reliability of its in species identification by surachit waengsothorn
TRANSCRIPT
Reliability of ITS in Species Identification
by
Surachit Waengsothorn
What’s ITS
ITS stands for Internal Transcribed Spacer regions
Where are they?
These regions are located in ribosome.
Ribosomal RNA
5S rRNS 5.8s rRNA 18s rRNS
120bp 160bp ~1900bp
ITS1 ITS2
What’s ITS
ITS stands for Internal Transcribed Spacer regions
Where are they?
These regions are located in ribosome.
Why do I pick ITS?
rRNA is highly conserved across texa while the ITS may be species-specific.
rRNA evolution rate use
Small-subunit very slow distantly related organisms
Mitocondrial more rapidly family level
ITS fastest variation among species
Species
In the past 30 years, over six concepts have been proposed.
Species is a very simple word BUT its definition is not that easy.
Three majors concepts:
-The biological species concept
- The phylogenetic species concept
- The morphospeceis concept
The biological species concept• proposed in 1942 by Ernst Mayr
• used by many zoologists
• defined “species” in Endangered Species Act
Criterion: reproductive isolation (lack of gene flow)
• populations do not hybridize
• populations fail to produce fertile offspring
Cons:
• can be applied to only living organisms
• difficult to keep tract on all populations
The phylogenetic species concept
Criterion: monophyly
Populations contain all the know descendants of a single common ancestor.
Species are the smallest diagnosable monophyletic groups.
The morphospeceis concept: used by paleontologists
They define species on the basis of morphological differences among fossils.
All concepts share three things in common:
1) Species consist of interbreeding populations.
2) Species are a fundamental unit of evolution.
3) Species share a distinguishing characteristic.
Why is species identification so important?
Species plays a major role in all conservation aspects.
Species identification is a starting point of life science disciplines i.e. biology, ecology, forestry, biotechnology, etc.
Species identification is daily used in many careers such as farmers, foresters, lawyers, gardeners, researchers, scientists, curators, ete.
MethodData collections:
Lab work:- extract DNA from a sugar maple sample.
- amplify ITS region using PCR technique.
- perform fragment sequencing.
5s RNA 5.8s RNA 18s RNA
ITS1 primer:TCCGTAGGTGAACCTGCGG
ITS4 primer: TCCTCCGCTTATTGATATGC
Method (cont.)
Office work:
- search around the cool web (NCBI home page) and collect ITS data of maples.
- use GCG to perform pileup, pretty - consensus, tofasta.
- put fasta file in clastalW, and get the tree from Treeview
Data collections:
Results
• 15 species of maples (genus Acer)
• 3 sample per species except sugar maple has only 2 samples + 1 sample of mine.
Pretty -consensus
Results
•15 species of maples (genus Acer)
•3 sample per species except sugar maple has only 2 samples + 1 sample of mine.
Pretty -consensus
Clustal W
Treeview
Data Interpretation
Recommendations
Unknown sample(s) is(are) recommended to compare with at least three sequences of a known species, and several species in the same genus or different genus in the same family.
ITS is a powerful tool to discriminate species. 42 of 45 sequences (>93%) support the hypothesis.