaea; Codon usage bias; Eubacteria; Generation time; Overlapping genes; rRNA multiplicity; tRNA multiplicity