Multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine

Table 4 Statistics of alignments based on sequence similarity of gene, transcript and protein comparisons

(A) EXAMPLE 1
	Query length	Subject length	Query coverage	Subject coverage	Identity/alig. Length	Positives/alig. Length	Score	e-value
Solyc07g008880.2 versus VIT_09s0002g07070
Gene vs Gene	12,772	12,589	7556/12772	7575/12589	6338/7556	–	6808	0
mRNA vs mRNA	2559	2476	2289/2559	2289/2476	2152/2289	2200/2289	5385	0
Protein vs Protein	2384	2348	2336/2384	2340/2348	2267/2343	2306/2343	4737	0
Solyc06g043160.1 versus VIT_09s0002g07070
Gene vs Gene	159	12,589	154/159	154/12589	118/154	–	82	3e⁻¹⁵
mRNA vs mRNA	53	2476	53/53	53/2476	43/53	47/53	111	7e⁻²⁶
Protein vs Protein	52	2348	52/52	52/2348	42/52	46/52	95	5e⁻²⁴
(B) EXAMPLE 2
Solyc01g111530.2 versus VIT_03s0038g02340
Gene vs Gene	11,273	26,647	5531/11273	5540/26647	4318/5531	–	3116	0
mRNA vs mRNA	2044	1986	1681/2044	1681/1986	1287/1681	1447/1681	2927	0
Protein vs Protein	1860	1897	1860/1860	1896/1897	1500/1914	1669/1914	2689	0
Solyc01g111530.2 versus VIT_04s0023g03830
Gene vs Gene	11,273	10,303	3225/11273	3228/10303	2548/3225	–	2024	2e⁻⁹⁸
mRNA vs mRNA	2044	1932	1499/2044	1499/1932	1093/1499	1258/1499	2558	0
Protein vs Protein	1860	1811	1764/1860	1799/1811	1190/1830	1407/1830	2210	0
(C) EXAMPLE 3
Solyc01g007530.2 versus VIT_10s0092g00760
Gene vs Gene	1813	3870	1024/1813	1034/3870	910/1024	–	1127	0
mRNA vs mRNA	353	318	160/353	160/318	130/160	141/160	336	4e⁻⁵⁴
Protein vs Protein	SEQUENCE SIMILARITY NOT DETECTED

The first three alignments of each example lead to the prediction of an orthology relationship by the multilevel approach proposed in this work: (A) Solyc07g008880.2 versus VIT_09s0002g07070, (B) Solyc01g111530.2 versus VIT_03s0038g02340 and (C) Solyc01g007530.2 versus VIT_10s0092g00760. The second triplets of alignments of (A) and (B) lead to the prediction of an orthology relationship by The Ensembl Plants / Gramene pipelines involving the same tomato or grapevine gene implicated in the relationship inferred by our approach (Solyc06g043160.1 versus VIT_09s0002g07070 and Solyc01g111530.2 versus VIT_04s0023g03830). Query length and query coverage are referred to the tomato gene loci, subject length and subject coverage are referred to grapevine gene loci

ISSN: 1471-2105