Table II.

Parallels in gene expression between tracheary element differentiation in Z. elegans and strawberry development and ripening

Z. elegansGeneReference2-aStrawberry (PRI Clone)Homolog Definition (GenBank Accession No.) (E Value)2-bRatio2-c
Activation of protein synthesis apparatus and dedifferentiation
 ZeRPS Fukuda (1997) F18740S Ribosomal protein S13 (AB043974) (3e-54)0.91.5 2.6
 ZeRPS3aC2360S Ribosomal protein L13E (AJ132537) (6e-60) 10.6 2.1 2.9
 ZeRPPOH88QM-like protein (AF295636) (1e-52) 2.7 1.8 2.2
 ZeEF1β Fukuda (1997) C197Elongation factor 1α (1) (AJ223969) (3e-69) 4.0 1.51.7
 TED4 Fukuda (2000) B90Lipid transfer protein (2) (X79604) (4e-18)1.3 3.8 1.7
 TED 63.30L.T. Koonce (19952-d)B105Nuclear protein (AL357612) (2e-11)0.71.5 2.4
Changes in cytoskeleton including actin reorganization
 ZeTub1,2 Yoshimura et al. (1996) G84Beta-tubulin (1) (D63138) (3e-80) 12.5 6.5 1.5
H54Alpha-tubulin (2) (U12589) (2e-66) 3.4 2.31.8
 NgrC122Profilin (AF129427) (4e-49) 13.9 8.2 1.8
 NgrH78Annexin (AF188832) (3e-59)2.5 3.5 1.2
Primary and secondary cell wall metabolism
 ZePel Domingo et al. (1998) D86Pectate lyase (1) (U63550) (3e-78) 4.8 0.80.6
 ZeExp1,2,3 Im et al. (2000) F39Expansin (1) (AF159563) (3e-28) 23.3 1.61.2
 Ngr Fukuda (1997 2-e)D56Extensin (2) (AF026382) (3e-43) 6.5 0.50.6
 ZePG1Y. Ohdaira et al. (20012-d)D15Polygalacturonase (2) (U20431) (1e-19) 4.0 1.20.6
Phenylpropanoid pathway and lignification
 ZCAD1 Fukuda (2000) F122Cinnamyl ADH (1) (U63534) (8e-57) 4.3 5.2 3.5
F138Cinnamyl ADH (2) (D13991) (3e-65) 4.2 3.5 1.5
F193Cinnamyl ADH (3) (U63534) (2e-53) 16.0 8.2 1.8
 NgrJB116CCR (1) (AJ295838) (3e-49) 3.5 1.50.8
JB196CCR (2) (X79566) (1e-06) 4.0 1.60.9
 CAOMT Ye and Varner (1995) F102 O-methyl transferase (2) (AF220491) (1e-18) 2.6 1.01.3
Programmed cell death
 ZCP-4 Fukuda (1997) C56Cys proteinase (3) (Z14028) (8e-42) 4.1 1.31.0
 P48h-17 Ye and Varner (1996) JB202Cys proteinase (7) (Z99954) (3e-68) 4.7 1.60.6
 TED2 Fukuda (2000) E149Quinone reductase-like protein (AL16372) (3e-36) 3.3 3.7 1.8
 Ngr Woffenden et al. (1988 2-e)JB75Ubiquitin (1) (U29159) (2e-81) 4.9 0.91.5
D53Ubiquitin extension protein (AJ223329) (7e-48) 2.9 1.31.4
  • F2-a  Report on expression of the corresponding gene in Z. elegans (depicted under Z. elegans Gene) during TE differentiation.

  • F2-b  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.

  • F2-c  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.

  • F2-d  Unpublished data (only sequence is currently available).

  • F2-e  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.