Molecular analyses display the increasing diversity of Podostemaceae in China.

•Four newly recorded species of Podostemaceae from southern China were identified by molecular and morphological evidence.•17 plastomes of Podostemaceae were newly sequenced and two novel polymorphic barcodes (ccsA and ndhA) detected.•Our findings reveal greater species richness (15 species from five genera) of Podostemaceae in China and supply molecular resources for research on taxonomy and phylogenomics of this enigmatic aquatic family.

Distinct hybridization modes in wide- and narrow-ranged lineages of Causonis (Vitaceae).

BACKGROUND: Explaining contrasting patterns of distribution between related species is crucial for understanding the dynamics of biodiversity. Despite instances where hybridization and whole genome duplication (WGD) can yield detrimental outcomes, a role in facilitating the expansion of distribution range has been proposed. The Vitaceae genus Causonis exhibits great variations in species' distribution ranges, with most species in the derived lineages having a much wider range than those in the early-diverged lineages. Hybridization and WGD events have been suggested to occur in Causonis based on evidence of phylogenetic discordance. The genus, therefore, provides us with an opportunity to for explore different hybridization and polyploidization modes in lineages with contrasting species' distribution ranges. However, the evolutionary history of Causonis incorporating potential hybridization and WGD events remains to be explored. RESULTS: With plastid and nuclear data from dense sampling, this study resolved the phylogenetic relationships within Causonis and revealed significant cyto-nuclear discordance. Nuclear gene tree conflicts were detected across the genus, especially in the japonica-corniculata clade, which were mainly attributed to gene flow. This study also inferred the allopolyploid origin of the core Causonis species, which promoted the accumulation of stress-related genes. Causonis was estimated to have originated in continental Asia in the early Eocene, and experienced glaciation in the early Oligocene, shortly after the divergence of the early-divergent lineages. The japonica-corniculata clade mainly diversified in the Miocene, followed by temperature declines that may have facilitated secondary contact. Species distribution modeling based on current climate change predicted that the widespread C. japonica tends to be more invasive, while the endemic C. ciliifera may be at risk of extinction. CONCLUSIONS: This study presents Causonis, a genus with complex reticulate evolutionary history, as a model of how hybridization and WGD modes differ in lineages of contrasting species' geographic ranges. It is important to consider specific evolutionary histories and genetic properties of the focal species within conservation strategies.

Development of genomic resources for Wenchengia alternifolia (Lamiaceae) based on genome skimming data.

Wenchengia alternifolia (Lamiaceae), the sole species of the genus Wenchengia is extremely rare and is currently listed as Critically Endangered (CR) on the IUCN Red List. The species had long been considered endemic to Hainan Island, China and was once believed to be extinct until a small remnant population was rediscovered at the type locality in 2010. Four more populations were later found on Hainan and in Vietnam. In order to develop genomic resources for further studies on population genetics and conservation biology of this rare species, we identified infraspecific molecular markers in the present study, using genome skimming data of five individuals collected from two populations on Hainan Island and three populations in Vietnam respectively. The length of plastome of the five individuals varied from 152,961 bp to 150,204 bp, and exhibited a typical angiosperm quadripartite structure. Six plastid hotspot regions with the Pi > 0.01 (trnH-psbA, psbA-trnK, rpl22, ndhE, ndhG-ndhI and rps15-ycf1), 1621 polymorphic gSSRs, as well as 1657 candidate SNPs in 237 variant nuclear genes were identified, thereby providing important information for further genetic studies.

Molecular and morphological evidence for a new species of Pogostemon (Lamiaceae) from Hainan Island, China.

