Flavia J. Krsticevic, Débora P. Arce, Joaquín Ezpeleta, and Elizabeth Tapia

G3 (Genes, Genomes, Genetics) October 2016 6:3027-3034. (doi:10.1534/g3.116.032045)

Abstract

In 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 were investigated. A sHSP gene family of 33 members was established. Remarkably, roughly half of the members of this family can be explained by nine independent tandem duplication events that determined, evolutionarily, their functional fates. Within a mitochondrial class subfamily, only one duplicated member, Solyc08g078700, retained its ancestral chaperone function, 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. Subfunctionalization occurred within a new subfamily, whose two members, Solyc04g082720 and Solyc04g082740, show heterogeneous differential expression profiles 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 a baseline protection during both fruit ripening and heat shock stress in different tomato tissues.

See: http://www.g3journal.org/content/6/10/3027.abstract?etoc

Figure 3. Phylogenetic relationships in the sHSP family of the S. lycopersicum (cv. Heinz 1706) genome. Amino acid sequences deduced from the 33 members of sHSP gene family were used. Gene expression profiles during fruit ripening are shown. Differential expression is measured at the MR stage relative to the MG reference stage. Different symbols are used for depicting upregulated and downregulated, not differentially expressed (NDE), and not expressed (NE) genes. Aiming to highlight tandem duplication events that happened during the evolutionary history of this family, the chromosome localization of sHSP genes is used for branch labeling. Nine tandem duplication events are present: one in chromosome 1 involving the pair Solyc01g009200–Solyc01g009220, one in chromosome 4 involving the pair Solyc04g082720–Solyc04g082740, two in chromosome8 involving the pair Solyc08g062340–Solyc08g062350, and the trio Solyc08g078700–Solyc08g078710–Solyc08g078720, three in chromosome 6 involving the quartet Solyc06g076520–Solyc06g076540–Solyc06g076560–Solyc06g076570, and one in chromosome 9 involving the pair Solyc09g015000–Solyc09g015020.