How to find out human mtDNA genes in d-loop control region for Indian origin only

Question

[SV]

Hi everyone,
I need help to find out the list of all mtDNA genes of Indian origin in the d-loop control region of mtDNA. I searched for databases/tools that can help me find out a list of genes, but most of the mtDNA specific databases are not working or not updated, so I don't know exactly how I should proceed for this. Can anybody help?
Thanks in advance!

[microfuge]

I am not entirely sure but NCBI popset database (https://www.ncbi.nlm.nih.gov/popset) might also be of some help as well especially the advanced search filters. For example I searched haplogroup M (as mentioned by Jeremy) https://www.ncbi.nlm.nih.gov/popset?term=((((haplogroup%20M)%20AND%20india))%20AND%20haplogroup%20M)%20AND%20human%5BOrganism%5D

[WouterDeCoster]

Do you expect different mitochondrial genes depending on the geographical origin?

[SV]

Yes, mtDNA genes based on geographical origin as Indian, but genes from the d-loop region of mtDNA.

[Gabriel R.]

But there are many different haplotypes in India. What do you mean Indian origin?

Answer 1

[Jeremy Leipzig]

I think you mean variants, not genes

The defining variants for haplogroup M, which is what most people on the Indian subcontinent fall into, are 489C, 10400T, 14783C, 15043A, 15301A

I think only 489C is in the D-loop. There are a bunch of variants that define subclades of M that also fall within the d-loop control region. I'm not sure what you are looking for but this page might help:

https://www.mitomap.org/foswiki/bin/view/MITOMAP/HaplogroupMarkers

Answer 2

[grant.hovhannisyan]

D-loop is a non-coding region, so it does not contain genes. Most probably you are looking for mtDNA haplogroups defined with D-loop. Also, take into account that the geographic origin of most of the mtDNA lineages is not known, and the most frequent haplogroup in a population might not have originated in that population (could be a founder effect, genetic drift, selection, etc). So finding the haplogroups of Indian origin can be very speculative.

For the databases, as @Jeremy mentioned, MITOMAP is the most comprehensive one, you also have hmtdb https://www.hmtdb.uniba.it/ which has more functionality compared to MITOMAP, but it was updated almost a year ago. On the other hand, its always more reliable to go through papers from large scale projects, I am pretty sure there are some for India.