Two novel SiC phases: structure, mechanical, and transport properties

Two novel phases of SiC are put forward in this paper, in which the crystal structural, mechanical, and electronic properties, as well as effective mass and carrier mobility of SiC in the Pnnm phase ( Pnnm -SiC) and Pm phase ( Pm -SiC) are researched utilizing first principles calculations. Both of the novel SiC phases are certificated to have good mechanical and dynamic stability. Through analysis of the three-dimensional perspective of Young’s modulus, shear modulus and Poisson’s ratio, visible anisotropies of mechanical properties are found. The band structure calculations predict two wide bandgap semiconductors, that the Pnnm -SiC is an indirect with a bandgap value of 3.12 eV, While the Pm -SiC is a quasi-direct with a bandgap value of 2.64 eV, which indicates the Pm -SiC has a higher application potential in the optoelectronic device area. An extremely large electronic mobility (7200 cm ^2 V ^−1 s ^−1 ) is found in the Pnnm -SiC. Based on the wide band gap, large carrier mobility, good mechanical and dynamic stability, the Pnnm -SiC is a promising material in the field of high performance electronic device in harsh environment

Characterization of the complete mitochondrial genome of Haemadipsa tianmushana Song 1977 (Hirudiniformes, Haemadipsidae) and its phylogenetic analysis

The complete mitochondrial genome of Haemadipsa tianmushana Song 1977 from China has been determined and reported for the first time in this study. It was 14,625 bp in length and consisted of 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes (PCGs), and 3 control regions. The nucleotide base content of the complete mitogenome for this species was 35.1% A, 10.5% C, 11.6% G, and 42.8% T. The tRNA genes were ranged from 57 bp (SerTCT) to 66 bp (GlnTTG) in length. The phylogenetic analyses indicated that Hirudinea is a mono-phyletic clade. And it includes Whitmania acranulata, Whitmania pigra, Whitmania laevis, Zeylanicobdella arugamensis, Ozobranchus jantseanus and Placobdella lamothei. In Hirudiniformes, H. tianmushana and three species of Haemopidae were obviously clustered into two independent branches. This result is consistent with a taxonomy that they all belong to the same suborder. This study adds to the genetic resources currently available for the species

First-Principles Study on III-Nitride Polymorphs: AlN/GaN/InN in the Pmn21 Phase

The structural, mechanical, and electronic properties, as well as stability, elastic anisotropy and effective mass of AlN/GaN/InN in the Pmn21 phase were determined using density functional theory (DFT). The phonon dispersion spectra and elastic constants certify the dynamic and mechanical stability at ambient pressure, and the relative enthalpies were lower than those of most proposed III-nitride polymorphs. The mechanical properties reveal that Pmn21-AlN and Pmn21-GaN possess a high Vickers hardness of 16.3 GPa and 12.8 GPa. Pmn21-AlN, Pmn21-GaN and Pmn21-InN are all direct semiconductor materials within the HSE06 hybrid functional, and their calculated energy band gaps are 5.17 eV, 2.77 eV and 0.47 eV, respectively. The calculated direct energy band gaps and mechanical properties of AlN/GaN/InN in the Pmn21 phase reveal that these three polymorphs may possess great potential for industrial applications in the future

The complete chloroplast genome and phylogenetic analysis of Bupleurum yinchowense Shan & Yin Li

Bupleurum yinchowense Shan & Yin Li was first described as a new Bupleurum species in 1974, but its classification status has always been disputed. Here, its complete chloroplast genome was provided to resolve this issue. The length of the B. yinchowense chloroplast genome is 155,851 bp and composed of two inverted repeats (IR: 26,307 bp), a large single-copy region (LSC: 85,625 bp), and a small single-copy region (SSC: 17,612 bp). The overall GC content is 37.6%. The chloroplast genome consists of 113 genes, including 79 protein-coding genes, four rRNA genes, and 30 tRNA genes. Phylogenetic analysis suggested that Bupleurum yinchowense holds a distinct phylogenetic position and can be considered as an accepted species

Validation of the shotgun metabarcoding approach for comprehensively identifying herbal products containing plant, fungal, and animal ingredients.

