Search

Castanopsis orthacantha Franch. 1899 is one representative tree species distributed in the evergreen broad-leaved forests of southwestern China. This species is an important source of timber for manufacturing furniture, floors, and paper. It also plays a significant role in maintaining ecological balance and stability. To help with the genetic diversity assessment of C. orthacantha, we sequenced and assembled the first complete chloroplast genome. The length of the chloroplast genome was 160,588 bp, with a typical quadripartite structure (GenBank accession no. OR900101). The large single-copy (LSC), small single-copy (SSC), and two inverted repeats (IRs) were 90,237 bp, 18,953 bp, and 25,699 bp in length, respectively. We annotated one hundred and thirty genes across the chloroplast genome, including 86 protein-coding genes (79 are unique), 37 tRNA genes (29 are unique), and eight rRNA genes (four are unique). Seventeen genes had one intron, and four were detected with two introns. The maximum likelihood phylogeny suggested that C. orthacantha, C. lamontii, C. sclerophylla, and C. hainanensis formed a clade with a high bootstrap value. This newly sequenced chloroplast genome assembly will aid in the population genetic and phylogenetic studies of Castanopsis species in the future. [ABSTRACT FROM AUTHOR]

The mountainous region of southern China has been characterized by its complicated environment and topography. Amorphophallus kiusianus Makino 1913 is a representative species of extreme habitat preference that resides mainly in this region. To help study the genetic differentiation mechanisms of A. kiusianus populations, we sequenced the first chloroplast genome of this species using next-generation sequencing. The chloroplast genome was 166,269 bp in length with an average GC content of 36% (GenBank accession number: PP072243). The lengths of the large single-copy region (LSC), small single-copy region (SSC), and two inverted repeats (IRs) were 90,701 bp, 14,802 bp, 31,383 bp, and 31,383 bp, respectively. One hundred and twenty-nine genes were annotated in the chloroplast genome, including 84 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The phylogenetic tree suggested a close relationship among A. kiusianus, A. yunnanensis, and A. coaetaneus. The chloroplast genome reported in this study provides valuable genomic resources for the future phylogeographic research of A. kiusianus. [ABSTRACT FROM AUTHOR]

Konjac glucomannan consists of D-mannose and D-glucose units and is a hydrocolloid obtained from the corm of Amorphophallus species. Due to its bioactive properties, biodegradability, and hydrophilic ability, glucomannan is widely used in the fields of food, medicine, and industry. Amorphophallus species have been cultivated as cash crops in many Asian countries. Amorphophallus kachinensis Engler & Gehrmann 1911 is naturally distributed in southwestern China, Laos, and northern Thailand. To help the genetic assessment and conservation of this species, the first chloroplast genome of A. kachinensis was sequenced on the Illumina sequencing platform. We assembled the chloroplast genome using the software GetOrganelle and annotated the genome by Geseq and Cpgavas 2. The assembled chloroplast genome was 173,330 bp long, and the average GC content was 35% (GenBank accession number: PP072244). The chloroplast genome of A. kachinensis contained one large single copy, one small single copy, and two inverted repeats, with lengths of 92,030 bp, 15,118 bp, 33,091 bp, and 33,091 bp, respectively. We successfully annotated 132 genes across the genome, which was consistent with other Amorphophallus species. The phylogenetic tree indicates a sub-divergence in the Amorphophallus genus with two main genetic groups detected among eight species. The two genetic groups should be treated as distinct evolutionarily significant units when making conservation strategies. Our study enriched the chloroplast genome resources of the Amorphophallus genus and could help future phylogeographic studies, protection, and utilization of wild resources. [ABSTRACT FROM AUTHOR]

