Comparison of homoeolocus organisation in paired BAC clones from white clover (Trifolium repens L.) and microcolinearity with model legume species

Table 2 Measures of identity and similarity between homoeologous genes identified across four regions of the white clover genome

Gene	Putative function	Average exon nucleotide identity (%)	Average intron nucleotide identity (%)	Protein sequence identity (%)	Protein similarity (%)	Ks	Ka
A.5	Predicted protein 2	99.1	99.8	98.8	99	0.0019	0.0026
A.6	Predicted protein 3	99.1	100	98.3	99	0.0165	0.0074
A.7	Galactose oxidase	99.9	98.6	99.7	99.7	0	0.0011
A.10	Adenine phosphoribosyltransferase	100	99.8	100	100	0	0
A.11	ZPT2	97.1	-	97.9	98.4	0.0409	0.0022
B.5	Bristled 1	85.9	88.4	86.3	87.5	0.0797	0.0059
B.6	Ethylene insensitive 3	94.2^a
B.7	bZIP transcription factor	97.1	62.6	97.1	98.2	0.0715	0.0125
B.8	Acyl-CoA oxidase 2	98.4	86.8	99	99.6	0.0552	0.0046
B.9	Predicted protein 9	95.8	75.1	94.9	95.6	0.1019	0.0175
B.10	DREB3	96.8	-	97	98.4	0.1179	0.0127
C.7	SH3 domain-containing protein 2 (SH3P2)	98.7	82.6	98.9	99.4	0.0368	0.0051
C.8	MKRP2	98.5	92.2	99.3	99.7	0.0465	0.0062
C.9	Salt tolerance homolog 2	95.2	94.7	95.1	95.8	0.0586	0.0062
C.10	DHNb	96.8	85.2	97.2	98.2	0.1050	0.0099
C.11	Transcription factor/zinc-mediated transcriptional activator (SHL1)	90.7^a
D.2	Anthocyanidin reductase	97.8	83.7	98.8	99.1	0.0706	0.0039
D.3	Serine/threonine kinase	98.2	91.7	96.8	97.9	0.0252	0.0162
Average		97.15	88.66	97.19	97.84	0.0518	0.0071

^a Due to an unequal number of exons and introns within these homoeologues, nucleotide identity was calculated from the genomic sequence including both the exons and introns. Protein identity and similarity were not calculated.

ISSN: 1471-2229