Chloroplast genome sequencing based on genome skimming for identification of Eriobotryae Folium

Background Whole chloroplast genome (cpDNA) sequence is becoming widely used in the phylogenetic studies of plant and species identification, but in most cases the cpDNA were acquired from silica gel dried fresh leaves. So far few reports have been available to describe cpDNA acquisition from crude drugs derived from plant materials, the DNA of which usually was seriously damaged during their processing. In this study, we retrieved cpDNA from the commonly used crude drug Eriobotryae Folium (Pipaye in Chinese, which is the dried leaves of Eriobotrya japonica, PPY) using genome skimming technique. Results We successfully recovered cpDNA sequences and rDNA sequences from the crude drug PPY, and bioinformatics analysis showed a high overall consistency between the cpDNA obtained from the crude drugs and fresh samples. In the ML tree, each species formed distinct monophyletic clades based on cpDNA sequence data, while the phylogenetic relationships between Eriobotrya species were poorly resolved based on ITS and ITS2. Conclusion Our results demonstrate that both cpDNA and ITS/ITS2 are effective for identifying PPY and its counterfeits derived from distantly related species (i.e. Dillenia turbinata and Magnolia grandiflora), but cpDNA is more effective for distinguishing the counterfeits derived from the close relatives of Eriobotrya japonica, suggesting the potential of genome skimming for retrieving cpDNA from crude drugs used in Traditional Chinese Medicine for their identification.

Gymnocolea borealis (Anastrophyllaceae, Marchantiophyta) in Asia and Russia: morphology, ecology, distribution, and differentiation

Gymnocolea borealis is reported for the first time for Asia from Russia based on the morphological and subsequent molecular-genetic comparison of rbcL cpDNA sequence of the specimen from the Gydansky Peninsula, West Siberian Arctic. An extended morphological description, generalizing the species characters throughout its range, and data on its variation, differentiation and ecology, and photomicrographs are provided. The occurrence of G. borealis growing as separate shoots among dense mire vegetation makes it easy to overlook. Presently known isolated records of G. borealis support its disjunctive circumpolar distribution.

Structure and Phylogeny of the Curly Birch Chloroplast Genome

Curly birch [Betula pendula var. carelica (Merckl.) Hämet-Ahti] is a relatively rare variety of silver birch (B. pendula Roth) that occurs mainly in Northern Europe and northwest part of Russia (Karelia). It is famous for the beautiful decorative texture of wood. Abnormal xylogenesis underlying this trait is heritable, but its genetic mechanism has not yet been fully understood. The high number of potentially informative genetic markers can be identified through sequencing nuclear and organelle genomes. Here, the de novo assembly, complete nucleotide sequence, and annotation of the chloroplast genome (plastome) of curly birch are presented for the first time. The complete plastome length is 160,523 bp. It contains 82 genes encoding structural and enzymatic proteins, 37 transfer RNAs (tRNAs), and eight ribosomal RNAs (rRNAs). The chloroplast DNA (cpDNA) is AT-rich containing 31.5% of A and 32.5% of T nucleotides. The GC-rich regions represent inverted repeats IR1 and IR2 containing genes of rRNAs (5S, 4.5S, 23S, and 16S) and tRNAs (trnV, trnI, and trnA). A high content of GC was found in rRNA (55.2%) and tRNA (53.2%) genes, but only 37.0% in protein-coding genes. In total, 384 microsatellite or simple sequence repeat (SSR) loci were found, mostly with mononucleotide motifs (92% of all loci) and predominantly A or T motifs (94% of all mononucleotide motifs). Comparative analysis of cpDNA in different plant species revealed high structural and functional conservatism in organization of the angiosperm plastomes, while the level of differences depends on the phylogenetic relationship. The structural and functional organization of plastome in curly birch was similar to cpDNA in other species of woody plants. Finally, the identified cpDNA sequence variation will allow to develop useful genetic markers.

Hybridization in the Temperate Bamboos (Poaceae: Bambusoideae: Arundinarieae): A Phylogenetic Study Using AFLPs and cpDNA Sequence Data

Abstract—The temperate bamboos are a taxonomically difficult group with nearly 600 species in approximately 30 genera and at least 12 constituent lineages. In this study, phylogenetic relationships were explored using amplified fragment length polymorphism (AFLP) data in comparison with a phylogeny based on plastid DNA sequences, with an emphasis onArundinariaof North America and its allies in East Asia (theArundinariaclade). Molecular analyses involved 248 individuals in 10 genera and 60 species. Hybridization was detected both within and among genera. Comparative analyses indicated hybrid origins for species in several widespread and well-known genera, includingHibanobambusa,Sasaella, andSemiarundinaria. Evidence also indicated thatPseudosasa japonica(the type species ofPseudosasa) is an intergeneric hybrid involvingPleioblastusandSasamorpha. In addition, cryptic hybrids were detected within and amongPleioblastus,Sasa, andSasamorpha. After accounting for hybrids, phylogenetic analyses of AFLP data provided resolution for core lineages in theArundinariaclade, includingPleioblastussensu stricto,Sasas. s., andSasamorpha.AFLP data also provided evidence for the monophyly of the North American cane bamboos (Arundinaria, three species) but failed to identify their closest relative among the East Asian taxa. The broader evolutionary implications of hybridization in the temperate bamboos are discussed along with recommendations for future studies.

