Highly asymmetric rice genomes

BMC Genomics

Table 2 Statistics of genes in genome, chromosome 10 and four gene groups.

Gene group^a	Symmetric or asymmetric	Known function^b	Multigene family^c	Clustered genes^c	Total
Inserts in Table 1
In Nipponbare	P/A	13	3	1	20
	P/A_d	43	56	8	56
	AL	37	46	11	56
In 93-11	P/A	45	1	0	62
	P/A_d	23	35	6	35
	AL	72	36	9	100
	Total asy.-genes	233	177	35	329
Chromosome 10
Genes in Nip.	Symmetric^d			284	2,572
	P/A	40(18)	2(1)	0(0)	56(26)
	P/A_d	49(31)	64(45)	2(1)	64(45)
	AL	32(23)	17(12)	2(2)	49(40)
	ND^e				80
Genes in 93-11	Symmetric^d				2,556
	P/A	46(30)	15(11)	5(4)	68(48)
	P/A_d	49(40)	72(60)	2(2)	72(60)
	AL	37(24)	11(4)	1(0)	46(31)
	ND^e				6
	Total asy.-genes	253(166)	181(133)	12(9)	355(250)
Gene family R-gene	Symmetric	339	35	132	339
	P/A	105	0	57	105
	P/A_d	42	42	37	42
	AL	116	38	88	116
	Total asy.-genes	263	80	182	263
	Total
RLK	Symmetric	264	99	111	264
	P/A	17	4	10	17
	AL	102	60	72	102
	Total asy.-genes	119	64	82	119
Myb&MADS	Symmetric	200	26	22	200
	P/A	6	0	ND	6
	AL	4	2	0	4
	Total asy.-genes	10	2	0	10

^a Asymmetric genes include P/A, P/A_d and AL genes. The genes in unknown function, in single gene families and in non-clustered genes are equal to the total number of genes subtracts the genes in known function, in multigene families and in clustered genes, respectively.
^b The genes in the group of function known are determined by GO (gene ontology) classification.
^c The definition of multigene or clustered gene is described in Methods.
^d The symmetric genes between Nipponbare and 93-11 should be equal. However when an allele is a pseudogene, we still classify this gene into symmetric group because it has an allelic sequence. Therefore the numbers are not equal; the numbers in parentheses represent the P/A, P/A_d and AL genes identified by the first method (see Methods for details), respectively. Otherwise the numbers stand for the asymmetric genes identified by the second method.
^e ND, not determined by the incomplete genome sequences (mainly in 93-11).

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