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PubMed2004

Characterization and comparative genomic analysis of intronless Adams with testicular gene expression.

ADAM (a disintegrin and metalloprotease) family members with testis-specific or -predominant gene expression are divided phylogenically into two groups: ADAMs 2, 3, 5, 27, and 32 (the first group) and ADAMs 4, 6, 20, 21, 24, 25, 26, 29, 30, and 34 (the second group). We cloned and sequenced cDNAs for previously unidentified mouse Adams that belong to the second group. We found that all the Adam genes in the second phylogenic group are transcribed by both somatic and germ cells in mouse testis, representing a unique expression pattern different from that of the first-group Adams. Genomic analyses revealed that all the second-group Adam genes lack introns interrupting protein-coding sequences and many of them are present as multicopy genes, resulting in total of 14 functional mouse genes in this phylogenic group. Comparing the mouse and human ADAM genes, we found that a number of these mouse Adam genes do not have human orthologues and, even if they exist, some orthologues are pseudogenes in human. These results suggest the differential expansion of the second-group Adam genes in the mouse genome during evolution and a relationship between these Adams and male reproduction unique to mouse.

Amino Acid Sequence↗
PubMed2025

PSIA: A Comprehensive Knowledgebase of Plant Self-incompatibility.

Self-incompatibility (SI) is an important genetic mechanism in angiosperms that prevents inbreeding and promotes outcrossing, with significant implications for crop breeding, including genetic diversity, hybrid seed production, and yield optimization. In eudicots, SI is typically governed by a single S-locus containing tightly linked pistil and pollen S-determinant genes. Despite major advances in SI research, a centralized, comprehensive resource for SI-related genomic data remains lacking. To address this gap, we developed the Plant Self-Incompatibility Atlas (PSIA), a systematically curated knowledgebase providing an extensive compilation of plant SI, including genomic resources for SI species, S gene annotations, molecular mechanisms, phylogenetic relationships, and comparative genomic analyses. The current release of PSIA includes over 500 genome assemblies from 469 SI species. Using known S genes as queries, we manually identified and rigorously curated 3700 S genes. PSIA provides detailed S-locus information from assembled genomes of SI species and offers an interactive platform for browsing, BLAST searches, S gene analysis, and data retrieval. Additionally, PSIA serves as a unique platform for comparative genomic studies of S-loci, facilitating exploration of the dynamic processes underlying the origin, loss, and regain of SI. As a comprehensive and user-friendly resource, PSIA will greatly advance our understanding of angiosperm SI and serve as a valuable tool for crop breeding and hybrid seed production. PSIA is freely available at http://www.plantsi.cn.

Self-Incompatibility in Flowering Plants↗
PubMed2002

The Feline Genome Project.

The compilation of a dense gene map and eventually a whole genome sequence (WGS) of the domestic cat holds considerable value for human genome annotation, for veterinary medicine, and for insight into the evolution of genome organization among mammals. Human association and veterinary studies of the cat, its domestic breeds, and its charismatic wild relatives of the family Felidae have rendered the species a powerful model for human hereditary diseases, for infectious disease agents, for adaptive evolutionary divergence, for conservation genetics, and for forensic applications. Here we review the advantages, rationale, and present strategy of a feline genome project, and we describe the disease models, comparative genomics, and biological applications posed by the full resolution of the cat's genome.

Animals↗
PubMed2005

[Differentiation of the Mycobacterium tuberculosis W-Beijing family strains from the Russian Federation by the VNTR-typing].

