The microsynteny of genes functionally related with the fruit ripening process in Solanaceae species

CACCHIARELLI, P.; ARCE, D.P.; EZPELETA, J.; PRATTA, G.R.; TAPIA, E.; KRSTICEVIC, F.J.

Buenos AIres

Conferencia; ISCB Latin America 2016 - VII Argentinean Conference on Bioinformatics and Computational Biology; 2016

International Society of Computational Biology - A2B2C

Small heat shock proteins (sHSP) are induced during tomato (Solanum lycopersicum) ripening, a model species for fleshy fruits, to maintain cellular homeostasis. Previous analysis identified 4 cytosolic class I (CI) sHSP genes mapping together with a 17.9 kbp region of chromosome 6 in S. lycopersicum cv. Heinz 1706 that are highly abundant and strongly induced during ripening. We evaluated the gene microsynteny of the chromosome 6 region across related Solanaceae species. We considered the genomes (g) and transcriptomes (tr) of 2 commercial tomato cultivars (Heinz 1706 (g) and Ohio 824 (g)), 2 accessions (LA1589 (g, tr) and LA0722 (g)) of the wild red-fruited S. pimpinellifolium, 2 wild green-fruited species (S. pennelli and S. peruvianum) and 3 related Solanaceae species (S. tuberosum (g, tr), S. melongena (g) and Capsicum annuum (g)). Gene microsynteny revealed variability in the number and position of genes, frequent gene movement during evolution, showing 8 gene gain/loss events. Phylogenetic analysis suggests that new chromosome configurations originated from the tomato and potato ancestors (~8 mya). Comparison of Ka/Ks ratios indicates that orthologous and paralogous CI sHSP genes are highly conserved due to strong negative selection. Differences in the number of CI sHSP genes were observed among S. pimpinellifolium accessions, a lower number of CI sHSP genes being putatively associated to a shorter fruit shelf life. Increasing knowledge on co-localized and functionally related genes in tomato wild species facilitates introgression of natural genetic variations in breeding programs, allowing a more efficient development of new commercial varieties.