Pogostemonhainanensis, a new species of Lamiaceae from Hainan Island, China, is described. The phylogenetic position of the new species within Pogostemon was investigated based on analyses of the nuclear ribosomal internal transcribed spacer (nrITS) and five plastid markers (viz. matK, psbA-trnH, rbcL, rsp16, trnL-F). The results show that P.hainanensis is supported to be a member of subgenus Pogostemon and is sister to P.parviflorus, a species widely distributed from Eastern Himalaya, through the Indo-China peninsula to China. Morphologically, the new species can be distinguished from all the other taxa of subgenus Pogostemon in having long petioles usually 4.5‒11.5 cm in length, and the calyx teeth 2/3 to subequal as long as the calyx tube. The new species differs from P.parviflorus further by its obviously double serrate leaf margin, spikes of inflorescence usually 2.5-8.0 cm long, calyx 4‒5 mm long and corolla 6-7 mm long.

The complete chloroplast genome sequence of Phyllagathi hainanensis (Melastomataceae) and phylogenetic analysis.

Phyllagathi hainanensis (Merr. et Chun) C. Chen is a small shrubs of Melastomataceae. It is only distributed in Hainan provinces of China. The complete chloroplast genome of P. hainanensis is reported in this study. The complete chloroplast genome of P. hainanensis is 156,123 bp in length with a typical quadripartite structure, consisting of a large single-copy region (LSC, 85,497 bp), a single-copy region (SSC, 17,076 bp), and a pair of inverted repeats (IRs, 26,775 bp). There are 129 genes annotated, including 37 transfer RNA genes, 8 ribosomal RNA genes, and 84 proteincoding genes. The complete plastome sequence of P. hainanensis will provide a useful resource for phylogenetic studies in Melastomataceae.

Characterization of the complete chloroplast genome of Scorpiothyrsus erythrotrichus (Melastomataceae), an endemic to Hainan.

Scorpiothyrsus erythrotrichus belongs to Melastomataceae. Here, we present its complete plastome. To our knowledge, this is the first reported complete chloroplast genome of S. erythrotrichus. The complete plastome of S. erythrotrichus is 160,731 bp in length with a typical quadripartite structure, consisting of four regions: large single-copy (LSC) region (85,483 bp), small single-copy (SSC) region (17,007 bp), and two inverted repeat regions (IRs, 26,780 bp). It contains 128 genes (79 coding genes, four rRNAs, and 30 tRNAs). The overall GC content is 36.9% and in the LSC, SSC, and IR regions are 34.70%, 30.40%, and 42.50%, respectively. Our study contributes to the molecular phylogenetic studies of Scorpiothyrsus and Melastomataceae.

Comparative Plastome Analysis of Root- and Stem-Feeding Parasites of Santalales Untangle the Footprints of Feeding Mode and Lifestyle Transitions.

In plants, parasitism triggers the reductive evolution of plastid genomes (plastomes). To disentangle the molecular evolutionary associations between feeding on other plants below- or aboveground and general transitions from facultative to obligate parasitism, we analyzed 34 complete plastomes of autotrophic, root- and stem-feeding hemiparasitic, and holoparasitic Santalales. We observed inexplicable losses of housekeeping genes and tRNAs in hemiparasites and dramatic genomic reconfiguration in holoparasitic Balanophoraceae, whose plastomes have exceptionally low GC contents. Genomic changes are related primarily to the evolution of hemi- or holoparasitism, whereas the transition from a root- to a stem-feeding mode plays no major role. In contrast, the rate of molecular evolution accelerates in a stepwise manner from autotrophs to root- and then stem-feeding parasites. Already the ancestral transition to root-parasitism coincides with a relaxation of selection in plastomes. Another significant selectional shift in plastid genes occurs as stem-feeders evolve, suggesting that this derived form coincides with trophic specialization despite the retention of photosynthetic capacity. Parasitic Santalales fill a gap in our understanding of parasitism-associated plastome degeneration. We reveal that lifestyle-genome associations unfold interdependently over trophic specialization and feeding mode transitions, where holoparasitic Balanophoraceae provide a system for exploring the functional realms of plastomes.

Tissue-specific and maturity-dependent distribution of pyridine alkaloids in Areca triandra.

