CRISPR/Cas9 Editing Sites Identification and Multi-Elements Association Analysis in Camellia sinensis

Abstract

CRISPR/Cas9 is an efficient genome-editing tool, and the identification of editing sites and potential influences in the Camellia sinensis genome have not been investigated. In this study, bioinformatics methods were used to characterise the Camellia sinensis genome including editing sites, simple sequence repeats (SSRs), G-quadruplexes (GQ), gene density, and their relationships. A total of 248,134,838 potential editing sites were identified in the genome, and five PAM types, AGG, TGG, CGG, GGG, and NGG, were observed, of which 66,665,912 were found to be specific, and they were present in all structural elements of the genes. The characteristic region of high GC content, GQ density, and PAM density in contrast to low gene density and SSR density was identified in the chromosomes in the joint analysis, and it was associated with secondary metabolites and amino acid biosynthesis pathways. CRISPR/Cas9, as a technology to drive crop improvement, with the identified editing sites and effector elements, provides valuable tools for functional studies and molecular breeding in Camellia sinensis.

The Characterization of G-Quadruplexes in Tobacco Genome and Their Function under Abiotic Stress

“…The appearance of these structures increases the instability of genes and may affect the process of gene expression, including DNA replication, repair, and transcription. In specific areas of the tea genome, a correlation between SSR density and the G-quadruplex, GC density, gene density, and CRISPR editing site density was found, and these areas were related to the secondary metabolism of tea [42]. In addition to SSRs, there are other types of tandem repeats and scattered repeats in the plant genome, including satellite DNA and transposons.…”