Identifying specific expanded genes

[romseg]

Dear author,

I am wondering if it's possible to identify the genes that were expanded, and not only the Orthogroup family? I launched cafe5 to identify gene family expansion/contractions with the following command using inputs from Orthofinder:

cafe5 -t SpeciesTree_rooted.ultrametric.tre -i cafe.input.tsv -k 3 -p -o gammak3out

cafe.input.tsv

Desc	Orthogroup	Ahypochondriacus	Athaliana	Bvulgarisssp_vulgaris	Cquinoa	Pamilis	Soleracea	Stuberosum	Utuberii	Zmays
(null)	OG0000017	15	1	3	25	27	6	97	24	12
(null)	OG0000020	5	4	16	37	59	27	32	7	2
(null)	OG0000021	0	0	0	47	11	34	2	93	0
(null)	OG0000023	4	6	15	43	54	13	11	1	27

After parsing the results Gamma_change.tab file for expanded families in Utuberii only:

FamilyID	Utuberii<3>
OG0000017	2
OG0000039	2
OG0000050	3
OG0000053	2

What I understand is that for example, the Orthogroup OG0000017 have 24 genes belonging to Utuberii species (cafe.input.tsv), and from these genes only 2 genes from OG0000017 were expanded in Utuberii. So cafe5 reports OG0000017 as a family in expansion. And I am wondering how to identify the identity of those two expanded genes?

I am trying to determine Gene Ontology terms enriched in the set of expanded gene families, but it seems to me that it would be more accurate to do this with only the two genes that were expanded, instead of the 24 from Orthogroup OG0000017. Maybe this is not the right approach and I will be happy to know it. Thank you.

Best regards,
Rom

[benfulton]

I'm afraid CAFE only identifies which families are expanded, and not which copies are the new ones. Dr. Hahn tells me it's a very hard problem, and I can't think of any solutions for you.