Complete chloroplast genomes of five Cuscuta species and their evolutionary significance in the Cuscuta genus.

BACKGROUND: Cuscuta, a parasitic plant species in the Convolvulaceae family, grows in many countries and regions. However, the relationship between some species is still unclear. Therefore, more studies are needed to assess the variation of the chloroplast (cp) genome in Cuscuta species and their relationship with subgenera or sections, thus, providing important information on the evolution of Cuscuta species. RESULTS: In the present study, we identified the whole cp genomes of C. epithymum, C. europaea, C. gronovii, C. chinensis and C. japonica, and then constructed a phylogenetic tree of 23 Cuscuta species based on the complete genome sequences and protein-coding genes. The complete cp genome sequences of C. epithymum and C. europaea were 96,292 and 97,661 bp long, respectively, and lacked an inverted repeat region. Most cp genomes of Cuscuta spp. have tetragonal and circular structures except for C. epithymum, C. europaea, C. pedicellata and C. approximata. Based on the number of genes and the structure of cp genome and the patterns of gene reduction, we found that C. epithymum and C. europaea belonged to subgenus Cuscuta. Most of the cp genomes of the 23 Cuscuta species had single nucleotide repeats of A and T. The inverted repeat region boundaries among species were similar in the same subgenera. Several cp genes were lost. In addition, the numbers and types of the lost genes in the same subgenus were similar. Most of the lost genes were related to photosynthesis (ndh, rpo, psa, psb, pet, and rbcL), which could have gradually caused the plants to lose the ability to photosynthesize. CONCLUSION: Our results enrich the data on cp. genomes of genus Cuscuta. This study provides new insights into understanding the phylogenetic relationships and variations in the cp genome of Cuscuta species.

The complete chloroplast genome and phylogenetic analysis of Stewartia sichuanensis (Theaceae), a Chinese endemic tree with narrow distribution.

Stewartia sichuanensis is a rare plant species of Theaceae and is endemic to China. Its distribution area is highly restricted, and genomic information is extremely limited. The present study reports the first complete chloroplast of S. sichuanensis. The chloroplast genome length was 158,903 bp, with a GC content of 37.3%. The chloroplast genome was comprised of an 87,736 bp long large single copy (LSC), an 18,435 bp long small single copy (SSC), and two copies of inverted repeat (IR) regions of 26,366 bp. It contained 129 genes, including 85 encoding, 36 transfer RNA, and eight ribosomal RNA genes. The phylogenetic analysis suggested that S. sichuanensis was closely related to S. laotica and S. pteropetiolata.

Insight into the differences in carbon dots prepared from fish scales using conventional hydrothermal and microwave methods.

The preparation of carbon dots (CDs) from waste fish scales is an attractive and high-value transformation. In this study, fish scales were used as a precursor to prepare CDs, and the effects of hydrothermal and microwave methods on their fluorescence properties and structures were evaluated. The microwave method was more conducive to the self-doping of nitrogen due to rapid and uniform heating. However, the low temperature associated with the microwave method resulted in insufficient dissolution of the organic matter in the fish scales, resulting in incomplete dehydration and condensation and the formation of nanosheet-like CDs, whose emission behavior had no significant correlation with excitation. Although the CDs prepared using the conventional hydrothermal method showed lower nitrogen doping, the relative pyrrolic nitrogen content was higher, which was beneficial in improving their quantum yield. Additionally, the controllable high temperature and sealed environment used in the conventional hydrothermal method promoted dehydration and condensation of the organic matter in the fish scales to form CDs with a higher degree of carbonization, uniform size, and higher C = O/COOH content. CDs prepared using the conventional hydrothermal method exhibited higher quantum yields and excitation wavelength-dependent emission behavior.

Parasitism Shifts the Effects of Native Soil Microbes on the Growth of the Invasive Plant Alternanthera philoxeroides.

