Analysis on the complete chloroplast genome of Grevillea robusta

Abstract

Grevillea robusta is an important plant in Proteaceae, decoding and understanding the chloroplast genome of G. robusta is of great theoretical significance and practical value to the genetic diversity and phylogenetic relationships of Proteaceae. In this work, the chloroplast genome of G. robusta was sequenced, characterized, and compared to the other Proteaceae species to provide chloroplast genetic resources and because the information on chloroplast genes is scarce in the Proteaceae, we also examined the affinities between G. robusta and species of various families within Proteales to determine G. robusta’s phylogenetic position. Based on the illumina sequencing data of G. robusta, the sequencing results were assembled and annotated utilizing the software tools GetOrganelle and CPGAVAS2. The chloroplast genome data for the genera Macadamia, Helicia, and Protea were obtained from the NCBI database. Subsequently, the chloroplast genomes of four genera within the Proteaceae family were subjected to analysis using various programs including MISA, REPuter, IRscope, and IQtree. The chloroplast genome of G. robusta was 158,642 bp in length and consists of 129 genes, including 84 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Fifty-six simple repeat sequences were obtained from G. robusta, of which single-nucleotide repeats were the most (66.07%) and the six nucleotide repeats were the least (1).Simultaneously, the chloroplast genome of G. robusta exhibited the presence of 34 repeats, primarily consisting of palindrome repeats (16). The inverted repeat (IR) region of G. robusta did not undergo a significant contraction/expansion event, in contrast to the notable contraction observed in Protea kilimandscharica. Analysis of gene selection pressure indicated positive selection signals in the ycf1 genes. Furthermore, examination of RNA editing sites revealed the occurrence of 148 RNA editing sites within the protein-coding genes of the chloroplast genome of G. robusta, with the majority consisting of C/U editing, accounting for 54.73% of the total. Phylogenetic analysis confirmed that G. robusta belongs to Proteaceae, and grouped with Helicia and Macadamia, with a support value of 100%. The chloroplast genome of G. robusta was assembled successfully, which is closely related to the chloroplast genomes of Helicia and Macadamia, and belongs to the same clade as Proteaceae. The results of this study laid a foundation for understanding the systematic evolution of Proteaceae plants and provide rich data to support the development of molecular biological information, such as molecular markers.