- Eukaryote microbial genomics
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Syllabus - What you will learn from this course. Video 6 videos. Reading 4 readings. Supplementary materials: Definition 10m. Supplementary materials: Cell Biology 10m. Supplementary materials: Phylogenetic tree 10m. Supplementary materials: Ecology of protists 10m. Quiz 5 practice exercises. Quiz 6m. Quiz 2m. Quiz 4m. Control test 15m. Video 5 videos. Mineral skeleton 4m.
Reading 3 readings. Supplementary materials 10m. Supplementary materials: Protistan skeletons 10m. Supplementary materials: Pseudopodia 10m. Quiz 6 practice exercises.ncof.co.uk/el-libro-interior-una-comunicacin-amena-con.php
Eukaryote microbial genomics
Quiz 20m. Quiz 18m. Control test 30m. Video 9 videos. Reading 7 readings. Supplementary materials: Axoneme 10m.
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- Comparative genomics of eukaryotic microbes: Genomes in flux, and flux between genomes?
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Supplementary materials: Centriole 10m. Supplementary materials: kDNA 10m. Supplementary materials: Hydrogenosome 10m. Supplementary materials: Glycosome 10m. Supplementary materials: Haptonema 10m. It retains 54 genes for biosynthesis of crucial amino acids, but no longer has pathways for those amino acids that the host can synthesize. Pathways for nucleotide biosynthesis are gone from many reduced genomes. Those anabolic pathways that evolved through niche adaptation remain in particular genomes.
The hypothesis that unused genes are eventually removed does not explain why many of the removed genes would indeed remain helpful in obligate pathogens. For example, many eliminated genes code for products that are involved in universal cellular processes, including replication, transcription , and translation. Even genes supporting DNA recombination and repair are deleted from every small genome.
In addition, small genomes have fewer tRNAs , utilizing one for several amino acids. So, a single codon pairs with multiple codons, which likely yields less-than-optimal translation machinery.
It is unknown why obligate intracellular pathogens would benefit by retaining fewer tRNAs and fewer DNA repair enzymes. Another factor to consider is the change in population that corresponds to an evolution towards an obligately pathogenic life. Such a shift in lifestyle often results in a reduction in the genetic population size of a lineage, since there is a finite number of hosts to occupy.
This genetic drift may result in fixation of mutations that inactivate otherwise beneficial genes, or otherwise may decrease the efficiency of gene products. Hence, not will only useless genes be lost as mutations disrupt them once the bacteria has settled into host dependency , but also beneficial genes may be lost if genetic drift enforces ineffective purifying selection. The number of universally maintained genes is small and inadequate for independent cellular growth and replication, so that small genome species must achieve such feats by means of varying genes.
This is done partly through nonorthologous gene displacement. That is, the role of one gene is replaced by another gene that achieves the same function. Redundancy within the ancestral, larger genome is eliminated. The descendant small genome content depends on the content of chromosomal deletions that occur in the early stages of genome reduction.
The very small genome of M. In a study in which single genes of this organism were inactivated using transposon-mediated mutagenesis , at least of its ORGs were not required for growth. A much smaller genome than that of the M. One theory predicts that bacteria have smaller genomes due to a selective pressure on genome size to ensure faster replication.
The theory is based upon the logical premise that smaller bacterial genomes will take less time to replicate. Subsequently, smaller genomes will be selected preferentially due to enhanced fitness. A study done by Mira et al. Still, many researchers believe there is some selective pressure on bacteria to maintain small genome size. Selection is but one process involved in evolution. Two other major processes mutation and genetic drift can account for the genome sizes of various types of bacteria. Results indicated that mutational deletions tend to be larger than insertions in bacteria in the absence of gene transfer or gene duplication.
Assuming a lack of these processes, genomes will tend to reduce in size in the absence of selective constraint. Evidence of a deletional bias is present in the respective genome sizes of free-living bacteria, facultative and recently derived parasites and obligate parasites and symbionts. Free-living bacteria tend to have large population-sizes and are subject to more opportunity for gene transfer.
As such, selection can effectively operate on free-living bacteria to remove deleterious sequences resulting in a relatively small number of pseudogenes. Continually, further selective pressure is evident as free-living bacteria must produce all gene-products independent of a host. Given that there is sufficient opportunity for gene transfer to occur and there are selective pressures against even slightly deleterious deletions, it is intuitive that free-living bacteria should have the largest bacterial genomes of all bacteria types.
Recently-formed parasites undergo severe bottlenecks and can rely on host environments to provide gene products. As such, in recently-formed and facultative parasites, there is an accumulation of pseudogenes and transposable elements due to a lack of selective pressure against deletions.
The population bottlenecks reduce gene transfer and as such, deletional bias ensures the reduction of genome size in parasitic bacteria. Obligatory parasites and symbionts have the smallest genome sizes due to prolonged effects of deletional bias. Parasites which have evolved to occupy specific niches are not exposed to much selective pressure.
As such, genetic drift dominates the evolution of niche-specific bacteria. Extended exposure to deletional bias ensures the removal of most superfluous sequences. Symbionts occur in drastically lower numbers and undergo the most severe bottlenecks of any bacterial type. There is almost no opportunity for gene transfer for endosymbiotic bacteria, and thus genome compaction can be extreme. One of the smallest bacterial genomes ever to be sequenced is that of the endosymbiont Carsonella rudii.
Molecular phylogenetics has revealed that every clade of bacteria with genome sizes under 2 Mb was derived from ancestors with much larger genomes, thus refuting the hypothesis that bacteria evolved by the successive doubling of small-genomed ancestors. Bacteria were cultured introducing frequent bottlenecks and growing cells in serial passage to reduce gene transfer so as to mimic conditions of endosymbiotic bacteria.
The data predicted that bacteria exhibiting a one-day generation time lose as many as 1, kbp in as few as 50, years a relatively short evolutionary time period. Furthermore, after deleting genes essential to the methyl-directed DNA mismatch repair MMR system, it was shown that bacterial genome size reduction increased in rate by as much as 50 times. This is not to suggest that all bacterial genomes are reducing in size and complexity. While many types of bacteria have reduced in genome size from an ancestral state, there are still a huge number of bacteria that maintained or increased genome size over ancestral states.
While deletional bias tends to remove unnecessary sequences, selection can operate significantly amongst free-living bacteria resulting in evolution of new genes and processes. Unlike eukaryotes, which evolve mainly through the modification of existing genetic information, bacteria have acquired a large percentage of their genetic diversity by the horizontal transfer of genes. This creates quite dynamic genomes, in which DNA can be introduced into and removed from the chromosome.
Bacteria have more variation in their metabolic properties, cellular structures, and lifestyles than can be accounted for by point mutations alone. For example, none of the phenotypic traits that distinguish E. On the contrary, evidence suggests that horizontal gene transfer has bolstered the diversification and speciation of many bacteria.
Horizontal gene transfer is often detected via DNA sequence information. Tools Request permission Export citation Add to favorites Track citation. Share Give access Share full text access. Share full text access.
Corradi Lab - Evolutionary Genetics and Genomics of Unique Eukaryotic Microbes - Home
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