Biogeography and assembly processes of abundant and rare soil microbial taxa in the southern part of the Qilian Mountain National Park, China.

Soil microorganisms play vital roles in regulating multiple ecosystem functions. Recent studies have revealed that the rare microbial taxa (with extremely low relative abundances, which are still largely ignored) are also crucial in maintaining the health and biodiversity of the soil and may respond differently to environmental pressure. However, little is known about the soil community structures of abundant and rare taxa and their assembly processes in different soil layers on the Qinghai-Tibet Plateau (QTP). The present study investigated the community structure and assembly processes of soil abundant and rare microbial taxa on the northeastern edge of the QTP. Soil microbial abundance was defined by abundant taxa, whereas rare taxa contributed to soil microbial diversity. The results of null model show that the stochastic process ruled the assembly processes of all sub-communities. Dispersal limitation contributed more to the assembly of abundant microbial taxa in the different soil layers. In contrast, drift played a more critical role in the assembly processes of the rare microbial taxa. In addition, in contrast to previous studies, the abundant taxa played more important roles in co-occurrence networks, most likely because of the heterogeneity of the soil, the sparsity of amplicon sequencing, the sampling strategy, and the limited samples in the present study. The results of this study improve our understanding of soil microbiome assemblies on the QTP and highlight the role of abundant taxa in sustaining the stability of microbial co-occurrence networks in different soil layers.

Assembly and comparative analysis of the complete mitochondrial genome of Trigonella foenum-graecum L.

BACKGROUND: Trigonella foenum-graecum L. is a Leguminosae plant, and the stems, leaves, and seeds of this plant are rich in chemical components that are of high research value. The chloroplast (cp) genome of T. foenum-graecum has been reported, but the mitochondrial (mt) genome remains unexplored. RESULTS: In this study, we used second- and third-generation sequencing methods, which have the dual advantage of combining high accuracy and longer read length. The results showed that the mt genome of T. foenum-graecum was 345,604 bp in length and 45.28% in GC content. There were 59 genes, including: 33 protein-coding genes (PCGs), 21 tRNA genes, 4 rRNA genes and 1 pseudo gene. Among them, 11 genes contained introns. The mt genome codons of T. foenum-graecum had a significant A/T preference. A total of 202 dispersed repetitive sequences, 96 simple repetitive sequences (SSRs) and 19 tandem repetitive sequences were detected. Nucleotide diversity (Pi) analysis counted the variation in each gene, with atp6 being the most notable. Both synteny and phylogenetic analyses showed close genetic relationship among Trifolium pratense, Trifolium meduseum, Trifolium grandiflorum, Trifolium aureum, Medicago truncatula and T. foenum-graecum. Notably, in the phylogenetic tree, Medicago truncatula demonstrated the highest level of genetic relatedness to T. foenum-graecum, with a strong support value of 100%. The interspecies non-synonymous substitutions (Ka)/synonymous substitutions (Ks) results showed that 23 PCGs had Ka/Ks < 1, indicating that these genes would continue to evolve under purifying selection pressure. In addition, setting the similarity at 70%, 23 homologous sequences were found in the mt genome of T. foenum-graecum. CONCLUSIONS: This study explores the mt genome sequence information of T. foenum-graecum and complements our knowledge of the phylogenetic diversity of Leguminosae plants.

Assembly and Characterization of the Mitochondrial Genome of Fallopia aubertii (L. Henry) Holub.

