TU Genome based species taxonomy 11/10 Flashcards
Cladistics
is a method of classifying organisms based on shared derived characteristics (synapomorphies). This approach emphasizes evolutionary relationships and aims to construct a phylogenetic tree (cladogram) that represents these relationships.
DNA-DNA hybridization (Bacterial taxonomy)
is a molecular technique used to determine the genetic relatedness between different organisms or species. It involves the binding of complementary DNA strands from different sources, allowing researchers to assess genetic similarities and differences
ribosomal RNA (16S rRNA) analysis (Bacterial taxonomy)
The 16S ribosomal RNA gene, which encodes a component of the small subunit of the ribosome, is highly conserved across different species, making it an ideal target for studying evolutionary relationships
Average Nucleotide Identity (ANI)
ANI calculates the percentage identity between orthologous genes across genomes. When genomes share more than 94% ANI, they are considered the same species. This method provides a precise framework for bacterial classification.
A genomic technique used to measure the similarity between the genomes of different organisms by calculating the percentage of identical nucleotide sequences, providing insights into their taxonomic relationships and potential species boundaries.
ANI is generally calculated by comparing whole-genome sequences to assess genomic similarity, but it can also be calculated using a set of orthologous genes when whole-genome data is not available.
Core Nucleotide Identity (CNI)
Similar to ANI, CNI is based on nucleotide identity within conserved single-copy genes across genomes. It helps define species by offering higher resolution in distinguishing between closely related species.
A measure of genomic similarity that calculates the average nucleotide identity of a core set of conserved genes shared among different genomes, providing insights into their evolutionary relationships and taxonomic classification.
Processes in Molecular Evolution
Gene Duplication: A process where a segment of DNA is copied, resulting in two or more identical or similar copies of a gene within a genome. This redundancy can provide raw material for evolutionary innovation, allowing one copy to maintain its original function while the other may acquire mutations and potentially evolve new functions.
Divergence: The process by which gene copies or species accumulate differences over time due to mutations, natural selection, or genetic drift. Divergence leads to increased genomic diversity and can result in the development of distinct traits, functions, or species from a common ancestor.
Speciation: The evolutionary process by which new biological species arise, typically as a result of reproductive isolation. Speciation can occur through mechanisms such as geographic separation, ecological differentiation, or genetic divergence, ultimately leading to the formation of distinct species that can no longer interbreed.
Hidden Markov Models (HMMs)
Used for identifying single-copy orthologous genes in large genomes, HMMs are statistical models that help predict gene sequences based on probabilistic patterns.
MAFFT (Multiple Alignment using Fast Fourier Transform) (Multiple Sequence Alignment, what said in samenvatting)
(Multiple Alignment using Fast Fourier Transform) is a widely used software tool designed for performing multiple sequence alignments of DNA, RNA, or protein sequences.
Genomic Quality Control:
* Genome completeness and redundancy assessments are crucial in verifying the accuracy of species identification.
* Techniques like MAFFT (Multiple Sequence Alignment) are used to ensure that alignments are of high quality before determining species classifications.