Phylogenetic position of Miliusa vidalii (Miliuseae, Annonaceae) inferred from chloroplast DNA and morphology

A molecular phylogenetic study was conducted to determine the position of the Philippine endemic Miliusa vidalii in the tribe Miliuseae of family Annonaceae utilizing the combined cpDNA sequence data (trnL-F-matK-ndhF-psbA-trnH-ycf1). Bayesian inference and Maximum parsimony analyses revealed a robustly supported monophyletic Miliusa clade (PP=1.00; BS=93%). Miliusa vidalii nested within clade D (PP=1.00; BS=85%) shares similar features by having terminal inflorescences and a notably long pedicel. M. vidalii is resolved as sister to M. lanceolata, which shares morphological features such as length of pedicels, number of secondary veins, shape of leaf apex, and apiculate monocarp. This present study revealed that M. vidalii possesses a conspicuous glandular structure in the inner petals, a feature that is common only to species found in clade A. Therefore, increased taxon sampling is necessary to construct a stronger phylogenetic relationship within the genus.

Genetic diversity and species limits in Veltheimia (Asparagaceae: Scilloideae): insights from noncoding cpDNA sequence data

Veltheimia is a genus of two species of bulbous flowering angiosperms restricted to southern Africa. Both parsimony and Bayesian analysis of 1829 nucleotides of DNA sequence data, from three non-coding chloroplast regions from multiple samples of both species, indicates that specimens of V. bracteata form a monophyletic clade together with three specimens named as V. capensis. This clade receives low support and is embedded within a paraphyletic grade of specimens of V. capensis. A Median Joining Network analysis of a subset of samples revealed nine haplotypes, the relationships of which mirrored the relationships resolved by the Bayesian analysis. With the exception of the V. capensis members of the V. bracteata clade, the remaining specimens are from the summer rainfall thicket and coastal forests. The samples of the basal V. capensis grade are found in the winter rainfall regions of southern Africa. These results indicate that there is limited genetic diversity within the genus, and there is no clear distinction between these two species based on plastid non-coding DNA data. This may be due to their recent divergence and incomplete lineage sorting, or recent or ongoing hybridisation and / or introgression.

Eutrema nanum (Brassicaceae), a new species from Chola Shan, Southwest China

Eutremananum, a new high-elevation (4500–4600 m) species from Chola Shan, Sichuan (Southwest China), is described and illustrated. It is similar morphologically to E.nepalense but is readily distinguished by having oblong to elliptic or obovate to spatulate (vs. suborbicular to broadly ovate) leaves, glabrous (vs. puberulent) sepals and ovate to oblong fruit 4–7 × 2–3 mm with flattened valves (vs. ovoid to subglobose fruit 2–3 × 1.8–2 mm with rounded valves). The genetic differences amongst E.nanum, E.nepalense and other close relatives are further confirmed by phylogenetic analyses using ITS and cpDNA sequence variations. The new combination E.sinense is proposed.

Eutrema nanum (Brassicaceae), a new species from Chola Shan, Southwest China

Eutremananum, a new high-elevation (4500–4600 m) species from Chola Shan, Sichuan (Southwest China), is described and illustrated. It is similar morphologically to E.nepalense but is readily distinguished by having oblong to elliptic or obovate to spatulate (vs. suborbicular to broadly ovate) leaves, glabrous (vs. puberulent) sepals and ovate to oblong fruit 4–7 × 2–3 mm with flattened valves (vs. ovoid to subglobose fruit 2–3 × 1.8–2 mm with rounded valves). The genetic differences amongst E.nanum, E.nepalense and other close relatives are further confirmed by phylogenetic analyses using ITS and cpDNA sequence variations. The new combination E.sinense is proposed.

Identifying the generic limits of the Cheilanthoid genus Doryopteris

Morphology-based delimitation of genera in the Cheilanthoid ferns has proved to be problematic and understanding of the phylogeny and relationships amongst Cheilanthoid ferns based on morphological characters has posed even further difficulties, owing perhaps in large part to adaptation by many taxa to xeric habitats, as well as convergent evolution. It is only now with the application of DNA sequence data that relationships of species and genera are becoming clear. Here, we present results of cpDNA sequence data from species that have been traditionally placed in the genus Doryopteris and, based on both these results, and morphological and distribution data, this study helps clarify the concept of the genus Doryopteris its position within the Cheilanthoid ferns and the status of Lytoneuron. As a result, three genera are redefined: Doryopteris, Lytoneuron and Ormopteris.