Biomedical subjects

Genomics

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At least 433 records · Page 24Linked to original sources

PubMed2006

Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing.

BACKGROUND: Whole genome amplification is an increasingly common technique through which minute amounts of DNA can be multiplied to generate quantities suitable for genetic testing and analysis. Questions of amplification-induced error and template bias generated by these methods have previously been addressed through either small scale (SNPs) or large scale (CGH array, FISH) methodologies. Here we utilized whole genome sequencing to assess amplification-induced bias in both coding and non-coding regions of two bacterial genomes. Halobacterium species NRC-1 DNA and Campylobacter jejuni were amplified by several common, commercially available protocols: multiple displacement amplification, primer extension pre-amplification and degenerate oligonucleotide primed PCR. The amplification-induced bias of each method was assessed by sequencing both genomes in their entirety using the 454 Sequencing System technology and comparing the results with those obtained from unamplified controls. RESULTS: All amplification methodologies induced statistically significant bias relative to the unamplified control. For the Halobacterium species NRC-1 genome, assessed at 100 base resolution, the D-statistics from GenomiPhi-amplified material were 119 times greater than those from unamplified material, 164.0 times greater for Repli-G, 165.0 times greater for PEP-PCR and 252.0 times greater than the unamplified controls for DOP-PCR. For Campylobacter jejuni, also analyzed at 100 base resolution, the D-statistics from GenomiPhi-amplified material were 15 times greater than those from unamplified material, 19.8 times greater for Repli-G, 61.8 times greater for PEP-PCR and 220.5 times greater than the unamplified controls for DOP-PCR. CONCLUSION: Of the amplification methodologies examined in this paper, the multiple displacement amplification products generated the least bias, and produced significantly higher yields of amplified DNA.

Bias↗

PubMed2000

Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs).

BACKGROUND: Standard archival sequence databases have not been designed as tools for genome annotation and are far from being optimal for this purpose. We used the database of Clusters of Orthologous Groups of proteins (COGs) to reannotate the genomes of two archaea, Aeropyrum pernix, the first member of the Crenarchaea to be sequenced, and Pyrococcus abyssi. RESULTS: A. pernix and P. abyssi proteins were assigned to COGs using the COGNITOR program; the results were verified on a case-by-case basis and augmented by additional database searches using the PSI-BLAST and TBLASTN programs. Functions were predicted for over 300 proteins from A. pernix, which could not be assigned a function using conventional methods with a conservative sequence similarity threshold, an approximately 50% increase compared to the original annotation. A. pernix shares most of the conserved core of proteins that were previously identified in the Euryarchaeota. Cluster analysis or distance matrix tree construction based on the co-occurrence of genomes in COGs showed that A. pernix forms a distinct group within the archaea, although grouping with the two species of Pyrococci, indicative of similar repertoires of conserved genes, was observed. No indication of a specific relationship between Crenarchaeota and eukaryotes was obtained in these analyses. Several proteins that are conserved in Euryarchaeota and most bacteria are unexpectedly missing in A. pernix, including the entire set of de novo purine biosynthesis enzymes, the GTPase FtsZ (a key component of the bacterial and euryarchaeal cell-division machinery), and the tRNA-specific pseudouridine synthase, previously considered universal. A. pernix is represented in 48 COGs that do not contain any euryarchaeal members. Many of these proteins are TCA cycle and electron transport chain enzymes, reflecting the aerobic lifestyle of A. pernix. CONCLUSIONS: Special-purpose databases organized on the basis of phylogenetic analysis and carefully curated with respect to known and predicted protein functions provide for a significant improvement in genome annotation. A differential genome display approach helps in a systematic investigation of common and distinct features of gene repertoires and in some cases reveals unexpected connections that may be indicative of functional similarities between phylogenetically distant organisms and of lateral gene exchange.

Archaea↗

PubMed2024

Genomic prediction and genome-wide association studies of morphological traits and distraction index in Korean Sapsaree dogs.

