Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signatures

Iandolino, Alberto; Nobuta, Kan; da Silva, Francisco Goes; Cook, Douglas R; Meyers, Blake C

doi:10.1186/1471-2229-8-53

Table 4 Grape ESTs derived from distinct tissue types matched by MPSS signatures (only from Vitis vinifera).

From: Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signatures

Categories	Contigs
A. EST contigs.
Berry pre-veraison	79
Berry veraison	117
Berry post-veraison	359
Subtotal berry	555
Compound bud	87
Flower	132
Seed	1
Petiole	63
Stem	67
Leaf	332
Roots	5
Subtotal from single organ library (excluding berry libraries)	687
Subtotal from single organ library ^a	1,242
2-Organs	1,520
3-Organs	1,084
4-Organs	763
5-Organs	491
6-Organs	312
7-Organs	181
8-Organs	135
9-Organs	46
All 10 sampled organs	10
Subtotal from multiple organ libraries ^b	4,542
Subtotal non-ESTs	6
Total matched contigs and non-EST sequences	5,791
Total matched contigs not previously associated with any berry library^c	1,038
Total matched contigs previously associated with berry libraries^f	4,753
A. Total matched contigs from other grape berry libraries^d	3,439
B. Total matched contigs with ≥1 EST derived from stage II berry libraries^e	1,314
Total unmatched contigs and non-EST sequences	7,567
C. Total unmatched contigs from all libraries except (D)	6,990
D. Total unmatched contigs corresponding to UCD stage II berry libraries^h	577
B. EST singletons.
Categories	Contigs
Berry pre-veraison	177
Berry veraison	343
Berry post-veraison	389
Subtotal berry	909
Compound bud	45
Flower	231
Seed	16
Petiole	34
Stem	89
Leaf	414
Roots	49
Subtotal from other libraries (excluding berry libraries)	878
Total matched singletons	1,787
A. Total matched singletons with ≥ 1 EST derived from stage II berry libraries	207
Total unmatched singletons	9,754
B. Total unmatched singletons from all libraries except (D)	8,947
C. Total unmatched singletons corresponding to UCD stage II berry libraries	807

Only 7,686 distinct, reliable and significant, 17-base MPSS signatures were used in this analysis.
^a Matched contigs with at least one EST derived from berry libraries excluding those from UCD. Berry libraries in this category include multiple developmental stages and growing conditions [4].
^b Matched contigs with ESTs found in cDNA libraries originated from at least two or more different grapevine organs. It may or may not simultaneously include berry libraries.
^cIndicates matched contigs assembled with ESTs not previously associated with berry libraries
^dIndicates matched contigs assembled with ESTs not previously associated with the UCD flower-berry libraries. This number includes contigs with at least one EST derived from flower-berry libraries reported by other groups.
^e Indicates contigs containing at least one EST produced from the flower-berry UCD libraries [4].
^fCorresponds to the sum of A and B.
^gTotal number of contigs and non-ESTs sequences [4] not matched by 17-mer reliable and significant tags. This value corresponds to the sum of C and D.
^h Contigs with at least one EST derived from SII berry libraries [4] but not matched by 17-mer reliable and significant tags.

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ISSN: 1471-2229

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