The tribe Phlomideae (Lamiaceae: Lamioideae) is divided into the three genera Phlomis, Phlomoides (incl. Pseuderemostachys, Lamiophlomis and Notochaete), and Eremostachys (incl. Paraeremostachys), contains about 278 species and has a distribution range extending from Europe to Mongolia, China, and India. Here, we present a phylogenetic analysis based on nuclear ribosomal (ITS) and cpDNA (partial trnK, rpl32-trnL, and trnT-A) sequence data of 56 accessions representing all genera and major subgeneric taxa of Phlomideae. Taxon sampling covered the genera Phlomoides and Eremostachys more intensively than previous phylogenetic investigations of the tribe. Parsimony and Bayesian analyses of each marker, as well as the combined plastid datasets, produced nearly congruent trees. Monophyly of Phlomis s.str. is confirmed here, although only few representatives of this genus were included. In all obtained trees a core group of Phlomoides and Eremostachys is strongly supported. In accordance with morphological evidence, molecular data confirm the inclusion of Eremostachys, Notochaete, and Paraeremostachys in Phlomoides. In conclusion, the number of recognized genera in Phlomideae is reduced to two: Phlomis and Phlomoides. The necessary new combinations are proposed.

The chloroplast genome harbors plenty of valuable information for phylogenetic research. Illumina short-read data is generally used for de novo assembly of whole plastomes. PacBio or Oxford Nanopore long reads are additionally employed in hybrid approaches to enable assembly across the highly similar inverted repeats of a chloroplast genome. Unlike for Pac-Bio, plastome assemblies based solely on Nanopore reads are rarely found, due to their high error rate and non-random error profile. However, the actual quality decline connected to their use has rarely been quantified. Furthermore, no study has employed referencebased assembly using Nanopore reads, which is common with Illumina data. Using Leucanthemum Mill. as an example, we compared the sequence quality of seven chloroplast genome assemblies of the same species, using combinations of two sequencing platforms and three analysis pipelines. In addition, we assessed the factors which might influence Nanopore assembly quality during sequence generation and bioinformatic processing. The consensus sequence derived from de novo assembly of Nanopore data had a sequence identity of 99.59% compared to Illumina short-read de novo assembly. Most of the errors detected were indels (81.5%), and a large majority of them is part of homopolymer regions. The quality of reference-based assembly is heavily dependent upon the choice of a closeenough reference. When using a reference with 0.83% sequence divergence from the studied species, mapping of Nanopore reads results in a consensus comparable to that from Nanopore de novo assembly, and of only slightly inferior quality compared to a referencebased assembly with Illumina data. For optimal de novo assembly of Nanopore data, appropriate filtering of contaminants and chimeric sequences, as well as employing moderate read coverage, is essential. Based on these results, we conclude that Nanopore long reads are a suitable alternative to Illumina short reads in plastome phylogenomics. Few errors remain in the finalized assembly, which can be easily masked in phylogenetic analyses without loss in analytical accuracy. The easily applicable and cost-effective technology might warrant more attention by researchers dealing with plant chloroplast genomes.

No abstract

No abstract

No abstract