BACKGROUND: Fallopia aubertii (L. Henry) Holub is a perennial semi-shrub with both ornamental and medicinal value. The mitochondrial genomes of plants contain valuable genetic traits that can be utilized for the exploitation of genetic resources. The parsing of F. aubertii mitochondrial genome can provide insight into the role of mitochondria in plant growth and development, metabolism regulation, evolution, and response to environmental stress. METHODS: In this study, we sequenced the mitochondrial genome of F. aubertii using the Illumina NovaSeq 6000 platform and Nanopore platform. We conducted a comprehensive analysis of the mitochondrial genome of F. aubertii, which involved examining various aspects such as gene composition, repetitive sequences, RNA editing sites, phylogeny, and organelle genome homology. To achieve this, we employed several bioinformatics methods including sequence alignment analysis, repetitive sequence analysis, phylogeny analysis, and more. RESULTS: The mitochondrial genome of F. aubertii has 64 genes, including 34 protein-coding genes (PCGs), three rRNAs, and 27 tRNAs. There were 77 short tandem repeat sequences detected in the mitochondrial genome, five tandem repeat sequences identified by Tandem Repeats Finder (TRF), and 50 scattered repeat sequences observed, including 22 forward repeat sequences and 28 palindrome repeat sequences. A total of 367 RNA coding sites were predicted in PCGs, with the highest number (33) found within ccmB. Ka/Ks values estimated for mitochondrial genes of F. aubertii and three closely related species representing Caryophyllales were less than 1 for most of the genes. The maximum likelihood evolutionary tree showed that F. aubertii and Nepenthes ×ventrata are most closely related. CONCLUSIONS: In this study, we obtained basic information on the mitochondrial genome of F. aubertii and this study investigated repeat sequences and homologous segments, predicted RNA editing sites, and utilized the Ka/Ks ratio to estimate the selection pressure on mitochondrial genes of F. aubertii. We also discussed the systematic evolutionary position of F. aubertii based on mitochondrial genome sequences. Our study revealed variations in the sequence and structure of mitochondrial genomes in Caryophyllales. These findings are of great significance for identifying and improving valuable plant traits and serve as a reference for future molecular studies of F. aubertii.

Comprehensive transcriptomic profiling and mutational landscape of primary gastric linitis plastica.

BACKGROUND: Primary gastric linitis plastica (GLP) is a distinct phenotype of gastric cancer with poor survival. Comprehensive molecular profiles and putative therapeutic targets of GLP remain undetermined. METHODS: We subjected 10 tumor-normal tissue pairs to whole exome sequencing (WES) and whole transcriptome sequencing (WTS). 10 tumor samples were all GLP which involves 100% of the gastric wall macroscopically. TCGA data were compared to generate the top mutated genes and the overexpressed genes in GLP. RESULTS: Our results reveal that GLP has distinctive genomic and transcriptomic features, dysfunction in the Hippo pathway is likely to be a key step during GLP development. 6 genes were identified as significantly highly mutated genes in GLP, including AOX1, ANKRD36C, CPXM1, PTPN14, RPAP1, and DCDC1). MUC6, as a previously identified gastric cancer driver gene, has a high mutation rate (20%) in GLP. 20% of patients in our GLP cohort had CDH1 mutations, while none had RHOA mutations. GLP exhibits high immunodeficiency and low AMPK pathway activity. Our WTS results showed that 3 PI3K-AKT pathway-related genes (PIK3R2, AKT3, and IGF1) were significantly up-regulated in GLP. Two genes were identified using immunohistochemistry (IHC), IGF2BP3 and MUC16, which specifically expressed in diffuse-type-related gastric cancer cell lines, and its knockdown inhibits PI3K-AKT pathway activity. CONCLUSIONS: We provide the first integrative genomic and transcriptomic profiles of GLP, which may facilitate its diagnosis, prognosis, and treatment.

Transcriptome analysis of halophyte Nitraria tangutorum reveals multiple mechanisms to enhance salt resistance.

As a typical halophyte, Nitraria tangutorum Bobr. has attracted the interest of many researchers with the excellent salt tolerance. Elucidation of the mechanism of N. tangutorum salinity tolerance will facilitate the genetic improvement of productive plants faced with salinity. To reveal the molecular response to gradually accumulated salt stress in N. tangutorum, RNA-sequencing and analysis of gradually accumulated NaCl treated samples and control samples were performed, and a total of 1419 differentially expressed genes were identified, including 949 down-regulated genes and 470 up-regulated genes. Detailed analysis uncovered that the catabolism of organic compounds mainly based on oxidative phosphorylation genes was up-regulated. Additionally, various antioxidant genes, especially anthocyanin-related genes, were found to help N. tangutorum remove reactive oxygen species. Moreover, the Mitogen activated protein kinase signaling pathway and other signaling pathways co-regulated various salt tolerance activities. Additionally, intracellular ion homeostasis was maintained via regulation of osmotic regulator-related genes, cutin-related genes, and cell elongation-related genes to retain cellular water and reduce ion concentration. In particularly, simultaneous up-regulation in cytoskeleton-related genes, cell wall-related genes, and auxin-related genes, provided evidence of important role of cell expansion in plant salt tolerance. In conclusion, complex regulatory mechanisms modulated by multiple genes might contribute to the salt tolerance by N. tangutorum.

The complete chloroplast genome and phylogenetic analysis of Syringa reticulata subsp. amurensis (Rupr.) P.S.Green & M.C.Chang from Qinghai Province, China.

