Hierarchical alignments with the <em>Helianthus annuus</em> genome as reference

Gene Search

Species

Gene ID

Example:

Or, Query Sequence

Example:

Hierarchical alignments with the Helianthus annuus genome as reference

Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Asteraceae genomes. We used Helianthus annuus as a reference, and by comparing homologous gene locus maps and Ks values between Helianthus annuus and other Asteraceae, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We constructed a 40×70, 843 macro-matrices.

Query Sequence

Or, Gene ID

Species

Hean_1	Cobi_1	Bial_1	Bial_2	Dapi_1	Dapi_2	Hetu_1	Hetu_2	Hetu_3	Amtr_1	Smso_1	Smso_2	Taer_1	Fro_1	Fso_1	Ftr_1	Fra_1	Fli_1	Stre_1	Mimi_1	Hean_2	Cobi_2	Bial_3	Bial_4	Dapi_3	Dapi_4	Hetu_4	Hetu_5	Hetu_6	Amtr_2	Smso_3	Smso_4	Taer_2	Fro_2	Fso_2	Ftr_2	Fra_2	Fli_2	Stre_2	Mimi_2
Hean17g04441	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04442	Cobi5g02906	Bial21g02663	Bial9g02744	.	Dapi21g00089	.	.	.	Amtr10g04101	Smso4g01301	Smso21g01332	.	Fro13g00089	Fso12g00087	.	Fra13g00738	Fli9g00088	Stre11g00100	Mimi2g00060	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04443	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04444	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04445	Cobi5g02904	Bial21g02662	Bial9g02743	.	Dapi21g00091	.	.	.	Amtr10g04106	Smso4g01305	Smso21g01271	Taer9g03148	Fro13g00090	Fso12g00088	Ftr6g00064	Fra13g00737	Fli9g00089	Stre11g00101	Mimi2g00061	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04446	Cobi5g00069	Bial21g02661	Bial9g02742	.	Dapi21g00094	Hetu50g03622	Hetu51g03987	.	Amtr10g04111	Smso4g01308	Smso21g01274	.	.	.	.	.	.	Stre11g00102	Mimi2g00062	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04448	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04449	Cobi5g02902	Bial21g02660	Bial9g02741	.	Dapi21g00095	Hetu50g03620	Hetu51g03986	.	Amtr10g04118	Smso4g01309	Smso21g01275	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04450	Cobi5g00076	Bial21g02614	Bial9g02692	.	Dapi21g00096	.	.	.	Amtr10g04119	Smso4g01310	Smso21g01276	Taer9g03144	Fro13g00091	Fso12g00090	Ftr6g00065	Fra13g00736	Fli9g00090	Stre11g00123	Mimi2g00064	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
10	95396738	95400183	-	AtrifAMIRv0_Chr10g0664751	Amtr10g04101	4101
10	95559139	95561113	+	AtrifAMIRv0_Chr10g0664801	Amtr10g04106	4106
10	95683431	95693735	-	AtrifAMIRv0_Chr10g0664851	Amtr10g04111	4111
10	95772274	95776930	+	AtrifAMIRv0_Chr10g0664921	Amtr10g04118	4118
10	95780979	95782947	-	AtrifAMIRv0_Chr10g0664931	Amtr10g04119	4119
9	72084962	72086979	+	g77072.t1	Bial9g02692	2692
9	72872434	72876941	-	g77121.t1	Bial9g02741	2741
9	72901551	72906131	+	g77122.t1	Bial9g02742	2742
9	72930964	72934578	-	g77123.t1	Bial9g02743	2743
9	72956284	72960457	+	g77124.t1	Bial9g02744	2744
21	69281524	69283541	+	g62382.t1	Bial21g02614	2614
21	70068996	70073503	-	g62428.t1	Bial21g02660	2660
21	70098113	70102693	+	g62429.t1	Bial21g02661	2661
21	70127526	70131140	-	g62430.t1	Bial21g02662	2662
21	70150216	70157019	+	g62431.t1	Bial21g02663	2663
5	1264440	1268350	+	h2tg000038l_1.g23817.t1	Cobi5g00069	69
5	1327419	1329311	-	h2tg000038l_1.g23810.t1	Cobi5g00076	76
5	79928137	79937469	-	h2tg000020l_1.g9878.t1	Cobi5g02902	2902
5	79968860	79972523	-	h2tg000020l_1.g9876.t1	Cobi5g02904	2904
5	80003272	80007490	+	h2tg000020l_1.g9874.t1	Cobi5g02906	2906
21	1817187	1820964	-	h1tg000096l.g113473.t1	Dapi21g00089	89
