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PubMed2003

Statistical bioinformatic methods in microbial genome analysis.

It is probable that, increasingly, genome investigations are going to be based on statistical formalization. This review summarizes the state of art and potentiality of using statistics in microbial genome analysis. First, I focus on recent advances in functional genomics, such as finding genes and operons, identifying gene conversion events, detecting DNA replication origins and analysing regulatory sites. Then I describe how to use phylogenetic methods in genome analysis and methods for genome-wide scanning for positively selected amino acids. I conclude with speculations on the future course of genome statistical modeling.

Computational Biology↗
PubMedDate not supplied

Parasite genome analysis. A global map of the Leishmania major genome: prelude to genomic sequencing.

In 1994, the World Health Organization (TDR) launched a new strategic initiative in parasite genome analysis, establishing international genome networks for filariae, Schistosoma, Leishmania, Trypanosoma brucei and T. cruzi. For Leishmania, a number of different but complementary approaches have been adopted by members of the Leishmania Genome Network. Our laboratory has been using cosmid clone fingerprinting to produce a physical map of the genome. Progress towards the completion of an integrated physical and biological map of L. major, and the preparations for genomic sequencing, are described.

Animals↗
PubMed2000

Comparative genome analysis reveals extensive conservation of genome organisation for Arabidopsis thaliana and Capsella rubella.

Genome colinearity has been studied for two closely related diploid species of the Brassicaceae family, Arabidopsis thaliana and Capsella rubella. Markers mapping to chromosome 4 of A. thaliana were found on two linkage groups in Capsella and colinear segments spanning more than 10 cM were revealed. Detailed analysis of a 60 kbp region in A. thaliana and its counterpart in C. rubella showed virtually complete conservation of gene repertoire, order and orientation. The comparison of orthologous genes revealed very similar exon-intron structures and sequence identities of 90% or more were found for exon sequences. This extensive genome colinearity at the genetic and molecular level allows the efficient transfer of data from the well-studied A. thaliana genome to other species in the Brassicaceae family, substantially facilitating genome analysis studies for species of this family.

Amino Acid Sequence↗
PubMed2025

Whole-Genome Analysis and Growth-Promoting Mechanism of Klebsiella pneumoniae YMK25 from Maize Rhizobacteria.

Plant growth-promoting rhizobacteria (PGPR) are microorganisms that enhance plant growth through various mechanisms. In the context of global agriculture, which faces fertilizer dependency and environmental pollution, developing eco-friendly microbial fertilizers has become crucial for enhancing agricultural sustainability. To identify highly effective PGPR, we isolated 102 bacterial strains from maize rhizosphere soil using the dilution plating method. The strains were screened for growth-promoting abilities using functional media, resulting in the selection of strain YMK25 for its exceptional capabilities in nitrogen fixation, solubilization of inorganic and organic phosphorus, indole-3-acetic acid (IAA) production, and siderophore production. Strain YMK25 produced IAA at a concentration of 80.49 ± 0.68 μg/mL and exhibited a relative siderophore expression level of 43.68%. Morphological analysis, 16S rDNA gene sequence analysis, and whole-genome sequencing confirmed that strain YMK25 is Klebsiella pneumoniae. Whole-genome analysis revealed a total genome length of 5,115,280 bp, a GC content of 57.61%, and it contained 4746 coding genes. Gene annotation results indicated genes involved in siderophore synthesis, phosphatase activity, and other plant growth-promoting functions, which align with the verified characteristics of strain YMK25. Furthermore, this strain exhibited significant metabolic capabilities. The pot experiment demonstrated that strain YMK25 promotes maize plant growth and assists in nutrient fixation in these plants. In conclusion, strain YMK25 is a high-quality PGPR with substantial potential for application in agricultural production, presenting promise for widespread use in sustainable agriculture.

Klebsiella pneumoniae↗
PubMed2005

Developmental expression and comparative genomic analysis of Xenopus cardiac myosin heavy chain genes.

Myosin heavy chains (MHC) are cytoskeletal motor proteins essential to the process of muscle contraction. We have determined the complete sequences of the Xenopus cardiac MHC genes, alpha-MHC and ventricular MHC (vMHC), and have characterized their developmental expression profiles. Whereas alpha-MHC is expressed from the earliest stages of cardiac differentiation, vMHC transcripts are not detected until the heart has undergone chamber formation. Early expression of vMHC appears to mark the cardiac conduction system, but expression expands to include the ventricle and outflow tract myocardium during subsequent development. Sequence comparisons, transgenic expression analysis, and comparative genomic studies indicate that Xenopus alpha-MHC is the true orthologue of the mammalian alpha-MHC gene. On the other hand, we show that the Xenopus vMHC gene is most closely related to chicken ventricular MHC (vMHC1) not the mammalian beta-MHC. Comparative genomic analysis has allowed the detection of a mammalian MHC gene (MyH15) that appears to be the orthologue of vMHC, but evidence suggests that this gene is no longer active.

