Bioinformatics Analysis and Characterization of RuBisCO's large subunit in some lettuce genotypes

Abstract

Objective Lettuce is among one of the oldest vegetables in the world originally lodge in India and Central Asia. This study aims to evaluate the genetic diversity of fifteen lettuce genotypes by using the rbcl gene and protein sequences. Material and Methods Using sequencing method, the rbcl gene sequence of of fifteen lettuce were sequenced. Chromas 2.1.1 software, MegAlign ver5 software (using ClustalW approach) were applied for generating the similarity matrix, genetic distances as the same as building phylogram of the studied sequences. The modeling and validation of rbcl protein structure were performed through SWISS-MODEL and QMEAN, respectively. Further steps were progressed using Ramadan and Pro-SAP servers. Results Investigating protein-protein cross-links using STRING showed most of proteins encoded by matK, psb (A, D and C)-tranH have the interaction with rbcl protein. The results of cluster analysis, similarity matrix, molecular-variance and dn/ds was indicated that the sequence of rbcl gene and protein is very similar and conserve among all genotypes. Conclusion The results were indicated that the rbcl sequence is not useful to study the phylogenetic relationships inter-species. Therefore, this point is trustworthy to say that one of the reasons for failing the segregation all lettuce genotypes is the tiny diversity of rbcl gene.

Keywords

• lettuce
• dn/ds
• lactucin
• genetic diversity
• rbcl gene