The Korean Sapsaree dog is a native breed known for its distinctive appearance and historical significance in Korean culture. The accurate estimation of breeding values is essential for the genetic improvement and conservation of such indigenous breeds. This study aimed to evaluate the accuracy of breeding values for body height, body length, chest width, hair length, and distraction index (DI) traits in Korean Sapsaree dogs. Additionally, a genome-wide association study (GWAS) was conducted to identify the genomic regions and nearby candidate genes influencing these traits. Phenotypic data were collected from 378 Korean Sapsaree dogs, and of these, 234 individuals were genotyped using the 170k Illumina CanineHD BeadChip. The accuracy of genomic predictions was evaluated using the traditional BLUP method with phenotypes only on genotyped animals (PBLUP-G), another traditional BLUP method using a pedigree-based relationship matrix (PBLUP) for all individuals, a GBLUP method based on a genomic relationship matrix, and a single-step GBLUP (ssGBLUP) method. Heritability estimates for body height, body length, chest width, hair length, and DI were 0.45, 0.39, 0.32, 0.55, and 0.50, respectively. Accuracy values varied across methods, with ranges of 0.22 to 0.31 for PBLUP-G, 0.30 to 0.57 for PBLUP, 0.31 to 0.54 for GBLUP, and 0.39 to 0.67 for ssGBLUP. Through GWAS, 194 genome-wide significant SNPs associated with studied Sapsaree traits were identified. The selection of the most promising candidate genes was based on gene ontology (GO) terms and functions previously identified to influence traits. Notable genes included CCKAR and DCAF16 for body height, PDZRN3 and CNTN1 for body length, TRIM63, KDELR2, and SUPT3H for chest width, RSPO2, EIF3E, PKHD1L1, TRPS1, and EXT1 for hair length, and DDHD1, BMP4, SEMA3C, and FOXP1 for the DI. These findings suggest that significant QTL, combined with functional candidate genes, can be leveraged to improve the genetic quality of the Sapsaree population. This study provides a foundation for more effective breeding strategies aimed at preserving and enhancing the unique traits of this Korean dog breed.

Animals↗

PubMedDate not supplied

Applications of genomic medicine in endocrinology and post-genomic endocrine research.

In the mid 1980's, two advances revolutionized Medicine in a way that is comparable only to some of the most important events in the approximately 3,000 years of its history. The first was the introduction of the concept of "positional cloning", i.e. the idea that one can identify genes for human disease though knowing nothing or very little about their function. The second was the discovery of the method of polymerase chain reaction (PCR) which made DNA easier to work with for all biomedical researchers and clinicians. Fresh in the history of Endocrinology were the great discoveries of neuroendocrinology, and even more contemporary and potent, the influence of the then emerging field of molecular endocrinology. Cancer medicine and traditional human genetics were the fields that benefited most from the first applications of the new genomic concepts and technologies. Almost two decades later, and after the first successful applications of positional cloning in Endocrine Genetics with the identification of RET, menin, PTEN and PRKAR1A in the various forms of multiple endocrine tumor syndromes, and a number of other genes in developmental diseases affecting the pituitary, thyroid, parathyroid, pancreas, adrenal and gonadal glands, endocrinology has made a comeback to the forefront of "genomically"- influenced as well as post-genomic Medicine. This report, using the example of endocrine tumor genetics, presents the process and some of the accomplishments of positional cloning and discusses the influence of endocrinology on contemporary translational research. The author suggests that some of the most traditional endocrine concepts, established in the previous two centuries, could help us understand the complex pathways recently unraveled in cancer genetics and, consequently, other fields. It is suggested that "Endocrine" genes that control cellular signaling act as "conductor" since they regulate differentiation, growth and proliferation. Their complex function and resultant "transcriptomes" are now being investigated by post-genomic Medicine. In cancer research, endocrine genes defy classic definitions of tumor suppressors and oncogenes and regulate gatekeepers, caretakers, and landscapers. In the post-genomic, translational Medicine, Endocrinology once again could help us to understand cellular regulation and pathophysiology and to design new treatments.

Chromosome Mapping↗

PubMed2004

Yeast as a touchstone in post-genomic research: strategies for integrative analysis in functional genomics.

The new complexity arising from the genome sequencing projects requires new comprehensive post-genomic strategies: advanced studies in regulatory mechanisms, application of new high-throughput technologies at a genome-wide scale, at the different levels of cellular complexity (genome, transcriptome, proteome and metabolome), efficient analysis of the results, and application of new bioinformatic methods in an integrative or systems biology perspective. This can be accomplished in studies with model organisms under controlled conditions. In this review a perspective of the favourable characteristics of yeast as a touchstone model in post-genomic research is presented. The state-of-the art, latest advances in the field and bottlenecks, new strategies, new regulatory mechanisms, applications (patents) and high-throughput technologies, most of them being developed and validated in yeast, are presented. The optimal characteristics of yeast as a well-defined system for comprehensive studies under controlled conditions makes it a perfect model to be used in integrative, "systems biology" studies to get new insights into the mechanisms of regulation (regulatory networks) responsible of specific phenotypes under particular environmental conditions, to be applied to more complex organisms (e.g. plants, human).

