Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing

Schlueter, Jessica A; Lin, Jer-Young; Schlueter, Shannon D; Vasylenko-Sanders, Iryna F; Deshpande, Shweta; Yi, Jing; O'Bleness, Majesta; Roe, Bruce A; Nelson, Rex T; Scheffler, Brian E; Jackson, Scott A; Shoemaker, Randy C

doi:10.1186/1471-2164-8-330

BMC Genomics

Table 2 Duplicate gene homeology/paralogy between BAC pairs

From: Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing

BAC homeologs	Putative function	# of exons	Coding length^a	Nucleotide identity	Protein identity	Protein similarity	Ks	Ka	Date (Mya)
gmw1-74i13 gmw1-52d3	^b	^b	^b	89.8	88.0	90.7	0.1490	0.0335	12.2
gmw1-105h23 gmw1-15k6	^d	^d	^d	90.7	88.9	90.4	0.1061	0.0326	8.70
UMb001-24d13	DNA binding	6	1338	92.7	88.7	92.2	0.1177	0.0468	9.65
UMb001-5f5	DNA binding	7	1473
UMb001-24d13	Gamma response I	9	987	95.9	95.7	96.3	0.1405	0.0152	11.52
UMb001-5f5	Gamma response I	9	984
UMb001-24d13	Selenium binding	4	1881	56.3	54.6	56.4	0.1709	0.0575	14.01
UMb001-5f5	Selenium binding	5	585
gmw1-103e11	A. thaliana-like NAP	7	510	96.4	95.8	97.2	0.0933	0.0188	7.65
gmw1-5g16	A. thaliana-like NAP	7	1002
gmw1-103e11	Beta-fructofuranosidase	6	1944	94.4	92.7	94.1	0.0716	0.0276	5.87
gmw1-5g16	Beta-fructofuranosidase	6	1956
gmw1-103e11	Galactinol synthase	4	732	90.5	93.5	94.7	0.3208	0.0316	26.30
gmw1-5g16	Galactinol synthase	3/4	669/987
gmw1-103e11	RAD-like protein	6/7	564/900	96.9	92.9	97.6	0.0432	0.0442	3.54
gmw1-5g16	RAD-like protein	5	240
gmw2-133d1	GTPase	14	3183	96.9	98.1	99.1	0.1055	0.0084	8.65
gmw1-93l19	GTPase	16	3480
gmw2-133d1	Cellulose synthase	9	2211	67.6	65.1	67.0	0.1109	0.0438	9.09
gmw1-93l19	Cellulose synthase	5	924
gmw2-133d1	Chain A protein	1	1608	81.1	76.4	80.1	0.1856	0.077	15.21
gmw1-93l19	Chain A protein	1	1452
gmw1-13o17	Raffinose synthase	5	2277	66.4	71.5	81.5	2.5495	0.2051	208.98
gmw1-8g7	Raffinose synthase	6	2190
gmw1-57d24	Phospholipase C	8	1308	80.5	78.7	87.6	0.5457	0.114	44.73
gmw1-58k3	Phospholipase C	8	1299
gmw1-57d24	COMT	5	747	79.7	79.0	88.3	0.6442	0.1204	52.80
gmw1-58k3	COMT	4/5	615/354
gmw1-58k3	COMT	4/5	615/354	73.6	76.3	87.7	1.7076	0.1667	139.97
gmw1-27d20	COMT	5	744
gmw1-58k3	Otubain	6	1992	53.7	42.5	53.3	4.024	0.3023	329.84
gmw1-27d20	Otubain	7	1860
gmw1-57d24	CBS	6/8	399/687	74.9	73.7	89.5	2.0095	0.1562	164.71
gmw1-27d20	CBS	8	678
gmw1-57d24	COMT	5	747	74.1	81.6	91.0	1.5875	0.1196	130.12
gmw1-27d20	COMT	5	744
	Average			*86.6*	*85.4*	*88.8*	*0.4239*	*0.0577*	*34.75*
	Recalculated average 1 ^d			89.8	88.2	90.1	0.1179	0.0341	9.665
	Recalculated average 2 ^e			71.8	71.9	82.7	1.8668	0.1691	153

^a Coding length in base pairs based upon CDS (from start to stop not including introns).
^b The values for homeologs between gmw1-74i13 and gmw1-52d3 are previously reported (Schlueter et al. 2006). Identity, similarity, Ks, Ka and Dates shown are average across BACs.
^c The values for homeologs between gmw1-105h23 and gmw1-15k6 are previously reported (Schlueter et al. 2007). Identity, similarity, Ks, Ka and Dates shown are average across BACs.
^d Recalculated average not including the highly divergent homeologs from gmw1-13o17, gmw1-8g7, gmw1-57d24, gmw1-58k3 and gmw1-27d20.
^e Recalculated average for just the highly divergent homeologs from gmw1-13o17, gmw1-8g7, gmw1-57d24, gmw1-58k3 and gmw1-27d24.

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