Annotated Trees Research Articles

The complete mitogenome sequence of the coral lily (Lilium pumilum) and the Lanzhou lily (Lilium davidii) in China.

BackgroundThe mitogenomes of higher plants are conserved. This study was performed to complete the mitogenome of two China Lilium species (Lilium pumilum Redouté and Lilium davidii var. unicolor (Hoog) cotton).MethodsGenomic DNA was separately extracted from the leaves of L. pumilum and L. davidii in triplicate and used for sequencing. The mitogenome of Allium cepa was used as a reference. Genome assembly, annotation and phylogenetic tree were analyzed.ResultsThe mitogenome of L. pumilum and L. davidii was 988,986 bp and 924,401 bp in length, respectively. There were 22 core protein-coding genes (including atp1, atp4, atp6, atp9, ccmB, ccmC, ccmFc, ccmFN1, ccmFN2, cob, cox3, matR, mttB, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7 and nad9), one open reading frame and one ribosomal protein-coding gene (rps12) in the mitogenomes. Compared with the A. cepa mitogenome, the coding sequence of the 24 genes and intergenic spacers in L. pumilum and L. davidii mitogenome contained 1,621 and 1,617 variable sites, respectively. In the phylogenetic tree, L. pumilum and L. davidii were distinct from A. cepa (NC_030100).Conclusions L. pumilum and L. davidii mitogenomes have far distances from other plants. This study provided additional information on the species resources of China Lilium.

A Language and Methodology based on Scenarios, Grammars and Views, for Administrative Business Processes Modelling

In Business Process Management (BPM), process modelling has been solved in various ways. However, there are no commonly accepted modelling tools (languages). Some of them are criticized for their inability to capture both the lifecycle, informational and organizational models of processes. For some others, process modelling is generally done using a single graph; this does not facilitate modularity, maintenance and scalability. In addition, some of these languages are very general; hence, their application to specific domain processes (such as administrative processes) is very complex. In this paper, we present a new language and a new methodology, dedicated to administrative process modelling. This language is based on a variant of attributed grammars and is able to capture the lifecycle, informational and organizational models of such processes. Also, it proposes a simple graphical formalism allowing to model each process's execution scenario as an annotated tree (modularity). In the new language, a particular emphasis is put on modelling (using "views") the perceptions that actors have on processes and their data.

HaploGrouper: a generalized approach to haplogroup classification.

We introduce HaploGrouper, a versatile software to classify haplotypes into haplogroups on the basis of a known phylogenetic tree. A typical use case for this software is the assignment of haplogroups to human mitochondrial DNA (mtDNA) or Y-chromosome haplotypes. Existing state-of-the-art haplogroup-calling software is typically hard-wired to work only with either mtDNA or Y-chromosome haplotypes from humans. HaploGrouper exhibits comparable accuracy in these instances and has the advantage of being able to assign haplogroups to any kind of haplotypes from any species-given an extant annotated phylogenetic tree defined by sequence variants. The software is available at the following URL https://gitlab.com/bio_anth_decode/haploGrouper. Supplementary data are available at Bioinformatics online.

Neural machine translation with Gumbel Tree-LSTM based encoder

Neural machine translation has improved the translation accuracy greatly and received great attention of the machine translation community. Tree-based translation models aim to model the syntactic or semantic relation among long-distance words or phrases in a sentence. However, it faces the difficulties of expensive manual annotation cost and poor automatic annotation accuracy. In this paper, we focus on how to encode a source sentence into a vector in a unsupervised-tree way and then decode it into a target sentence. Our model incorporates Gumbel Tree-LSTM, which can learn how to compose tree structures from plain text without any tree annotation. We evaluate the proposed model on both spoken and news corpora, and show that the performance of our proposed model outperforms the attentional seq2seq model and the Transformer base model.

Hierarchically Labeled Database Indexing Allows Scalable Characterization of Microbiomes.