Forecasting↗

PubMed2005

The genome of model malaria parasites, and comparative genomics.

The field of comparative genomics of malaria parasites has recently come of age with the completion of the whole genome sequences of the human malaria parasite Plasmodium falciparum and a rodent malaria model, Plasmodium yoelii yoelii. With several other genome sequencing projects of different model and human malaria parasite species underway, comparing genomes from multiple species has necessitated the development of improved informatics tools and analyses. Results from initial comparative analyses reveal striking conservation of gene synteny between malaria species within conserved chromosome cores, in contrast to reduced homology within subtelomeric regions, in line with previous findings on a smaller scale. Genes that elicit a host immune response are frequently found to be species-specific, although a large variant multigene family is common to many rodent malaria species and Plasmodium vivax. Sequence alignment of syntenic regions from multiple species has revealed the similarity between species in coding regions to be high relative to non-coding regions, and phylogenetic footprinting studies promise to reveal conserved motifs in the latter. Comparison of non-synonymous substitution rates between orthologous genes is proving a powerful technique for identifying genes under selection pressure, and may be useful for vaccine design. This is a stimulating time for comparative genomics of model and human malaria parasites, which promises to produce useful results for the development of antimalarial drugs and vaccines.

Animals↗

PubMed2026

Whole-Genome Analysis of Bacillus Licheniformis Ali5 and Synthesis of Lichenysin via Genome Shuffling.

Whole-genome sequencing of Bacillus licheniformis Ali5 was performed via MGI-seq PE150 and Nanopore single-molecule real-time sequencing. The strain has a 4,114,664 bp circular genome encoding 4030 protein-coding genes. Functional annotation across NR, COG, GO, KEGG, CARD, BacMet, and CAZy databases identified 4025, 2812, 988, 1242, 72, 69, and 94 corresponding genes, respectively, and antiSMASH 6.0 revealed multiple antimicrobial biosynthetic gene clusters, including intact lichenysin and lichenicidin VK21 A1/A2 gene clusters. Three rounds of recursive protoplast fusion-based genome shuffling, paired with a dual-index screening system, significantly improved strain growth and lichenysin biosynthesis. Recombinants exhibited shortened lag phase, enhanced proliferation, improved stationary-phase stability, and higher diauxic peak biomass. PP3-176 and PP3-186 showed 4.6%-8.1% higher 12-h shake-flask titer and 3.1%-4.0% higher maximum titer than the parental average, with excellent fermentation stability. 1-L bioreactor validation confirmed strong scale-up potential. PP3-186 achieved 27.2% and 31.6% titer increases at 12 h and 20 h, while PP3-176 yielded 20.4% and 14.6% improvements with robust metabolic performance. This study validates genome shuffling as an effective strategy for enhancing lichenysin production, providing candidate strains and technical support for industrial application.

Bacillus licheniformis↗

PubMed2026

Comparative genomics approaches to identify genomic regions associated with the antimicrobial activity of Pseudomonas protegens PBL3.

The environmental bacterium Pseudomonas protegens PBL3 has antagonistic activity against the plant pathogenic bacterium Burkholderia glumae, an important pathogen in rice. The antimicrobial activity of P. protegens PBL3 was found in the bacteria-free secreted fraction (secretome), but the specific molecules, as well as the genetic basis of that activity, have not been identified. In this study, we integrated genomic information with antimicrobial assays on P. protegens PBL3 and additional six Pseudomonas spp. strains, to identify putative genomic regions in P. protegens PBL3 associated with antimicrobial activity. We hypothesized that Pseudomonas spp. strains with antimicrobial activity against B. glumae have conserved genes with P. protegens PBL3 that are absent in strains lacking activity. Comparative genomics analyses with anvi'o and progressiveMauve, and using P. protegens PBL3 as the reference genome, revealed 188 genes uniquely present in antimicrobial-producing strains. Seven of those genes were annotated as biosynthetic gene clusters predicted to encode secondary metabolites; additional genes were grouped into 25 contiguous clusters with functions annotated as secretion, signal transduction, regulation, transport/efflux, carbohydrate metabolism and one with an additional uncharacterized function. Altogether, this study uncovered a complex and multi-functional network of candidate genes, suggesting that the antimicrobial activity in P. protegens PBL3 is not limited to biosynthetic pathways but also involves additional regulatory, metabolic and export modules to synthesize and deploy antimicrobials.

