Task 1.2 Background
“The taxonomy browser is an NCBI-derived search tool that allows an individual to search the taxonomy database. Using the
taxonomy browser, information may be retrieved on available nucleotide, protein, and structure records for a particular species
or higher taxon. The taxonomy database contains the names and lineages of every organism that is represented by at least one
nucleotide or protein sequence in the NCBI genetic databases.”i
Task 1.2 Scenario
One of your fictitious coworkers at Clearsighted Biotechnologies, Inc., Dr. Paul E. Morrfism is studying insect genes. He hopes
to better understand the genetic changes that take place as an insect population evolves the resistance to toxins (pesticides). In
addition he is interested in the possibility of using this understanding to develop insects that would have the ability to clean up
toxins in polluted environments. Currently he is studying how insect genes have changed over very long periods of time.
In 1993 it was reported that DNA had been recovered from an extinct organism, Lebanorhinus succinusii. This insect was
preserved for more than 120 million years in amber. One of the genes from this extinct organism was amplified and sequenced,
and then it was submitted to the Genbank database. Dr. Morrfism would like to know how/if this gene has changed over time.
Your task is to use the Taxonomy Browser at NCBI to learn more about this organism and the DNA sequence that was
recovered from it. Then you are to find matching sequences from extant insects and describe any differences between
the genes of the extinct and modern species.
Step
A
To get started you need to learn a little
more about the taxonomy of
Lebanorhinus succinus. Use the
Taxonomy Browser at the NCBI
website and locate the list of Extinct
Organisms in the Taxonomy Database.
Hints
There are many ways to find this information here is one method. Navigate to the
Taxonomy database home by selecting “Taxonomy” from the pull down database menu
bar at the top of the NCBI homepage and click “go”.
(1)Scroll down and search for the link to “Taxonomy Home” along the left-hand side of
the page. Follow this link to the home page then look for the Extinct Organisms link
on the lower left side of this page.
B
Find and view the taxonomic lineage of
an extinct “beetle from Lebanese
amber”. This will show you all the
categories (taxons) that are used to
classify Lebanorhinus succinus.
(1) Scroll down the list of extinct organisms until you find the section labeled Insects:
(2) Click on the link for Libanorhinus succinus
C
Dr. Morrfism would like an update on
your progress. He is curious to know
more about this extinct organism and
other organisms that are closely related
to it.
In the space below provide the name for
each of the following taxonomical
categories of the extinct Lebanorhinus
succinus.
 Superkingdom:
 Kingdom:
 Phylum:
 Class:
 Order:
 Family:
 Genus:
List the common names of 3 other
organisms in this same phylum.
1.
2.
3.
D
In order to learn about the gene
sequence that was recovered from the
amber, visit the Genbank report to get a
description of this DNA and learn about
the gene’s product.
(1)Click on the word “Lineage” to alternate between the abbreviated and the full lineage.
Note that the lineage of an organism may contain extra descriptive categories that are
not assigned a taxonomic rank.
(2)Scroll over each word in the lineage to see a pop-up label describing its taxonomical
rank. In the example below the superkingdom (domain) is the category Eukaryota
(1)Identify the phylum and click on this word.
(2)Click on the phylum link depicted below.
Then select 3 common names of organisms that are listed as sub headings below the
Arthropoda heading.
(1) There are many ways to get to the Genbank summary report. One method is to click
the direct link to the nucleotide database which is provided in the window you should
still have open. See the image below for help:
Then click the Genbank accession number, which is a link to the report summary and
nucleotide sequence.
(2)Another method to find the Genbank record is to search the nucleotide sequence
database for L succinus. This can be done easily from the homepage. The search bar
is at the top of the page, see the image below.
E
Note the definition line in this summary
report, it provides some information
about the product of this DNA
sequence. Follow the PubMed link to
read the abstract of the scientific paper
published about the DNA extracted
from the amber.
(1) Click on the link depicted in the image below.
F
Its time to report to Dr. Morrfism what
you have learned from the Genbank
record and the abstract provided by
PubMed. Record you answers on the
hanout.
(1) Refer to Genbank report or the abstract provided by PubMed for this information.
(2) From the Genbank record:
1. Describe the product or function of
this gene?
From the Abstract provided by PubMed:
2. What is different about the age of this
DNA when compared to DNA
previously extracted from extinct
organisms?
G
Now its time to determine what modern
organisms contain a similar gene using
a nucleotide BLAST search. Another
method to search the Nucleotide
Database is to use the accession number
instead of the nucleotide sequence. Use
the accession number to complete a
BLASTn search. This will allow you to
discover sequences that closely match
the DNA recovered from the extinct L.
succinus.
(1) Copy the accession number from the Genbank summary report, navigate to the
BLASTn page and paste the number into BLAST Query text box. Select “Nucleotide
Collection” from the database pull-down menu and enter a job title before clicking
the BLAST button.
(2) Copy the accession number
top of the
then click on
Click this double helix icon
at the
page to return to the NCBI homepage and
the
link in the menu bar.
Run nucleotide BLAST program by clicking
Paste the accession number into the query text box
Change the search name if you would like
Select the Nucleotide Collection from the pull-down menu of databases
Click the BLAST button at the bottom of the page
H
Visit the Taxonomy Report to
determine the type of organisms that
have similar DNA to that recovered
from the amber. You can might be able
to find images of these organisms with a
Google image search.
.
(1) From the BLAST results page click on the link to the taxonomy reports. It will open
in a new window or tab.
(2) See the image below to find the link to the Taxonomy Reports
I
View the alignment data for several of
the closest matching sequences to see
how closely they are aligned. Recall
that high Bit Scores and low E-values
indicate significant alignment. E-values
are often given in scientific notation.
For example 2e-163=2x10-163.
J
Dr. Morrfism has some questions about
the results of your BLAST search.
(1) Close the taxonomy report window or tab to see the BLAST results again. Click on
the Max Score number in the table for one of the hits near the top of the table.
(2) View the image below to get a sense of which links to follow in order to view the
detailed alignments data.
(1)Refer to the Taxonomy Report for help with this question
(2)Look on the report for the common name of the organisms that are listed there,
especially those with the highest alignment scores
1. What group of organisms (common
name) with DNA in the database is
the source of the closest matching
sequences?
K
1. Looking at the alignment data for
the first hit in the table. Notice how
the index numbers in both sequences
are perfectly aligned Why is the first
hit in the BLAST results table a
perfect match for the DNA you
submitted?
(1)Look closely at the first record, the definition or description will give you some hints
about the source of the DNA. Then click the max score for that record to link to the
alignment data.
(2)Look at the image below to see how the two sequences of DNA are the same DNA.
L
Find the alignment data for the
sequence with Accession Number
AJ841532.1 (it is in the top 10 hits).
Describe how well it aligns with the
DNA from L. succinus.
(1)The number of identities (identical matches) will also tell you how many mismatches
there are by comparing it to the total number of letters in the query sequence. The
number of gaps is also given in these details.
(2)Look at the image below for help finding the data to answer these questions. Recall
that the E-value is the number of chance matches expected to exist in a database that
would have the same (or higher) alignment score.
1. How many gaps and mismatches?
2. How does the hit score compare to
perfect match?
3. How many matches of this quality
would be expected in a randomly
generated database of the same size?
M
Congratulations! You have
completed this task for Dr. Morrfism.
Now its time for Assessment 1.
i
National Library of Medicine and National Institutes of Health. National Center for Biotechnology Information Website.
http://www.ncbi.nlm.nih.gov/About/primer/phylo.html
ii
Nature. 1993 Jun 10; 363(6429):536-8.