Soil microbes play an important role in plant invasion, and parasitic plants regulate the growth of invasive plants. However, the mechanisms by which parasitic plants regulate the effects of soil microbes on invasive plants have not been investigated. Here, we used the invasive plant Alternanthera philoxeroides and the holoparasitic plant Cuscuta grovonii to test whether and how C. grovonii parasitism shifts the effect of native soil microbes on the growth of A. philoxeroides. In a factorial setup, A. philoxeroides was grown in pots with the presence versus absence of parasitism and the presence versus absence of native soil microbes. The findings showed that native soil microbes increased the biomass and clonal growth of A. philoxeroides only in the absence of a parasite, whereas parasitism decreased the biomass and clonal growth of A. philoxeroides only in the presence of soil microbes. In addition, the presence of soil microbes increased the deleterious effects of the parasite on A. philoxeroides. These results indicate that parasitism can shift the effects of native soil microbes on the growth of the invasive plant A. philoxeroides. Our results enrich the understanding of the mechanisms underlying the success of plant invasion.

Adaptive genetic diversity of dominant species contributes to species co-existence and community assembly.

The synthesis of evolutionary biology and community ecology aims to understand how genetic variation within one species can shape community properties and how the ecological properties of a community can drive the evolution of a species. A rarely explored aspect is whether the interaction of genetic variation and community properties depends on the species' ecological role. Here we investigated the interactions among environmental factors, species diversity, and the within-species genetic diversity of species with different ecological roles. Using high-throughput DNA sequencing, we genotyped a canopy-dominant tree species, Parashorea chinensis, and an understory-abundant species, Pittosporopsis kerrii, from fifteen plots in Xishuangbanna tropical seasonal rainforest and estimated their adaptive, neutral and total genetic diversity; we also surveyed species diversity and assayed key soil nutrients. Structural equation modelling revealed that soil nitrogen availability created an opposing effect in species diversity and adaptive genetic diversity of the canopy-dominant Pa. chinensis. The increased adaptive genetic diversity of Pa. chinensis led to greater species diversity by promoting co-existence. Increased species diversity reduced the adaptive genetic diversity of the dominant understory species, Pi. kerrii, which was promoted by the adaptive genetic diversity of the canopy-dominant Pa. chinensis. However, such relationships were absent when neutral genetic diversity or total genetic diversity were used in the model. Our results demonstrated the important ecological interaction between adaptive genetic diversity and species diversity, but the pattern of the interaction depends on the identity of the species. Our results highlight the significant ecological role of dominant species in competitive interactions and regulation of community structure.

Opening a door to the spatiotemporal history of plants from the tropical Indochina Peninsula to subtropical China.

The complexity of global biodiversity in the tropical Indochina Peninsula and subtropical China bioregions has fascinated biologists for decades, but little is known about the spatiotemporal patterns in these regions. Accordingly, the aims of present study were to investigate the evolutionary and distribution patterns of Engelhardia in these regions and establish a model for examining biogeographic patterns and geological events throughout the tropical Indochina Peninsula and subtropical China. The effects of geological events occurring in the area between the Indochina Peninsula and subtropical China bioregions on the two trees species (i.e., E. roxburghiana and E. fenzelii) were evaluated. A robust phylogenetic framework of 884 individuals from 79 populations was used to generate time-calibrated cytoplasmic and nuclear phylogenetic frameworks based on cpDNA, nrDNA, and nSSR data, respectively. When considered along with ancestral area reconstructions, the genetic data were also used to assess and reconstruct the species' population genetic structure and diversity. These analyses yielded important information about the (1) historical distribution relationships between the tropical and subtropical flora of China; (2) effects of the East Asian summer monsoon (EASM) on the evolutionary history of Asia's plants; and (3) importance of biogeography in conservation planning. Although cytoplasmic-nuclear discordance indicated cpDNA and nrDNA were subject to distinct evolutionary mechanisms that reflected respective evolutionary histories of the plastid and nuclear genomes of prior demographic and biogeographic events. The tropical elements of Engelhardia occupied the Indochina Peninsula during the early Eocene, whereas the subtropical elements were transformed from the tropical elements during Miocene cooling and the onset of the EASM at the Oligocene-Miocene boundary, intensified during the late Miocene and Pliocene, facilitating the transformation of Engelhardia from the tropical Indochina Peninsula to subtropical China. Demographic history provided insights into prominent planning frameworks in conservation biology, namely that subtropical China functioned as a refugium during past climate oscillations and will continue to serve in this capacity in the future.