Recent phylogenetic studies allowed the Mycobacterium tuberculosis complex to be divided into a number of the strain families. The W-Beijing family is one of most widespread M. tuberculosis variants frequently causing epidemic outbreaks. This family is genetically homogenous and conserved so that ETR A, B, C, D, E - typing is insufficient for the W-Beijing differentiation. All W-Beijing isolates have common profile (42435). This led to the false clustering in the molecular epidemiology study, especially in the region of predominance of the W-Beijing family. In this investigation we searched for the VNTR loci with high evolution rate, which were polymorphic in the W-Beijing genome. Eleven VNTR-loci were assayed in the DNA panel of 99 M. tuberculosis isolates from the tuberculosis patients in North-West and West-Siberian regions of Russia during the period from 2000 to 2001. Ninety nine strains of M. tuberculosis were divided into 74 VNTR-types, 51 isolates of the W-Beijing family were subdivided into 30 VNTR-types. The Hunter-Gudson index (HGDI) for all studied loci (ETR-A, ETR-C, ETR-E, V, V2, V3, V4, V5, V6, V10, V11) was close to one of the IS6110 RFLP indices being "the gold standard" of the M. tuberculosis complex genotyping. The V2, V3 loci located in the sequences of the PPE gene family, were highly polymorphic and more discriminative then others (HGDI is about 0.8). The congruence between the IS6110 RFLP-typing and 11 loci VNTR-typing was measured during genotyping for 23 isolates of the W-Beijing family. The isolates were divided into 9 genotypes by the IS6110 RFLP and into 13 variants by the VNTR-typing. The profiles correlation coefficient was 0.767689 that reflected the differences in the rate and type of the given genome target evolution.

Bacterial Typing Techniques↗
PubMed1999

Contribution of genomics to bacterial pathogenesis.

Genomics is changing the landscape of modern biology. The impact is far-reaching because it provides both the most economical means of acquiring large amounts of information and because it has forced the creation of new technologies to exploit this information. Five of the six genomes published in the year from August 1998 to August 1999 were human pathogens, all of which are highly host-adapted. Four of these are obligate intracellular pathogens and the study of these genomes is providing novel insights into the intricacies of pathogen-host interactions and co-evolution. These genomes are also significant because they mark the beginning of an important trend in the sequencing of closely related genomes, including the sequencing of more than one strain from a single pathogenic species. As comparative genomics truly comes of age, the ability to compare the genomes of pathogenic and non-pathogenic organisms will hopefully provide insight into what makes certain bacterial strains and species pathogens.

Bacteria↗
PubMed2006

Divergent evolution of a structural proteome: phenomenological models.

We develop models of the divergent evolution of genomes; the elementary object of sequence dynamics is the protein structural domain. To identify patterns of organization that reflect mechanisms of evolution, we consider the individual genomes of many procaryote species, studying the arrangement of protein structural domains in the space of all polypeptide structures. We view the network of structural similarities as a graph, called the organismal Protein Domain Universe Graph (oPDUG); vertices represent types of structural domains and edges represent strong structural similarity. As observed before, each oPDUG is a highly nonrandom graph, as evidenced in the vertex degree distribution, which resembles a Pareto law (which has a power-law asymptotic). To explain this and other peculiar properties of the oPDUGs, we construct an evolving-graph model for the long-timescale evolutionary dynamics of oPDUGs, containing only divergent mechanisms of domain discovery. The model generates degree distributions (resembling Pareto laws) and clustering-coefficient distributions that are characteristic of the oPDUGs. In the infinite-graph limit, we analytically compute the exponent for specific biological parameters, as well as the complete phase diagram of the model, finding two distinct regimes of domain innovation dynamics. Thus, divergent evolutionary dynamics quantitatively explains the nonrandom organization of oPDUGs.

Bacterial Proteins↗
PubMed2004

Functional and evolutionary genomics of Mycobacterium tuberculosis: insights from genomic deletions in 100 strains.

To better understand genome function and evolution in Mycobacterium tuberculosis, the genomes of 100 epidemiologically well characterized clinical isolates were interrogated by DNA microarrays and sequencing. We identified 68 different large-sequence polymorphisms (comprising 186,137 bp, or 4.2% of the genome) that are present in H37Rv, but absent from one or more clinical isolates. A total of 224 genes (5.5%), including genes in all major functional categories, were found to be partially or completely deleted. Deletions are not distributed randomly throughout the genome but instead tend to be aggregated. The distinct deletions in some aggregations appear in closely related isolates, suggesting a genomically disruptive process specific to an individual mycobacterial lineage. Other genomic aggregations include distinct deletions that appear in phylogenetically unrelated isolates, suggesting that a genomic region is vulnerable throughout the species. Although the deletions identified here are evidently inessential to the causation of disease (they are found in active clinical cases), their frequency spectrum suggests that most are weakly deleterious to the pathogen. For some deletions, short-term evolutionary pressure due to the host immune system or antibiotics may favor the elimination of genes, whereas longer-term physiological requirements maintain the genes in the population.

Evolution, Molecular↗
PubMed1994

Rates and patterns of chloroplast DNA evolution.

