Phylogenomic and evolutionary dynamics of inverted repeats across Angelica plastomes

Abstract

Background Angelica L. (family Apiaceae) is an economically important genus comprising ca. One hundred ten species. Angelica species are found on all continents of the Northern Hemisphere, and East Asia hosts the highest number of species. Morphological characters such as fruit anatomy, leaf morphology and subterranean structures of Angelica species show extreme diversity. Consequently, the taxonomic classification of Angelica species is complex and remains controversial, as the classifications proposed by previous studies based on morphological data and molecular data are highly discordant. In addition, the phylogenetic relationships of major clades in the Angelica group, particularly in the Angelica s. s. clade, remain unclear. Chloroplast (cp) genome sequences have been widely used in phylogenetic studies and for evaluating genetic diversity. Results In this study, we sequenced and assembled 28 complete cp genomes from 22 species, two varieties and two cultivars of Angelica. Combined with 36 available cp genomes in GenBank from representative clades of the subfamily Apioideae, the characteristics and evolutionary patterns of Angelica cp genomes were studied, and the phylogenetic relationships of Angelica species were resolved. The Angelica cp genomes had the typical quadripartite structure including a pair of inverted repeats (IRs: 5836–34,706 bp) separated by a large single-copy region (LSC: 76,657–103,161 bp) and a small single-copy region (SSC: 17,433–21,794 bp). Extensive expansion and contraction of the IR region were observed among cp genomes of Angelica species, and the pattern of the diversification of cp genomes showed high consistency with the phylogenetic placement of Angelica species. Species of Angelica were grouped into two major clades, with most species grouped in the Angelica group and A. omeiensis and A. sinensis grouped in the Sinodielsia with Ligusticum tenuissimum. Conclusions Our results further demonstrate the power of plastid phylogenomics in enhancing the phylogenetic reconstructions of complex genera and provide new insights into plastome evolution across Angelica L.

Comparative And Phylogenetic Analyses of Six Kenya Polystachya (Orchidaceae) Species Based On The Complete Chloroplast Genome Sequences

“…The GC content in six Polystachya species was almost similar (36.9%-37.0%). Although Polystachya cp genomes were AT rich, the higher GC content in IRs region, is most likely due to the presence of rrn4.5, rrn5, rrn16, and rrn23 [56][57][58], which is consistent with the previously published Orchidaceae cp genomes [59,60]. Non-coding region, especially introns may have accumulated mutations more rapidly than coding region, hence have an in uence at gene expression level [61].…”

Chloroplast phylogenomics and divergence times of Lagerstroemia (Lythraceae)

“…However, the genetic background of the cultivars was unclear, and these markers were not informative to infer the relationship of those species. The chloroplast genome has become an efficient option for increasing plant phylogenomics at multiple taxonomic levels during the past years [ 24 – 29 ]. We had used the chloroplast genome data to infer phylogenetic relationships of six Lagerstroemia species, and discovered that the chloroplast genome sequences had effective information to infer the phylogeny of this genus [ 15 ].…”

Heterogeneous Genetic Diversity Estimation of a Promising Domestication Medicinal Motherwort Leonurus Cardiaca Based on Chloroplast Genome Resources

“…Owing to rare recombination, small genome size, uniparental transmission, and moderate evolution rate, chloroplast genome research has been used extensively in different scientific fields. In molecular phylogeny, it can clearly reflect the relationship at different taxonomic levels, such as Chaenomeles , Juglans , Coryloideae, Angelica, and Distylium, and even difficult relationships within Fabaceae can be addressed ( Dong et al, 2017 ; Hu et al, 2017 ; Dong et al, 2018 ; Hu et al, 2020 ; Sun et al, 2020 ; Zhang et al, 2020 ; Wang et al, 2021a ; Dong et al, 2021 ) . In phylogeographical analysis, the advantage of the chloroplast genome in non-recombination and uniparental inheritance can allow for successfully estimation of divergence times and determine a biogeographic history ( Zhang et al, 2017 ; Liu et al, 2018 ; Zhao et al, 2019 ; del Valle et al, 2019 ).…”