Amino Acid Sequence↗
PubMed1995

[Usefulness of genome analysis methods for diagnosis of giardiasis and cryptosporidiosis].

The article comprises a critical review on practical applications of molecular technology in parasitological diagnostics in a broad sense, also as a diagnosis of species and a method of epidemiological analysis. Techniques of genome analysis at different levels, as specific nucleic acid probes, DNA restriction profiles (RFLP), hybridization techniques, pulse-field gel electrophoresis, in vitro nucleic acid amplification, and DNA fingerprint technique used in studies on Giardia and Cryptosporidium were discussed. The essential reservation as far as this technology is concerned refers to its usefulness in parasitological diagnostics; there is no sense in working out methods for recognizing parasites which could otherwise be identified by well trained parasitologists and simple microscopic methods. The improved diagnosis of parasites resulting from the application of molecular technology significantly contributed to the armarium of parasitologists. Application of recent molecular technology in diagnosis of giardiasis and cryptosporidiosis may basically support clinical diagnosis which provides possibilities of early and selective treatment and makes possible epidemiological studies. These assays will permit not only a rapid diagnosis and exact differentiation but will also enable a better recognition of Giardia and Cryptosporidium genome organization. However, in spite of the wide availability of this new techniques they have not been fully applied--as yet--in diagnosis and in epidemiological studies on these parasites. The authors share the opinion of Busch (1991) on the need of proper recognition of high-quality and rigorous work in employing new molecular assays, because their wide availability and high sensitivity could cause "false-positive" results by contamination with amplified DNA sequences.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2005

Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis.

BACKGROUND: A major challenge in computational genomics is the development of methodologies that allow accurate genome-wide prediction of the regulatory targets of a transcription factor. We present a method for target identification that combines experimental characterization of binding requirements with computational genomic analysis. RESULTS: Our method identified potential target genes of the transcription factor Ndt80, a key transcriptional regulator involved in yeast sporulation, using the combined information of binding affinity, positional distribution, and conservation of the binding sites across multiple species. We have also developed a mathematical approach to compute the false positive rate and the total number of targets in the genome based on the multiple selection criteria. CONCLUSION: We have shown that combining biochemical characterization and computational genomic analysis leads to accurate identification of the genome-wide targets of a transcription factor. The method can be extended to other transcription factors and can complement other genomic approaches to transcriptional regulation.

Amino Acid Motifs↗
PubMed1993

Use of reference libraries and hybridisation fingerprinting for relational genome analysis.

The concept of relational genome analysis by hybridisation has been developed into a working system. Various genomic and cDNA libraries have been generated and are distributed via a reference system. Analysis procedures have been tested successfully in the mapping of the entire Schizosaccharomyces pombe genome. In another test-case for their refinement, analyses on the Drosophila genome are well under way. Human and mouse libraries are being studied on all levels, from generating YAC maps to partially sequencing representative cDNA libraries. The automation of the involved processes and the development of improved image detection and analysis are well advanced.

Animals↗
PubMed2006

Seventh international meeting on single nucleotide polymorphism and complex genome analysis: 'ever bigger scans and an increasingly variable genome'.

In September 2005, the seventh international meeting on single nucleotide polymorphism (SNP) and complex genome analysis was held in Hinckley, near Leicester, UK and the meeting was organised by Anthony Brookes, Stephen Chanock, Ivo Gut, Alec Jeffreys and Pui-Yan Kwok. Similar to prior meetings, the 3-day meeting focused on new trends and methods in the analysis of SNPs and complex human disease. A substantial portion of the meeting was devoted to preliminary analyses of data emerging from the International HapMap Consortium and addressed key issues in patterns of recombination, linkage disequilibrium and population genetics. Of great interest were the sessions that addressed SNP analysis in other species and the emerging field of copy number variation. Overall, there have been a number of recent advances in genomics that promise to accelerate the pace of dissecting the genetic basis of many complex diseases in humans-and perhaps in other species.

Evolution, Molecular↗
PubMed1990

Human genome analysis and the concept of human nature.

The possibilities opened up by human genome analysis appear to provide support for quasi-deterministic views of human nature but an analysis of the debate over sociobiology shows that we cannot derive a theory of human nature directly from biological and genetic evidence. From this perspective human genome analysis and the forms of human genetic engineering that it makes possible cannot alter our concept of human nature although they make us more aware of the 'plasticity' of the human. The possibility envisaged by some neo-eugenicists (and often accepted by their opponents) of a radical reshaping of human nature is as misconceived as the view of some sociobiologists that human nature is biologically determined. Human genome analysis raises formidable ethical, social and legal problems and we need to develop criteria that will enable us to decide which kinds of genetic manipulation will help to enhance human life and which will not. This will involve having a clear concept of human nature and the values it implies. But we shall not derive this concept of human nature from genetics itself.

