Phytop: a tool for visualizing and recognizing signals of incomplete lineage sorting and hybridization using species trees output from ASTRAL.

Incomplete lineage sorting (ILS) and introgression/hybridization (IH) are prevalent in nature and thus frequently result in discrepancies within phylogenetic tree topologies, leading to misinterpretation of phylogenomic data. Despite the availability of numerous tools for detecting ILS and IH among species, many of these tools lack effective visualization, or are time-consuming, or require prior predetermination. Here, we addressed these shortcomings by developing a fast-running, user-friendly tool called Phytop.

Characterization of chloroplast genome and phylogenetic analysis of the Elaeagnus hybrid variety E. 'viridis' (Elaeagnaceae).

'viridis', an artificial hybrid of (♂) Thunb. (1784) × (♀) Thunb. (1784), is known for its economic and ecological value.

Anthocyanin metabolism in Nelumbo: translational and post-translational regulation control transcription.

Background: Lotus (Nelumbo Adans.) is used as an herbal medicine and the flowers are a source of natural flavonoids. 'Da Sajin', which was firstly found in the plateau area, is a natural mutant in flower color with red streamers dyeing around white petals.

Chromosome-Level Genome Assembly of a Fragrant Rice Cultivar 'Changxianggeng 1813' Provides Insights into Genomic Variations between Fragrant and Non-Fragrant Rice.

East Asia has an abundant resource of fragrant japonica rice that is gaining increasing interest among both consumers and producers. However, genomic resources and in particular complete genome sequences currently available for the breeding of fragrant japonica rice are still scarce. Here, integrating Nanopore long-read sequencing, Illumina short-read sequencing, and Hi-C methods, we presented a high-quality chromosome-level genome assembly (~378.

Abundant Allelochemicals and the Inhibitory Mechanism of the Phenolic Acids in Water Dropwort for the Control of Blooms.

In recent years, with the frequent global occurrence of harmful algal blooms, the use of plant allelopathy to control algal blooms has attracted special and wide attention. This study validates the possibility of turning water dropwort into a biological resource to inhibit the growth of harmful blooms via allelopathy. The results revealed that there were 33 types of allelopathic compounds in the water dropwort culture water, of which 15 were phenolic acids.

Characterization of the Non-specific Phospholipase C Gene and Its Involvement in the Salt Stress Response.

is a medicinal halophyte that inhabits sandy beaches and has high ecological and commercial value. However, the molecular mechanism of salt adaptation in remains largely unknown. Here, we cloned and identified a non-specific phospholipase C gene () from , which conferred lipid-mediated signaling during the salt stress response.

Characterization and phylogenetic analysis of the complete chloroplast genome of , traditional Chinese medicine plant.

is a traditional Chinese medicine plant. In this study, we characterized the complete chloroplast (cp) genome sequence of to investigate its phylogenetic relationship. The cp genome of was 157,743 bp in length with 37.

The complete chloroplast genome sequence of Sims. (Aquifoliaceae), a folk herbal medicine plant in China.

The complete chloroplast (cp) genome of , an important economic plant with ornamental and ecological values, was sequenced to investigate its phylogenetic relationship. The entire cp genome of was 157,885 bp in length with 37.61% overall GC content, including a large single-copy (LSC) region of 87,289 bp, and a small single-copy (SSC) region of 18,388 bp, which were separated by a pair of inverted repeats (IRs) of 52,208 bp.

The complete chloroplast genome sequence and phylogenetic analysis of Ilex × Koehneana 'Wirt L. Winn' (Aquifoliaceae).

Ilex × Koehneana 'Wirt L. Winn', an important ornamental tree, has been widely distributed in southeastern China. In this study, we assembled and characterized the complete chloroplast (cp) genome of I.

The complete chloroplast genome of 'Tall Boy', × (Aquifoliaceae).

Thecomplete chloroplast (cp) genome of 'Tall Boy', an important economic plant with ornamental and ecological values, was sequenced to investigate its phylogenetic relationship. The entire cp genome of 'Tall Boy' was 157,527 bp in length with 37.65% overall GC content, including a large single-copy (LSC) region of 87,044 bp and a small single-copy (SSC) region of 18,429 bp, which were separated by a pair of inverted repeats (IRs) of 52,054 bp.

The complete chloroplast genome sequence and phylogenetic analysis of 'Beryl', a hybrid of × (Aquifoliaceae).

'Beryl' is an ornamental and ecological tree widespread in southeastern China. In this study, the complete chloroplast (cp) genome of 'Beryl' was assembled and characterized to investigate its phylogenetic relationship. The entire cp genome of 'Beryl' was a typical quadripartite structure with 157,575 bp in length, including a large single-copy (LSC) region of 87,080 bp and a small single-copy (SSC) region of 18,427 bp, which were separated by a pair of inverted repeats (IRs) of 52,068 bp.

The complete chloroplast genome of Ilex 'Emily Bruner', Ilex cornuta 'Burfordii' × Ilex latifolia (Aquifoliaceae).

'Emily Bruner' is an important economic plant with ornamental and ecological functions in southeastern China. In this study, we characterized the complete chloroplast (cp) genome sequence of 'Emily Bruner' to investigate its phylogenetic relationship. The entire cp genome of 'Emily Bruner' was 157,216 bp in length with 37.

Selection and Validation of Reference Genes for Normalisation of Gene Expression in Glehnia littoralis.

Glehnia littoralis is an important medicinal halophyte-the dried root of which is used as Chinese herbal medicine. However, the use, selection and stability of reference genes are rarely verified in studies of G. littoralis, which hampers investigation of its salt tolerance and metabolism.

Nutrients resorption and stoichiometry characteristics of different-aged plantations of Larix kaempferi in the Qinling Mountains, central China.

Elucidating the stoichiometry and resorption patterns of multiple nutrients is of essential importance to holistically understanding plant nutrition and biogeochemical cycling. Although many studies on ecological stoichiometry have been carried out, surprisingly few of them were simultaneously done on the investigation of both nutrient resorption efficiency and stoichiometry for different-aged plantations of a perennial tree. Here, both green and senesced leaf samples were collected from four Larix kaempfer plantations aged of 8, 15, 22, and 32 years in the Qinling Mountains to examine nutrients resorption efficiency and stoichiometry characteristics.

Gene Expression Profile in the Long-Living Lotus: Insights into the Heat Stress Response Mechanism.

Lotus (Nelumbo Adans) is an aquatic perennial plant that flourished during the middle Albian stage. In this study, we characterized the digital gene expression signatures for China Antique lotus under conditions of heat shock stress. Using RNA-seq technology, we sequenced four libraries, specifically, two biological replicates for control plant samples and two for heat stress samples.

Molecular Evidence for the Hybrid Origin of Ilex dabieshanensis (Aquifoliaceae).

Ilex, the largest genus of dioecious woody plants, is a good study system to assess the role of hybridization in speciation and evolution. Ilex dabieshanensis, a tree endemic to Dabieshan Mountains region, was initially described as a new species. Based on morphological intermediacy and sympatric distribution with its putative parental species, I.

[Patch diversity and spatial structure of wild Thymus quinquecostatus].

With the combination of ISSR (inter-simple sequence repeats), SRAP (sequence-related amplified polymorphism) and spatial autocorrelation, the genetic diversity and spatial structure per unit patch of three Huaiyuan populations of Thymus quinquecostatus in southeast China were analyzed. The results showed that there existed higher levels of genetic and clonal diversity among the patches within the wild T. quinquecostatus populations, with the percentage of polymorphic loc being 75.