Answers.Body: <p>Gene naming is pretty subjective and even a single gene can have many names. If you're lucky orthologs will be named the same in different lineages, but you can't rely on it. Better to use gene ids (e.g. from Ensembl) and an <a href="https://questfororthologs.org/orthology_databases" rel="nofollow noreferrer">ortholog db</a> to map the orthologs. However, if you're looking at different strains, this is more tricky since most db don't go below the species level</p>
  
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Answers.CreationDate: 2021-05-30T13:26:56.127Z
Answers.Text: Thanks for your answer. I was wondering if two genes belong to two different isolates of E. coli (i.e., they are still the same species but different isolates), should we call them ortholog or paralog
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Answers.CreationDate: 2021-06-30T15:56:08.240Z
Answers.Text: Gene IDs are not perfect either. Those can change as well, even between different versions of the annotation for the same species.
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Body: <p>To be specific, we have different lineages of E. coli. I wondered if the ortholog genes among them should all have the same name in all lineages or can they also have different names?</p>
  
Tags: <phylogenetics><sequence-homology><orthologues>
Title: Can ortholog genes have different names among different species?
ThreadText: # Can ortholog genes have different names among different species?
  
  (Asked by: username_0 on 2021-05-28)
  
  To be specific, we have different lineages of E. coli. I wondered if the ortholog genes among them should all have the same name in all lineages or can they also have different names?
  
  **Tags:** phylogenetics, sequence-homology, orthologues
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2021-05-29. Score: 3
  
  Gene naming is pretty subjective and even a single gene can have many names. If you're lucky orthologs will be named the same in different lineages, but you can't rely on it. Better to use gene ids (e.g. from Ensembl) and an [ortholog db](https://questfororthologs.org/orthology_databases) to map the orthologs. However, if you're looking at different strains, this is more tricky since most db don't go below the species level
  
  > **Comments:**
  > **username_0**: Thanks for your answer. I was wondering if two genes belong to two different isolates of E. coli (i.e., they are still the same species but different isolates), should we call them ortholog or paralog  
  > **username_2**: Gene IDs are not perfect either. Those can change as well, even between different versions of the annotation for the same species.  
  
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