Authors: Cacchiarelli, Paolo; Krsticevic Flavia; Spetale Flavio Ezequiel; Pratta, Guillermo; Tapia Elizabeth.
Resumen: 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 tomatogermplasm, 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, whichwere 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 inS. 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-guidedassemblies 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.
Meeting type: Conferencia.
Type of job: Artículo Breve.
Production: In silico analysis of gene copy number of small heat shock proteins in tomato wild species.
Scientific meeting: V International Society for Computational Biology Latin America, SOIBIO and EMBnet Joint Bioinformatics Conference 2018.
Meeting place: Viña del mar.
It's published?: Yes
Publication place: London
Meeting month: 11