Areca nuts (seeds of Areca catechu L.) are a traditional and popular masticatory in India, Bangladesh, Malaysia, certain parts of China, and some other countries. Four related pyridine alkaloids (arecoline, arecaidine, guvacoline, and guvacine) are considered being the main functional ingredients in areca nut. Until now, A. catechu is the only known species producing these alkaloids in the Arecaceae family. In the present study, we investigated alkaloid contents in 12 Arecaceae species and found that only Areca triandra Roxb. contained these pyridine alkaloids. We further analyzed in more detail tissue-specific and development-related distribution of these alkaloids in leaves, male and female flowers and fruits in different stages of maturity in A. triandra by ultra-performance liquid chromatography-quadrupole/time-of-flight mass spectrometry. Results revealed that the alkaloids were most abundant in young leaves, the pericarp of ripe fruits and the endosperm of unripe fruits in developmental stage 2. Abundance of the 4 different alkaloids in A. triandra fruits varied during maturation. Pericarps of ripe fruits had the highest arecaidine concentration (4.45 mg g-1) and the lowest guvacoline concentration (0.0175 mg g-1), whereas the endosperm of unripe fruits of developmental stage 2 contained the highest guvacoline concentration (3.39 mg g-1) and the lowest guvacine concentration (0.245 mg g-1). We conclude that A. triandra is useful in future as a further valuable source of Areca alkaloids.

Correction: Taxonomic and phylogenetic diversity of vascular plants at Ma'anling volcano urban park in tropical Haikou, China: Reponses to soil properties.

[This corrects the article DOI: 10.1371/journal.pone.0198517.].

Taxonomic and phylogenetic diversity of vascular plants at Ma'anling volcano urban park in tropical Haikou, China: Reponses to soil properties.

Anthropogenic processes and socio-economic factors play important roles in shaping plant diversity in urban parks. To investigate how plant diversity of Ma' anling urban volcano park in Hainan Province, China respond to these factors, we carried out a field investigation on the taxonomic and phylogenetic diversity of vascular plants and soil properties in this area. We found 284 species of vascular plants belonging to 88 families and 241 genera, which included 194 native species, 23 invasive species, 31 naturalized species, 40 cultivars, and 4 rare / endangered plant species. Tree composition and richness significantly varied between different vegetation formations (plantation, secondary forest, and abandoned land). Plant species richness and community composition were significantly affected by elevation (El), soil water content (WC), total soil nitrogen (TN) and soil organic matter (SOM). There were significant diversity differences between plantations and abandoned lands, but not between the plantations and secondary forests. The flora in the study site was tropical in nature, characterized by pantropic distributions. Compared to adjacent areas, floristic composition in the study site was most similar to that of Guangdong, followed by that of Vietnam. Our study revealed the diversity patterns of volcanic plants and provided the basis for future planning of plant conservation, such as preserving plant species, maintaining plant habitats, and coordinating plant management in this region.

Complete chloroplast genome sequence of Scurrula notothixoides (Loranthaceae): a hemiparasitic shrub in South China.

Scurrula notothixoides (Loranthaceae) is a hemiparasitic shrub distributed in forest margins of Southeast Asian countries. Here, we report and characterize the complete plastid genome sequence of S. notothixoides in an effort to provide genomic resources useful for the phylogenetic studies for Santalales. The complete plastome is 123,810 bp in length and contains the typical structure and gene content of angiosperm plastomes, including two inverted repeat (IR) regions of 23,101 bp, a large single copy (LSC) region of 71,448 bp and a small single copy (SSC) region of 6160 bp. The plastome contains 88 genes, consisting of 61 unique protein-coding genes, 23 unique tRNA genes and four unique rRNA genes. The overall A/T content in the plastome of S. notothixoides is 62.7%. Phylogenetic analyses were performed using the entire plastome, including spacers, introns, etc. and we recovered that S. notothixoides and Taxillus sutchuenensis was closely related. The complete plastome sequence of S. notothixoides will provide a useful resource for the phylogenetic studies for Santalales.