Genetics, Medical↗
PubMed2003

Buccal cells as a source of DNA for comparative animal genomic analysis.

The source of DNA of adequate quality and quantity is an important consideration in genome analysis. In many animal and livestock species, easy access to DNA will facilitate the rapid and reliable genotyping of a large number of individual individuals. Here, we describe the use, for the first time, of buccal cells from non-human mammalian species as a source of DNA template for PCR and restriction analysis. The buccal cells from the pig, cow and human, were used to amplify PCR fragments that were scanned SNPs and for comparative genome analysis. The work indicates that buccal cells are also adequate sources of DNA for genome analysis of animals that have been identified as priorities in comparative genomics.

Animals↗
PubMed2005

Identification of cyanobacterial non-coding RNAs by comparative genome analysis.

BACKGROUND: Whole genome sequencing of marine cyanobacteria has revealed an unprecedented degree of genomic variation and streamlining. With a size of 1.66 megabase-pairs, Prochlorococcus sp. MED4 has the most compact of these genomes and it is enigmatic how the few identified regulatory proteins efficiently sustain the lifestyle of an ecologically successful marine microorganism. Small non-coding RNAs (ncRNAs) control a plethora of processes in eukaryotes as well as in bacteria; however, systematic searches for ncRNAs are still lacking for most eubacterial phyla outside the enterobacteria. RESULTS: Based on a computational prediction we show the presence of several ncRNAs (cyanobacterial functional RNA or Yfr) in several different cyanobacteria of the Prochlorococcus-Synechococcus lineage. Some ncRNA genes are present only in two or three of the four strains investigated, whereas the RNAs Yfr2 through Yfr5 are structurally highly related and are encoded by a rapidly evolving gene family as their genes exist in different copy numbers and at different sites in the four investigated genomes. One ncRNA, Yfr7, is present in at least seven other cyanobacteria. In addition, control elements for several ribosomal operons were predicted as well as riboswitches for thiamine pyrophosphate and cobalamin. CONCLUSION: This is the first genome-wide and systematic screen for ncRNAs in cyanobacteria. Several ncRNAs were both computationally predicted and their presence was biochemically verified. These RNAs may have regulatory functions and each shows a distinct phylogenetic distribution. Our approach can be applied to any group of microorganisms for which more than one total genome sequence is available for comparative analysis.

Base Sequence↗
PubMed2026

LCR-modules: a collection of workflows for cancer genome analysis.

MOTIVATION: The surge of genomic data from advanced sequencing technologies is outpacing current analytical pipelines. We introduce LCR-modules, an open-source suite of bioinformatics tools designed for flexible and automated cancer genome data analysis. LCR-modules enables reproducible analysis of diverse cancer genomics data at scale. The suite comprises 49 Snakemake-based workflows organized into three levels, facilitating tasks from low-level quality control to complex cohort-level analyses. LCR-modules supports various sequencing types and integrates pipelines such as mutation calling, expression quantification, and cohort-level aggregation, ensuring flexibility and reproducibility. LCR-modules represents a significant advancement in genomic data analysis, reducing barriers in reproducibility and scalability and has already been applied to a combination of exomes and genomes from over 10 800 samples. AVAILABILITY: No new data were generated in support of this research. The source code for the LCR-modules is openly available at https://github.com/LCR-BCCRC/lcr-modules.

Software↗
PubMed1994

Analysis of products of the Escherichia coli genomic genes and regulation of their expressions: an applicable procedure for genomic analysis of other microorganisms.

A partial library of the Escherichia coli genomic genes has been constructed, in which each clone has part of a genomic gene fused in frame with the lacZ gene in addition to its promoter and operator. DNA of randomly selected clones was sequenced, and the resultant deduced N-terminal amino acid sequences showed that 17 out of 26 genes analyzed encode unknown proteins. Genomic locations of the cloned genes and their expressional regulations under the aerobic and anaerobic conditions were also analyzed. These results suggest that this library is useful for the global analysis of the E. coli genomic genes and that this strategy may be applicable to the genomic analysis of other microorganisms.

Bacterial Proteins↗
PubMed2006

CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes.