SummaryIncreasingly available microbial reference data allow interpreting the composition and function of previously uncharacterized microbial communities in detail, via high-throughput sequencing analysis. However, efficient methods for read classification are required when the best database matches for short sequence reads are often shared among multiple reference sequences. Here, we take advantage of the fact that microbial sequences can be annotated relative to established tree structures, and we develop a highly scalable read classifier, PRROMenade, by enhancing the generalized Burrows-Wheeler transform with a labeling step to directly assign reads to the corresponding lowest taxonomic unit in an annotation tree. PRROMenade solves the multi-matching problem while allowing fast variable-size sequence classification for phylogenetic or functional annotation. Our simulations with 5% added differences from reference indicated only 1.5% error rate for PRROMenade functional classification. On metatranscriptomic data PRROMenade highlighted biologically relevant functional pathways related to diet-induced changes in the human gut microbiome.

Khmer Treebank Construction via Interactive Tree Visualization

Despite the fact that there are a number of researches working on Khmer Language in the field of Natural Language Processing along with some resources regarding words segmentation and POS Tagging, we still lack of high-level resources regarding syntax, Treebanks and grammars, for example. This paper illustrates the semi-automatic framework of constructing Khmer Treebank and the extraction of the Khmer grammar rules from a set of sentences taken from the Khmer grammar books. Initially, these sentences will be manually annotated and processed to generate a number of grammar rules with their probabilities once the Treebank is obtained. In our experiments, the annotated trees and the extracted grammar rules are analyzed in both quantitative and qualitative way. Finally, the results will be evaluated in three evaluation processes including Self-Consistency, 5-Fold Cross-Validation, Leave-One-Out Cross-Validation along with the three validation methods such as Precision, Recall, F1-Measure. According to the result of the three validations, Self-Consistency has shown the best result with more than 92%, followed by the Leave-One-Out Cross-Validation and 5-Fold Cross Validation with the average of 88% and 75% respectively. On the other hand, the crossing bracket data shows that Leave-One-Out Cross Validation holds the highest average with 96% while the other two are 85% and 89%, respectively.

Tree Annotations in LiDAR Data Using Point Densities and Convolutional Neural Networks

LiDAR provides highly accurate 3D point clouds. However, data needs to be manually labelled in order to provide subsequent useful information. Manual annotation of such data is time consuming, tedious and error prone, and hence in this paper we present three automatic methods for annotating trees in LiDAR data. The first method requires high density point clouds and uses certain LiDAR data attributes for the purpose of tree identification, achieving almost 90% accuracy. The second method uses a voxel-based 3D Convolutional Neural Network on low density LiDAR datasets and is able to identify most large trees accurately but struggles with smaller ones due to the voxelisation process. The third method is a scaled version of the PointNet++ method and works directly on outdoor point clouds and achieves an F_score of 82.1% on the ISPRS benchmark dataset, comparable to the state-of-the-art methods but with increased efficiency.

A classification of liquid chromatography mass spectrometry techniques for evaluation of chemical composition and quality control of traditional medicines

Natural products (NPs) and traditional medicines (TMs) are used for treatment of various diseases and also to develop new drugs. However, identification of drug leads within the immense biodiversity of living organisms is a challenging task that requires considerable time, labor, and computational resources as well as the application of modern analytical instruments. LC–MS platforms are widely used for both drug discovery and quality control of TMs and food supplements. Moreover, a large dataset generated during LC–MS analysis contains valuable information that could be extracted and handled by means of various data mining and statistical tools. Novel sophisticated LC–MS based approaches are being introduced every year. Therefore, this review is prepared for the scientists specialized in pharmacognosy and analytical chemistry of NPs as well as working in related areas, in order to navigate them in the world of diverse LC–MS based techniques and strategies currently employed for NP discovery and dereplication, quality control, pattern recognition and sample comparison, and also in targeted and untargeted metabolomic studies. The suggested classification system includes the following LC–MS based procedures: elemental composition determination, isotopic fine structure analysis, mass defect filtering, de novo identification, clustering of the compounds in Molecular Networking (MN), diagnostic fragment ion (or neutral loss) filtering, manual dereplication using MS/MS data, database-assisted peak annotation, annotation of spectral trees, MS fingerprinting, feature extraction, bucketing of LC–MS data, peak profiling, predicted metabolite screening, targeted quantification of biomarkers, quantitative analysis of multi-component system, construction of chemical fingerprints, multi-targeted and untargeted metabolite profiling.

