Appendix S1. Phylogenetic analysis of tomato TF families in comparison with
Arabidopsis TF families
In an attempt to reveal tomato specificity as well as the significance of certain genes
during fruit development and ripening a phylogenetic analysis was carried out on the
basis of protein sequences using Arabidopsis TF sequences as comparison (Figure S4
– S6). We first focused on the “early response” AP2-EREBP family genes, because this
is one of the most significantly changing families of TFs during fruit development and
ripening (a total 26.0% of genes of this family were altered, see Table S1), which were
clustered into 15 sub-groups (Nakano et al., 2006) (Figure S4). In sub-family group
Aintegumenta-like, one gene which increased during fruit development and ripening
(J0048) was the homologous gene of At5g10510 (PLT3) in Arabidopsis (Table S1). In
Arabidopsis, PLT3 was reported as a regulator of different facets of plant development
such as floral growth (Krizek, 2009) and root initiation (Galinha et al., 2007). Sub-family
group IX is potentially a tomato specific cluster, given that 13 tomato genes of a total of
17 genes were clustered in this sub-family. In sub-family VIII, gene expression of J0065
and J0066 significantly increased during fruit development. A BLAST search indicated
that At5g51190 was the Arabidopsis homolog of both tomato genes. At5g51190 was
reported to be a growth related TF gene, since its expression was up-regulated in the
sweetie mutant affected in carbohydrate metabolism and defective in the control of
growth, development and senescence (Veyres et al., 2008). Sub-family group IV
represents the DREB sub-family. This sub-family includes DREB2A and DREB2B which
are involved in response to water stress (Sakuma et al., 2006b) and drought (Sakuma et
al., 2006a). Expression of the tomato gene J0035, which is a member of the DREB subfamily, increased during fruit development and ripening. Whilst SlAP2 was not on our
platform, a homologous gene (J0062) increased during ripening as would perhaps, be
anticipated on the basis of studies of SlAP2 (Chung et al., 2010; Vrebalov et al., 2002).
Figure S5 shows the phylogenetic analysis of the NAC gene family (Hu et al.,
2010) as an example of “late response”. In Arabidopsis, NAC genes have diverse
functions in apical meristem formation, tissue development (Kunieda et al., 2008;
Raman et al., 2008; Willemsen et al., 2008), senescence (Balazadeh et al., 2010; Kim et
al., 2009; Yabuta et al., 2010), secondary wall formation (Ohashi-Ito et al., 2010) and
flavonoid biosynthesis (Morishita et al., 2009) besides others. In the phylogenetic
analysis shown in Figure S5, many genes in the sub-family of NAC-d were significantly
increased. In the NAC-d sub-family, a sub-cluster including ANAC018 (At1g52880) and
ANAC056 (At3g15510), tomato NAC genes J0813, J0814 and J0824 were considerably
affected during ripening. On the basis of work in Arabidopsis, this sub-cluster includes
embryogenesis related genes (Kunieda et al., 2008). A further NAC cluster containing
ANAC103 (At5g64060) and ANAC82 (At5g09330), as well as two tomato NACs (J0828
and J0831) which both showed a significantly increased expression during fruit ripening.
This cluster is suggested as development related given that ANAC82 regulates xylem
vessel formation in Arabidopsis (Yamaguchi et al., 2010). In addition, J0820 is a
homologous gene of At5g04410 (ANAC78) which is a known regulator of flavonoid
biosynthesis (Morishita et al., 2009). The gene expression of J0820 also increased
significantly during fruit ripening.
The functions of some MYB TFs have been well-characterized in Arabidopsis
being regulators of secondary metabolism (Borevitz et al., 2000; Hirai et al., 2007;
Stracke et al., 2007; Zhou et al., 2007) meristem initiation (Byrne et al., 2002; Keller et
al., 2006; Muller et al., 2006) and stress tolerance (Ding et al., 2009; Hemm et al., 2001;
Mengiste et al., 2003). Figure S6 represents the phylogenetic analysis of the tomato
MYB family in comparison to Arabidopsis. These analyses included tomato MYBs which
are homologous genes of those in Arabidopsis which affect the metabolism of flavonoids
(J0730 and J0737) and phenylpropanoids (J0724). The expression of these homologous
genes did not change during ripening. However, expression of several tomato MYBs
including J0691, J0707, J0712 and J0703 increased during breaker stage. The tomato
homologous gene to AtMYB4, a negative regulator of phenylpropanoid synthesis (Hemm
et al., 2001), is decreased after breaker stage (J0708). By contrast the homologue to
AtMYB39 (At4g17785) and AtMYB91 (At2g37630), J0703 increased after breaker stage.
