Skmer approach improves species discrimination in taxonomically problematic genus (Theaceae).

Genome skimming has dramatically extended DNA barcoding from short DNA fragments to next generation barcodes in plants. However, conserved DNA barcoding markers, including complete plastid genome and nuclear ribosomal DNA (nrDNA) sequences, are inadequate for accurate species identification. Skmer, a recently proposed approach that estimates genetic distances among species based on unassembled genome skims, has been proposed to effectively improve species discrimination rate.

The gut microbiota-aromatic hydrocarbon receptor (AhR) axis mediates the anticolitic effect of polyphenol-rich extracts from .

Inflammatory bowel disease (IBD) is a significant global health concern. The gut microbiota plays an essential role in the onset and development of IBD. (SH), a traditional Chinese medicinal mushroom, has excellent anti-inflammatory effects and is effective at modulating the gut microbiota.

Young evolutionary origins of dioecy in the genus Asparagus.

Premise: Dioecy (separate sexes) has independently evolved numerous times across the angiosperm phylogeny and is recently derived in many lineages. However, our understanding is limited regarding the evolutionary mechanisms that drive the origins of dioecy in plants. The recent and repeated evolution of dioecy across angiosperms offers an opportunity to make strong inferences about the ecological, developmental, and molecular factors influencing the evolution of dioecy, and thus sex chromosomes.

Phylogenetic Relationships and Next-Generation Barcodes in the Genus Reveal a High Proportion of Misidentified Cultivated Plants.

Accurate species identification is key to conservation and phylogenetic inference. Living plant collections from botanical gardens/arboretum are important resources for the purpose of scientific research, but the proportion of cultivated plant misidentification are un-tested using DNA barcodes. Here, we assembled the next-generation barcode (complete plastid genome and complete nrDNA cistron) and mitochondrial genes from genome skimming data of species with multiple accessions for each species to test the species discrimination and the misidentification proportion of cultivated plants used in studies.

[Advances and Prospect of Sampling Techniques and Analytical Methods for Trace Elements in the Ocean: Progress of Trace Element Platform Construction in Xiamen University].

Trace elements, which are important chemical components in the ocean, generally refer to those chemical elements with concentrations below 10 μmol·kgin seawater. Some trace elements, such as Fe and Zn, serve as essential micronutrients for marine organisms, which regulate marine primary productivity and are closely related to the biogeochemical cycle of carbon and nitrogen and therefore affect the global environment and climate change. In contrast, some elements, such as Pb, are anthropogenic pollutants largely released by human activities.

Phylogenomics and the flowering plant tree of life.

The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent.

DNA barcoding of Cymbidium by genome skimming: Call for next-generation nuclear barcodes.

Cymbidium is an orchid genus that has undergone rapid radiation and has high ornamental, economic, ecological and cultural importance, but its classification based on morphology is controversial. The plastid genome (plastome), as an extension of plant standard DNA barcodes, has been widely used as a potential molecular marker for identifying recently diverged species or complicated plant groups. In this study, we newly generated 237 plastomes of 50 species (at least two individuals per species) by genome skimming, covering 71.

Species discrimination in Schima (Theaceae): Next-generation super-barcodes meet evolutionary complexity.

Plastid genome and nuclear ribosomal DNA (nrDNA) arrays, proposed recently as "super-barcodes," might provide additional discriminatory power and overcome the limitations of traditional barcoding loci, yet super-barcodes need to be tested for their effectiveness in more plant groups. Morphological homoplasy among Schima species makes the genus a model for testing the efficacy of super-barcodes. In this study, we generated multiple data sets comprising standard DNA barcodes (matK, rbcL, trnH-psbA, nrITS) and super-barcodes (plastid genome, nrDNA arrays) across 58 individuals from 12 out of 13 species of Schima from China.

Blood Lead and High-Density Lipoprotein Concentrations in Relation to Human Blood Pressure: A Cross Sectional Study.

Background: While the relationship between blood pressure and blood lead has been studied more extensively, the effect of high-density lipoprotein (HDL) concentration on this relationship remains uncertain. Therefore, this study aimed to determine the effect of HDL concentration on the relationship between blood lead and blood pressure.