The chloroplast genome (cpDNA) of plants has been a focus of research in plant molecular evolution and systematics. Several features of this genome have facilitated molecular evolutionary analyses. First, the genome is small and constitutes an abundant component of cellular DNA. Second, the chloroplast genome has been extensively characterized at the molecular level providing the basic information to support comparative evolutionary research. And third, rates of nucleotide substitution are relatively slow and therefore provide the appropriate window of resolution to study plant phylogeny at deep levels of evolution. Despite a conservative rate of evolution and a relatively stable gene content, comparative molecular analyses reveal complex patterns of mutational changes. Non-coding regions of cpDNA diverge through insertion/deletion changes that are sometimes site dependent. Coding genes exhibit different patterns of codon bias that appear to violate the equilibrium assumptions of some evolutionary models. Rates of molecular change often vary among plant families and orders in a manner that violates the assumption of a simple molecular clock. Finally, protein-coding genes exhibit patterns of amino acid change that appear to depend on protein structure, and these patterns may reveal subtle aspects of structure/function relationships. Only comparative studies of molecular sequences have the resolution to reveal this underlying complexity. A complete description of the complexity of molecular change is essential to a full understanding of the mechanisms of evolutionary change and in the formulation of realistic models of mutational processes.

Biological Evolution↗
PubMed2005

Genome duplication, extinction and vertebrate evolution.

Vertebrate evolution has been punctuated by three episodes of widespread gene or genome duplication, which have been linked with the origin of vertebrates, gnathostomes and teleosts, respectively. These three events coincide with bursts of character acquisition and increases in phenotypic complexity, and many researchers have suggested a causal relationship between the two. However, this pattern is derived from data for living taxa only; we argue here that, when fossils are taken into account, bursts of character acquisition disappear and gen(om)e duplication in vertebrate phylogeny can no longer be correlated with the origin of body plans. If patterns of character acquisition or morphological gaps between higher taxa are a reflection of phenotypic complexity, then more inclusive data sets incorporating fossil taxa provide no support for hypotheses linking gen(om)e duplications and the evolution of complexity in vertebrates.

Journal Article↗
PubMed2005

Towards a prokaryotic genomic taxonomy.

One of the most interesting developments in the field of modern-day microbiology is the ever increasing number of whole-genome sequences that is publicly available. There is an increasing interest in the use of these genome sequences to assess evolutionary relationships among microbial taxa, as it is anticipated that much additional taxonomic information can be extracted from these sequences. In a first part of the present review, mechanisms that are responsible for the evolution of genomes will be discussed. Subsequently, we will give an overview of approaches that are presently available to assess the taxonomic relationships between prokaryotic species based on complete genome sequences, followed by a brief discussion of the potential implications of these novel approaches for bacterial taxonomy in general and our thinking about the bacterial species concept in particular.

Bacteria↗
PubMed2006

Using partial genomic fosmid libraries for sequencing complete organellar genomes.

Organellar genome sequences provide numerous phylogenetic markers and yield insight into organellar function and molecular evolution. These genomes are much smaller in size than their nuclear counterparts; thus, their complete sequencing is much less expensive than total nuclear genome sequencing, making broader phylogenetic sampling feasible. However; for some organisms, it is challenging to isolate plastid DNA for sequencing using standard methods. To overcome these difficulties, we constructed partial genomic libraries from total DNA preparations of two heterotrophic and two autotrophic angiosperm species using fosmid vectors. We then used macroarray screening to isolate clones containing large fragments of plastid DNA. A minimum tiling path of clones comprising the entire genome sequence of each plastid was selected, and these clones were shotgun-sequenced and assembled into complete genomes. Although this method worked well for both heterotrophic and autotrophic plants, nuclear genome size had a dramatic effect on the proportion of screened clones containing plastid DNA and, consequently, the overall number of clones that must be screened to ensure full plastid genome coverage. This technique makes it possible to determine complete plastid genome sequences for organisms that defy other available organellar genome sequencing methods, especially those for which limited amounts of tissue are available.

DNA↗
PubMed2006

The complete nucleotide sequence of the mitochondrial genome of Tetraodon nigroviridis.