Syringa reticulata subsp. amurensis (Rupr.) P. S. Green & M. C. Chang (Oleaceae) is a shrub or tree with high medicinal value as well as great ecological significance as an urban garden plant. To better understand the molecular genetics and evolutionary of S. reticulata subsp. amurensis, its complete chloroplast genome was sequenced and annotated. The assembled chloroplast genome is a circular 156,141 bp sequence, consisting of 87,108 bp large single copy (LSC) region and 17,239 bp small single copy (SSC) region, which were flanked by a pair of 25,897 bp inverted repeats (IRs). The GC content of the chloroplast genome is 36.14%. Moreover, a total of 132 functional genes were annotated, including 88 protein-coding, 36 tRNA, and eight rRNA genes. Phylogenetic analysis showed that S. reticulata subsp. amurensis was most closely related to S. reticulata subsp. Pekinensis and the genus Syringa is paraphyletic group. This study provides important information for further phylogenetic studies on S. reticulata subsp. amurensis and its allies.

Environmental filtering affects fungal communities more than dispersal limitation in a high-elevation hyperarid basin on Qinghai-Tibet Plateau.

The Qaidam Basin is the most extensive (120 000 km2) basin on the Qinghai-Tibet Plataea (QTP). Recent studies have shown that environmental selection and dispersal limitation influence the soil fungal community significantly in a large-scale distance. However, less is known about large-scale soil fungal community assemblages and its response to the elevation gradient in the high-elevation basin ecosystems. We studied fungal assemblages using Illumina sequencing of the ITS1 region from 35 sites of the Qaidam Basin. As the increase of elevation, fungal species richness and Chao1 index also increased. The Ascomycota was the most abundant phylum (more than 70% of total sequences), and six of the 10 most abundance fungal family was detected in all 35 soil samples. The key factors influencing the soil fungal community composition in the Qaidam Basin were environmental filtering (soil properties and climate factors). The Mantel test showed no significant relationship between geographic distance and community similarity (r = 0.05; p = 0.81). The absence of the distance effect might be caused by lacking dispersal limitation for the soil fungal community.

The complete chloroplast genome of Thalictrum baicalense Turcz. ex Ledeb.

Thalictrum baicalense Turcz. ex Ledeb. is a well-known herbaceous perennid that has been used as a traditional medicine to treat influenza, hepatitis, and detoxfeaction. In this study, we release and detail the complete chloroplast genome sequences of T. baicalense. The whole chloroplast genome was 155,859 bp in length and comprised 130 genes, including 84 protein-coding genes, 37 tRNA genes, eight rRNA genes. The T. baicalense chloroplast genome had a GC content of 38.39%. The phylogenetic relationships inferred that T. baicalense, T. tenue, T. minus and T. petaloideum are closely related to each other within the genus Thalictrum.

Characterization of the complete chloroplast genome of Cornus bretschneideri (cornaceae).

Cornus bretschneideri L.Henry (Cornaceae), a shrub or small tree, is a potential horticultural plant or a soil-fixing plant. In this study, the complete sequence and characterization of the chloroplast genome of C. bretschneideri was studied. The size of the chloroplast genome is 158,270 bp in length, including a large single copy region (LSC) of 87,466 bp, a small single copy region (SSC) of 18,730 bp, and a pair of inverted repeat (IR) regions with 26,037 bp. The GC content of the chloroplast genome was 37.86%. Moreover, a total of 132 functional genes were annotated, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The neighbor-joining phylogenetic tree suggested that C. bretschneideri was closely related to C. sanguinea and C. macrophylla.

Genome-wide identification and evolution of HECT genes in wheat.

BACKGROUND: As an important class of E3 ubiquitin ligases in the ubiquitin proteasome pathway, proteins containing homologous E6-AP carboxyl terminus (HECT) domains are crucial for growth, development, metabolism, and abiotic and biotic stress responses in plants. However, little is known about HECT genes in wheat (Triticum aestivum L.), one of the most important global crops. METHODS: Using a genome-wide analysis of high-quality wheat genome sequences, we identified 25 HECT genes classified into six groups based on the phylogenetic relationship among wheat, rice, and Arabidopsis thaliana. RESULTS: The predicted HECT genes were distributed evenly in 17 of 21 chromosomes of the three wheat subgenomes. Twenty-one of these genes were hypothesized to be segmental duplication genes, indicating that segmental duplication was significantly associated with the expansion of the wheat HECT gene family. The Ka/Ks ratios of the segmental duplication of these genes were less than 1, suggesting purifying selection within the gene family. The expression profile analysis revealed that the 25 wheat HECT genes were differentially expressed in 15 tissues, and genes in Group II, IV, and VI (UPL8, UPL6, UPL3) were highly expressed in roots, stems, and spikes. This study contributes to further the functional analysis of the HECT gene family in wheat.

