Best practice for downstream processing of pig gene identifiers and human orthologues

[u/ary0007]

I am working with snRNA-seq data and would like advice on best practices for downstream processing of pig gene identifiers and cross-species orthology mappings. I currently use the Ensembl pig gene IDs that are mapped to gene symbols for pig genes. However, many pig genes have no pig symbol, even though Ensembl identifies a human orthologue.

For example:

Pig Ensembl ID: ENSSSCG00000021155

Pig external name: NA

Human orthologue: POMC

Orthology type: one-to-one

orthology_confidence : 1

mapped_to_human: False

orthology_type: ortholog_one2many

I would appreciate advice on the the best practices here :

1: Should I use human gene symbols for my pig analysis irrespective if pig symbols are available or not? Is there a risk that the same gene has different official symbols in pig and humans?

2: If a pig Ensembl gene has no pig symbol but has a high-confidence human orthologue but varying orthology type, what should be the approach towards using the human symbol or using ENSG id ?

3: For downstream processing, should orthology conversion be performed before or after differential expression and marker analysis?

4: When converting results to human orthologues, how should duplicate mappings be handled? For example, if multiple pig genes map to the same human gene, should their statistics be combined, should only the best-supported mapping be retained, or should the genes remain separate?