Marsupials and monotremes possess a novel family of MHC class I genes that is lost from the eutherian lineage


Table S3. Number of domain matches found in the genomes of each species using custom profile hidden Markov models. 

Species Number of domain matches

Class 

Figure S1 .

 S1 Figure S1. Sensitive protein and genome search method workflows. 


Figure S2 .

 S2 Figure S2. The posterior probability of the phylogeny of 449 predicted MHC class I peptides generated by 4 MCMCs using BEAST2, started from random trees and sampled every 1000 steps. 


Figure S3 .

 S3 Figure S3. Maximum likelihood tree (JTT+IGF model) of selected proteins including UT family members. Numbers at nodes indicate bootstrap support. 


Figure S4 .Figure S5 .

 S4S5 Figure S4. UT gene family tree was estimated by maximum likelihood using the JTT+IGF model and reconciled with the species tree using NOTUNG. Predicted gene losses are shown in grey. Predicted duplications are indicated by a "D" at internal nodes. Bootstrap support is shown in red. 




  


Table S1 .

 S1 Overgo sequences used to isolate tammar wallaby and platypus BACs containing UT loci. 


	Gene symbol	Overgo A	Overgo B	BACs
	me_UT21	CATGTGGGTCAGTTCACTGCAGTG GAGAATGGATTGTGCCCACTGCAG 289L16, 370J4
	me_UT20	CACCACAAGCACATAGCTCAGTTC TTGTGCCCACTGCAGTGAACTGAG 289L16, 370J4
	me_UT18	GTCTGAGGATCAGGATCAAAGAAC GTCCTCTCCCTAGAATGTTCTTTG	No BACs
	me_UT16	CACCCTTGAGATGTGTTTCACAGC CTTTGTTGTACCTACTGCTGTGAA	334C11, 352G17, 432E9
	me_UT19	GTTTGTGGGTCAGTTCACTGCAGT TTTTGTGCTTGTGCCCACTGCAGT	289L16, 370J4
	me_UT14	ATTTCACTGCAGTGGGCACAGCCA AAGTTCAGCAGGGAGCTGGCTGTG 334C11, 352G17, 432E9
	me_UT15	CAAGGTCTCTCAAACCTCATAGTC CATCCACAGAACTGATGACTATGA	334C11, 352G17, 432E9
	me_UT21	TAGGCCCATGAATGATGGATTTTC CACTAGACAGCAGATAGAAAATCC	289L16, 370J4

Table S2 .

 S2 RT-PCR primers for opossum UT exons 2 and 3. 


	Gene	Exon 2/3 primers
	mdUT1	5' GTTCTGCAGCTCACCACAAAC 3'
		5' CATGGTGTCAATACAATATTCTTGC 3'
	mdUT2	5' ACAGCCTGGAGATCCAGTTCA 3'
		5' GTTCCAGGACAATCTTCAGAAA 3'

Table S7 .

 S7 The pairwise backbone Root Mean Square Deviation (Å) between the α 1 and α 2 domains of the opossum UT4, UT5, and UT8 modeling structures, several of the top 10 closest structural analogs identified using I-TASSER, and selected classical and non-classical MHC class I proteins from human and mouse. 


	Human Protein		I APD 8468 UT4	Ig 17738 UT5	C-terminal 25836 UT8	Class II beta 24437 Comment
	Mouse mdUT4	-	7718 0	19763 1.716	0.936	25160		24902
	Cow mdUT5	-	9752 1.716	0	17066	1.449	33669		22055
	Dog mdUT8	-	6663 0.936	18066 1.449	0	22088		21248
	Opossum		2127		3571		5028		5546
	Tammar wallaby ggYF1	3P73*	212 2	295 1.79	1.953	53		38
	Tasmanian devil ggB4	4G43*	3728 1.02	4147 1.368	1.22	4093		6992
	Platypus ggB21	3BEV*	795 1.041	4651 1.969	0.501	5480	5469 Binds 11mer peptide
	Chicken ggB21	2YF6*	3075 3.356	8752 1.884	0.871	10813	11979 Binds 10mer peptide
	Zebrafinch		4069		10490		13807		14411
	Turkey btMR1	4IIQ*	2833 2.387	7236 2.308	2.308	9760		10959
	Green anole mmH-2Kb1	1S7Q*	4528 2.492	8813 2.979	2.959	9732		14282
	Frog hsMR1	4L4T*	1541 3.399	4996 3.402	3.296	2673		8766
	Zebrafish Tetraodon hsAZGP1	3ES6*	4674 930 3.121	9489 2887 3.941	3.462	10040 4448		16523 3706
	Lamprey hsFcRn	1EXU	263 1.941	927 2.881	4.288	658		328
	Sea squirt hsHFE	1A6Z	606 2.657	588 2.977	2.919	403		1537
	Fruitfly hsMICA	1HYR	644 4.519	779 6.291	5.534	1455		1762
	Yeast hsMICB	1JE6	108 62734 6.989	107 140361 7.94	118 185314 8.283	178 195118
	hsULBP	1KCG	22.309	7.634	4.986		
	hsCD1a	1ONQ	12.601	13.225	4.042		
	hsCD1b	1GZQ	7.31	5.466	3.49		
	hsPROCR	1L8J	6.17	6.669	4.545		

*From top 10 templates for all the UTs
Anthony T Papenfuss, Zhi-Ping Feng, Katina Krasnec, Janine E Deakin, Michelle L Baker, Robert D Miller
Marsupials and monotremes possess a novel family of MHC class I genes that is lost from the eutherian lineage