BACKGROUND: The recent accumulation of closely related genomic sequences provides a valuable resource for the elucidation of the evolutionary histories of various organisms. However, although numerous alignment calculation and visualization tools have been developed to date, the analysis of complex genomic changes, such as large insertions, deletions, inversions, translocations and duplications, still presents certain difficulties. RESULTS: We have developed a comparative genome analysis tool, named CGAT, which allows detailed comparisons of closely related bacteria-sized genomes mainly through visualizing middle-to-large-scale changes to infer underlying mechanisms. CGAT displays precomputed pairwise genome alignments on both dotplot and alignment viewers with scrolling and zooming functions, and allows users to move along the pre-identified orthologous alignments. Users can place several types of information on this alignment, such as the presence of tandem repeats or interspersed repetitive sequences and changes in G+C contents or codon usage bias, thereby facilitating the interpretation of the observed genomic changes. In addition to displaying precomputed alignments, the viewer can dynamically calculate the alignments between specified regions; this feature is especially useful for examining the alignment boundaries, as these boundaries are often obscure and can vary between programs. Besides the alignment browser functionalities, CGAT also contains an alignment data construction module, which contains various procedures that are commonly used for pre- and post-processing for large-scale alignment calculation, such as the split-and-merge protocol for calculating long alignments, chaining adjacent alignments, and ortholog identification. Indeed, CGAT provides a general framework for the calculation of genome-scale alignments using various existing programs as alignment engines, which allows users to compare the outputs of different alignment programs. Earlier versions of this program have been used successfully in our research to infer the evolutionary history of apparently complex genome changes between closely related eubacteria and archaea. CONCLUSION: CGAT is a practical tool for analyzing complex genomic changes between closely related genomes using existing alignment programs and other sequence analysis tools combined with extensive manual inspection.

Algorithms↗
PubMed2006

Comparative genomic analysis of Campylobacter jejuni strains reveals diversity due to genomic elements similar to those present in C. jejuni strain RM1221.

Analysis of the complete genomic sequence of Campylobacter jejuni strain RM1221 identified four large genomic elements, Campylobacter jejuni-integrated elements (CJIEs), that were absent from C. jejuni strain NCTC 11168. To further investigate the genomic diversity of Campylobacter, we conducted a comparative genomic analysis from a collection of 67 C. jejuni and 12 Campylobacter coli strains isolated from various geographical locations and clinical and veterinary sources. Utilizing PCR, we demonstrated that 55% of the C. jejuni strains examined were positive for at least one RM1221-like genomic element and 27% were positive for two or more of these CJIEs. Furthermore, many C. coli strains were positive for either genomic element CJIE1 or CJIE3. To simultaneously assess for the presence or absence of several genes that comprise the various CJIEs, we developed a multistrain C. jejuni DNA microarray that contained most of the putative coding sequences for strains NCTC 11168 and RM1221. A comparative genomic hybridization (CGH) analysis of 35 of the 67 C. jejuni strains confirmed the presence of genomic elements similar to those in strain RM1221. Interestingly, the DNA microarray analysis demonstrated that these genomic elements in the other C. jejuni strains often exhibited modular patterns with some regions of the CJIEs present and other regions either absent or highly divergent compared to strain RM1221. Our CGH method also identified 18 other intraspecies hypervariable regions, such as the capsule and lipooligosaccharide biosynthesis regions. Thus, the inclusion of genes from these integrated genomic elements and the genes from the other intraspecies hypervariable regions contributes to a better assessment of the diversity in C. jejuni and may increase the usefulness of DNA microarrays as an epidemiological genotyping tool. Finally, we also showed that in CJIE1, a Campylobacter Mu-like phage, is located differentially in other strains of C. jejuni, suggesting that it may integrate essentially randomly.

Campylobacter jejuni↗
PubMed2000

Arabidopsis genome analysis as exemplified by analysis of chromosome 4.

During the last decade the small cruciferous plant Arabidopsis thaliana has become a model organism for flowering plants. Sequencing and analysis of the Arabidopsis genome is nearing completion. Beside an overview on methods and strategies for Arabidopsis genome analysis, a summary of the results from the first analysis is presented. This includes an overview on chromosomal organisation and topological features as well as a first comparison with other genomes.

Arabidopsis↗
PubMed2004

Rapid and sensitive dot-matrix methods for genome analysis.

MOTIVATION: Dot-matrix plots are widely used for similarity analysis of biological sequences. Many algorithms and computer software tools have been developed for this purpose. Though some of these tools have been reported to handle sequences of a few 100 kb, analysis of genome sequences with a length of >10 Mb on a microcomputer is still impractical due to long execution time and computer memory requirement. RESULTS: Two dot-matrix comparison methods have been developed for analysis of large sequences. The methods initially locate similarity regions between two sequences using a fast word search algorithm, followed with an explicit comparison on these regions. Since the initial screening removes most of random matches, the computing time is substantially reduced. The methods produce high quality dot-matrix plots with low background noise. Space requirements are linear, so the algorithms can be used for comparison of genome size sequences. Computing speed may be affected by highly repetitive sequence structures of eukaryote genomes. A dot-matrix plot of Yeast genome (12 Mb) with both strands was generated in 80 s with a 1 GHz personal computer.

Algorithms↗