Tandem duplication events in the expansion of the small heat shock protein gene family in Solanum lycopersicum (cv. Heinz 1706)

Abstract

ABSTRACTIn plants, fruit maturation and oxidative stress can induce small heat shock protein (sHSP) synthesis to maintain cellular homeostasis. Although the tomato reference genome was published in 2012, the actual number and functionality of sHSP genes remain unknown. Using a transcriptomic (RNA-seq) and evolutionary genomic approach, putative sHSP genes in the Solanum lycopersicum (cv. Heinz 1706) genome are investigated. A sHSP gene family of 33 members is established. Remarkably, roughly half of themembers of this family can be explained by nine independent tandem duplication eventsthat evolutionarily determined their functional fates. Within a mitochondrial class subfamily, only one duplicated member, Solyc08g078700, retained its ancestral chaperonefunction, while the others, Solyc08g078710 and Solyc08g078720,likely degenerated under neutrality and lack ancestral chaperone function. Functional conservation occurred within a cytosolic class I subfamily, whose four members, Solyc06g076570, Solyc06g076560, Solyc06g076540 and Solyc06g076520, support ~57% of the total sHSP RNAm in the red ripe fruit. Sub-functionalization occurred within a new subfamily, whose twomembers, Solyc04g082720 and Solyc04g082740, show heterogeneous differential expressionprofiles during fruit ripening. These findings, involving the birth/death of some genes or the preferential/plastic expression of some others during fruit ripening, highlight the importance of tandem duplication events in the expansion of the sHSP gene family in the tomato genome. Despite its evolutionary diversity, the sHSP gene family in the tomato genome seems to be endowed with a core set of four homeostasis genes: Solyc05g014280, Solyc03g082420, Solyc11g020330 and Solyc06g076560, which appear to provide abaseline protection during both fruit ripening and heat shock stress in different tomato tissues.