Characterization of the complete chloroplast genome of Allium mongolicum.

Allium mongolicum is a kind of wild vegetable with high nutritional value and even a traditional Chinese medicine. Here, we reported the complete chloroplast genome sequence of Allium mongolicum. The size of the chloroplast genome is 153,376 bp in length, including a large single copy region (LSC) of 82,912 bp, a small single copy region (SSC) of 18,054 bp, and a pair of inverted repeated regions of 26,205 bp. The Allium mongolicum chloroplast genome encodes 115 genes, including 69 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Phylogenetic tree showed that Allium mongolicum is closely related to Allium przewalskianum.

Characterization of the complete chloroplast genome of Syringa wolfii.

Syringa wolfii (Syringa: Syringeae), an upright shrub, is ornamental species used in urban greenification. In this study, we determined the complete chloroplast (cp) genome of S. wolfii using next-generation sequencing (NGS). The size of the chloroplast genome is 156,571 bp in length, including a large single-copy region (LSC) of 86,684 bp, a small single-copy region (SSC) of 19,109 bp, and a pair of inverted repeat (IR) regions with 25,362 bp. The GC content of the chloroplast genome was 37.95%. Moreover, a total of 131 functional genes were annotated, including 87 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The neighbor-joining phylogenetic tree suggested that S. wolfii was closely related to S. yunnansis.

Deregulation of CSMD1 targeted by microRNA-10b drives gastric cancer progression through the NF-κB pathway.

Aim: This study aimed to investigate the oncogenic activity of microRNA-10b by targeting CUB and sushi multiple domains protein 1 (CSMD1) in human gastric cancer (GC) and the underlying mechanisms. Methods: The expression of CSMD1 in human GC tissues was evaluated by real-time reverse transcription polymerase chain reaction (RT-PCR), immunoblotting, and immunohistochemical analysis. The expressive abundance of microRNA-10b was detected by stem-loop RT-PCR. Molecular and cellular techniques, including lentiviral vector-mediated knockdown or overexpression, were used to elucidate the effect of microRNA-10b on the expression of CSMD1. Results: CSMD1 was targeted and downregulated by microRNA-10b in human GC tissues and cells, and the down-regulated expression of CSMD1 contributed to poor survival. The knockdown of microRNA-10b expression inhibited cell proliferation in GC cells in vitro and tumor growth in vivo. The inhibition of microRNA-10b expression repressed invasion and migration of HGC27 cells and retarded GC cells metastasis to the liver in Balb/c nude mice. The up-regulated expression of microRNA-10b promoted the proliferation and metastasis of MKN74 cell in vitro. Intratumoral injection of microRNA-10b mimic also promoted the growth and metastasis of tumor xenografts in Balb/c nude mice. Mechanistically, microRNA-10b promoted the invasion and metastasis of human GC cells through inhibiting the expression of CSMD1, leading to the activation of the nuclear factor-κB (NF-κB) pathway that links inflammation to carcinogenesis, subsequently resulting in the upregulation of c-Myc, cyclin D1 (CCND1), and epithelial-mesenchymal transition (EMT) markers. Conclusions: The findings established that microRNA-10b is an oncomiR that drives metastasis. Moreover, a set of critical tumor suppressor mechanisms was defined that microRNA-10b overcame to drive human GC progression.

Large-scale distribution of bacterial communities in the Qaidam Basin of the Qinghai-Tibet Plateau.

