Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees.

Evolview is an online visualization and management tool for customized and annotated phylogenetic trees. It allows users to visualize phylogenetic trees in various formats, customize the trees through built-in functions and user-supplied datasets and export the customization results to publication-ready figures. Its 'dataset system' contains not only the data to be visualized on the tree, but also 'modifiers' that control various aspects of the graphical annotation. Evolview is a single-page application (like Gmail); its carefully designed interface allows users to upload, visualize, manipulate and manage trees and datasets all in a single webpage. Developments since the last public release include a modern dataset editor with keyword highlighting functionality, seven newly added types of annotation datasets, collaboration support that allows users to share their trees and datasets and various improvements of the web interface and performance. In addition, we included eleven new 'Demo' trees to demonstrate the basic functionalities of Evolview, and five new 'Showcase' trees inspired by publications to showcase the power of Evolview in producing publication-ready figures. Evolview is freely available at: http://www.evolgenius.info/evolview/.

EvolView, an online tool for visualizing, annotating and managing phylogenetic trees.

EvolView is a web application for visualizing, annotating and managing phylogenetic trees. First, EvolView is a phylogenetic tree viewer and customization tool; it visualizes trees in various formats, customizes them through built-in functions that can link information from external datasets, and exports the customized results to publication-ready figures. Second, EvolView is a tree and dataset management tool: users can easily organize related trees into distinct projects, add new datasets to trees and edit and manage existing trees and datasets. To make EvolView easy to use, it is equipped with an intuitive user interface. With a free account, users can save data and manipulations on the EvolView server. EvolView is freely available at: http://www.evolgenius.info/evolview.html.

Complete genome sequence of a high cesium ion- tolerating bacterium Bacillus sp. Cs-700 isolated from the South China Sea sediment.

Generally, cesium ion (Cs+) which concentration of above the millimolar order is toxic to microorganisms. In this study we report the isolation and genomic characteristics of Bacillus sp. Cs-700, which can grow in media supplemented with 700 mM Cs+ and was one of the most Cs+ tolerating bacteria been reported. Bacillus sp. Cs-700 was isolated from the South China Sea, and comprised one circular chromosome of 4,297,839 bp (40.32 mol% G + C content), containing 4366 predicted protein-coding sequences. We predict that numerous genes related to high cesium tolerating, and the genome of Bacillus sp. Cs-700 will be helpful for further insights into the mechanism of bacterial resistance to excess Cs+ conditions and the bioremediation of radiocesium-polluting environments.

Rewiring of Microbiota Networks in Erosive Inflammation of the Stomach and Small Bowel.

The development of non-invasive, inexpensive, and effective early diagnosis tests for gastric and small-bowel lesions is an urgent requirement. The introduction of magnetically guided capsule endoscopy (MGCE) has aided examination of the small bowel for diagnoses. However, the distribution of the fecal microbiome in abnormal erosions of the stomach and small bowel remains unclear. Herein, alternations in the fecal microbiome in three groups [normal, small-bowel inflammation, and chronic gastritis (CG)] were analyzed by metagenomics and our well-developed method [individual-specific edge-network analysis (iENA)]. In addition to the dominant microbiota identified by the conventional differential analysis, iENA could recognize novel network biomarkers of microbiome communities, such as the genus Bacteroide in CG and small-bowel inflammation. Combined with differential network analysis, the network-hub microbiota within rewired microbiota networks revealed high-ranked iENA microbiota markers, which were disease specific and had particular pathogenic functions. Our findings illuminate the components of the fecal microbiome and the importance of specific bacteria in CG and small-bowel erosions, and could be employed to develop preventive and non-invasive therapeutic strategies.

Specific TP53 subtype as biomarker for immune checkpoint inhibitors in lung adenocarcinoma.

BACKGROUND: Although TP53 co-mutation with KRAS/ATM/EGFR/STK11 have been proved to have predictive value for response to immune checkpoint inhibitors (ICIs), not all TP53 mutations are equal in this context. As the main part of TP53 mutant types, Missense and Nonsense alternations in TP53 as independent factors to predict the response to ICIs within Lung Adenocarcinoma (LUAD) patients have not yet been reported. METHODS: An integrated analysis based on multiple-dimensional data types including genomic, transcriptomic, proteomic and clinical data from published lung adenocarcinoma data and local database of LUAD taking immune checkpoint inhibitors. Gene set enrichment analysis (GSEA) was used to determine potentially relevant gene expression signatures between specific subgroups. Single-sample GSEA (GSVA) is conducted to calculate the score for enrichment of a set of genes regulating DNA damage repair (DDR) pathway. FINDINGS: The TP53-missense-mutation group showed increased PD-L1 (CD274) level and enriched IFN-γ signatures compared with the TP53-wild-type subgroup, but no differences were noted in patients with nonsense-mutant vs wild-type p53. Furthermore, a group of suppressor Immune cells like M2 Macrophage and Neutrophils are found enriched in nonsense group. On the other-side, both TP53 missense and nonsense mutations are associated with elevated TMB and neoantigen levels and contribute equally to DNA damage repair deficiency. The distribution regarding to multi-dimensional factors determining the efficacy of ICIs finally transformed into diverse clinical benefits for LUAD. TP53 missense but not -nonsense Mutants are associated with better clinical benefits taking antiPD-1/1L. However, all such TP53 subgroups responds well to nivolumab (antiPD-L1) plus ipilimumab (antiCTLA-4) therapy. INTERPRETATION: Our study demonstrated that not all TP53 mutations are equal in predicting efficacy in patients with LUAD treated with ICIs. Multi-center data showed that TP53 missense and nonsense mutations were significantly different in terms of associations with PD-L1 expression, IFN-γ signatures and TME composition. Special attention should be paid to potential TP53 mutation heterogeneity when evaluating TP53 status as biomarker for ICIs. FUNDING: The study was supported by Key Lab System Project of Guangdong Science and Technology Department - Guangdong Provincial Key Lab of Translational Medicine in Lung Cancer (Grant No. 2017B030314120, to Yi-Long WU).

