4 Types of molecular data

(a)  

4 DNA Fragments

(a)  

Refers to the sequence of nucleotide in a particular region of the DNA in a given taxon.

(a)  

Each nucleotide position is a ___ and the actual nucleotide that is present at that site is the ___.

(a)  

4 nucleotide bases

(a)  

A character can be (a)   when nucleotide changes are shared by two or more taxa.

A character can be (a)   when all nucleotides are the same among taxa, or when only a single taxon has a different nucleotide.

Three major sources of genes (DNA) for plants

(a)  

replicate and divide independently of the nucleus and it is transmitted to offspring only maternally

(a)  

Chloroplast and Mitochondrial DNA

genomes were acquired from __or__ millions of years ago (endosymbiosis)

(a)  

derived from endosymbiosis of cyanobacteria

(a)  

Shape of Chloroplast DNA

(a)  

Stable within cells and species (more so than

mitochondrial genome)

(a)  

Rearrangements are rare enough in evolution that they can

be used to demarcate major groups.

(a)  

Three zones of Chloroplast DNA

(a)  

Draw Chloroplast Genes Table

(a)  

Usually chosen because it is almost universal among plants, it is fairly long, and has many copies in the cell.

(a)  

not explored in plant systematics

(a)  

used to a lesser degree in plant systematics

(a)  

2 useful types of nuclear DNA sequences include

(a)  

2 Non coding regions of nrDNA

(a)  

-codes for ribosomal RNA

-occur in tandem repeats

(a)  

-3 highly conserved coding units

-useful in providing information at higher taxonomic levels

(a)  

Lies between 18S and 26S nrDNA

(a)  

Divided into 2 sub regions separated by 5.8S nrDNA:

(a)  

-Lies between 26S and 18S nrDNA

-Contain more sequence variations than ITS and is useful for analysis at lower taxonomic levels (genus)

(a)  

-stretch of DNA sequences located between genes; not transcribed

-higher degree of variability- thus more useful for analysis at the species or infraspecies

level

(a)  

also called spacer DNA

(a)  

considered the most conserved (least variable) gene in all cells (Smith et al. 2007)

(a)  

genes that encode the rRNA (rDNA) are sequenced

(a)  

thousands of rRNA sequences are known and stored in specialized databases such as__ and __

(a)  

Nuclear, Chloroplast, Mitochondrial Genomes in Comparison

Table

Indicate:

Genome, Genome Size , Inheritance, Shape

(a)  

Steps in acquiring DNA sequence data

(a)  

can control the temperature of the samples that are put into the machine

(a)  

can be programmed to go to different

temperatures and “hold” them for different

times, then repeat the cycle

(a)  

the determination of the precise sequence of nucleotides in a sample of DNA

(a)  

most popular method

(a)  

dideoxy method is named after

(a)  

the target DNA is copied many times, making fragments of different lengths

(a)  

fluorescent “ (a)   ” nucleotides mark the ends of the fragments and allow the sequence to be determined

Ingredients of Sanger method

(a)  

-synthetic nucleotides

-lack the -OH at the 3′carbon atom

-chain elongation stops because there is no 3′ - OH for the next nucleotide to be attached to

-also called the chain termination method.

(a)  

DNA strands can be scanned during (a)   .

arranging the sequences of DNA to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences (homologous sequences)

(a)  

-mismatches can be interpreted as

-gaps

(a)  

there is a substitution since their

divergence.

(a)  

no change since their

divergence

(a)  

_____ : substitutions from A to G; G to A; C to T; T to C.

___ : substitutions from G to C; C to G; T to A;

A to T.

___ : removal of one or more nucleotides.

___ : addition of one or more nucleotides.

___ :180 °C rotation of a double strande•.d DNA

segment compromising 2 or more base pairs

(a)  

Region that has the same genes in all species

(a)  

-If two sequences in an alignment share a common ancestor (homologous sequences)

-the absence of substitutions in a particular region of the sequence

the conservation of base pairs can indicate a similar functional or structural role

(a)  

-bossy genes are powerful — they can turn on all the genes necessary to build a working eye!

(a)  

-very short or very similar sequences can be aligned by hand

-alignment of lengthy, highly variable or extremely numerous sequences can be done by computational approaches (computer algorithms)

(a)  

2 types of Alignment

(a)  

-align every nucleotide bases in every sequence

-most useful when the sequences in the query set are

similar and of roughly equal size

-usually done for comparing homologous genes

(a)  

identify regions of similarity within long sequences that are often widely divergent

used to find homologous domains in otherwise non- homologous genes.

(a)  

-used to find the best-matching piecewise (local) or global alignments of two query sequences

-can only be used between two sequences at a time

(a)  

an extension of pairwise alignment to incorporate more than two sequences at a time

(a)  

Two major tree building methods

(a)  

Phenetic methods based on

(a)  

Cladistic methods based on characters:

(a)  

Give the family name, scientific name, common name

Specific epithet= spicata

genus= distichlis

authors=grenne;linnaeus

common name= coastal saltgrass

family=poaceae

(a)  

Give the family name, scientific name, common name

Specific epithet= caroliniana

genus= lanchnanthes

authors=dandy; lam

common name= carolina redroot

family=haemodoraceae

(a)  

Give the order in naming a scientific name

(a)