Southwestern China is a biodiversity hotspot due to its diverse topography and environment. Amorphophallus yunnanensis is a species of perennial herb that is mainly distributed throughout southwestern China. The genetic diversity and divergence in this species have not been assessed largely due to a lack of genomic resources. To help with the phylogeographic study, we sequenced and assembled the first complete chloroplast genome sequence of A. yunnanensis. The length of the chloroplast genome was 164,417 bp, with an average GC content of 36% (GenBank accession no. OR400247). The genome possessed a typical quadripartite structure, and the lengths of the large single-copy (LSC), small single-copy (SSC), and two inverted repeat (IR) regions were 92,149 bp, 15,182 bp, 28,543bp, and 28,543bp, respectively. A total of 128 genes were annotated across the genome, including 82 protein-coding genes, 8 rRNAs, and 38 tRNAs. The maximum likelihood (ML) phylogeny confirmed the phylogenetic position of Amorphophallus within Araceae, with the Amorphophallus species forming a single monophyletic clade with a high bootstrap value. The ML tree also indicated that A. yunnanensis was most closely related to A. coaetaneus. This newly sequenced chloroplast genome assembly will aid in future studies of genetic diversity, historical population dynamics, and geographic differentiation patterns of A. yunnanensis. [ABSTRACT FROM AUTHOR]

Plants in the genus Amorphophallus, many of which possess high konjac glucomannan content, are considered important cash crops in many Asian countries. Wild relatives of cultivated Amorphophallus species are valuable resources for the genetic improvement of these crops. To aid in future genetic research of wild germplasm resources of Amorphophallus, a single individual of Amorphophallus krausei Engler, Pflanzenr 1911 was collected from southwestern China, and its chloroplast genome was sequenced using next-generation sequencing technologies. The assembled chloroplast genome was 172,418 bp in length with a GC content of 35.23% (GenBank accession no. OR416863). A typical quadripartite structure was found in the genome, which was comprised of one large single-copy (LSC), one small single-copy (SSC), and two inverted repeats (IRs), with lengths of 91,983 bp, 15,591 bp, 32,422 bp, and 32,422 bp, respectively. A total of 132 genes were annotated in the genome, including 86 protein-coding genes, 38 tRNAs, and 8 rRNAs. A maximum likelihood (ML) tree of A. krausei and 17 other species in the family Araceae suggested that all Amorphophallus species formed a single monophyletic clade. A close relationship among A. konjac, A. albus, and A. krausei was also revealed by the phylogenetic tree. The newly sequenced chloroplast genome of A. krausei will support future genetic studies, particularly the assessment of genetic diversity, resource conservation, and phylogeographic research. [ABSTRACT FROM AUTHOR]

Amorphophallus coaetaneus S. Y. Liu & S. J. Wei 1986 is a perennial herb belonging to the Araceae family in southwestern China (Guangxi and Yunnan provinces). Although this species have not been list in the red list of International Union for Conservation of Nature (IUCN), the populations are declining due to human over exploitation. To help to genetic diversity studies, we sequenced and assembled the complete chloroplast (cp) genome of A. coaetaneus (GenBank accession number of national center for biotechnology information (NCBI): OQ404947). The assembled genome revealed 175,465 bp in length with a GC content of 34.90%, including a large single-copy (LSC) region (98,561 bp), a small single-copy (SSC) region (16,504 bp) and two inverted repeat regions (IRs) (30,200 bp each). A total of 133 genes were annotated, of which 85 are protein-coding genes, 40 are tRNA genes and 8 are rRNA genes. As an output of this study, a maximum likelihood (ML) phylogenetic inference of 16 Araceae species clustered all four Amorphophallus species in one clade, and showed a relatively close relationship between the tribes Pythonieae and Colocasieae. The cp genome will serve as a basis in a more extensive molecular works covering all possible extant population of Amorphophallus, as well as conservation, breeding, and other ethnobotanical utilization of this species. [ABSTRACT FROM AUTHOR]

The southwest mountainous region of China has been characterized as one of the worldwide biodiversity hotspots, but mechanisms underlying diversification of organisms in this region are still not clear. We assessed whether fragmented mountainous habitats and Pleistocene climate changes impacted the genetic diversity and diversification patterns of the hoary bamboo rat (Rhizomys pruinosus Blyth), a widely distributed species of rodent in SW China. Genetic diversity analyses were undertaken based on four mitochondrial DNA regions and 12 nuclear microsatellite loci (simple sequence repeats), representing 153 individuals from 24 populations across SW China. Moreover, we investigated correlations between genotype and geographical components, and predicted species distribution models for R. pruinosus under the historical and present climate conditions. Both mitochondrial DNA and simple sequence repeat markers revealed substantial genetic diversity and strong differentiation between populations. Phylogeographical analyses revealed two phylogenetic clades that were consistent with their geographical distributions (eastern and western clades). We inferred that the divergence of R. pruinosus was largely driven by Quaternary climatic oscillations and regionally fragmented mountainous habitats with environmental and geographical heterogeneity. Overall, our study revealed diversification patterns of R. pruinosus—patterns that may be shared by small alpine vertebrates in SW China. [ABSTRACT FROM AUTHOR]

