Characteristics analysis of chloroplast genome and molecular evolution of chloroplast genes in Amaryllidaceae plants

Abstract

AbstractBackgroundAmaryllidaceaeis a family of Monocotyledons inLiliflorae, and is considered an important ornamental and economic plant due to its usually showy flowers, and theAmaryllidaceaealso has enormous medicinal value. Currently, the gene structure characteristics and molecular function analysis of all chloroplast genomes inAmaryllidaceaeare rarely reported, so this study mainly analyzed the gene structure characteristics and molecular function of all chloroplast genomes inAmaryllidaceaeto reveal the characteristics of the chloroplast genome ofAmaryllidaceaeplants and explore their evolution and development patterns, and it usedbioinformaticsmethods to analyze the chloroplast genome sequences of 64Amaryllidaceaeplants that have been published on NCBI. Results Among the 64 species ofAmaryllidaceaeplants, the species with a gene number of 86 had the most chloroplasts, with 38 species accounting for approximately 59%. The number of rRNAs in its chloroplast genome is all 8. There are 55 species of plants in theAmaryllidaceaewith 38 tRNAs, and only a few species have abnormal tRNA numbers in their chloroplast genomes due to the loss or duplication of tRNA genes. The GC content of chloroplast genomes in all species ranges from 36–39%, indicating that their AT content is roughly between 61–64%. The high proportion of AT content in chloroplast genomes indicates that chloroplast codons prefer to use A/T bases. By constructing a phylogenetic evolution tree, it was found that the 64 species ofAmaryllidaceaeplants can be divided into 12 evolutionary groups.Lycoris longitubaandLycoris anhuiensishave the fastest evolutionary speed, whileAllium przewalskianumandAllium polyrhizum CMS-Shave the most primitive and slowest evolutionary speed. By analyzing the codon preference of chloroplast genomes, it was found that plants in theAmaryllidaceaeprefer to use synonymous codons ending in A/U, and their chloroplast genome codon usage bias is weak. Conclusion Our results preliminarily explored the relationship between each species in Amaryllidaceae, and the characteristics of the entire chloroplast genome sequence ofAmaryllidaceaewere revealed, these results provide a certain theoretical basis for further research on the plants of theAmaryllidaceaefamily in the future.