Molecular markers for phylogenetic applications derived from comparative plastome analysis of Prunus species

Abstract

Interspecific and intergeneric relationships of Prunus s.l. are still unclear due to low levels of genetic variation among species, and resulting partially unresolved phylogenetic inferences. Here we sequenced and compared six complete plastomes from two subgenera of Prunus in order to choose molecular markers to increase the amount of genetic variation suitable for inference of Prunus phylogeny. The plastomes range between 157 817 and 158 995 bp in length, and we found different levels of inverted repeat (IR) contraction among the three sampled subgenera of Prunus s.l. Most regions in Prunus plastomes considered individually provide low phylogenetic resolution at the subgenus or species level compared to a tree constructed using all 78 coding regions combined. We compared levels of variation among 206 coding regions and noncoding (intergenic and intron) plastid regions and inferred phylogenies from each region considered individually. We then chose using two regions together for future studies of relationships in Prunus, ycf1 and trnT‐L, that display high to moderate levels of variation among coding and intergenic regions, respectively, and that individually permit inference of resolved species‐level trees in Prunus with moderate to strong branch support. Considered together, these two regions allow inference of the same topology of Prunus inferred using all coding plastid regions combined, with comparable levels of tree support to the full plastome set. These two loci should therefore be useful as a plastid phylogenetic marker set for further inference of relationships within Prunus s.l.

The complete chloroplast genome of Prunus apetala, a native deciduous flowering cherry of Japan

“…Cerasus , similar to the previous results (Kim et al. 2019 ), and P. apetala is sister to Prunus serrulata var. spontanea ( Figure 1 ).…”

On the Species Delimitation of the Maddenia Group of Prunus (Rosaceae): Evidence From Plastome and Nuclear Sequences and Morphology

“…In addition, the GC content in the IRs was higher than that in LSC and SSC, which is due to the presence of rRNA genes with high GC content (Kim and Lee, 2004). The conserved genome size, GC content, and gene number of Maddenia plastomes resemble other Amygdaloideae species (Wang et al, 2013;Kim et al, 2018). Although gene rearrangement events have been reported in some genera of other families, such as Lasthenia of Asteraceae (Walker et al, 2014), Anemone of Ranunculaceae (Liu et al, 2018), and Passiflora of Passifloraceae (Rabah et al, 2018), we observed no such events in Maddenia plastomes (Supplementary Figure 1).…”

Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China

“…Once sequenced, the complete plastome sequence can be screened for potential taxon-specific, hyper-variable gene regions that are likely to be a more cost-effective, yet useful, species identification tool, than the entire plastome [15,26]. Although this strategy has worked for a number of gene regions across a range of taxa (i.e., the ycf1 gene region within Pterocarpus [27] and Prunus [28]; the trnC-rps16, trnS-trnG, and trnE-trnM gene regions for Panax [22]; and trnQ-psbK, trnR-atpA, trnS-psbZ and rpl33-rps18 for Oresitrophe [26]) to date, there are no reported sequences for the plastomes of any Calligonum species, nor has a genome-wide search for taxon-specific barcodes been completed for the group.…”