Comparative Analysis and Phylogenetic Implications of Plastomes of Five Genera in Subfamily Amyridoideae (Rutaceae)

Abstract

In the most recent classification of Rutaceae, Amyridoideae is the largest and most diverse subfamily. In Amyridoideae, the genera Phellodendron, Tetradium, Toddalia and Zanthoxylum were proposed as “proto-Rutaceae”due to substantial phytochemical similarities. In this study, we investigated the plastome varia-tions in eight species representing these four genera and Melicope. All plastomes exhibited a typical quadripartite structure with four regions (LSC, SSC, IRa and IRb). The whole chloroplast genome size ranged from 158,383 bp to 159,014 bp and the gene number ranged from 115 to 116. By comparative analyses, we found that there were structural variations at the LSC/IR and SSC/IR borders of the plastomes in the five genera, especially in Melicope. Three most divergent regions (trnH-psbA, trnE-trnT and psaB) were found from the LSC region, which had great potential for developing effective genetic markers. In addition, we conducted a phylogenomic analyses of the “proto-Rutaceae”and related taxa with plastomes data from 36 species. Our results showed that (1) Phellodendron, Tetradium, Toddalia and Zanthoxylum were confirmed as close relatives and grouped together as the ‘proto-Rutaceae’, (2) Phellodendron was sister to Tetradium, and Toddalia was deeply nested within Zanthoxylum, and (3) Toddalia asiatica was closely related to the Southwest Pacific and East Asian species of Zanthoxylum, and Melicope pteleifolia was more closely related to Acronychia than it is to Tetradium. This study provided new insights into the plastome structural varia-tions in subfamily Amyridoideae, and demonstrated that the plastomes data were sufficiently robust to explore implications of the phylogeny for the previous phylogenetic hypotheses.

Incompatibility Phylogenetic Signals between Double-Digest Restriction Site-Associated DNA Sequencing and Plastid Genomes in Chinese Curcuma (Zingiberaceae)—A Recent Qinghai–Tibetan Plateau Diversification Genera

“…Topological incompatibility among the six datasets (corresponding to chloroplast and ddRAD) was also distinct in the visualization of topological scores (Table 2). Phylogenetic analysis of our chloroplast genome and ddRAD data corroborated the rapid diversification of the interspecific divergence of Chinese Curcuma, which resulted in the inconsistency in topologies [65]. Altogether, Curcuma in the QTP showed a complex history of ecological diversification in this study, which is consistent with a previous study [9].…”

Comparative analysis of the complete plastid genomes in Prunus subgenus Cerasus (Rosaceae): Molecular structures and phylogenetic relationships

“…l . [ 7 – 10 ], only one phylogenetic study has included 13 taxa from subg. Cerasus and was based on a minimal number of molecular markers [ 8 ].…”

The use of African medicinal plants in cancer management

“…Fagaropsis are mostly shrubs or deciduous trees with buttress roots. The plant species Fagaropsis angolensis is found in Angola, Ethiopia, Kenya, Namibia, Tanzania, Uganda, and Zimbabwe; F. hildebrandtii is primarily found in Ethiopia, Kenya, Somalia, and Tanzania while F. velutina and F. glabra occur endemically in Madagascar ( Sun et al, 2021 ). F. angolensis whole root methanol extracts have been shown to exhibit antitumor activity against throat cancer cells (Hep2) at an IC 50 value of 10.05 ± 2.15 μg/mL.…”