Delineation of the Olive Pollen Proteome and Its Allergenome Unmasks Cyclophilin as a Relevant Cross-Reactive Allergen.

Olive pollen is a major allergenic source worldwide due to its extensive cultivation. We have combined available genomics data with a comprehensive proteomics approach to get the annotated olive tree (Olea europaea L.) pollen proteome and define its complex allergenome. A total of 1907 proteins were identified by LC-MS/MS using predicted protein sequences from its genome. Most proteins (60%) were predicted to possess catalytic activity and be involved in metabolic processes. In total, 203 proteins belonging to 47 allergen families were found in olive pollen. A peptidyl-prolyl cis-trans isomerase, cyclophilin, produced in Escherichia coli, was found as a new olive pollen allergen (Ole e 15). Most Ole e 15-sensitized patients were children (63%) and showed strong IgE recognition to the allergen. Ole e 15 shared high sequence identity with other plant, animal, and fungal cyclophilins and presented high IgE cross-reactivity with pollen, plant food, and animal extracts.

Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees.

Evolview is an interactive tree visualization tool designed to help researchers in visualizing phylogenetic trees and in annotating these with additional information. It offers the user with a platform to upload trees in most common tree formats, such as Newick/Phylip, Nexus, Nhx and PhyloXML, and provides a range of visualization options, using fifteen types of custom annotation datasets. The new version of Evolview was designed to provide simple tree uploads, manipulation and viewing options with additional annotation types. The ‘dataset system’ used for visualizing tree information has evolved substantially from the previous version, and the user can draw on a wide range of additional example visualizations. Developments since the last public release include a complete redesign of the user interface, new annotation dataset types, additional tree visualization styles, full-text search of the documentation, and some backend updates. The project management aspect of Evolview was also updated, with a unified approach to tree and project management and sharing. Evolview is freely available at: https://www.evolgenius.info/evolview/.

Interactive Tree Of Life (iTOL) v4: recent updates and new developments.

The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. The current version introduces four new dataset types, together with numerous new features. Annotation options have been expanded and new control options added for many display elements. An interactive spreadsheet-like editor has been implemented, providing dataset creation and editing directly in the web interface. Font support has been rewritten with full support for UTF-8 character encoding throughout the user interface. Google Web Fonts are now fully supported in the tree text labels. iTOL v4 is the first tool which supports direct visualization of Qiime 2 trees and associated annotations. The user account system has been streamlined and expanded with new navigation options, and currently handles >700 000 trees from more than 40 000 individual users. Full batch access has been implemented allowing programmatic upload and export of trees and annotations.

Towards animal-friendly machines

AbstractSemi-autonomous machines, autonomous machines and robots inhabit closed, semi-closed and open environments. There they encounter domestic animals, farm animals, working animals and/or wild animals. These animals could be disturbed, displaced, injured or killed. Within the context of machine ethics, the School of Business FHNW developed several design studies and prototypes for animal-friendly machines,which can be understood as moral machines in the spirit of this discipline. They were each linked with an annotated decision tree containing the ethical assumptions or justifications for interactions with animals. Annotated decision trees are seen as an important basis in developing moral machines. They are not without problems and contradictions, but they do guarantee well-founded, secure actions that are repeated at a certain level. This article documents completed and current projects, compares their relative risks and benefits, and makes proposals for future developments in machine ethics. The findings in this article and proposals for the future hope to systemically promote animal well-being and prevent animal suffering in encounters between machines and animals.

Discerning three novel chromate reduce and transport genes of highly efficient Pannonibacter phragmitetus BB: From genome to gene and protein