Methods: The research used cross-sectional data from the 2005 to 2014 National Health and Nutrition Examination Survey (NHANES), which included 16,451 participants aged 20-60 years.

Testing the Complete Plastome for Species Discrimination, Cryptic Species Discovery and Phylogenetic Resolution in (Cephalotaxaceae).

Species of have great economic and ecological values. However, the taxonomy and interspecific phylogenetic relationships within the genus have been controversial and remained not fully resolved until now. To date, no study examined the efficiency of the complete plastome as super-barcode across species with multiple samples per taxon.

Genome Skimming Contributes to Clarifying Species Limits in Section (Melanthiaceae).

Paris L. section H. Li (Melanthiaceae) is a taxonomically perplexing taxon with considerable confusion regarding species delimitation.

Cryptic Species Diversification of the Complex (Orobanchaceae) in the Mountains of Southwest China Since the Pliocene.

Morphological approaches often fail to delimit species in recently derived species complexes. This can be exacerbated in historical collections which may have lost key features in specimen preparation and preservation. Here, we examine the complex, endemic to the Mountains of Southwest China.

Organelle Phylogenomics and Extensive Conflicting Phylogenetic Signals in the Monocot Order Poales.

The Poales is one of the largest orders of flowering plants with significant economic and ecological values. Reconstructing the phylogeny of the Poales is important for understanding its evolutionary history that forms the basis for biological studies. However, due to sparse taxon sampling and limited molecular data, previous studies have resulted in a variety of contradictory topologies.

Organelle Genomes and Transcriptomes of Reveal the Interplay between Intron Splicing and RNA Editing.

Posttranscriptional modifications, including intron splicing and RNA editing, are common processes during regulation of gene expression in plant organelle genomes. However, the intermediate products of intron-splicing, and the interplay between intron-splicing and RNA-editing were not well studied. Most organelle transcriptome analyses were based on the Illumina short reads which were unable to capture the full spectrum of transcript intermediates within an organelle.

Plastome Evolution in the Hyperdiverse Genus (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region.

With 2,000 species, is one of the largest angiosperm genera, yet a lack of chloroplast genome (plastome) resources impedes a better understanding of its evolution. In this study, we assembled and annotated 28 plastomes from Euphorbiaceae, of which 15 were newly sequenced. Phylogenomic and comparative analyses of 22 plastome sequences from all four recognized subgenera within revealed that plastome length in is labile, presenting a range of variation 42 kb.

Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron.

Standard plant DNA barcodes based on 2-3 plastid regions, and nrDNA ITS show variable levels of resolution, and fail to discriminate among species in many plant groups. Genome skimming to recover complete plastid genome sequences and nrDNA arrays has been proposed as a solution to address these resolution limitations. However, few studies have empirically tested what gains are achieved in practice.

Plastid NDH Pseudogenization and Gene Loss in a Recently Derived Lineage from the Largest Hemiparasitic Plant Genus Pedicularis (Orobanchaceae).

The plastid genome (plastome) is highly conserved in both gene order and content and has a lower mutation rate than the nuclear genome. However, the plastome is more variable in heterotrophic plants. To date, most such studies have investigated just a few species or only holoheterotrophic groups, and few have examined plastome evolution in recently derived lineages at an early stage of transition from autotrophy to heterotrophy.

assembling a complete mitochondrial genome of (Orobanchaceae) using GetOrganelle toolkit.

We reported the first mitogenome of from (Orobanchaceae), which is endemic to SW China. The complete mitochondrial genome (mitogenome or chondriome) was a single circular chromosome that was 219,859 bp in length. It contains 56 genes, including 34 protein-coding ( and with two copies), 19 transfer RNA (tRNA), and three ribosomal RNA (rRNA) genes.

GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes.

GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads using a modified "baiting and iterative mapping" approach, conducts de novo assembly, filters and disentangles the assembly graph, and produces all possible configurations of circular organelle genomes. For 50 published plant datasets, we are able to reassemble the circular plastomes from 47 datasets using GetOrganelle.