The fresh water pufferfish Tetraodon nigroviridis is a model organism for studying evolution of genome and gene functions, but its mitochondrial genome (mtDNA) sequence is still not available. We determined the complete nucleotide sequence of its mtDNA using shotgun sequencing. The T. nigroviridis mtDNA was 16,462 bp, and contained 13 protein coding genes, 22 tRNAs, 2 rRNAs and a major non-coding region. The gene order was identical to the common type of vertebrate mtDNA, whereas the G + C content in the sense strand was 46.9%, much higher than most other fish species. One hundred and three SNPs were detected in the control region of the mtDNA of 35 individuals, a majority of SNPs were detected in the 5' end of the control region. A phylogenetic study including 21 fish species was performed on concatenated amino acid sequences of 12 protein coding genes, and revealed that the T. nigroviridis was clustered with Fugu rubripes into a group. The complete mtDNA sequence and SNPs in its control region will be useful in studying fish evolution, in differentiating different Tetraodon species and in analyzing genetic diversity within T. nigroviridis.

Animals↗
PubMed2002

Long terminal repeat retrotransposons of Oryza sativa.

BACKGROUND: Long terminal repeat (LTR) retrotransposons constitute a major fraction of the genomes of higher plants. For example, retrotransposons comprise more than 50% of the maize genome and more than 90% of the wheat genome. LTR retrotransposons are believed to have contributed significantly to the evolution of genome structure and function. The genome sequencing of selected experimental and agriculturally important species is providing an unprecedented opportunity to view the patterns of variation existing among the entire complement of retrotransposons in complete genomes. RESULTS: Using a new data-mining program, LTR_STRUC, (LTR retrotransposon structure program), we have mined the GenBank rice (Oryza sativa) database as well as the more extensive (259 Mb) Monsanto rice dataset for LTR retrotransposons. Almost two-thirds (37) of the 59 families identified consist of copia-like elements, but gypsy-like elements outnumber copia-like elements by a ratio of approximately 2:1. At least 17% of the rice genome consists of LTR retrotransposons. In addition to the ubiquitous gypsy- and copia-like classes of LTR retrotransposons, the rice genome contains at least two novel families of unusually small, non-coding (non-autonomous) LTR retrotransposons. CONCLUSIONS: Each of the major clades of rice LTR retrotransposons is more closely related to elements present in other species than to the other clades of rice elements, suggesting that horizontal transfer may have occurred over the evolutionary history of rice LTR retrotransposons. Like LTR retrotransposons in other species with relatively small genomes, many rice LTR retrotransposons are relatively young, indicating a high rate of turnover.

Animals↗
PubMed2002

Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution.

Mycoplasmas evolved by a drastic reduction in genome size, but their genomes contain numerous repeated sequences with important roles in their evolution. We have established a bioinformatic strategy to detect the major recombination hot-spots in the genomes of Mycoplasma pneumoniae, Mycoplasma genitalium, Ureaplasma urealyticum and Mycoplasma pulmonis. This allowed the identification of large numbers of potentially variable regions, as well as a comparison of the relative recombination potentials of different genomic regions. Different trends are perceptible among mycoplasmas, probably due to different functional and structural constraints. The largest potential for illegitimate recombination in M.pulmonis is found at the vsa locus and its comparison in two different strains reveals numerous changes since divergence. On the other hand, the main M.pneumoniae and M.genitalium adhesins rely on large distant repeats and, hence, homologous recombination for variation. However, the relation between the existence of repeats and antigenic variation is not necessarily straightforward, since repeats of P1 adhesin were found to be anti-correlated with epitopes recognized by patient antibodies. These different strategies have important consequences for the structures of genomes, since large distant repeats correlate well with the major chromosomal rearrangements. Probably to avoid such events, mycoplasmas strongly avoid inverse repeats, in comparison to co-oriented repeats.

Adhesins, Bacterial↗
PubMed2002

[Chromosomal localization of rice field eel Hox genes by PRINS].

The genome duplication and chromosome rearrangement are two kinds of evolution models at the chromosome level during the evolution of vertebrate genome. And Hox genes are the powerful proves to support the evolution theory of genome duplication, which has been found recently. In this study, the chromosomal localization of rice field eel Hox genes has been carried out by PRINS. The mapping results indicated that 6 Hox clusters might exist in rice field eel genome, and these clusters were localized on chromosome 1, 2, 3, 6, 8, 10 and at the position of 28.24 +/- 2.88, 4.55 +/- 1.39, 13.89 +/- 2.03, 74.32 +/- 1.86, 38.03 +/- 2.41, 58.18 +/- 2.05 from the centromere respectively. The mapping results that Hox genes were localized on chromosome 1, 3, 6 and 10 in the study are corresponding to that by chromosome microdissection. The chromosomal localization of rice field eel Hox genes will help us to discover the origin and evolution of rice field eel chromosomes, and provide cellular genetic proves of this special species to support the evolution theory of genome duplication.