Many studies have investigated patterns of soil microbial communities over large spatial scales. However, these studies mainly focused on a few sites. Here, we studied the near-surface (0-30 cm) soil microbial communities of 35 soil samples collected from most of the areas of the Qaidam Basin, which is the largest basin on the Qinghai-Tibet Plateau. A total of 32 phyla and 838 genera were detected from all the samples, in which Actinobacteria, Proteobacteria, Bacteroidetes, and Acidobacteria were the most dominant and cosmopolitan phyla. The most abundant phyla (relative abundance > 5%) detected in all 35 soil samples were also the most dominant, which could be explained by their great dispersal ability. The microbial community structures correlated strongly with variations in pH and Mg2+ and were distinct between the high Mg2+ content (>20 g/kg) samples and other samples (Acidobacteria, Actinobacteria, and Chloroflexi were significantly less abundant in the high Mg2+ content group, but the abundance of Firmicutes was significantly greater). Finally, the microbial spatial pattern was influenced by both the local environment and spatial distance, but environmental factors were the primary drivers of microbial spatial patterns in the Qaidam Basin.

Characterization of the complete chloroplast genome of Pterygocalyx volubilis (Gentianaceae).

Pterygocalyx volubilis Maxim. (Gentianaceae) is a traditional Chinese medicine, and its whole grass is used in the treatment of pulmonary tuberculosis and other conditions. Here, the complete chloroplast genome sequence of P. volubilis was reported based on the Illumina HiSeq Platform. The chloroplast genome genome is 154,365 bp in length, containing a pair of inverted repeated (IR) regions (25,928 bp) that are separated by a large single copy (LSC) region of 84,033 bp, and a small single copy (SSC) region of 18,476 bp. Moreover, a total of 130 functional genes were annotated, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. In the maximum-likelihood (ML) phylogenetic tree, Pterygocalyx clustered with the genus Swertia. This sequenced chloroplast genome of P. volubilis supports that Pterygocalyx belongs to subtribe Swertiinae.

Characterization of the complete chloroplast genome of Allium tuberosum.

Allium tuberosum is a popular vegetable, condiment, and even a traditional Chinese medicine. Here, the complete chloroplast genome sequence of Allium tuberosum was reported. The size of the chloroplast genome is 154,056 bp in length, including a large single copy region (LSC) of 83,068 bp, a small single copy region (SSC) of 17,958 bp, and a pair of inverted repeat (IR) regions with 26,515 bp. The Allium tuberosum chloroplast genome encodes 132 genes, including 87 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic tree analysis suggested that Allium tuberosum was closely related to Allium sativum.

Complete plastome sequence of Eustoma grandiflorum (Gentianaceae), a popular cut flower.

Eustoma grandiflorum (Raf.) Shinners is a popular cut flower due to its beautiful morphological characteristics and extended vase life. Here, the complete plastome sequence of E. grandiflorum was reported based on the Illumina HiSeq Platform. The plastome sequence is 154,230 bp in length with a typical quadripartite structure, containing a pair of inverted repeated (IR) regions (25,755 bp) that are separated by a large single copy (LSC) region of 84,297 bp, and a small single copy (SSC) region of 18,423 bp. A total of 130 functional genes were annotated, including 84 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The complete plastome sequence of E. grandiflorum will provide a valuable resource for its garden utilization and the phylogenetic studies of Gentianaceae.

Characterization of the complete plastome of Elymus tangutorum (Poaceae: Triticeae).

Elymus tangutorum (Nevski) Handel-Mazzetti (Poaceae: Triticeae), a hexaploid perennial herb, is a kind of forage plant with large biomass. In this study, the complete plastome sequence of E. tangutorum was reported. The size of the plastome is 134,949 bp in length, including a large single copy region (LSC) of 80,556 bp, a small single copy region (SSC) of 12,767 bp, and a pair of inverted repeat (IR) regions with 20,813 bp. Moreover, a total of 131 functional genes were annotated, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The maximum likelihood (ML) phylogenetic tree suggested that E. tangutorum was closely related to Elymus libanoticus and Dasypyrum villosum.

Complete chloroplast genome of Exacum affine (Gentianaceae): the first plastome of the tribe Exaceae in the family Gentianaceae.

Exacum affine Balf.f. ex Regel is a traditional medicinal plant in Yemen and also a popular potted plant. In this study, we sequenced the complete chloroplast genome of E. affine on the Illumina HiSeq Platform. The plastome sequence is 153,311 bp in length with a typical quadripartite structure, containing a pair of inverted repeated (IR) regions of 26,079 bp that are separated by a large single copy (LSC) region of 83,724 bp, and a small single copy (SSC) region of 17,509 bp. The GC content of the whole cp genome was 43.14%. A total of 132 functional genes were annotated, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The complete plastome sequence of E. affine will provide genetic and genomic information to promote its horticulture, officinal utilisation and systematics research of Gentianaceae (especially the tribe Exaceae).