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

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.

Comparative Chloroplast Genomics of Sophora Species: Evolution and Phylogenetic Relationships in the Early-Diverging Legume Subfamily Papilionoideae (Fabaceae)

“…In the present study, except in morphological confusing species S. albescens , S. dunnii , and S. velutina , the rps12 gene lost an intron in this genus which was specific to Desmodieae ( Jin et al, 2019 ). We also identified the addition of an intron in ndhA , atpF , rps16 , and rpoC1 , a finding which differs from those of previous studies ( Li et al, 2021 ; Oyebanji et al, 2020 ; Zhao et al, 2020 ; Guo et al, 2021 ). Compared to the two species ( S. macrocarpa and S. toromiro ) distributed in Chile, the ycf3 gene was increased by one to two introns and the gene rrn23 lost introns within each of the taxa distributed in China.…”

“…AT/AT repeats, AAT/AAT repeats, and AAAT/AAAT repeats were prevalent in all species ( Figure 3A ). This phenomenon may occur because the A/T variation occurs more easily than the G/C mutation ( Li et al, 2021 ). Similar cases has been reported in previous study in which SSRs generally consist of polyA or polyT repeats, and rarely contain G or C repeats ( Zha et al, 2020 ).…”

The Conservation of Chloroplast Genome Structure and Improved Resolution of Infrafamilial Relationships of Crassulaceae

“…This result indicated these protein-coding genes are under strong structural and functional constraints. The absence of positive selection in most protein-coding genes of chloroplast genome was also found in Euonymus ( Li et al, 2021 ) and Quercus ( Yin et al, 2018 ).…”

“…Chloroplasts are semi-autonomous replication organelles, originating in endosymbiosis between cyanobacteria and non-photosynthetic host, and play crucial roles in photosynthesis and physiology of plants ( Gao et al, 2019a ; Huo et al, 2019 ; Li et al, 2021 ). The chloroplast genome is mostly a typical quadripartite circular DNA genome comprising a small single-copy (SSC), a large single-copy (LSC), and two inverted repeats (IRs) ( Hu et al, 2016 ; Chang et al, 2020 ).…”

Authentication of Zingiber Species Based on Analysis of Metabolite Profiles

“…In this paper, 110 SSRs were identified from the cp genomes of two Zingiber species, and the most abundant repeat type was AT/TA, followed by A/T mononucleotide repeat. Previous studies found that cp genome SSRs always consists of short poly-A or poly-T repeats, and most plants rarely contain tandem G or C repeats ( Li et al, 2021 ). At present, SSR markers have been widely used in the fields of species identification, genetic diversity, population structure evaluation, comparative genomics, and marker-assisted selection breeding ( Zhang et al, 2019 ; Liang et al, 2020 ).…”