Variation and Evolution of the Whole Chloroplast Genomes of Fragaria spp. (Rosaceae).

Species identification is vital for protecting species diversity and selecting high-quality germplasm resources. Wild Fragaria spp. comprise rich and excellent germplasm resources; however, the variation and evolution of the whole chloroplast (cp) genomes in the genus Fragaria have been ignored. In the present study, 27 complete chloroplast genomes of 11 wild Fragaria species were sequenced using the Illumina platform. Then, the variation among complete cp genomes of Fragaria was analyzed, and phylogenetic relationships were reconstructed from those genome sequences. There was an overall high similarity of sequences, with some divergence. According to analysis with mVISTA, non-coding regions were more variable than coding regions. Inverted repeats (IRs) were observed to contract or expand to different degrees, which resulted in different sizes of cp genomes. Additionally, five variable loci, trnS-trnG, trnR-atpA, trnC-petN, rbcL-accD, and psbE-petL, were identified that could be used to develop DNA barcoding for identification of Fragaria species. Phylogenetic analyses based on the whole cp genomes supported clustering all species into two groups (A and B). Group A species were mainly distributed in western China, while group B contained several species from Europe and Americas. These results support allopolyploid origins of the octoploid species F. chiloensis and F. virginiana and the tetraploid species F. moupinensis and F. tibetica. The complete cp genomes of these Fragaria spp. provide valuable information for selecting high-quality Fragaria germplasm resources in the future.

Complete chloroplast genome sequence of Mirabilis himalaica (Nyctaginaceae).

Mirabilis himalaica (Nyctaginaceae) is endemic to the Himalayas where it is used in traditional Tibetan folk medicine. In this study, we first presented the complete chloroplast genome of M. himalaica. Complete genome size of M. himalaica ranged from 154,348 to 154,388 bp. The length varied from 85,808 to 85,845 bp in the (large single-copy) LSC region, from 17,935 to 17,938 bp in the (small single-copy) SSC region, and from 25,302 to 25,303 bp in the inverted repeat (IR) region. The overall GC contents of the chloroplast genome sequences were around 36%. Annotation analysis revealed a total of 112 genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis with three M. himalaica samples and five other Nyctaginaceae species showed that Mirabilis including two species was clustered with high bootstrap support. The complete chloroplast genome sequences obtained in this study will provide valuable data for wider studies into the phylogenetics and conservation biology of M. himalaica.

Design and evaluation of a brinzolamide drug-resin in situ thermosensitive gelling system for sustained ophthalmic drug delivery.

In this study a brinzolamide drug-resin ophthalmic thermosensitive in situ gelling system was developed and evaluated. Brinzolamide was combined with ion exchange resins to prolong the retention time of drugs in the eye and to reduce ocular and systemic side effects. Poloxamer F127 was used as gelling vehicle in combination with carbopol 934P, which acted as a viscosity-enhancing agent. They were prepared using the cold method. The optimized formulation exhibited a sol-gel transition at 33.2±1.1°C with pseudoplastic flow behavior. This formulation was stable and nonirritant to rabbit eyes. In vitro release studies demonstrated diffusion-controlled release of brinzolamide from the combined solutions over a period of 8 h. In vivo evaluation (the elimination of brinzolamide through tears and absorption of brinzolamide in aqueous humor) indicated that the solution combination was better able to retain the drug than commercial preparations. Thus this formulation is safe for ophthalmic use and significantly increases brinzolamide bioavailability in aqueous humor.