Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding

Table 2 Single nucleotide variations statistics for the S. incanum and S. aethiopicum transcriptomes

SNVs intraspecific variations			INDELs	SNPs	Total SNVs
	S. incanum		535	11,861	12,396
		filtered	28	385
	S. aethiopicum		4,556	159,571	164,127
		filtered	312	5,804
	S. melongena		120	2,660	2,780
		filtered	6	57
	S. torvum		6,318	18,829	25,147
		filtered	26	90
SNVs interspecific variations			INDELs	SNPs	Total SNVs
	S. incanum and S. aethiopicum		586	14,576	15,162
		filtered	29	649
	S. incanum and S. melongena		3,673	102,104	105,777
		filtered	253	4,184
	S. incanum and S. torvum		96,799	491,965	588,764
		filtered	760	3,995
	S. aethiopicum and S. melongena		2,392	73,059	75,451
		filtered	165	3,277
	S. aethiopicum and S. torvum		83,106	420,685	503,791
		filtered	604	3,229
	S. melongena and S. torvum		92,323	464,071	556,394
		filtered	722	3,682
	S. incanum, S. aethiopicum and S. melongena		108	41	149
		filtered	8	2
	S. incanum, S. aethiopicum and S. torvum		908	198	1,106
		filtered	10	3
	S. incanum, S. melongena and S. torvum		8,022	1,265	9,287
		filtered	118	15
	S. aethiopicum, S. melongena and S. torvum		6,986	886	7,872
		filtered	102	12
	S. incanum, S. aethiopicum, S. melongena and S. torvum		50	0	50
		filtered	2	0

SNVs (SNPs and INDELs) have been identified by the Freebayes SNP caller. The interspecific and intraspecific variations, as well as all species combination, have been determined by filtering ID (identification) species number. Every species and species comparison present an unambiguous identification number. The INDELs have been separated from SNPs applying the VKF filter to the total SNVs. The filtered SNPs and INDELs have been obtained by adding the CS60, HV0.05, CL60 and CEF filters

ISSN: 1471-2164