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"?
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Organelle genomes may be separately sequenced and thus may have their own RefSeq entries. Here are five genomes from the organism you refer to : https://www.ncbi.nlm.nih.gov/nuccore/?term=ddbj_embl_genbank%5Bfilter%5D+AND+txid37727%5Borgn%3Anoexp%5D+AND+complete-genome%5Btitle%5D+AND+mitochondrion%5Bfilter%5D
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Are you sure the sequences don't exist - could it be that the viewer does not show them?
Please keep in mind that posting the same question to multiple sites can be perceived as bad etiquette, because efforts may be made to address a problem that has already been solved elsewhere in the meantime.
The helpful thing to do if you do decide to post on multiple forums is to add a link to the other forum posts on each post so people will look at the other posts before investing their effort.
Link to post on bioinfo SE: https://bioinformatics.stackexchange.com/questions/22246/why-many-organisms-even-though-they-possess-mitochondrial-dna-mtdna-it-is-not
Thank you I will keep that in mind!