The linear correlation between genome size and the size of the non-transcribing region

Abstract

BackgroundThe genome sizes of organisms vary widely (C-value paradox). There are non-transcribing regions in the genome that neither encode proteins nor RNA entities. There are several hypotheses about the function of these regions: one suggests that they are unannotated functional areas, while another views them as genomic isolation zones that reduce mutations in coding regions. MethodStatistical analysis was conducted on the transcribing regions (including areas annotated as genes and transcribed pseudogenes) and non-transcribing regions, protein-coding regions (Coding sequence, CDS), and genome sizes using annotation files from 63,866 species genomes in the NCBI RefSeq database. ResultsThere is a significant linear relationship between the size of non-transcribing genomic regions and overall genome size across species, with varying proportional coefficients among different phyla (realms for viruses). As genome size increases, the proportion of non-transcribing regions gradually rises, eventually approaching a linear proportional limit, resembling one arm of hyperbolic functions. Eukaryotes show high linear correlation, with the highest in Streptophyta and the lowest in Apicomplexa. In eukaryotes, the size of the coding region increases with genome size, but the increasing trend diminishes (proportionally decreases). In non-eukaryotes, the size of the coding region maintains a linear relationship with genome size. ConclusionThe size of non-transcribing region in species may be subject to some strict quantitative control mechanism, showing that genome and non-transcribing genome sizes increase proportionally with the expansion of the transcribing genome, indicating a strict balance between expansion and energy conservation. The proportion of non-transcribed genomes in eukaryotes is conservative (although the sequences are not), and the presence of non-transcribing genomes has significant implications for the evolution or survival of species. Thus, I propose a new hypothesis about the non-transcribing genome, that it is a space for generating new genes from scratch, and the different proportional coefficients among phyla are due to their different positions in energy transfer. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/613789v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@dc3e88org.highwire.dtl.DTLVardef@18d70e8org.highwire.dtl.DTLVardef@efb92corg.highwire.dtl.DTLVardef@66068b_HPS_FORMAT_FIGEXP M_FIG C_FIG