Backbone phylogeny and evolution of Apioideae (Apiaceae): New insights from phylogenomic analyses of plastome data.

Traditional phylogenies inferred from chloroplast DNA fragments have not obtained a well-resolved evolutionary history for the backbone of Apioideae, the largest subfamily of Apiaceae. In this study, we applied the genome skimming approach of next-generation sequencing to address whether the lack of resolution at the tip of the Apioideae phylogenetic tree is due to limited information loci or the footprint of ancient radiation. A total of 90 complete chloroplast genomes (including 23 newly sequenced genomes and covering 20 major clades of Apioideae) were analyzed (RAxML and MrBayes) to provide a phylogenomic reconstruction of Apioideae. Dating analysis was also implemented using BEAST to estimate the origin and divergence time of the major clades. As a result, the early divergences of Apioideae have been clarified but the relationship among its distally branching clades (Group A) was only partially resolved, with short internal branches pointing to an ancient radiation scenario. Four major clades, Tordyliinae I, Pimpinelleae I, Apieae and Coriandreae, were hypothesized to have originated from chloroplast capture events induced by early hybridization according to the incongruence between chloroplast-based and nrDNA-based phylogenetic trees. Furthermore, the variable and nested distribution of junction positions of LSC (Large single copy region) and IRB (inverted repeat region B) in Group A may reflect incomplete lineage sorting within this group, which possibly contributed to the unclear phylogenetic relationships among these clades inferred from plastome data. Molecular clock analysis revealed the chloroplast capture events mainly occurred during the middle to late Miocene, providing a geological and climate context for the evolution of Apioideae.

The chloroplast genome of Archontophoenix alexandrae (Arecaceae): an important landscape tree for the subtropics.

Archontophoenix alexandrae, known as king palm, is an important landscape tree for the subtropics and potential sources of dietary fiber. In this study, the complete chloroplast genome of A. alexandrae was determined through Illumina sequencing method. The chloroplast genome was 159,196 bp in length and contained a small single-copy region (17,763 bp), a large single-copy region (87,055 bp) and a pair of IR regions (27,189 bp). 135 genes were determined in the A. alexandrae chloroplast genome, including 86 CDS, 39 tRNA genes, and 8 rRNA genes. Archontophoenix alexandrae showed the closest relationship with Veitchia arecina in the phylogenetic analysis.

Characterization of the complete chloroplast genome of Plumeria rubra cv. Acutifolia (Apocynaceae).

Plumeria rubra cv. Acutifolia is a widely planted landscape tree in the subtropics. In this study, the complete chloroplast genome of P. rubra cv. Acutifolia was determined through Illumina sequencing method. The complete chloroplast genome has a length of 153,912 bp, containing a small single-copy region (18,036 bp), a large single-copy region (84,852 bp), and a pair of IR regions (25,512 bp). The chloroplast genome possesses 130 genes, including 85 CDS, 37 tRNA genes and 8 rRNA genes. P. rubra cv. Acutifolia exhibited the closest relationship with P. cubensis in phylogenetic analysis.

Plastomes of eight Ligusticum species: characterization, genome evolution, and phylogenetic relationships.

BACKGROUND: The genus Ligusticum consists of approximately 60 species distributed in the Northern Hemisphere. It is one of the most taxonomically difficult taxa within Apiaceae, largely due to the varied morphological characteristics. To investigate the plastome evolution and phylogenetic relationships of Ligusticum, we determined the complete plastome sequences of eight Ligusticum species using a de novo assembly approach. RESULTS: Through a comprehensive comparative analysis, we found that the eight plastomes were similar in terms of repeat sequence, SSR, codon usage, and RNA editing site. However, compared with the other seven species, L. delavayi exhibited striking differences in genome size, gene number, IR/SC borders, and sequence identity. Most of the genes remained under the purifying selection, whereas four genes showed relaxed selection, namely ccsA, rpoA, ycf1, and ycf2. Non-monophyly of Ligusticum species was inferred from the plastomes and internal transcribed spacer (ITS) sequences phylogenetic analyses. CONCLUSION: The plastome tree and ITS tree produced incongruent tree topologies, which may be attributed to the hybridization and incomplete lineage sorting. Our study highlighted the advantage of plastome with mass informative sites in resolving phylogenetic relationships. Moreover, combined with the previous studies, we considered that the current taxonomy system of Ligusticum needs to be improved and revised. In summary, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of Ligusticum species.

Tongoloa arguta (Apiaceae), a new species from southwest China.

A new species Tongoloa arguta (Apiaceae) is described and illustrated in this article. The new species grows in alpine bushes and meadows in south-western China. It resembles T. silaifolia, but differs from the latter by the length of the stem, ultimate segments of leaf and rays of the umbel. Phylogenetic analysis, based on nuclear ribosomal DNA internal transcribed spacer (ITS) sequences, is provided, as well as comparative morphology between related species.

Characterization of the complete chloroplast genome of Taibaisanqi (Tongoloa silaifolia).

Tongoloa silaifolia, known as a traditional Chinese medicine Taibaisanqi, is a perennial herb of Apiaceae. In this study, the complete chloroplast genome of T. silaifolia was determined through Illumina sequencing method. The chloroplast genome of T. silaifolia was 161,122 bp in length and contained a pair of IR regions (30,824 bp) separated by a small single-copy region (17,553 bp) and a large single-copy region (81,921 bp). This chloroplast genome is encoded with 137 genes including 92 CDS, 37 tRNA genes, and 8 rRNA genes. The overall GC content of T. silaifolia cp genome is 37.7%. By phylogenetic analysis using maximum likelihood method, T. silaifolia showed the closest relationship with Chuanminshen violaceum and Hansenia species.