AtMYB91 is an auxin related regulator for asymmetric leaf growth (Morimoto et al.,
2009).
Literature:
Balazadeh, S., Siddiqui, H., Allu, A.D., Matallana-Ramirez, L.P., Caldana, C.,
Mehrnia, M., Zanor, M.I., Kohler, B. and Mueller-Roeber, B. (2010) A gene regulatory
network controlled by the NAC transcription factor ANAC092/AtNAC2/ORE1 during saltpromoted senescence. Plant J., 62, 250-264.
Borevitz, J.O., Xia, Y.J., Blount, J., Dixon, R.A. and Lamb, C. (2000) Activation
tagging identifies a conserved MYB regulator of phenylpropanoid biosynthesis. Plant
Cell, 12, 2383-2393.
Byrne, M.E., Simorowski, J. and Martienssen, R.A. (2002) ASYMMETRIC LEAVES1
reveals knox gene redundancy in Arabidopsis. Development, 129, 1957-1965.
Chung, M.Y., Vrebalov, J., Alba, R., Lee, J., McQuinn, R., Chung, J.D., Klein, P. and
Giovannoni, J. (2010) A tomato (Solanum lycopersicum) APETALA2/ERF gene,
SlAP2a, is a negative regulator of fruit ripening. Plant J., 64, 936-947.
Ding, Z.H., Li, S.M., An, X.L., Liu, X.J., Qin, H.M. and Wang, D. (2009) Transgenic
expression of MYB15 confers enhanced sensitivity to abscisic acid and improved
drought tolerance in Arabidopsis thaliana. J. Genet. Genomics, 36, 17-29.
Galinha, C., Hofhuis, H., Luijten, M., Willemsen, V., Blilou, I., Heidstra, R. and
Scheres, B. (2007) PLETHORA proteins as dose-dependent master regulators of
Arabidopsis root development. Nature, 449, 1053-1057.
Hemm, M.R., Herrmann, K.M. and Chapple, C. (2001) AtMYB4: a transcription factor
general in the battle against UV. Trends Plant Sci., 6, 135-136.
Hirai, M.Y., Sugiyama, K., Sawada, Y., Tohge, T., Obayashi, T., Suzuki, A., Araki, R.,
Sakurai, N., Suzuki, H., Aoki, K., Goda, H., Nishizawa, O.I., Shibata, D. and Saito, K.
(2007) Omics-based identification of Arabidopsis Myb transcription factors regulating
aliphatic glucosinolate biosynthesis. Proc. Natl. Acad. Sci. U. S. A., 104, 6478-6483.
Hu, R.B., Qi, G.A., Kong, Y.Z., Kong, D.J., Gao, Q.A. and Zhou, G.K. (2010)
Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus
trichocarpa. Bmc Plant Biology, 10, 23.
Keller, T., Abbott, J., Moritz, T. and Doerner, P. (2006) Arabidopsis REGULATOR OF
AXILLARY MERISTEMS1 controls a leaf axil stem cell niche and modulates vegetative
development. Plant Cell, 18, 598-611.
Kim, J.H., Woo, H.R., Kim, J., Lim, P.O., Lee, I.C., Choi, S.H., Hwang, D. and Nam,
H.G. (2009) Trifurcate Feed-Forward Regulation of Age-Dependent Cell Death Involving
miR164 in Arabidopsis. Science, 323, 1053-1057.
Krizek, B.A. (2009) AINTEGUMENTA and AINTEGUMENTA-LIKE6 Act Redundantly to
Regulate Arabidopsis Floral Growth and Patterning. Plant Physiol., 150, 1916-1929.
Kunieda, T., Mitsuda, N., Ohme-Takagi, M., Takeda, S., Aida, M., Tasaka, M.,
Kondo, M., Nishimura, M. and Hara-Nishimura, I. (2008) NAC Family Proteins
NARS1/NAC2 and NARS2/NAM in the Outer Integument Regulate Embryogenesis in
Arabidopsis. Plant Cell, 20, 2631-2642.
Mengiste, T., Chen, X., Salmeron, J. and Dietrich, R. (2003) The BOTRYTIS
SUSCEPTIBLE1 gene encodes an R2R3MYB transcription factor protein that is required
for biotic and abiotic stress responses in Arabidopsis. Plant Cell, 15, 2551-2565.
