Answers.Body: <p>The most obvious answer is wet-lab rather than bioinformatics: mtDNA can get removed in the DNA extraction process. As a control group, in bacterial drug-resistance studies the plasmids are frequently lost. mtDNA at ~15KB is smaller than a regular bacterial plasmid.</p>
  <p>On the bioinformatics front there would be an issue about reference genome assemblies as well, i.e. if mtDNA genome isn't present then it will not appear as a separate genome.</p>
  
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Body: <p><a href="https://www.biostars.org/p/9589320/" rel="nofollow noreferrer">Also posted on biostars</a></p>
  <p>While I was searching the genomes of some eukariotic organisms (fungi,plants,protists) even though I knew that they had mitochondrial DNA,when I searched their genome structure I couldn't find any &quot;chromosome&quot; labeled as &quot;mtDNA&quot;. Here I give some links of genomes that show this:
  <a href="https://www.ncbi.nlm.nih.gov/genome/gdv/browser/genome/?id=GCF_016861865.1" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/genome/gdv/browser/genome/?id=GCF_016861865.1</a>
  <a href="https://www.ncbi.nlm.nih.gov/genome/gdv/browser/genome/?id=GCF_009556855.1" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/genome/gdv/browser/genome/?id=GCF_009556855.1</a></p>
  <p>Why does this happens? How can I find if the mtDNA sequence is inluded in these &quot;chromosomes&quot;?</p>
  
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Comments.Text: Note how in https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_016861865.1/, the number of "organelles" is listed as 0 for RefSeq but 1 in GenBank. I would guess you can find a mitochondrial sequence in GenBank.
Comments.UserDisplayName: terdon
Tags: <genome><sequence-annotation><reference-genome><mtdna>
Title: Why is mtDNA not labelled as such for many organisms?
ThreadText: # Why is mtDNA not labelled as such for many organisms?
  
  (Asked by: username_0 on 2024-03-06)
  
  [Also posted on biostars](https://www.biostars.org/p/9589320/)
  
  While I was searching the genomes of some eukariotic organisms (fungi,plants,protists) even though I knew that they had mitochondrial DNA,when I searched their genome structure I couldn't find any "chromosome" labeled as "mtDNA". Here I give some links of genomes that show this:
  <https://www.ncbi.nlm.nih.gov/genome/gdv/browser/genome/?id=GCF_016861865.1>
  <https://www.ncbi.nlm.nih.gov/genome/gdv/browser/genome/?id=GCF_009556855.1>
  
  Why does this happens? How can I find if the mtDNA sequence is inluded in these "chromosomes"?
  
  **Tags:** genome, sequence-annotation, reference-genome, mtdna
  
  > **Comments:**
  > **username_1**: Note how in https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_016861865.1/, the number of "organelles" is listed as 0 for RefSeq but 1 in GenBank. I would guess you can find a mitochondrial sequence in GenBank.  
  
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  ## 1 answers
  
  ### Answer by username_2 on 2024-03-06. Score: 1
  
  The most obvious answer is wet-lab rather than bioinformatics: mtDNA can get removed in the DNA extraction process. As a control group, in bacterial drug-resistance studies the plasmids are frequently lost. mtDNA at ~15KB is smaller than a regular bacterial plasmid.
  
  On the bioinformatics front there would be an issue about reference genome assemblies as well, i.e. if mtDNA genome isn't present then it will not appear as a separate genome.
  
  
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