In eukaryotes mainly:
1. Mitochondria (animals & plants),
2. Chloroplast (plants)
3. Extra chromosomal circular DNA (eccDNA):
which are the tendom repeats in chromosomal DNA deleted from their origin and form circular formation, sometimes can replicate independently.
Mitochondrial and chloroplast DNA can be identified by mapping reads to the available mitochondrial and chloroplast sequences.
eccDNA can be identified by isolating microDNA sequences from the sample following by paired end sequencing, perfectly paired mapped reads identification, and one end of the paired end reads should have mapped to the start or end of the sequence where another end of paired end reads were mapped (to identify circularity).
Is there any approach if I have whole genomic library rather than microDNA library.
plz suggest me as soon as possible.
Thanks!
Hi Hemant
One approach would be to construct a genetic map and look for extra linkage groups. Until now, extra linkage groups usually meant large gaps among markers from the same chromosome. However, the use of NGS data should ensure you do not have such gaps and therefore, any extra LG should be extrachromosomal.
Pablo
@Mathew A Beale, Here in this question, Extrachoromosomal DNA didnt mean contaminated DNA but it is also a part of genome and need to be identified besides than chromosomal DNA.
By the way Mathew, your approach to remove contaminated sequences from the data is quite useful and I will use this one whenever I will require.
Thanks!
any further answers will be appreciated.
@Mathew, I completely agree with you and its a kind of useful approach to remove contamination from the data. But "The sequences DNA other than chromosome (which generally found outside of the nucleus), So your mitochondrial, chloroplast or other circular repitative sequences will be defined as Extra-chromosomal DNA" and it cant be said as contamination because its a part of your cell.
Hope It is clear now!
By the way thanks for answering ..
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