Phylogenomic analysis of vertebrate thrombospondins reveals fish-specific paralogues, ancestral gene relationships and a tetrapod innovation

Table 1 Dataset of vertebrate TSPs compiled from fully-sequenced genomes and genome-predicted proteins for this study.

TSP	TSP-1	TSP-2	TSP_3	TSP-4	TSP-5/COMP
Species
T. rubripes	a: SINFRUP00000078556 (scaffold_376) b: SINFRUP00000091179 (scaffold_260)	SINFRUP00000052212 (scaffold_1131)	SINFRUP00000068259 (scaffold_3664)	a:SINFRUP00000074734 (scaffold_1187) b:SINFRUP00000057986 (scaffold_305)
T.nigroviridis	a :CAG03524 (chro 14) b :CAG10667 (Chro 10)	CAG09456 (chro 17)		a:CAG07859 (chro 12) b:CAG00605 (chro 1) c:CAG06350 (chro 4)
D.rerio	CAI20599 (chro 20)	a:ENSDARP00000057230 (chro 13) b:ENSDARP00000030477 (chro 12)	a:NP_775332 (chro 16) b:XP_699985 (chro19)	a:NP_775333 (unmap*) b:XP_690679 (unmap, Zv5 NA2846) c:ENSDARP00000022442 (partial sequence, chro 5)
X.tropicalis	Xt4l278562lestExt_gw1.C_2730021 (scaffold_273)	Xt4l302353le_gw1.2.579.1 (scaffold_2)	NP_001011401 (scaffolds_3931 and _3512)	Xt4l458958lestExt_fgenesh1_pg.C_5790005 (scaffold_579)	Xt4l387829le_gw1.580.20.1 (scaffold_580)
G.gallus	XP_421205 (chro 5)	XP_419599 (chro 3)	L81165 (unmap)	XP_424763 (chro Z)	XP_418238 (chro 28)
M.musculus	A40558 (chro2 band F)	Q03350 (chro17 band F)	NP_038719 (chro 3 band E3)	NP_035712 (chro13-52)	AF033530 (chro8-22)
H.sapiens	P07996 (chro15q15)	P35442 (chro6q27)	P49746 (chro1q21)	P35443 (chro5q23)	P49747 (chro19p13.1)

Predicted proteins are assigned by their BLASTP bit scores against the five human TSPs. Proteins are identified according to GenBank accession numbers where available. In the case of T. rubripes, the Fugu genome-predicted protein identifiers are given; for D. rerio, sequences not in GenBank are identified by their Ensembl DARP numbers. X. tropicalis proteins are identified according to the genome assembly 4.1 Gene Models (proteins) identifiers. Chromosomal locations are given in brackets for the physically mapped genomes and genomic scaffold numbers are provided for T. rubripes (as per Fugu Genome sequencing consortium) and X. tropicalis (as per JGI genome assembly v4.1). *, mapping uncertain until a finished clone for the region is completed in zebrafish genome assemby 5 (Wellcome Trust Sanger Institute).

ISSN: 2730-7182