Identifying plant, fungal, and animal ingredients in a specific mixture remains challenging during the limitation of PCR amplification and low specificity of traditional methods. Genomic DNA was extracted from mock and pharmaceutical samples. Four type of DNA barcodes were generated from shotgun sequencing dataset with the help of a local bioinformatic pipeline. Taxa of each barcode was assigned by blast to TCM-BOL, BOLD, and GenBank. Traditional methods including microscopy, thin layer chromatography (TLC), and high-performance liquid chromatography (HPLC) were carried out according to Chinese pharmacopoeia. On average, 6.8 Gb shotgun reads were sequenced from genomic DNA of each sample. Then, 97, 11, 10, 14, and one operational taxonomic unit (OTU) were generated for ITS2, psbA-trnH, rbcL, matK, and COI, respectively. All the labeled ingredients including eight plant, one fungal, and one animal species were successfully detected in both the mock and pharmaceutical samples, in which Chebulae Fructus, Poria, and Fritilariae Thunbergia Bulbus were identified via mapping reads to organelle genomes. In addition, four unlabeled plant species were detected from pharmaceutical samples, while 30 genera of fungi, such as Schwanniomyces, Diaporthe, Fusarium were detected from mock and pharmaceutical samples. Furthermore, the microscopic, TLC, and HPLC analysis were all in accordance with the standards stipulated by Chinese Pharmacopoeia. This study indicated that shotgun metabarcoding could simultaneously identified plant, fungal, and animal ingredients in herbal products, which has the ability to serve as a valuable complement to traditional methods

Division of developmental phases of freshwater leech Whitmania pigra and key genes related to neurogenesis revealed by whole genome and transcriptome analysis

Abstract The freshwater leech Whitmania pigra (W. pigra) Whitman (Annelida phylum) is a model organism for neurodevelopmental studies. However, molecular biology research on its embryonic development is still scarce. Here, we described a series of developmental stages of the W. pigra embryos and defined five broad stages of embryogenesis: cleavage stages, blastocyst stage, gastrula stage, organogenesis and refinement, juvenile. We obtained a total of 239.64 Gb transcriptome data of eight representative developmental phases of embryos (from blastocyst stage to maturity), which was then assembled into 21,482 unigenes according to our reference genome sequenced by single-molecule real-time (SMRT) long-read sequencing. We found 3114 genes differentially expressed during the eight phases with phase-specific expression pattern. Using a comprehensive transcriptome dataset, we demonstrated that 57, 49 and 77 DEGs were respectively related to morphogenesis, signal pathways and neurogenesis. 49 DEGs related to signal pathways included 30 wnt genes, 14 notch genes, and 5 hedgehog genes. In particular, we found a cluster consisting of 7 genes related to signal pathways as well as synapses, which were essential for regulating embryonic development. Eight genes cooperatively participated in regulating neurogenesis. Our results reveal the whole picture of W. pigra development mechanism from the perspective of transcriptome and provide new clues for organogenesis and neurodevelopmental studies of Annelida species

Phylogenomic analyses based on the plastid genome and concatenated nrDNA sequence data reveal cytonuclear discordance in genus Atractylodes (Asteraceae: Carduoideae)

Atractylodes species are widely distributed across East Asia and are cultivated as medicinal herbs in China, Japan, and Korea. Their unclear morphological characteristics and low levels of genetic divergence obscure the taxonomic relationships among these species. In this study, 24 plant samples were collected representing five species of Atractylodes located in China; of these, 23 belonged to members of the A. lancea complex. High-throughput sequencing was used to obtain the concatenated nrDNA sequences (18S-ITS1-5.8S-ITS2-28S) and plastid genomes. The concatenated nrDNA sequence lengths for all the Atractylodes species were 5,849 bp, and the GC content was 55%. The lengths of the whole plastid genome sequences ranged from 152,138 bp (A. chinensis) to 153,268 bp (A. lancea), while their insertion/deletion sites were mainly distributed in the intergenic regions. Furthermore, 33, 34, 36, 31, and 32 tandem repeat sequences, as well as 30, 30, 29, 30, and 30 SSR loci, were detected in A. chinensis, A. koreana, A. lancea, A. japonica, and A. macrocephala, respectively. In addition to these findings, a considerable number of heteroplasmic variations were detected in the plastid genomes, implying a complicated phylogenetic history for Atractylodes. The results of the phylogenetic analysis involving concatenated nrDNA sequences showed that A. lancea and A. japonica formed two separate clades, with A. chinensis and A. koreana constituting their sister clade, while A. lancea, A. koreana, A. chinensis, and A. japonica were found based on plastid datasets to represent a mixed clade on the phylogenetic tree. Phylogenetic network analysis suggested that A. lancea may have hybridized with the common ancestor of A. chinensis and A. japonica, while ABBA-BABA tests of SNPs in the plastid genomes showed that A. chinensis was more closely related to A. japonica than to A. lancea. This study reveals the extensive discordance and complexity of the relationships across the members of the A. lancea complex (A. lancea, A. chinensis, A. koreana, and A. japonica) according to cytonuclear genomic data; this may be caused by interspecific hybridization or gene introgression

Additional file 10 of Division of developmental phases of freshwater leech Whitmania pigra and key genes related to neurogenesis revealed by whole genome and transcriptome analysis

Additional file 10: Table S8. RNA-Seq results of eight phases