Single Gene Orthologs
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11.5 years ago
GR ▴ 400

Dear Everyone,

I have All-vs-All blast results of 10 species and I have to select genes that are Single gene orthologs (SGOs). Can any one please elaborate what are SGOs or provide some useful reference.

Thanks, R.

gene • 8.9k views
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Where did you find that expression ("SGO")? It does not sound familiar to me.

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11.5 years ago

Single-copy genes have clear one-to-one orthologs between species. Thus, you can easily assume that they are more similar to each other than they are to any other genes from organisms you compare.

In order to identify putative single-copy genes between two species (A and B) you should first perform all-against-all BLAST comparisons of:

  1. organism A -> organism B,
  2. organism B -> organism A,
  3. organism A -> organism A,
  4. organism B -> organism B.

Pairs of genes, one from either species (A and B), that are each other’s highest scoring BLAST match can be considered as orthologs. If these orthologous genes don't have such a symmetric best hit corresponding gene within their genomes you can classify them as single-copy orthologs.

I highly recommend this paper: Creevey, C. J., Muller, J., Doerks, T., Thompson, J. D., Arendt, D., & Bork, P. (2011). Identifying single copy orthologs in Metazoa. PLoS Computational Biology, 7(12), e1002269. doi:10.1371/journal.pcbi.1002269

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Thanks a lot everyone for you kind responses and useful references. This has helped me a lot.

Many thanks, R.

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Such a clear explanation. Thankyou!

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An how are they called if the genes have a symmetric best hit corresponding gene within their genomes? are those paralogues?

I'm working in something similar and I was also wondering why are paralogues not included in the core genome?

Thanks a lot for your explanations :)

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11.5 years ago

This should be genes that are present in each species in exactly one copy. The assumption is that these genes are essential: a species cannot be without them. They are also (in some sense) nice to work with because they lack paralogs and there is therefor no confusion about how to handle the redundancy.

Such genes are sometimes called "core genes". In practice, the "exactly one" property is often relaxed to "zero or one" copies.

Zmasek and Eddy (http://www.biomedcentral.com/1471-2105/3/14) introduced the concept of "super orthologs" which are pairs of orthologs that have no (known) history of gene duplications in between them. The paper is a nice introduction (and starting point) to why orthologs are interesting to study.

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While there is a tie in between duplicability and core genes, core genes CAN have experienced duplications. Usually the operational definition for core genes are those that are present in all, or nearly all, of the species/genomes under consideration.

Obviously the duplicability of core genes is affected by the complexity hypothesis, as these are often informational as opposed to metabolic genes, but it isn't strictly speaking part of the definition

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I was working in this topic and I was wondering why are paralogues not included in the core genome?

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11.5 years ago
DG 7.3k

I am going to guess what you are referring to are Single-Copy Gene Orthologs. If there have been gene duplications within a group you have several different types of orthology/paralogy relationships between genes that are possible. Sometimes, for certain types of analyses, you want to restrict yourself to genes that have not undergone any duplication events, at least within the clade of interest. In that case there are no paralogs for that gene, including in-paralogs and out-paralogs (within the same genome versus within another genome). This may be done because you want to compare some characteristic of genes that have never undergone duplications versus those that have for instance, or because you want to he absolutely sure that the orthology is correct. If duplications have occurred, especially if they were ancient, it can sometimes be difficult to get the exact oprtholog/paralog relationships correctly identified.

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