The Clay of Evolution - How to study genes and genomes.

How can genes get duplicated:
Whole genome duplication, partial genome duplication, single genes get duplicated (tandem repeats)

Whole genome duplication: frequent event in plants, also speculated to have occurred at least twice in the early evolution of vertebrates. 15% of the yeast genome is present in duplicated form, the currently accepted idea is that there was an ancient duplication followed by rearrangement and gene loss. The idea of genome duplications in early vertebrate evolution has become very popular, but phylogeny of regulatory proteins does not support this idea (see here and here for pro and here for contra).

The picture below is a comparison of the Yeast proteome with itself (the diagonal is removed).  It clearly shows many small regions of duplications.

Parts of chromosomes get duplicated: traces of this seen in Arabidopsis and Caenorhabditis

Single genes get duplicated -> gene families originally tandemly replicated (see the Caenorhabditis paper above)

Some TOOLS at NCBI

The NCBI provides several different interfaces to browse through and analyze genomes. For example, in the Borrelia genome, if you click on the complete genome, you get a graphical representation, further clicks move you down throw several levels to the nucleotide and encoded amino acid sequence. If you click on an ORF, you retrieve the sequence followed by an output of a blast search of this sequence against the nr database. The graphic representation shows you which part of the ORF generated the match, if you click on the number that represents the score, you open a new window with the alignment (again with nice graphics included). If you click on the number an window with the matching sequence in gb-format opens up. If the ORF is part of a cluster of putatively orthologous genes, you can get information on the cluster by clicking on the COGnumber.

From the Borrelia genome page, you can go to tables listing all ORF, or to taxtable, which provides an interesting nearest neighbor coloring of the genome. It is noteworthy that many of the pink dots are endonucleases. Also, there are many transporters among the odd colored genes.

In an attempt to capture some phylogenetic information in blast comparisons, Olendzenski et al. pioneered an approach to use multiple reference genomes to screen for putatively horizontally transferred genes (see Fig. 4). A similar approach, but using only two instead of three reference genomes is implemented in the TAX PLOT program at the NCBI's genome page (see below, if demo doesn't work).

You pick one genome to analyze, and two reference genomes. The program returns a plot of every ORF in the selected genome represented in a coordinate system, where the two coordinates are the highest alignment score with the two reference genomes:

Selected genome was from Borrelia burgdorferi. The list of selected genes is below:

Definition Blast2Seq GenBank Blink
V-type ATPase, subunit B (atpB) [Borrelia burgdorferi] 15594439 =>
aa V-TYPE ATP SYNTHASE BETA CHAIN (V-TYPE A 722 12585403 =>
aa ATP synthase F1 alpha subunit [Aquifex a 261 15606090 =>
V-type ATPase, subunit A (atpA) [Borrelia burgdorferi] 15594440 =>
aa H+-transporting ATP synthase, subunit A 1051 11498766 =>
aa ATP synthase F1 beta subunit [Aquifex ae 221 15607015 =>
prolyl-tRNA synthetase (proS) [Borrelia burgdorferi] 15594747 =>
aa prolyl-tRNA synthetase (proS) [Archaeogl 655 11499201 =>
aa proline-tRNA synthetase [Aquifex aeolicu 167 15605873 =>
phenylalanyl-tRNA synthetase, beta subunit (pheT) [Borrelia burgdorferi] 15594859 =>
aa phenylalanyl-tRNA synthetase, subunit be 709 11499019 =>
aa phenylalanyl-tRNA synthetase beta subuni 153 15606806 =>
chemotaxis histidine kinase (cheA-1) [Borrelia burgdorferi] 15594912 =>
aa chemotaxis histidine kinase (cheA) [Arch 798 11498645 =>
aa histidine kinase sensor protein [Aquifex 86 15605839 =>
methionyl-tRNA synthetase (metG) [Borrelia burgdorferi] 15594932 =>
aa methionyl-tRNA synthetase (metS) [Archae 873 11499048 =>
aa methionyl-tRNA synthetase alpha subunit 436 15606482 =>
spermidine/putrescine ABC transporter, ATP-binding protein (potA) [Borrelia burgdorferi] 15594987 =>
aa spermidine/putrescine ABC transporter, A 678 11499200 =>
aa ABC transporter [Aquifex aeolicus] 325 15607081 =>
lysyl-tRNA synthetase [Borrelia burgdorferi] 15595004 =>
aa lysyl-tRNA synthetase (lysS) [Archaeoglo 642 11498815 =>
aa cysteinyl-tRNA synthetase [Aquifex aeoli 92 15606347 =>

More on Comparing Genomes:

Genome dot plots allow to compare two genomes (or rather the ORFs encoded in these genomes). In contrast to a normal dot plot, one does not move a window through the sequence, rather one takes one ORF at a time and compares it to the other genome.

Robert L. Charlebois' genome and bioinformatics site performed these and other analysis.
Sadly, this site is no longer free.

For example BLASTP-based dot plot of Pyrococcus abyssi vs Pyrococcus horikoshii depicted below clearly reveals inversions, and a duplication (two parallel diagonals), the latter can also be detected by comparing a genome to itself.

See this paper from Tillier and Collins on a discussion of this and similar patterns.

 

Automation of Repetitive Tasks

SEALS demo.

(to look at the tree go to phylodendron, or copy paste into treeview)

 

Assignment #7:

Your name:
Your email address:

  1. Go to the taxonomy browser in Entrez. Can you use this to find the taxonomic position of Pyrococcus and Aeropyrum?
    To which kingdoms do they belong?

  2. Go to the ENTREZ genome section. Select the genome from Aeropyrum pernix. Explore the different genome views (click and explore the different options). Select TaxMap (also called TaxTable).


    How many ORFs do you find whose most similar sequence is a eukaryotic one?

    What could be the reason for this?

    How does the plot change, when you select different cut-off values?

  3. Select a microbial genome, and a question to address using TAX PLOT. Select two reference genomes appropriate for your question.

    Your question:

    Your genome:

    Your two reference genomes:

    Which candidate genes did you find?:

    For example:
    If you ask the question: which genes in Treponema pallidum are candidates for having been transferred from the archaeal domain into this genome, you go to the NCBI genomes page, select the Treponema pallidum genome (here), and then select TAX PLOT (here).

    To look for genes transferred from the archaea, you need to select one bacterial genome (a deep branching one would be nice, if there is such a thing), and an archaeal genome. Aquifex and Archaeoglobus would be suitable.


    If you look for halobacterial (archaeal) genes in cyanobacteria you could select B. subtilis (B.=Bacillus) and H. NRC1 (=Halobacterium, which is an archaeon, not a bacterium!) as reference genomes and the genome from Synechocystis sp PCC6803 as the genome to analyze.

Finished?

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