Morimoto, R., Nishioka, E., Murai, K. and Takumi, S. (2009) Functional conservation
of wheat orthologs of maize rough sheath1 and rough sheath2 genes. Plant Molecular
Biology, 69, 273-285.
Morishita, T., Kojima, Y., Maruta, T., Nishizawa-Yokoi, A., Yabuta, Y. and Shigeoka,
S. (2009) Arabidopsis NAC Transcription Factor, ANAC078, Regulates Flavonoid
Biosynthesis under High-light. Plant Cell Physiol., 50, 2210-2222.
Muller, D., Schmitz, G. and Theres, K. (2006) Blind homologous R2R3 Myb genes
control the pattern of lateral meristem initiation in Arabidopsis. Plant Cell, 18, 586-597.
Nakano, T., Suzuki, K., Fujimura, T. and Shinshi, H. (2006) Genome-wide analysis of
the ERF gene family in Arabidopsis and rice. Plant Physiol., 140, 411-432.
Ohashi-Ito, K., Oda, Y. and Fukuda, H. (2010) Arabidopsis VASCULAR-RELATED
NAC-DOMAIN6 Directly Regulates the Genes That Govern Programmed Cell Death and
Secondary Wall Formation during Xylem Differentiation. Plant Cell, 22, 3461-3473.
Raman, S., Greb, T., Peaucelle, A., Blein, T., Laufs, P. and Theres, K. (2008)
Interplay of miR164, CUP-SHAPED COTYLEDON genes and LATERAL SUPPRESSOR
controls axillary meristem formation in Arabidopsis thaliana. Plant J., 55, 65-76.
Sakuma, Y., Maruyama, K., Osakabe, Y., Qin, F., Seki, M., Shinozaki, K. and
Yamaguchi-Shinozaki, K. (2006a) Functional analysis of an Arabidopsis transcription
factor, DREB2A, involved in drought-responsive gene expression. Plant Cell, 18, 12921309.
Sakuma, Y., Maruyama, K., Qin, F., Osakabe, Y., Shinozaki, K. and YamaguchiShinozaki, K. (2006b) Dual function of an Arabidopsis transcription factor DREB2A in
water-stress-responsive and heat-stress-responsive gene expression. Proceedings of
the National Academy of Sciences, 103, 18822-18827.
Stracke, R., Ishihara, H., Barsch, G.H.A., Mehrtens, F., Niehaus, K. and Weisshaar,
B. (2007) Differential regulation of closely related R2R3-MYB transcription factors
controls flavonol accumulation in different parts of the Arabidopsis thaliana seedling.
Plant J., 50, 660-677.
Veyres, N., Danon, A., Aono, M., Galliot, S., Karibasappa, Y.B., Diet, A.,
Grandmottet, F., Tamaoki, M., Lesur, D., Pilard, S., Boitel-Conti, M., SangwanNorreel, B.S. and Sangwan, R.S. (2008) The Arabidopsis sweetie mutant is affected in
carbohydrate metabolism and defective in the control of growth, development and
senescence. Plant J., 55, 665-686.
Vrebalov, J., Ruezinsky, D., Padmanabhan, V., White, R., Medrano, D., Drake, R.,
Schuch, W. and Giovannoni, J. (2002) A MADS-box gene necessary for fruit ripening
at the tomato ripening-inhibitor (Rin) locus. Science, 296, 343-346.
Willemsen, V., Bauch, M., Bennett, T., Campilho, A., Wolkenfelt, H., Xu, J.,
Haseloff, J. and Scheres, B. (2008) The NAC Domain Transcription Factors FEZ and
SOMBRERO Control the Orientation of Cell Division Plane in Arabidopsis Root Stem
Cells. Dev. Cell, 15, 913-922.
Yabuta, Y., Morishita, T., Kojima, Y., Maruta, T., Nishizawa-Yokoi, A. and Shigeoka,
S. (2010) Identification of recognition sequece of ANAC078 protein by the cyclic
amplification and selection of targets technique. Plant Signaling & Behavior, 5, 3.
Yamaguchi, M., Ohtani, M., Mitsuda, N., Kubo, M., Ohme-Takagi, M., Fukuda, H.
and Demura, T. (2010) VND-INTERACTING2, a NAC Domain Transcription Factor,
Negatively Regulates Xylem Vessel Formation in Arabidopsis. Plant Cell, 22, 12491263.
Zhou, L., Zeng, H., Shi, M. and Xie, D. (2007) Establishment of transgenic
anthocyanin-producing tissue culture over-expressing a R2R3-MYB trascriptional factor.
Plant Biology (Rockville), 2007, 130-131.