21	1904727	1908160	+	h1tg000096l.g113471.t1	Dapi21g00091	91
21	1946284	1951762	-	h1tg000096l.g113468.t1	Dapi21g00094	94
21	2013415	2017965	+	h1tg000096l.g113467.t1	Dapi21g00095	95
21	2019408	2020505	-	h1tg000096l.g113466.t1	Dapi21g00096	96
9	1913195	1916652	-	FliAMIRv0_Chr09g0208551	Fli9g00088	88
9	1941320	1943464	+	FliAMIRv0_Chr09g0208561	Fli9g00089	89
9	1947131	1948234	-	FliAMIRv0_Chr09g0208571	Fli9g00090	90
13	34701182	34702288	+	FraAMIRv0_Chr13g0260441	Fra13g00736	736
13	34705873	34707964	-	FraAMIRv0_Chr13g0260451	Fra13g00737	737
13	34724559	34728010	+	FraAMIRv0_Chr13g0260461	Fra13g00738	738
13	1184188	1187634	-	FroAMIRv0_Chr13g0222731	Fro13g00089	89
13	1205442	1207682	+	FroAMIRv0_Chr13g0222741	Fro13g00090	90
13	1211281	1212372	-	FroAMIRv0_Chr13g0222751	Fro13g00091	91
12	1438588	1442043	-	FsoAMIRv0_Chr12g0290521	Fso12g00087	87
12	1462168	1464462	+	FsoAMIRv0_Chr12g0290531	Fso12g00088	88
12	1469874	1470731	-	FsoAMIRv0_Chr12g0290551	Fso12g00090	90
6	760044	762303	+	FtrAMIRv0_Chr06g0162141	Ftr6g00064	64
6	767386	768480	-	FtrAMIRv0_Chr06g0162151	Ftr6g00065	65
17	191462711	191462989	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830221	Hean17g04441	4441
17	191466971	191474080	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830231	Hean17g04442	4442
17	191471308	191473998	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830241	Hean17g04443	4443
17	191526077	191526598	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830251	Hean17g04444	4444
17	191541230	191545128	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830261	Hean17g04445	4445
17	191563528	191571740	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830271	Hean17g04446	4446
17	191594943	191598438	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830281	Hean17g04447	4447
17	191616536	191618541	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830291	Hean17g04448	4448
17	191636229	191644570	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830301	Hean17g04449	4449
17	191652158	191653261	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830311	Hean17g04450	4450
50	210028021	210035648	-	>Htub.h1tg000531l.g422.t1	Hetu50g03620	3620
50	210113849	210121042	+	>Htub.h1tg000531l.g424.t1	Hetu50g03622	3622
51	231048775	231054023	-	>Htub.h1tg000558l.g218.t1	Hetu51g03986	3986
51	231141944	231148223	+	>Htub.h1tg000558l.g219.t1	Hetu51g03987	3987
2	1651907	1655731	-	KAD7116476.1	Mimi2g00060	60
2	1685650	1687899	+	KAD7116477.1	Mimi2g00061	61
2	1726375	1727155	-	KAD7116478.1	Mimi2g00062	62
2	1826256	1827338	-	KAD7116480.1	Mimi2g00064	64
4	17461366	17465293	-	KAI3818154.1	Smso4g01301	1301
4	17510269	17513177	+	KAI3818158.1	Smso4g01305	1305
4	17533615	17539191	-	KAI3818161.1	Smso4g01308	1308
4	17572432	17577677	+	KAI3818162.1	Smso4g01309	1309
4	17583576	17584667	-	KAI3818163.1	Smso4g01310	1310
21	13336321	13339282	+	KAI3731477.1	Smso21g01271	1271
21	13355349	13360756	-	KAI3731480.1	Smso21g01274	1274
21	13380772	13384078	+	KAI3731481.1	Smso21g01275	1275
21	13387497	13388588	-	KAI3731482.1	Smso21g01276	1276
21	14117353	14119619	-	KAI3731538.1	Smso21g01332	1332
11	2616111	2622128	-	Streb.11G001000.1	Stre11g00100	100
11	2751435	2755642	+	Streb.11G001010.1	Stre11g00101	101
11	2835003	2844257	-	Streb.11G001020.1	Stre11g00102	102
11	3446618	3447875	-	Streb.11G001230.1	Stre11g00123	123
9	31486990	31489146	+	>KAK1413779.1	Taer9g03144	3144
9	31524185	31526138	-	>KAK1413783.1	Taer9g03148	3148

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