Table 1.

Statistical summary of the de novo and reference based assembly results

Sample ID*	Number of raw reads	Reference-guided assembled transcripts	De novo assembled transcripts	PASA alignment
Cortex1	28,688,674	54,198	33,909	29,533
Cortex2	34,602,978	51,586	29,001	25,339
Cortex3	29,332,631	49,470	26,746	23,988
Cortex4	30,473,993	49,434	26,909	23,799
Cortex5	27,773,042	49,387	26,249	23,456
Embryo3	13,580,328	46,827	21,362	19,547
Embryo4	22,817,240	52,203	28,728	25,371
Embryo5	20,596,516	50,390	26,655	24,038
Ghost3	20,131,210	53,322	31,702	28,050
Ghost4	24,729,472	54,355	33,985	29,612
Ghost5	21,893,808	52,645	30,382	27,037
Ovule1	28,983,033	53,794	34,796	30,060
Seed2	31,044,314	54,353	31,669	28,044
Pith1	26,828,710	53,968	33,015	28,971
Pith2	29,684,268	51,985	28,916	25,497
Pith3	32,039,484	50,854	28,047	24,757
Pith4	31,461,556	50,342	26,944	23,872
Pith5	35,919,060	51,016	27,727	24,411
Wall1	25,996,860	53,102	31,968	28,214
Wall2	29,527,238	53,552	32,761	28,780
Wall3	19,130,041	51,998	30,787	27,384
Wall4	27,737,593	52,606	31,071	27,423
Wall5	34,216,551	52,882	32,980	28,694
Leaf1	30,740,916	54,993	36,502	31,610
Seedling1	27,518,958	53,477	31,589	28,065
Total	685,448,474	1,302,739	754,400	665,552

*Sample name indicates tissue type and the number indicates stage (see Kang et al. [2]). Each sample reflects averaged data from two biological replicates. Sample descriptions are available at http://bioinformatics.towson.edu/strawberry/newpage/Tissue_Description.aspx.