Maleae consists of economically and ecologically important plants. However, there are considerable disputes on generic circumscription due to the lack of a reliable phylogeny at generic level. In this study, molecular phylogeny of 35 generally accepted genera in Maleae is established using 15 chloroplast regions.Gilleniais the most basal clade of Maleae, followed byKageneckia+Lindleya,Vauquelinia, and a typical radiation clade, the core Maleae, suggesting that the proposal of four subtribes is reasonable. In the core Maleae including 31 genera, chloroplast gene data support that the fourMalus-related genera should better be merged into one genus and the sixSorbus-related genera would be classified into two genera, whereas allPhotinia-related genera should be accepted as distinct genera. Although the phylogenetic relationships among the genera in Maleae are much clearer than before, it is still premature to make a formal taxonomic treatment for these genera.

DNA barcoding has been extensively used for species identification. However, species identification of mixed samples or degraded DNA is limited by current DNA barcoding methods. In this study, we use plant species in Juglandaceae to evaluate an assembly-free reads accurate identification (AFRAID) method of species identification, a novel approach for precise species identification in plants. Specifically, we determined (1) the accuracy of DNA barcoding approaches in delimiting species in Juglandaceae, (2) the minimum size of chloroplast dataset for species discrimination, and (3) minimum amount of next generation sequencing (NGS) data required for species identification. We found that species identification rates were highest when whole chloroplast genomes were used, followed by taxon-specific DNA barcodes, and then universal DNA barcodes. Species identification of 100% was achieved when chloroplast genome sequence coverage reached 20% and the original sequencing data reached 500,000 reads. AFRAID accurately identified species for all samples tested after 500,000 clean reads, with far less computing time than common approaches. These results provide a new approach to accurately identify species, overcoming limitations of traditional DNA barcodes. Our method, which uses next generation sequencing to generate partial chloroplast genomes, reveals that DNA barcode regions are not necessarily fixed, accelerating the process of species identification.

Whereas the presence of flowers on ornamental flowering plants is essential for their identification via traditional methods, ornamental flowering plants cannot be reliably identified in non‐flowering stages likewise. Here, DBALM (DNA Barcodes–Leaf Morphology), a new approach that combines DNA barcoding data with micromorphological features of the leaf epidermis and that is not limited by the flowering stage, was used to identify 16 evergreen rhododendron cultivars. First, the sequences of DNA barcodes, ITS, matK, psbA‐trnH, and rbcL, were obtained from the DNA of leaves. Phylogenetic analysis was conducted to clarify the groupings among all the samples based on the four markers. Then, microscopic features of the leaf epidermis were used to further distinguish individuals from the same clade. DNA barcoding permitted the 16 cultivars to be divided into eight groups. The microscopic features of the leaf epidermis permitted cultivars within the same clade to be distinguished. The matK + psbA‐trnH combination was the most effective barcode combination in this study. In addition, the new primer matK‐Rh_R was designed, and it increased the amplification rate of evergreen rhododendron cultivars to 100%. In sum, DBALM was capable of accurately identifying the 16 evergreen rhododendron cultivars using data collected from a single leaf in the vegetative growth stage. This method can greatly facilitate the identification and breeding of ornamental flowering plants.

Mnium is the type genus of the family Mniaceae, the species’ richest family of order Bryales (Bryophyte). Mnium marginatum is widely distributed worldwide. The complete chloroplast genome of M. marginatum was sequenced by high-throughput sequencing technology. The chloroplast genome is 124,935 bp in length with a quadripartite structure. The two inverted repeat regions are 9,910 bp long and separated by a large single-copy region of 86,572 bp and a small single-copy region of 18,543 bp. Based on the chloroplast genome data of 11 bryophytes downloaded from GenBank and one acquired in this study, phylogenetic trees were constructed.

Pohlia is a genus with many taxonomic and systematic controversies. In this study, the complete chloroplast genome of Pohlia cruda (Bryales, Bryophyte) was sequenced by high-throughput sequencing technology and described. The complete chloroplast genome is 125,114 bp in length and has a quadripartite structure. The two inverted repeat (IR) regions are 9921 bp long and separated by a large single-copy (LSC) region of 86,727 bp and a small single-copy (SSC) region of 18,545 bp. Phylogenetic trees were constructed based on the complete chloroplast genome sequences of 10 bryophytes downloaded from GenBank and one acquired in this study.