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.

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.

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.