Pseudomonas↗

PubMed2025

Genome sequencing and population genomics provide insights into the demographic history, genetic load, and local adaptation of an endangered Tertiary relict.

Endangered Tertiary relict trees represent an exceptional evolutionary heritage with small and isolated populations, yet little is known about how demographic history, local adaptation, and genetic load have affected their long-term survival and extinction risk. We performed whole-genome sequencing and population genomic analyses on Ulmus elongata L. K. Fu & C. S. Ding, an endangered Tertiary relict tree endemic to East Asia. By integrating genomes from U. elongata and seven other endangered trees from public databases, we identified rate-decelerated genes across endangered trees and genes under positive selection of U. elongata associated with tissue development, detoxification, and immune response, and signal transduction and regulation mechanisms potentially leading to endangered status. Demographic analyses revealed continuous population decline from the late Miocene to present, especially during the last glacial maximum (LGM) and last 10 000 years. Spearman correlation indicated a strong negative relationship between effective population size and human population density (rpopulation density = -0.90, P < 0.001) as well as cropland use (rcropland use = -0.89, P < 0.001). Genotype-environment association (GEA) analyses identified a set of candidate genes associated with temperature and precipitation, supporting a polygenic adaptation model in U. elongata. Overall, our findings underscore the severe population bottlenecks that have led to the fixation of strongly deleterious mutations and inbreeding, further compromising the adaptive potential and long-term viability of U. elongata. Furthermore, assessments of genomic vulnerability under future climate scenarios revealed higher genetic offsets in northern region of Fujian and Jiangxi populations, suggesting these regions require prioritized conservation efforts due to reduced adaptive capacity.

Endangered Species↗

PubMed1999

Comparative genomics: the key to understanding the Human Genome Project.

The sequencing of the human genome is well underway. Technology has advanced, such that the total genomic sequence is possible, along with an extensive catalogue of genes via comprehensive cDNA libraries. With the recent completion of the Saccharomyces cerevisiae sequencing project and the imminent completion of that of Caenorhabditis elegans, the most frequently asked question is how much can sequence data alone tell us? The answer is that that a DNA sequence taken in isolation from a single organism reveals very little. The vast majority of DNA in most organisms is noncoding. Protein coding sequences or genes cannot function as isolated units without interaction with noncoding DNA and neighboring genes. This genomic environment is specific to each organism. In order to understand this we need to look at similar genes in different organisms, to determine how function and position has changed over the course of evolution. By understanding evolutionary processes we can gain a greater insight into what makes a gene and the wider processes of genetics and inheritance. Comparative genomics (with model organisms), once the poor relation of the human genome project, is starting to provide the key to unlock the DNA code.

Animals↗

PubMed1998

Gene silencing in plants: relevance for genome evolution and the acquisition of genomic methylation patterns.

Transgenes often become silenced in plants because of repressive influences exerted by flanking plant DNA and/or because of interactions among multiple copies of closely linked transgenes. Repeated transgenes on different chromosomes can also interact in a way that leads to silencing and methylation, suggesting a previously unrecognized ability of unlinked homologous sequences to cross-talk in complex genomes. Non-Mendelian inheritance is a frequent consequence of these interactions because the silenced genes do not fully reactivate or lose methylation after segregating in progeny. Several examples of gene silencing in plants appear to reflect the action of genome defence system that methylates and inactivates foreign or invasive sequences such as transgenes and transposable elements. Because certain types of transposable elements are embedded in regulatory regions of plant genes and have become greatly amplified in plant genomes, they could contribute substantially to normal gene expression and to the generation of genomic methylation patterns. Polyploidy, which has been a major force in plant and vertebrate evolution, might encourage proliferation of transposable elements because genes in polyploids are duplicated and hence less susceptible to the consequences of insertional mutagenesis. Accordingly, the appearance of genome-wide methylation has often coincided with episodes of polyploidization.

DNA Methylation↗

PubMed2006

Array-comparative genomic hybridization of central chondrosarcoma: identification of ribosomal protein S6 and cyclin-dependent kinase 4 as candidate target genes for genomic aberrations.

