TY - JOUR T1 - The mysterious orphans of <em>Mycoplasmataceae</em> JF - bioRxiv DO - 10.1101/025700 SP - 025700 AU - Tatiana V. Tatarinova AU - Inna Lysnyansky AU - Yuri V. Nikolsky AU - Alexander Bolshoy Y1 - 2015/01/01 UR - http://biorxiv.org/content/early/2015/08/28/025700.abstract N2 - Background The length of a protein sequence is largely determined by its function, i.e. each functional group is associated with an optimal size. However, comparative genomics revealed that proteins’ length may be affected by additional factors. In 2002 it was shown that in bacterium Escherichia coli and the archaeon Archaeoglobus fulgidus, protein sequences with no homologs are, on average, shorter than those with homologs [1]. Most experts now agree that the length distributions are distinctly different between protein sequences with and without homologs in bacterial and archaeal genomes. In this study, we examine this postulate by a comprehensive analysis of all annotated prokaryotic genomes and focusing on certain exceptions.Results We compared lengths’ distributions of “having homologs proteins” (HHPs) and “non-having homologs proteins” (orphans or ORFans) in all currently annotated completely sequenced prokaryotic genomes. As expected, the HHPs and ORFans have strikingly different length distributions in almost all genomes. As previously established, the HHPs, indeed, are, on average, longer than the ORFans, and the length distributions for the ORFans have a relatively narrow peak, in contrast to the HHPs, whose lengths spread over a wider range of values. However, about thirty genomes do not obey these rules. Practically all genomes of Mycoplasma and Ureaplasma have atypical ORFans distributions, with the mean lengths of ORFan larger than the mean lengths of HHPs. These genera constitute over 80% of atypical genomes.Conclusions We confirmed on a ubiquitous set of genomes the previous observation that HHPs and ORFans have different gene length distributions. We also showed that Mycoplasmataceae genomes have very distinctive distributions of ORFans lengths. We offer several possible biological explanations of this phenomenon.List of abbreviationsCOG -a cluster of orthologous groups of genes; each COG consists of groups of proteins found to be orthologous across at least three lineagesHHP -having homologs protein; here COG-annotated proteinORF –an open reading frameORFan –non-HHP; here a protein-encoding gene that is not linked to any COGCG content -relative frequency of guanine and cytosineCG3 content -relative frequency of guanine and cytosine in the 3rd position of a codon ER -