Here, Pannonibacter phragmitetus BB was investigated at genomic, genetic and protein levels to explore molecular mechanisms of chromium biotransformation, respectively. The results of Miseq sequencing uncovered that a high-qualified bacterial genome draft was achieved with 5.07 Mb in length. Three novel genes involved in chromate reduce and transport, named nitR, chrA1 and chrA2, were identified by alignment, annotation and phylogenetic tree analyses, which encode a chromate reductase (NitR) and two chromate transporters (ChrA1 and ChrA2). Reverse transcription real-time polymerase chain reaction (RT-qPCR) analyses showed that the relative quantitative transcription of the three genes as the maximum reduction rate of Cr(VI) were significantly up-regulated with the increasing initial Cr(VI) concentrations. However, at the maximum cell growth points nitR was in a low transcription level, while the transcription of chrA1 and chrA2 were hold at a relatively high level and decreased with the increasing initial Cr(VI) concentrations. The ex-situ chromate reducing activity of NitR was revealed a Vmax of 34.46 µmol/min/mg enzyme and Km of 14.55 µmol/L, suggesting feasibility of the reaction with Cr(VI) as substrate. The multiple alignment demonstrates that NitR is potentially a nicotinamide adenine dinucleotide phosphate (NADPH) dependent flavin mononucleotide (FMN) reductase of Class I chromate reductases. Our results will prompt a large-scaled bioremediation on the contaminated soils and water by Pannonibacter phragmitetus BB, taking advantage of uncovering its molecular mechanisms of chromium biotransformation.

Bioinformatic Workflows for Generating Complete Plastid Genome Sequences-An Example from Cabomba (Cabombaceae) in the Context of the Phylogenomic Analysis of the Water-Lily Clade.

The sequencing and comparison of plastid genomes are becoming a standard method in plant genomics, and many researchers are using this approach to infer plant phylogenetic relationships. Due to the widespread availability of next-generation sequencing, plastid genome sequences are being generated at breakneck pace. This trend towards massive sequencing of plastid genomes highlights the need for standardized bioinformatic workflows. In particular, documentation and dissemination of the details of genome assembly, annotation, alignment and phylogenetic tree inference are needed, as these processes are highly sensitive to the choice of software and the precise settings used. Here, we present the procedure and results of sequencing, assembling, annotating and quality-checking of three complete plastid genomes of the aquatic plant genus Cabomba as well as subsequent gene alignment and phylogenetic tree inference. We accompany our findings by a detailed description of the bioinformatic workflow employed. Importantly, we share a total of eleven software scripts for each of these bioinformatic processes, enabling other researchers to evaluate and replicate our analyses step by step. The results of our analyses illustrate that the plastid genomes of Cabomba are highly conserved in both structure and gene content.

PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization.

Comparative and evolutionary studies utilize phylogenetic trees to analyze and visualize biological data. Recently, several web-based tools for the display, manipulation and annotation of phylogenetic trees, such as iTOL and Evolview, have released updates to be compatible with the latest web technologies. While those web tools operate an open server access model with a multitude of registered users, a feature-rich open source solution using current web technologies is not available. Here, we present an extension of the widely used PhyloXML standard with several new options to accommodate functional genomics or annotation datasets for advanced visualization. Furthermore, PhyD3 has been developed as a lightweight tool using the JavaScript library D3.js to achieve a state-of-the-art phylogenetic tree visualization in the web browser, with support for advanced annotations. The current implementation is open source, easily adaptable and easy to implement in third parties' web sites. More information about PhyD3 itself, installation procedures and implementation links are available at http://phyd3.bits.vib.be and at http://github.com/vibbits/phyd3/ . klaas.vandepoele@ugent.vib.be or michiel.vanbel@ugent.vib.be. Supplementary data are available at Bioinformatics online.

BRILIA: Integrated Tool for High-Throughput Annotation and Lineage Tree Assembly of B-Cell Repertoires.

