Lesson 2B: (Species Concept and Taxonomic Methods) Flashcards
that is, the strains composing the species should all share a recent common ancestor to the exclusion of other species
Monophyletic
Phylogenetic species concent for bacteri and archea:
Members of a species should be ____ and ____ cohesive
genetically
and phenotypically
combines the two principles above, thus, a species is a group of strains that share certain characteristic traits and which are genetically cohesive and share a unique recent common ancestor
Phylogenetic species concept
Species of ____ and ____ are defined operationally as a group of strains sharing a high degree of similarity in many traits and sharing a recent common ancestor for their SSU rRNA genes
Bacteria and Archaea
Bacteria and archea shares a recent ancestor for their ___ ____ genes
SSU rRNA genes
provides a measure of their genomic similarity between the two genomes of organisms
DNA-DNA hybridization
contains an ever-growing collection of these sequences and provides computational programs for their analysis and for the construction of phylogenetic trees
The Ribosomal Database Project
Different taxonomic methods
a. Gene Sequencing analysis
b. MLST (multilocus sequencing typing)
c. Genome fingerprinting
d. Multigene and Whole genom analyses
e. Phenotypic analyses
are commonly determined from PCR amplified fragments of DNA, and the sequences are analyzed using phylogenetic analyses
Gene sequences
are highly conserved, and while they provide valuable phylogenetic information, they are not always useful for distinguishing closely related species
SSU rRNA gene sequences
Other highly conserve genes
- recA, gyrB
A highly conserved gene that encodes recombinase protein
recA
a highly conserved gene that encodes DNA gyrase
gyrB
is a method that uses “housekeeping “genes from several related organisms , which are sequenced and the sequences used collectively to distinguish the organisms.
Multilocus sequence typing (MLST)
Genes that encode essential functions in cells and are always located on the chromosome rather than on a plasmid
Housekeeping genes
How many bp of genes is amplified and sequenced in MLST
450-base-pair sequence
a rapid approach for evaluating polymorphisms between strains of a species. The fingerprints are generally fragments of DNA generated from individual genes or whole genomes
Genome Fingerprinting
Example of Genome fingerprinting
Ribotyping
is a form of genome fingerprinting based on the localization of SSU rRNA genes on genome fragments.
Ribotyping
a kind of genome fingerprint
Ribotype
What causes ribotype
- changes in genome sequencing that can cause variations in restriction fragments
Other common genome finger printing methods
- rep-PCR (repetitive extragenic palindromic PCR)
- AFLP (amplified fragment Length Polymorphism)
this method is based on the presence of highly conserved repetitive DNA elements interspersed randomly around the bacterial chromosome
rep-PCR
is based on the digestion of genomic DNA with one or two restriction enzymes and selective PCR amplification of the resulting fragments, which are then separated by agarose gel electrophoresis.
AFLP