The genome evolution and domestication of tropical fruit mango.

BACKGROUND: Mango is one of the world's most important tropical fruits. It belongs to the family Anacardiaceae, which includes several other economically important species, notably cashew, sumac and pistachio from other genera. Many species in this family produce family-specific urushiols and related phenols, which can induce contact dermatitis. RESULTS: We generate a chromosome-scale genome assembly of mango, providing a reference genome for the Anacardiaceae family. Our results indicate the occurrence of a recent whole-genome duplication (WGD) event in mango. Duplicated genes preferentially retained include photosynthetic, photorespiration, and lipid metabolic genes that may have provided adaptive advantages to sharp historical decreases in atmospheric carbon dioxide and global temperatures. A notable example of an extended gene family is the chalcone synthase (CHS) family of genes, and particular genes in this family show universally higher expression in peels than in flesh, likely for the biosynthesis of urushiols and related phenols. Genome resequencing reveals two distinct groups of mango varieties, with commercial varieties clustered with India germplasms and demonstrating allelic admixture, and indigenous varieties from Southeast Asia in the second group. Landraces indigenous in China formed distinct clades, and some showed admixture in genomes. CONCLUSIONS: Analysis of chromosome-scale mango genome sequences reveals photosynthesis and lipid metabolism are preferentially retained after a recent WGD event, and expansion of CHS genes is likely associated with urushiol biosynthesis in mango. Genome resequencing clarifies two groups of mango varieties, discovers allelic admixture in commercial varieties, and shows distinct genetic background of landraces.

The Draft Genome Sequence of Pseudomonas frederiksbergensis Strain 11-D3 Reveals Its Ability To Mobilize Phosphorus.

Pseudomonas frederiksbergensis strain 11-D3 is a Gram-negative, nonmotile, aerobic bacterium isolated from a managed maize field in North China. This strain displays high efficiency for solubilization of inorganic phosphorus (P). We present the draft genome sequence of strain 11-D3 with P cycling genes which indicate the presence of a probable mechanism for P mobilization.

Leveraging Fecal Bacterial Survey Data to Predict Colorectal Tumors.

Colorectal cancer (CRC) ranks second in cancer-associated mortality and third in the incidence worldwide. Most of CRC follow adenoma-carcinoma sequence, and have more than 90% chance of survival if diagnosed at early stage. But the recommended screening by colonoscopy is invasive, expensive, and poorly adhered to. Recently, several studies reported that the fecal bacteria might provide non-invasive biomarkers for CRC and precancerous tumors. Therefore, we collected and uniformly re-analyzed these published fecal 16S rDNA sequencing datasets to verify the association and identify biomarkers to classify and predict colorectal tumors by random forest method. A total of 1674 samples (330 CRC, 357 advanced adenoma, 141 adenoma, and 846 control) from 7 studies were analyzed in this study. By random effects model and fixed effects model, we observed significant differences in alpha-diversity and beta-diversity between individuals with CRC and the normal colon, but not between adenoma and the normal. We identified various bacterial genera with significant odds ratios for colorectal tumors at different stages. Through building random forest model with 10-fold cross-validation as well as new test datasets, we classified individuals with CRC, advanced adenoma, adenoma and normal colon. All approaches obtained comparable performance at entire OTU level, entire genus level, and the common genus level as measured using AUC. When combined all samples, the AUC of random forest model based on 12 common genera reached 0.846 for CRC, although the predication performed poorly for advance adenoma and adenoma.

Draft Genome Sequence of Rhodococcus opacus Strain 04-OD7, Which Can Mobilize Phosphate.

Rhodococcus opacus strain 04-OD7 (=CCTCC AB 2017148) is a Gram-positive bacterium showing inorganic phosphate solubilization capacity for the first time in the genus Rhodococcus We present here the draft genome description of R. opacus 04-OD7 along with multiple phosphorus (P) mobilization-related genes, supporting its inorganic phosphate solubilization.

Comparative genomics reveals adaptive evolution of Asian tapeworm in switching to a new intermediate host.

Taenia saginata, Taenia solium and Taenia asiatica (beef, pork and Asian tapeworms, respectively) are parasitic flatworms of major public health and food safety importance. Among them, T. asiatica is a newly recognized species that split from T. saginata via an intermediate host switch ∼1.14 Myr ago. Here we report the 169- and 168-Mb draft genomes of T. saginata and T. asiatica. Comparative analysis reveals that high rates of gene duplications and functional diversifications might have partially driven the divergence between T. asiatica and T. saginata. We observe accelerated evolutionary rates, adaptive evolutions in homeostasis regulation, tegument maintenance and lipid uptakes, and differential/specialized gene family expansions in T. asiatica that may favour its hepatotropism in the new intermediate host. We also identify potential targets for developing diagnostic or intervention tools against human tapeworms. These data provide new insights into the evolution of Taenia parasites, particularly the recent speciation of T. asiatica.