This reposiory contains code and scripts for processing and analysing data for the TRIBE project.
Interspecific hybridization in tomato influences endogenous viral sRNAs and alters gene expression
- smallRNA-seq of Solanum Lycopersicum and Solanum Pennellii parents and crosses up to the F4 generation
- RNA-seq of Solanum Lycopersicum and Solanum Pennellii parents and crosses up to the F4 generation
Hybridization is associated with activation of transposable elements and changes in patterns of gene expression leading to phenotypic changes. However, the underlying mechanisms are not well understood.
Results: Here we describe changes to gene expression in interspecific Solanum hybrids that are associated with small RNAs derived from endogenous (para)retroviruses (EPRV). There were prominent changes to sRNA profiles in these hybrids involving 22nt species produced in the DCL2 biogenesis pathway and the hybridisation-induced changes to gene expression were similar to those in a dcl2 mutant.
Conclusions: These findings indicate that hybridization leads to activation of EPRV, perturbation of small RNA profiles and, consequently, changes in gene expression. Such hybridization-induced variation in gene expression could increase the natural phenotypic variation in natural evolution or in breeding for agriculture.
European Commission: TRIBE - Transgressive Inheritance in plant Breeding and Evolution (340642)
The same code as deposited here is also mirrored on zenodo:
