Table II.
Parallels in gene expression between tracheary element differentiation in Z. elegans and strawberry development and ripening
| Z. elegans Gene | Referencea | Strawberry (PRI Clone) | Homolog Definition (GenBank Accession No.) (E Value)b | Ratioc
|
||
|---|---|---|---|---|---|---|
| R:G | R:W | R:T | ||||
| Activation of protein synthesis apparatus and dedifferentiation | ||||||
| ZeRPS | Fukuda (1997) | F187 | 40S Ribosomal protein S13 (AB043974) (3e-54) | 0.9 | 1.5 | 2.6 |
| ZeRPS3a | C23 | 60S Ribosomal protein L13E (AJ132537) (6e-60) | 10.6 | 2.1 | 2.9 | |
| ZeRPPO | H88 | QM-like protein (AF295636) (1e-52) | 2.7 | 1.8 | 2.2 | |
| ZeEF1β | Fukuda (1997) | C197 | Elongation factor 1α (1) (AJ223969) (3e-69) | 4.0 | 1.5 | 1.7 |
| TED4 | Fukuda (2000) | B90 | Lipid transfer protein (2) (X79604) (4e-18) | 1.3 | 3.8 | 1.7 |
| TED 63.30 | L.T. Koonce (1995d) | B105 | Nuclear protein (AL357612) (2e-11) | 0.7 | 1.5 | 2.4 |
| Changes in cytoskeleton including actin reorganization | ||||||
| ZeTub1,2 | Yoshimura et al. (1996) | G84 | Beta-tubulin (1) (D63138) (3e-80) | 12.5 | 6.5 | 1.5 |
| H54 | Alpha-tubulin (2) (U12589) (2e-66) | 3.4 | 2.3 | 1.8 | ||
| Ngr | C122 | Profilin (AF129427) (4e-49) | 13.9 | 8.2 | 1.8 | |
| Ngr | H78 | Annexin (AF188832) (3e-59) | 2.5 | 3.5 | 1.2 | |
| Primary and secondary cell wall metabolism | ||||||
| ZePel | Domingo et al. (1998) | D86 | Pectate lyase (1) (U63550) (3e-78) | 4.8 | 0.8 | 0.6 |
| ZeExp1,2,3 | Im et al. (2000) | F39 | Expansin (1) (AF159563) (3e-28) | 23.3 | 1.6 | 1.2 |
| Ngr | Fukuda (1997e) | D56 | Extensin (2) (AF026382) (3e-43) | 6.5 | 0.5 | 0.6 |
| ZePG1 | Y. Ohdaira et al. (2001d) | D15 | Polygalacturonase (2) (U20431) (1e-19) | 4.0 | 1.2 | 0.6 |
| Phenylpropanoid pathway and lignification | ||||||
| ZCAD1 | Fukuda (2000) | F122 | Cinnamyl ADH (1) (U63534) (8e-57) | 4.3 | 5.2 | 3.5 |
| F138 | Cinnamyl ADH (2) (D13991) (3e-65) | 4.2 | 3.5 | 1.5 | ||
| F193 | Cinnamyl ADH (3) (U63534) (2e-53) | 16.0 | 8.2 | 1.8 | ||
| Ngr | JB116 | CCR (1) (AJ295838) (3e-49) | 3.5 | 1.5 | 0.8 | |
| JB196 | CCR (2) (X79566) (1e-06) | 4.0 | 1.6 | 0.9 | ||
| CAOMT | Ye and Varner (1995) | F102 | O-methyl transferase (2) (AF220491) (1e-18) | 2.6 | 1.0 | 1.3 |
| Programmed cell death | ||||||
| ZCP-4 | Fukuda (1997) | C56 | Cys proteinase (3) (Z14028) (8e-42) | 4.1 | 1.3 | 1.0 |
| P48h-17 | Ye and Varner (1996) | JB202 | Cys proteinase (7) (Z99954) (3e-68) | 4.7 | 1.6 | 0.6 |
| TED2 | Fukuda (2000) | E149 | Quinone reductase-like protein (AL16372) (3e-36) | 3.3 | 3.7 | 1.8 |
| Ngr | Woffenden et al. (1988e) | JB75 | Ubiquitin (1) (U29159) (2e-81) | 4.9 | 0.9 | 1.5 |
| D53 | Ubiquitin extension protein (AJ223329) (7e-48) | 2.9 | 1.3 | 1.4 | ||
Report on expression of the corresponding gene in Z. elegans (depicted under Z. elegans Gene) during TE differentiation.
Definition, accession no. (nucleotide sequence), and E value (see Altschul et al., 1990) of the first BLAST X homolog. Not always the described strawberry cDNA shows first homology to the corresponding Z. elegans gene in the BLAST search result. The no. in parentheses following the putative definitions represents the no. of the sequence contig in the case when more than one sequence showed similar BLAST result but did not align in the sequence alignment.
Expression ratios obtained in first three microarray experiments comparing red versus green (R:G), red versus white (R:W), and red versus turning (R:T) stages of fruit development. Values depicted in bold represent significant changes in expression (see “Materials and Methods”). The processes depicted above each gene set (in bold) are known to occur during TE differentiation in Z. elegans.
Unpublished data (only sequence is currently available).
Cases in which protein activity has been reported or suggested but not expression of the corresponding gene (ngr, no gene reported). If no report on protein exists, the association with TE differentiation was suggested in this study.