A statistical analysis of the three-fold evolution of genomic compression through frame overlaps in prokaryotes

Biology Direct

Table 1 A few representative studies on overlapping genes, organized alphabetically with summary of principle conclusions and data type

Authors	Year	Genomes	IE	VE	SM	Genes & Homology	Evolutionary Process
Lillo & Krakauer	2007	58 Prokaryote	RC & TC	MA & MB	NS	Study of E. coli genome	Neutrality & Selection
Boi et al [2]	2004	? Eukaryote	GR	NS	NS	NS	Selection on regulation
Das & Yanofsky [3]	1989	1 Prokaryote	TC	NS	NS	Study of 2 genes	Selection on expression
Fukuda et al. [6]	1999	2 Prokaryote	NS	NS	NE	Study of 480 & 677 genes	Neutral mutation to stop codon
Fukuda et al [7]	2003	3 Prokaryote	NS	NS	NS	NS	Neutral mutation to stop and start
Johnson & Chisholm [13]	2004	198 Prokaryote	TC	NS	NS	Study of 2 genomes	Selection on expression
Krakauer [15]	2000	NS	RC & TC	MA	NS	NS	Selection on replication and expression
Krakauer [16]	2002	NS	RC & TC	MA & MB	NS	NS	Selection on replication and expression
Makalowska et al. [22]	2005	7 Eukaryote	GR	NS	NS	NS	Neutrality
Merino et al. [25]	1994	28 Prok & 8 Euk	GR	NS	NS	Study of E. coli genome	Selection on regulation
Miyata & Yasunaga [24]	1978	1 Prokaryote	NS	MA	NS	Study of -x174	Selection on replication
Normark et al. [26]	1983	? Prokaryote	TC	NS	NS	NS	Selection on expression
Oppenheim & Yanofsky [28]	1980	1 Prokaryote	TC	NS	NS	E. coli Trp operon	Selection on expression
Pavesi et al. [29]	1997	? Viral	NS	MB	IC	NS	Selection on coding
Rogozin et al. [30]	2002	? Prokaryotes	NS	MB	NS	NS	Selection on coding
Sakharkar et al [31]	2005	9 Prokaryotes	RC	NS	NS	Study of 2 genomes	Selection on replication
Sander & Schulz [32]	1979	2 Prokaryote	NS	MB	NS	Study of SV40 & -x174 genes	Selection on coding
Welch et al. [39]	2000	1 Prokaryote	TC	NS	NS	Study of V anguillarum	Selection for iron biosynthesis

Key: IE – Immediate Effect, VE – variational effect, SM – Statistical Model NS – Not in Study, TC – translational coupling, RC – replicative compression, GR antisense gene regulation MB – mutational buffering, MA – mutational amplification, NE – Neutral expectation under statistical model, IC – Shannon information content of overlap. The ? symbols records an unknown number lineages. The column labeled "Genes and detailed homology" captures the pattern of many studies to couple the statistics of large databases with the detailed analysis of a small number of overlapping genes from well studied genomes. The difference between selection on expression versus selection on regulation seeks to discriminate between co-expression (as in a codon) and active inhibition or activation (such as through anti-sense), The difference between selection on replication and selection on coding reflects a difference only in emphasis as both imply a greater number of genes in a shorter sequence.

ISSN: 1745-6150