Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae.

Yongtan Li,Yichao Liu,Minsheng Yang,Yan Dong,Yinran Huang,Xiaoyue Yu

doi:10.3389/fpls.2020.593984

Abstract

In this study, we assembled and annotated the chloroplast (cp) genome of the Euonymus species Euonymus fortunei, Euonymus phellomanus, and Euonymus maackii, and performed a series of analyses to investigate gene structure, GC content, sequence alignment, and nucleic acid diversity, with the objectives of identifying positive selection genes and understanding evolutionary relationships. The results indicated that the Euonymus cp genome was 156,860–157,611bp in length and exhibited a typical circular tetrad structure. Similar to the majority of angiosperm chloroplast genomes, the results yielded a large single-copy region (LSC) (85,826–86,299bp) and a small single-copy region (SSC) (18,319–18,536bp), separated by a pair of sequences (IRA and IRB; 26,341–26,700bp) with the same encoding but in opposite directions. The chloroplast genome was annotated to 130–131 genes, including 85–86 protein coding genes, 37 tRNA genes, and eight rRNA genes, with GC contents of 37.26–37.31%. The GC content was variable among regions and was highest in the inverted repeat (IR) region. The IR boundary of Euonymus happened expanding resulting that the rps19 entered into IR region and doubled completely. Such fluctuations at the border positions might be helpful in determining evolutionary relationships among Euonymus. The simple-sequence repeats (SSRs) of Euonymus species were composed primarily of single nucleotides (A)n and (T)n, and were mostly 10–12bp in length, with an obvious A/T bias. We identified several loci with suitable polymorphism with the potential use as molecular markers for inferring the phylogeny within the genus Euonymus. Signatures of positive selection were seen in rpoB protein encoding genes. Based on data from the whole chloroplast genome, common single copy genes, and the LSC, SSC, and IR regions, we constructed an evolutionary tree of Euonymus and related species, the results of which were consistent with traditional taxonomic classifications. It showed that E. fortunei sister to the Euonymus japonicus, whereby E. maackii appeared as sister to Euonymus hamiltonianus. Our study provides important genetic information to support further investigations into the phylogenetic development and adaptive evolution of Euonymus species.

Highlights

Chloroplasts are ubiquitous in plants and originate from symbiotic cyanobacteria (Jin and Daniell, 2015; Gao et al, 2019) with independent genomes and evolutionary routes
The GC content of the chloroplast genome differed among locations and among genes coding for different functions
The structure, gene organization and gene content of the cp genome of Euonymus species were highly conserved, which is similar to the other Celastrineae species (Choi and Park, 2015; Cascales et al, 2017; Gu et al, 2018)

Summary

Introduction

Chloroplasts (cps) are ubiquitous in plants and originate from symbiotic cyanobacteria (Jin and Daniell, 2015; Gao et al, 2019) with independent genomes and evolutionary routes. It plays important roles in energy conversion, photosynthesis, and the synthesis of fatty acids, chlorophyll, carotene, amino acids, starch, and other compounds (Neuhaus and Emes, 2000; Jensen, 2013). Many mutational events often occur in cp genomes, including indels, substitutions, inversion, contraction, and expansion of inverted repeats and its effect on the number of genes such as gene loss, duplication, and pseudogenes (Abdullah et al, 2020a; Henriquez et al, 2020). Sequence rearrangements have been reported from various kinds of plants (Sun et al, 2017; Liu et al, 2018)

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Conclusion