In silico analysis of gene copy number of small heat shock proteins in tomato wild species

CACCHIARELLI, P.; KRSTICEVIC, F.J.; SPETALE, F.; PRATTA, G.; ELIZABETH, TAPIA

Viña del Mar

Conferencia; V International Society for Computational Biology Latin America, SOIBIO and EMBnet Joint Bioinformatics Conference 2018 (ISCB-LA SOIBIO EMBnet 2018); 2018

SoiBio

Small heat shock proteins (sHSPs) are a family of genes which are strongly induced and highly abundant during tomato (Solanum lycopersicum) ripening. Previous analysis identified 4 tandem duplicated intronless sHSP genes mapping within a ~17.9 kbp region of chromosome 6 in S. lycopersicum cv. Heinz 1706. Tandem duplications pose a computational challenge for assemblies. Aiming to accurately characterize tomato germplasm, we evaluated de novo assembly strategies to establish the sHSP gene copy number in this chromosomal region across related wild species. Genomes (g) and transcriptomes (tr) of Solanaceae species are derived from 2 sequencing projects,ERA282888 (g) and SRA320560 (tr). Both projects share in common 6 accessions, which were used for gene copy number determination. ERA282888 (g) accessions, which had been previously assembled in front reference, were reassembled de novo using SPAdes. On the other hand, SRA320560 (tr) accessions were de novo assembled using Trinity. While reference-guided genome assemblies always showed 4 sHSP copies, likely due to genome reference bias, de novo assemblies showed (g/tr): 6/5 copies in S. arcanum LA2172, 4/2 in S. habrochaites LA1777, 4/3 in S. habrochaites LA0407, 2/5 in S. pennellii LA0716, 3/3 in S. neorickii LA2133, and 2/3 in S. huaylasense LA1364. Variability in gene copy number could be better inferred through de novo assemblies, avoiding likely bias from reference-guided assemblies that belong to cultivated species to those wild species, and thus establishing the genetic variants that natural selection would have generated in the tomato germplasm biodiversity.