Animals↗
PubMed2004

Evolution of oxygenic photosynthesis: genome-wide analysis of the OEC extrinsic proteins.

The appearance of oxygenic photosynthesis was a key event in the evolution of our green biosphere. Oxygen in the atmosphere is generally believed to come from the biomolecular water-splitting reaction that occurs in oxyphotosynthetic organisms catalysed by the oxygen evolving centre (OEC) of Photosystem II. Using knowledge from complete genomes and current databases, we have investigated the nature and composition of the extrinsic proteins forming the OECs of different organisms, with particular focus on the manganese stabilizing protein that is present in all known oxyphototrophs. This analysis traces the evolution of the extrinsic proteins from ancient cyanobacteria to higher plants and gives hints about the ancestral form of the OEC.

Bacteria↗
PubMed1999

The cattle interleukin-13 gene: genomic organization, chromosomal location, and evolution of the promoter.

Interleukin (IL)-13 plays a key role in the T-helper 2 type immune response. In domestic animal species no sequence information is available for the IL13 gene. Here, we report the isolation and sequencing of the cattle IL13 gene. Since a heterologous cDNA probe failed to hybridize to cattle genomic DNA the gene was identified by a positional sequencing approach. In human and mouse both cytokines are located within a region of about 30 kilobases (kb). Therefore the region upstream of the cattle IL4 gene has been sequenced by a shotgun approach. The cattle IL13 gene was found to be located about 20 kb upstream of IL4 in a head-to-tail orientation. The exon-intron structure and the promoter region is well conserved across species. The alignment of the IL13 sequences from different species allowed the identification of highly conserved amino acid positions and transcriptional elements. Two conserved amino acid positions (glu(31) and pro(94)) are most probably homologous to the interleukin-4 signalling residues. One of the potential binding sites for transcription factors is located at position -197 to -189 and is closely related to the P elements of the IL4 promoter. Nevertheless, the overall identity of the promoter sequences of IL13 and IL4 is low. Therefore we conclude that both cytokines use diverse regulatory elements. There is evidence that IL-13, but not IL-14, is the key mediator in allergic asthma. Furthermore IL-13 is involved in resistance to some infections. Therefore IL-13 is of interest for disease association studies in domestic animals.

Amino Acid Sequence↗
PubMed2002

The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants.

The entire mitochondrial genome of rice (Oryza sativa L.), a monocot plant, has been sequenced. It was found to comprise 490,520 bp, with an average G+C content of 43.8%. Three rRNA genes, 17 tRNA genes and five pseudo tRNA sequences were identified. In addition, eleven ribosomal protein genes and two pseudo ribosomal protein genes were found, which are homologous to 13 of the 16 genes for ribosomal proteins in the mitochondrial genome of the liverwort (Marchantia polymorpha). A greater degree of variation in terms of presence/absence and integrity of genes was observed among the ribosomal protein genes and tRNA genes of rice, Arabidopsis and sugar beet. Transcription and post-transcriptional modification (RNA editing) in the rice mitochondrial sequence were also examined. In all, 491 Cs in the genomic DNA were converted to Ts in cDNA. The frequency of RNA editing differed markedly depending upon the ORF considered. Sequences derived from plastid and nuclear genomes make up 6.3% and 13.4% of the mitochondrial genome, respectively. The degree of conservation of plastid sequences in the mitochondrial genome ranged from 61% to 100%, suggesting that sequence migration has occurred very frequently. Three plastid DNA fragments that were incorporated into the mitochondrial genome were subsequently transferred to the nuclear genome. Nineteen fragments that were similar to transposon or retrotransposon sequences, but different from those found in the mitochondrial genomes of dicots, were identified. The results indicate frequent and independent DNA sequence flow to and from the mitochondrial genome during the evolution of flowering plants, and this may account for the range of genetic variation observed between the mitochondrial genomes of higher plants.

Biological Evolution↗