Domesticated species represent unique systems in which the evolutionary genomic consequences of intensive selective breeding and adaptation can be thoroughly investigated. Amorphophallus albus occurs naturally and is in cultivation throughout the downstream region of the Jinshajiang River in Southwest China. This species is characterised by high konjac glucomannan content, and has been cultivated in China for nearly 2,000 years. To study genetic differentiation and local adaption of A. albus , we sampled 13 distinct local cultivated populations of this species. Restriction site-associated DNA sequencing was conducted with 87 samples, resulting in 24,225 SNPs. The population structure analyses suggest two main genetic groups: one in the relatively upstream region, and one downstream. We found evidence of additional sub-structure within the upstream group, demonstrating the statistical power of genomic SNPs in discovering subtle genetic structure. The environmental and geographic factors were all identified as significant in shaping the genetic differentiation of this species. Notably, the proportion of environmental factors was larger than geographic factors in influencing the population genetic patterns of A. albus. We also discovered loci that were associated with local adaptation. These findings will help us understand the genetic differentiation of this newly domesticated species, thereby informing future breeding programs of A. albus. [ABSTRACT FROM AUTHOR]

The yellow-vented flowerpecker (Dicaeum chrysorrheum Temminck & Laugier) is a small bird in the Dicaeidae family. To explore the phylogenetic relationships within the genus Dicaeum, we sequenced the complete mitochondrial genome of D. chrysorrheum using a next generation sequencing platform. The mitogenome of D. chrysorrheum (GenBank accession number, MW629121) has a length of 16,818 bp, with a nucleotide composition of 30.62% A, 23.45% T, 31.34% C, and 14.59% G. The genome is comprised of 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes. The total length of the protein-coding genes is 11,402 bp, accounting for 67.8% of the total length of the mitochondrial genome. Of the 13 protein-coding genes, 10 have ATG start codons and three genes terminate with incomplete stop codons. A maximum-likelihood phylogenetic tree of 16 bird species placed D. chrysorrheum and D. agile as sister to the other three Dicaeum species (D. concolor, D. eximium and D. cruentatum). This new mitogenome will be useful for further phylogenetic studies of the genus Dicaeum. [ABSTRACT FROM AUTHOR]

To elucidate the characteristics of VOCs chemical components during heavy pollution episodes, hourly online VOCs data derived from 11 heavy pollution events in Tianjin from 2019 to 2020 were employed. The positive matrix factorization （PMF） and conditional bivariate probability function （CBPF） were employed to analyze the sources of VOCs during heavy pollution episodes. The results indicated that the average VOCs volume fraction during these episodes was recorded at 35.7×10 -9 . Furthermore, it was observed that during the winter emergency response period, there was a discernible increase in the volume fraction of VOCs when compared to that during the autumn season. Specifically, there was a notable upswing of 48% in the olefins category, whereas alkanes registered a 4% increase. Additionally, the VOCs component structure changed significantly during the heavy pollution episodes. During the orange warning period, the proportion of alkanes increased by 36%, and the proportion of acetylene decreased by 32%. During the yellow warning period, the proportion of alkanes increased by 14%, and the proportion of acetylene decreased by 5%. During the emergency response period, motor vehicle emission sources, natural gas evaporative sources, and solvent use sources were the main contributors of VOCs in environmental receptors, contributing 17.5%, 15.4%, and 15.2%, respectively. Compared with that during the period antecedent to the emergency response, the contribution of vehicle emission sources and diesel volatile sources to VOCs in environmental receptors decreased by 2.0% to 5.5% and 2.1% to 6.6%, respectively, and the contribution of solvent use sources decreased by 0.2% to 2.4% during the yellow warning period. During the orange warning period, the contribution of motor vehicle emission sources was reduced by 0.1% to 8.3%, and the contribution of solvent use sources was reduced by 0.5% to 6.2%.

