Tandem Duplication Events in the Expansion of the Small Heat Shock Protein Gene Family in Solanum lycopersicum (cv. Heinz 1706)

• Published in: G3 : genes - genomes - genetics 2016-10, Vol.6 (10), p.3027-3034
• Main Authors: Krsticevic, Flavia J, Arce, Débora P, Ezpeleta, Joaquín, Tapia, Elizabeth
• Format: Article
• Language: English
• Subjects: Computational Biology - methods; Gene Duplication; Gene Expression Profiling; Gene Expression Regulation, Plant; Genes, Plant; Heat-Shock Proteins, Small - classification; Heat-Shock Proteins, Small - genetics; Heat-Shock Proteins, Small - metabolism; Investigations; Lycopersicon esculentum - genetics; Lycopersicon esculentum - metabolism; Molecular Sequence Annotation; Multigene Family; Phylogeny; Protein Transport; ripening; RNA-seq; sHSP; tandem duplication; Tandem Repeat Sequences; tomato; Transcriptome
• ISSN: 2160-1836; 2160-1836
• 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.