In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure

BMC Research Notes

Table 1 Highest Volatility Candidates in Arabidopsis thaliana and dN/dS comparative sequence analysis to B. oleracea and A. lyrata

			Volatility Analysis	dN/dS Selection Analysis
			A. thaliana	A. thaliana vs B. oleraca		A. thaliana vs A. lyrata
Gene	Description	CDS (bp)	P-values	dN/dS	(%CDS)	dN/dS	(%CDS)
At1g62240	expressed protein	684	0.000000006			0.7975*	(100)
At1g64370	expressed protein	537	0.000000323			0.2567	(94)
At1g69440	PAZ domain-containing protein	2973	0.000008714	0.1098	(15)	0.0910	(93)
At2g27380	proline-rich family protein	2286	0.000000000			0.0412	(25)
At3g21420	oxidoreductase	1095			(22)	0.1173*	(88)
At3g21420	oxidoreductase	1095			(22)	0.0913	(84)
At3g28780	glycine-rich protein	1845				0.4217*	(95)
At3g28780	glycine-rich protein	1845				0.2545	(53)
At4g15430	early-responsive to dehydration	2271	0.000004120	0.3808	(17)
At4g31590	glycosyl transferase family 2	2079	0.000004420	0.2099	(29)	0.1028	(100)
At4g32420	peptidyl-prolyl cis-trans isomerase	2514	0.000005314			0.2893	(98)
At5g07570	glycine/proline-rich protein	4515	0.000001603			0.4833	(71)
At5g59990	expressed protein	726			(55)	0.1869*	(90)
						0.2227	(100)

The 11 most volatile genes in the A. thaliana genome with their corresponding volatility P- values (P < 10^-6). Conventional analyses using pairwise dN/dS ratios (CODEML M0 from PAML). Displayed are those comparisons that were possible between A. thaliana and homologous sequences, using shotgun sequencing reads (B. oleracea), close to full length sequences (A. lyrata) and four cloned genes (A. lyrata) marked by *.

ISSN: 1756-0500