BACKGROUND: Enchondromas are benign lesions that can occur as solitary tumors or multiple tumors (Ollier disease) and may be precursors of central chondrosarcomas. Recurrent chondrosarcomas can be of a higher grade compared with primary tumors, suggesting possible progression. METHODS: Genome-wide array-comparative genomic hybridization (CGH) was used to investigate copy number changes in enchondromas and central chondrosarcomas to elucidate both primary genetic events and the events related to tumor progression. Analyses of variance, Student t tests, and hierarchical clustering were used for the current analyses. Array-CGH data were compared with complementary DNA (cDNA) and quantitative reverse-transcriptase polymerase chain reaction expression array data. RESULTS: Genomic imbalances were rare in enchondromas and in grade I chondrosarcomas, whereas they were frequent in high-grade tumors. No genomic imbalances that were specific for Ollier disease were found. The authors identified 22 chromosome regions that were imbalanced in > or =25% of tumors, and 3 of those regions were located on chromosome 12 (12p13, 12p11.21-p11.23, and 12q13, containing among others the PTPRF-interacting protein-binding protein 1 (PPFIBP1) gene. Loss of chromosome 6 and gain of 12q12 were associated with higher grade. Comparison of array-CGH with cDNA expression showed correlations for the ribosomal protein S6 (RPS6) and cyclin-dependent kinase 4 (CDK4) genes. CONCLUSIONS: In the current study the authors identified genomic regions and new candidate genes (RPS6, CDK4, and PPFIBP1) that were associated with tumor progression and prognosis in patients with high-grade chondrosarcomas.

Adaptor Proteins, Signal Transducing↗

PubMed2002

Combined restriction landmark genomic scanning and virtual genome scans identify a novel human homeobox gene, ALX3, that is hypermethylated in neuroblastoma.

Restriction landmark genome scanning (RLGS) allows comparative analysis of several thousand DNA fragments in the genome and provides a means to identify CpG islands that are altered in tumor cells as a result of amplification, deletion, or methylation changes. We have developed a novel informatics tool, designated virtual genome scan (VGS), that makes it possible to predict automatically the sequence of fragments in RLGS patterns by matching to the human genome sequence. A combination of RLGS and VGS was utilized to identify changes of chromosome 1-derived fragments in neuroblastoma. A NotI-EcoRV fragment was found to be absent frequently in neuroblastoma cell line RLGS patterns. Sequence prediction by VGS as well as cloning of the fragment showed that it contained a CpG island that is part of the human orthologue of the hamster homeobox gene Alx3. Expression analysis in a panel of human and mouse tissues showed predominant expression of ALX3 in brain tissue. Methylation-sensitive sequence analysis of the promoter region in neuroblastoma cell lines indicated that methylation of specific sequences correlated with repression of the ALX3 gene. Expression was re-induced after treatment with the methylation inhibitor 5-aza-2'-deoxycytidine. Promoter methylation analysis of ALX3 in primary neuroblastoma tumors, using methylation-sensitive polymerase chain reaction, found preferential ALX3 methylation in advanced-stage tumors. The VGS approach we have implemented in combination with RLGS is useful for the identification of genomic CpG island-related methylation changes or deletions in cancer.

Adult↗

PubMed1993

Demonstration of hepatitis C virus genome in saliva and urine of patients with type C hepatitis: usefulness of the single round polymerase chain reaction method for detection of the HCV genome.

The possible transmission routes of hepatitis C virus (HCV) in patients without overt parenteral exposure (sporadic or community acquired form) were examined. Saliva and urine specimens obtained from type C hepatitis patients, whose sera were positive for the HCV genome, were examined by reverse transcription and polymerase chain reaction (RT-PCR). By analyzing the factors that influenced the detection of the HCV genome by PCR, we developed a single round method which enabled semiquantitative detection with higher sensitivity than that obtained with nested PCR. Single round PCR revealed that 34.8% (8 of 23) of saliva and 56.5% (13 of 23) of urine specimens from patients with type C hepatitis contained the HCV genome. The amounts of HCV genome in saliva and urine specimens correlated with those in serum. The relative amounts of HCV genome in serum, saliva, and urine from a chronic type C hepatitis patient were determined by comparing the reciprocal of the smallest volume of the specimens in which the PCR products were visualized in agarose gels (PCR units/ml), and the values were 1 x 10(5), 5 x 10(1), and 3 x 10(1) PCR units/ml for serum, saliva, and urine specimens, respectively.

Adolescent↗

PubMed2005

Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches.

