Complete Plastid Genome Sequence of the Basal Asterid Ardisia polysticta Miq. and Comparative Analyses of Asterid Plastid Genomes

Abstract

Ardisia is a basal asterid genus well known for its medicinal values and has the potential for development of novel phytopharmaceuticals. In this genus of nearly 500 species, many ornamental species are commonly grown worldwide and some have become invasive species that caused ecological problems. As there is no completed plastid genome (plastome) sequence in related taxa, we sequenced and characterized the plastome of Ardisia polysticta to find plastid markers of potential utility for phylogenetic analyses at low taxonomic levels. The complete A. polysticta plastome is 156,506 bp in length and has gene content and organization typical of most asterids and other angiosperms. We identified seven intergenic regions as potentially informative markers with resolution for interspecific relationships. Additionally, we characterized the diversity of asterid plastomes with respect to GC content, plastome organization, gene content, and repetitive sequences through comparative analyses. The results demonstrated that the genome organizations near the boundaries between inverted repeats (IRs) and single-copy regions (SCs) are polymorphic. The boundary organization found in Ardisia appears to be the most common type among asterids, while six other types are also found in various asterid lineages. In general, the repetitive sequences in genic regions tend to be more conserved, whereas those in noncoding regions are usually lineage-specific. Finally, we inferred the whole-plastome phylogeny with the available asterid sequences. With the improvement in taxon sampling of asterid orders and families, our result highlights the uncertainty of the position of Gentianales within euasterids I.

Complete chloroplast genome sequence of common bermudagrass (Cynodon dactylon (L.) Pers.) and comparative analysis within the family Poaceae

“…The procedures for sample preparation, sequencing, and assembly were based on those described in our previous studies [8–10]. Briefly, total genomic DNA was extracted using the Wizard Genomic DNA Purification Kit (Promega, USA) following the manufacturer's protocol.…”

Comparative chloroplast genomes of eleven Schima (Theaceae) species: Insights into DNA barcoding and phylogeny

“…Although the genes located at the IR junctions are identical in cp genomes of Schima and Camellia , the overall cp genome sequences of Schima are more homogenous as compared to Camellia , which was suggested to show more differences at the junction regions [26]. The cp genomes of Schima encode the same set of protein-coding genes as previously reported Camellia species, with the exception of Orf 42 and Orf 188 which were reported in Camellia [25], but not in other Ericales members such as Actinidia (Actinidiaceae) and Ardisia (Primulaceae) [46, 47]. For the whole cp genomes of Schima , 37 tRNA genes were annotated, which is consistent with Huang et al [26].…”

Phylogenetic and Cophylogenetic Analyses of the Leaf-Nodule Symbiosis inArdisiaSubgenusCrispardisia(Myrsinaceae): Evidence from Nuclear and Chloroplast Markers and BacterialrrnOperons

“…In future research, in addition to a more comprehensive sampling of Crispardisia taxa, it would be important to explore other host or symbiont markers that may provide better phylogenetic resolution, such as the nuclear LEAFY intron 2 region (Grob et al 2004), potentially more informative chloroplast markers (see Ku et al 2013), and protein-coding genes commonly used for bacterial phylogenetics (Santos and Ochman 2004). Additionally, temporal frameworks for phylogenies of both the hosts and the symbionts need to be constructed.…”