Plants species in the genus Amorphophallus are of great economic importance, as they are the only plants known to produce glucomannan. Although southwestern China has been recognized as one of the origin centres of Amorphophallus, only a few studies assessing its genetic diversity have been reported. To aid in the utilization and conservation of Amorphophallus species, we evaluated the genetic diversity and phylogenetic relationships among seven edible Amorphophallus species using three chloroplast DNA regions (rbcL, trnL and trnK-matK). The results showed that the genetic diversity at the population level was relatively low, with over half of the populations harbouring only one haplotype. The widely scattered species, A. konjac, had the largest genetic diversity, while the narrow endemic species, A. yuloensis, possessed only one haplotype. Phylogeny analysis identified three well-supported major lineages. Our study suggested that habitat fragmentation might be a driver of the genetic variation patterns within and between populations of Amorphophallus. A conservation strategy consisting of in situ conservation and germplasm collection is recommended.

Amorphophallus paeoniifolius, is a commercially important vegetable crop because of its high production potential. In this study, we generated a total of 166 Gb of genomic data from 16 wild and 20 cultivated A. paeoniifolius individuals in southwestern China using restriction site associated DNA sequencing (RAD-seq). We compared the genome-wide variations between the wild and cultivated populations. Wild populations exhibited higher genetic diversity than did cultivated populations based on private allele number, expected heterozygosity, observed heterozygosity and nucleotide diversity. STRUCTURE analysis, principal component analysis (PCA) and a maximum likelihood (ML) tree indicated that A. paeoniifolius populations could be divided into three groups (a cultivated group and two wild groups) with significant genetic differentiation. The low genetic diversity and shallow genetic differentiation found within cultivated populations are likely caused by continuous selection and the clonal propagation methods used during domestication. The significant differentiation between the wild populations may suggest strong genetic drift due to small populations and human disturbance. The genome-wide single nucleotide polymorphisms (SNPs) identified in our study will provide a valuable resource for further breeding improvement and effective use of the germplasm.

Objective: To evaluate the role of sclerostin in bone loss of postmenopausal Chinese women with type 2 diabetes mellitus., Methods: The postmenopausal patients suffering from type 2 diabetes mellitus and age, body mass index, and duration of menopause matched healthy controls were enrolled into this cross-sectional study according to criteria of inclusion and exclusion. The serum sclerostin level and bone mineral density of the anterior-posterior lumbar spine (L1-L4), femoral neck, and total hip were determined by using a quantitative sandwich ELISA kit and dual X-ray absorptiometry, respectively. Meanwhile, the clinical and laboratory indexes of bone mineral metabolism were analyzed. Associations between serum sclerostin level and bone mineral density as well as bone turnover markers were evaluated by linear regression analysis., Results: Finally, 265 postmenopausal women with type 2 diabetes and 225 non-diabetic women were recruited in the diabetic group and control group, respectively. Serum sclerostin level of the diabetic group was significantly higher than that of the control group (48.2±19.4 vs. 37.2±18.6 pmol/L, P<0.001) and was increased with age in both groups (diabetic group, r=0.374, P<0.001; control group, r=0.312, P<0.001). In type 2 diabetes patients, serum sclerostin concentration was positively correlated with hemoglobin A1c level (r=0.237; P=0.021). Biochemical bone turnover markers, intact parathyroid hormone and bone-specific alkaline phosphatase, were negatively associated with serum sclerostin level (r=-0.138, P=0.078 and r=-0.265, P<0.001). Conversely, the positive correlation between sclerostin and C-terminal cross-linking telopeptide of type I collagen was found in diabetic patients (r=0.354, P<0.001). Serum sclerostin levels of the diabetic group were positively correlated with bone mineral density of the lumbar spine, femoral neck, and total hip (r=0.324, 0.367, and 0.416, respectively; all P<0.001)., Conclusions: Sclerostin might participate in the pathogenesis of bone loss of type 2 diabetes. The high sclerostin level might serve as a marker of increased osteocyte activity in postmenopausal patients with type 2 diabetes mellitus.