Structural genomics is an international effort to determine the three-dimensional shapes of all important biological macromolecules, with a primary focus on proteins. Target proteins should be selected according to a strategy that is medically and biologically relevant, of good value, and tractable. As an option to consider, we present the "Pfam5000" strategy, which involves selecting the 5000 most important families from the Pfam database as sources for targets. We compare the Pfam5000 strategy to several other proposed strategies that would require similar numbers of targets. These strategies include complete solution of several small to moderately sized bacterial proteomes, partial coverage of the human proteome, and random selection of approximately 5000 targets from sequenced genomes. We measure the impact that successful implementation of these strategies would have upon structural interpretation of the proteins in Swiss-Prot, TrEMBL, and 131 complete proteomes (including 10 of eukaryotes) from the Proteome Analysis database at the European Bioinformatics Institute (EBI). Solving the structures of proteins from the 5000 largest Pfam families would allow accurate fold assignment for approximately 68% of all prokaryotic proteins (covering 59% of residues) and 61% of eukaryotic proteins (40% of residues). More fine-grained coverage that would allow accurate modeling of these proteins would require an order of magnitude more targets. The Pfam5000 strategy may be modified in several ways, for example, to focus on larger families, bacterial sequences, or eukaryotic sequences; as long as secondary consideration is given to large families within Pfam, coverage results vary only slightly. In contrast, focusing structural genomics on a single tractable genome would have only a limited impact in structural knowledge of other proteomes: A significant fraction (about 30-40% of the proteins and 40-60% of the residues) of each proteome is classified in small families, which may have little overlap with other species of interest. Random selection of targets from one or more genomes is similar to the Pfam5000 strategy in that proteins from larger families are more likely to be chosen, but substantial effort would be spent on small families.

Animals↗

PubMed2002

A whole genome amplification method to generate long fragments from low quantities of genomic DNA.

Several whole genome amplification strategies have been developed to preamplify the entire genome from minimal amounts of DNA for subsequent molecular genetic analysis. However, none of these techniques has proven to amplify long products from very low (nanogram or picogram) quantities of genomic DNA. Here we report a new whole genome amplification protocol using a degenerate primer (DOP-PCR) that generates products up to about 10 kb in length from less than 1 ng genomic template DNA. This new protocol (LL-DOP-PCR) allows in the subsequent PCR the specific amplification, with high fidelity, of DNA fragments that are more than 1 kb in length. LL-DOP-PCR provides significantly better coverage for microsatellites and unique sequences in comparison to a conventional DOP-PCR method.

DNA↗

PubMed2002

A technique for genome-wide identification of differences in the interspersed repeats integrations between closely related genomes and its application to detection of human-specific integrations of HERV-K LTRs.

We have developed a method of targeted genomic difference analysis (TGDA) for genomewide detection of interspersed repeat integration site differences between closely related genomes. The method includes a whole-genome amplification of the flanks adjacent to target interspersed repetitive elements in both genomic DNAs under comparison, and subtractive hybridization (SH) of the selected amplicons. The potential of TGDA was demonstrated by the detection of differences in the integration sites of human endogenous retroviruses K (HERV-K) and related solitary long terminal repeats (LTRs) between the human and chimpanzee genomes. Of 55 randomly sequenced clones from a library enriched with human-specific integration (HSI) sites, 33 (60%) represented HSIs. All the human-specific (Hs) LTRs belong to two related evolutionarily young groups, suggesting simultaneous activity of two master genes in the hominid lineage. No deletion/insertion polymorphism was detected for the LTR HSIs for 25 unrelated caucasoid individuals. We also discuss the possible research applications for TGDA research.

Animals↗

PubMed1997

The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression.

The goal of the fungal mitochondrial genome project (FMGP) is to sequence complete mitochondrial genomes for a representative sample of the major fungal lineages; to analyze the genome structure, gene content, and conserved sequence elements of these sequences; and to study the evolution of gene expression in fungal mitochondria. By using our new sequence data for evolutionary studies, we were able to construct phylogenetic trees that provide further solid evidence that animals and fungi share a common ancestor to the exclusion of chlorophytes and protists. With a database comprising multiple mitochondrial gene sequences, the level of support for our mitochondrial phylogenies is unprecedented, in comparison to trees inferred with nuclear ribosomal RNA sequences. We also found several new molecular features in the mitochondrial genomes of lower fungi, including: (1) tRNA editing, which is the same type as that found in the mitochondria of the amoeboid protozoan Acanthamoeba castellanii; (2) two novel types of putative mobile DNA elements, one encoding a site-specific endonuclease that confers mobility on the element, and the other constituting a class of highly compact, structured elements; and (3) a large number of introns, which provide insights into intron origins and evolution. Here, we present an overview of these results, and discuss examples of the diversity of structures found in the fungal mitochondrial genome.

Base Sequence↗