Dataset Information

Visualization of genome signatures of eukaryote genomes by batch-learning self-organizing map with a special emphasis on Drosophila genomes.

ABSTRACT: A strategy of evolutionary studies that can compare vast numbers of genome sequences is becoming increasingly important with the remarkable progress of high-throughput DNA sequencing methods. We previously established a sequence alignment-free clustering method "BLSOM" for di-, tri-, and tetranucleotide compositions in genome sequences, which can characterize sequence characteristics (genome signatures) of a wide range of species. In the present study, we generated BLSOMs for tetra- and pentanucleotide compositions in approximately one million sequence fragments derived from 101 eukaryotes, for which almost complete genome sequences were available. BLSOM recognized phylotype-specific characteristics (e.g., key combinations of oligonucleotide frequencies) in the genome sequences, permitting phylotype-specific clustering of the sequences without any information regarding the species. In our detailed examination of 12 Drosophila species, the correlation between their phylogenetic classification and the classification on the BLSOMs was observed to visualize oligonucleotides diagnostic for species-specific clustering.

SUBMITTER: Abe T

PROVIDER: S-EPMC3967822 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Visualization of genome signatures of eukaryote genomes by batch-learning self-organizing map with a special emphasis on Drosophila genomes.

Abe Takashi T Hamano Yuta Y Ikemura Toshimichi T

BioMed research international 20140311

A strategy of evolutionary studies that can compare vast numbers of genome sequences is becoming increasingly important with the remarkable progress of high-throughput DNA sequencing methods. We previously established a sequence alignment-free clustering method "BLSOM" for di-, tri-, and tetranucleotide compositions in genome sequences, which can characterize sequence characteristics (genome signatures) of a wide range of species. In the present study, we generated BLSOMs for tetra- and pentanuc ...[more]

PMID: 24741568

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Project description:Horizontal gene transfer (HGT) has been widely suggested to play a critical role in the environmental adaptation of microbes; however, the number and origin of the genes in microbial genomes obtained through HGT remain unknown as the frequency of detected HGT events is generally underestimated, particularly in the absence of information on donor sequences. As an alternative to phylogeny-based methods that rely on sequence alignments, we have developed an alignment-free clustering method on the basis of an unsupervised neural network "Batch-Learning Self-Organizing Map (BLSOM)" in which sequence fragments are clustered based solely on oligonucleotide similarity without taxonomical information, to detect HGT candidates and their origin in entire genomes. By mapping the microbial genomic sequences on large-scale BLSOMs constructed with nearly all prokaryotic genomes, HGT candidates can be identified, and their origin assigned comprehensively, even for microbial genomes that exhibit high novelty. By focusing on two types of Alphaproteobacteria, specifically psychrotolerant Sphingomonas strains from an Antarctic lake, we detected HGT candidates using BLSOM and found higher proportions of HGT candidates from organisms belonging to Betaproteobacteria in the genomes of these two Antarctic strains compared with those of continental strains. Further, an origin difference was noted in the HGT candidates found in the two Antarctic strains. Although their origins were highly diversified, gene functions related to the cell wall or membrane biogenesis were shared among the HGT candidates. Moreover, analyses of amino acid frequency suggested that housekeeping genes and some HGT candidates of the Antarctic strains exhibited different characteristics to other continental strains. Lys, Ser, Thr, and Val were the amino acids found to be increased in the Antarctic strains, whereas Ala, Arg, Glu, and Leu were decreased. Our findings strongly suggest a low-temperature adaptation process for microbes that may have arisen convergently as an independent evolutionary strategy in each Antarctic strain. Hence, BLSOM analysis could serve as a powerful tool in not only detecting HGT candidates and their origins in entire genomes, but also in providing novel perspectives into the environmental adaptations of microbes.

Project description:Background Micro-computed tomography (micro-CT) provides detailed 3-dimensional (3D) visualization of anatomical structures and encourages morphological reinvestigation of organs with delicate features. The low radiodensity of soft tissues necessitates preceding sample preparation to conduct X-ray imaging with decent contrast between different tissues. In this study, we demonstrate the preparation with three radiopaque agents in combination with elimination of liquids by critical point drying (CPD) introduced for ocular samples. Methods Enucleated porcine eyes were prepared with ethanolic iodine (EI), aqueous iodine-potassium iodide, or ethanolic phosphotungstic acid (EPTA). Micro-CT scans of the samples were conducted in a moist environment with an isotropic resolution of 9.2–12.5 µm voxel size. Subsequently, samples were chemically dehydrated and critical point (CP) dried to conduct a second scan in a dry environment with a resolution up to 4.7–5.4 µm in voxel size. The visualization effects were qualitatively and semi-quantitatively evaluated with regard to the generated contrast between different ocular tissues. Results All three contrast agents accumulated well in most of the investigated ocular tissues and lead to an increased X-ray attenuation which allowed for differentiated visualization of ocular structures. Problematic agent penetration into the lens was obvious for iodine-potassium iodide and EPTA. Artificial damages of the lens and thickness reduction for the cornea and sclera due to CPD were noticed. The effects of the different contrasting treatments are described and compared with regard to the effects of CPD. Exclusively CP dried samples that were not treated with contrast agents could also be visualized excellently with a good distinction of different ocular structures from each other. Conclusions All ocular structures can be visualized by micro-CT. To contrast moist samples, the best results were achieved with iodine potassium iodide (IPI). CPD improved the scan quality in all cases. Even without pretreatment with contrasting agents, the CP dried samples showed a contrast similar to the IPI treated samples.

Project description:BackgroundPlant inducible immunity includes the accumulation of a set of defense proteins during infection called pathogenesis-related (PR) proteins, which are grouped into families termed PR-1 to PR-17. The PR-5 family is composed of thaumatin-like proteins (TLPs), which are responsive to biotic and abiotic stress and are widely studied in plants. TLPs were also recently discovered in fungi and animals. In the poplar genome, TLPs are over-represented compared with annual species and their transcripts strongly accumulate during stress conditions.ResultsOur analysis of the poplar TLP family suggests that the expansion of this gene family was followed by diversification, as differences in expression patterns and predicted properties correlate with phylogeny. In particular, we identified a clade of poplar TLPs that cluster to a single 350 kb locus of chromosome I and that are up-regulated by poplar leaf rust infection. A wider phylogenetic analysis of eukaryote TLPs - including plant, animal and fungi sequences - shows that TLP gene content and diversity increased markedly during land plant evolution. Mapping the reported functions of characterized TLPs to the eukaryote phylogenetic tree showed that antifungal or glycan-lytic properties are widespread across eukaryote phylogeny, suggesting that these properties are shared by most TLPs and are likely associated with the presence of a conserved acidic cleft in their 3D structure. Also, we established an exhaustive catalog of TLPs with atypical architectures such as small-TLPs, TLP-kinases and small-TLP-kinases, which have potentially developed alternative functions (such as putative receptor kinases for pathogen sensing and signaling).ConclusionOur study, based on the most recent plant genome sequences, provides evidence for TLP gene family diversification during land plant evolution. We have shown that the diverse functions described for TLPs are not restricted to specific clades but seem to be universal among eukaryotes, with some exceptions likely attributable to atypical protein structures. In the perennial plant model Populus, we unravelled the TLPs likely involved in leaf rust resistance, which will provide the foundation for further functional investigations.

Dataset Information

Visualization of genome signatures of eukaryote genomes by batch-learning self-organizing map with a special emphasis on Drosophila genomes.

Publications

Visualization of genome signatures of eukaryote genomes by batch-learning self-organizing map with a special emphasis on Drosophila genomes.

Similar Datasets

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