Impacts of genomic localization on the evolutionary behavior of repetitive sequences in tandem in maize and relative species

Author(s)

Gabriel Fernando da Silva

• Document type: Master's Dissertation
• Press: Piracicaba.
• Institution: Universidade de São Paulo (USP). Escola Superior de Agricultura Luiz de Queiroz (ESALA/BC)
• Defense date: 2020-11-30

Examining board members

Mateus Mondin; Fábio de Oliveira Freitas; Gustavo Campos e Silva Kuhn

• Advisor: Mateus Mondin

Abstract

The satellite DNA evolution is led through the mechanisms of Concerted Evolution. Concerted evolution leads to the homogenization of motifs at the level of arrays. It is observed that concerted evolution has differences in its behavior between the motifs present in families of different species and has few reports on this evolutionary characteristic between families of the same genome. In order to increase the knowledge of the evolutionary studies of satellite DNA families present in the same genome, the goals of this work was to study the evolutionary behavior of two families named CentC and K180 present in maize and located in two different genomic contexts, the centromere and the knob, respectively. This work started with the search for the motifs of these satellite DNA families in the assembled genome of the lineage model of maize B73. Subsequently, the motifs were collected, organized and aligned to obtain the nucleotide diversity values, construction of the MLTree and observation of the motifs organization according to their position in the genome. From these analyzes, the results between these two satellite DNA families were compared and it was possible to see that the motifs located in the centromeric region (CentC) are more conserved in relation to the motifs in the knob region (K180) showing that the genomic context may influence the evolutionary behavior of satellites DNAs in maize. It was also observed that the CentC family has three groups of motifs that have distinct nucleotide diversity (highly conserved from 0% to 1,%, moderately conserved from 4% to 8% and more polymorphic from 13% to 17%) and that, possibly, may be associated with the functions centromere and with the association of centromeric proteins. Moreover, a new subfamily derived from K180 has been found that increases the great diversity that exists in this satellite DNA. This sub-family was called K180_B and is present in knobs of several species of the genus Zea and in the species Tripsacum dactyloides and absent in the species of Coix aquática and Coix lacryma-jobi. (AU)

• FAPESP's process: 18/09760-1 - Impacts of genomic location in the evolution of tandem repetitive sequence
• Grantee: Gabriel Fernando da Silva
• Support Opportunities: Scholarships in Brazil - Master