The somatic diversity of antigen-recognizing B-cell receptors (BCRs) arises from Variable (V), Diversity (D), and Joining (J) (VDJ) recombination and somatic hypermutation (SHM) during B-cell development and affinity maturation. The VDJ junction of the BCR heavy chain forms the highly variable complementarity determining region 3 (CDR3), which plays a critical role in antigen specificity and binding affinity. Tracking the selection and mutation of the CDR3 can be useful in characterizing humoral responses to infection and vaccination. Although tens to hundreds of thousands of unique BCR genes within an expressed B-cell repertoire can now be resolved with high-throughput sequencing, tracking SHMs is still challenging because existing annotation methods are often limited by poor annotation coverage, inconsistent SHM identification across the VDJ junction, or lack of B-cell lineage data. Here, we present B-cell repertoire inductive lineage and immunosequence annotator (BRILIA), an algorithm that leverages repertoire-wide sequencing data to globally improve the VDJ annotation coverage, lineage tree assembly, and SHM identification. On benchmark tests against simulated human and mouse BCR repertoires, BRILIA correctly annotated germline and clonally expanded sequences with 94 and 70% accuracy, respectively, and it has a 90% SHM-positive prediction rate in the CDR3 of heavily mutated sequences; these are substantial improvements over existing methods. We used BRILIA to process BCR sequences obtained from splenic germinal center B cells extracted from C57BL/6 mice. BRILIA returned robust B-cell lineage trees and yielded SHM patterns that are consistent across the VDJ junction and agree with known biological mechanisms of SHM. By contrast, existing BCR annotation tools, which do not account for repertoire-wide clonal relationships, systematically underestimated both the size of clonally related B-cell clusters and yielded inconsistent SHM frequencies. We demonstrate BRILIA’s utility in B-cell repertoire studies related to VDJ gene usage, mechanisms for adenosine mutations, and SHM hot spot motifs. Furthermore, we show that the complete gene usage annotation and SHM identification across the entire CDR3 are essential for studying the B-cell affinity maturation process through immunosequencing methods.

Ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data

Summary We present an r package, ggtree, which provides programmable visualization and annotation of phylogenetic trees. ggtree can read more tree file formats than other softwares, including newick, nexus, NHX, phylip and jplace formats, and support visualization of phylo, multiphylo, phylo4, phylo4d, obkdata and phyloseq tree objects defined in other r packages. It can also extract the tree/branch/node‐specific and other data from the analysis outputs of beast, epa, hyphy, paml, phylodog, pplacer, r8s, raxml and revbayes software, and allows using these data to annotate the tree. The package allows colouring and annotation of a tree by numerical/categorical node attributes, manipulating a tree by rotating, collapsing and zooming out clades, highlighting user selected clades or operational taxonomic units and exploration of a large tree by zooming into a selected portion. A two‐dimensional tree can be drawn by scaling the tree width based on an attribute of the nodes. A tree can be annotated with an associated numerical matrix (as a heat map), multiple sequence alignment, subplots or silhouette images. The package ggtree is released under the artistic‐2.0 license. The source code and documents are freely available through bioconductor (http://www.bioconductor.org/packages/ggtree).

The OGCleaner: filtering false-positive homology clusters

https://github.com/byucsl/ogcleaner CONTACT: sfujimoto@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online.

Identification of triacylglycerol using automated annotation of high resolution multistage mass spectral trees

High complexity of identification for non-target triacylglycerols (TAGs) is a major challenge in lipidomics analysis. To identify non-target TAGs, a powerful tool named accurate MSn spectrometry generating so-called ion trees is used. In this paper, we presented a technique for efficient structural elucidation of TAGs on MSn spectral trees produced by LTQ Orbitrap MSn, which was implemented as an open source software package, or TIT. The TIT software was used to support automatic annotation of non-target TAGs on MSn ion trees from a self-built fragment ion database. This database includes 19108 simulate TAG molecules from a random combination of fatty acids and corresponding 500582 self-built multistage fragment ions (MS ≤ 3). Our software can identify TAGs using a “stage-by-stage elimination” strategy. By utilizing the MS1 accurate mass and referenced RKMD, the TIT software can discriminate unique elemental composition candidates. The regiospecific isomers of fatty acyl chains will be distinguished using MS2 and MS3 fragment spectra. We applied the algorithm to the selection of 45 TAG standards and demonstrated that the molecular ions could be 100% correctly assigned. Therefore, the TIT software could be applied to TAG identification in complex biological samples such as mouse plasma extracts.

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.

Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. The current version was completely redesigned and rewritten, utilizing current web technologies for speedy and streamlined processing. Numerous new features were introduced and several new data types are now supported. Trees with up to 100,000 leaves can now be efficiently displayed. Full interactive control over precise positioning of various annotation features and an unlimited number of datasets allow the easy creation of complex tree visualizations. iTOL 3 is the first tool which supports direct visualization of the recently proposed phylogenetic placements format. Finally, iTOL's account system has been redesigned to simplify the management of trees in user-defined workspaces and projects, as it is heavily used and currently handles already more than 500,000 trees from more than 10,000 individual users.