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
Hean17g04461	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04462	.	Bial21g02623	.	.	Dapi21g00102	Hetu50g03612	Hetu51g03976	.	Amtr10g04126	Smso4g01315	Smso21g01284	Taer9g03137	Fro13g00097	Fso12g00095	Ftr6g00069	.	Fli9g00096	Stre11g00135	Mimi2g00069	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04463	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04464	Cobi5g00080	Bial21g02630	.	.	Dapi21g00103	Hetu50g03608	Hetu51g03975	.	.	Smso4g01316	Smso21g01285	.	.	.	.	.	.	Stre11g00136	Mimi2g00070	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04465	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04466	.	Bial21g02631	.	.	Dapi21g00104	.	.	.	Amtr10g04147	Smso4g01317	Smso21g01286	Taer9g03136	Fro13g00100	Fso12g00097	.	Fra13g00729	Fli9g00098	Stre11g00137	Mimi2g00071	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04467	Cobi5g00088	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Stre11g00140	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04468	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04469	.	.	.	.	.	.	.	.	.	Smso4g01320	Smso21g01288	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04470	Cobi5g02886	Bial21g02646	.	Dapi5g00070	Dapi21g00109	.	.	.	Amtr10g04155	Smso4g01321	Smso21g01289	.	.	.	.	.	.	Stre11g00142	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
10	95952728	95960721	-	AtrifAMIRv0_Chr10g0665001	Amtr10g04126	4126
10	96291435	96295280	+	AtrifAMIRv0_Chr10g0665211	Amtr10g04147	4147
10	96461114	96462819	+	AtrifAMIRv0_Chr10g0665291	Amtr10g04155	4155
21	69419821	69421970	-	g62391.t1	Bial21g02623	2623
21	69605516	69611538	+	g62398.t1	Bial21g02630	2630
21	69627889	69631347	+	g62399.t1	Bial21g02631	2631
21	69858846	69860870	+	g62414.t1	Bial21g02646	2646
5	1372344	1379666	+	h2tg000038l_1.g23806.t1	Cobi5g00080	80
5	1655390	1659096	-	h2tg000038l_1.g23798.t1	Cobi5g00088	88
5	79749823	79751803	+	h2tg000020l_1.g9894.t1	Cobi5g02886	2886
5	1586665	1589964	+	h1tg000132l.g124127.t1	Dapi5g00070	70
21	2160667	2167702	-	h1tg000096l.g113460.t1	Dapi21g00102	102
21	2193335	2196366	+	h1tg000096l.g113459.t1	Dapi21g00103	103
21	2232631	2237332	+	h1tg000096l.g113458.t1	Dapi21g00104	104
21	2349290	2351274	+	h1tg000096l.g113453.t1	Dapi21g00109	109
9	2090456	2097948	-	FliAMIRv0_Chr09g0208631	Fli9g00096	96
9	2167732	2172102	+	FliAMIRv0_Chr09g0208651	Fli9g00098	98
13	34574973	34579646	-	FraAMIRv0_Chr13g0260371	Fra13g00729	729
13	1298577	1299422	-	FroAMIRv0_Chr13g0222811	Fro13g00097	97
13	1339471	1343790	+	FroAMIRv0_Chr13g0222841	Fro13g00100	100
12	1528502	1536021	-	FsoAMIRv0_Chr12g0290601	Fso12g00095	95
12	1566672	1570726	+	FsoAMIRv0_Chr12g0290621	Fso12g00097	97
6	820011	823707	-	FtrAMIRv0_Chr06g0162191	Ftr6g00069	69
17	191844120	191846124	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830471	Hean17g04461	4461
17	191855347	191871234	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830481	Hean17g04462	4462
17	191891184	191893674	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830491	Hean17g04463	4463
17	191921177	191928569	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830501	Hean17g04464	4464
17	191949572	191950447	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830511	Hean17g04465	4465
17	191957644	191963932	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830521	Hean17g04466	4466
17	191990265	191997417	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830531	Hean17g04467	4467
17	192026772	192027151	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830551	Hean17g04468	4468
17	192055930	192057791	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830571	Hean17g04469	4469
17	192068407	192070927	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830581	Hean17g04470	4470
50	209521987	209528579	-	>Htub.h1tg000531l.g410.t1	Hetu50g03608	3608
50	209592351	209604193	+	>Htub.h1tg000531l.g414.t1	Hetu50g03612	3612
51	230745205	230750479	-	>Htub.h1tg000558l.g207.t1	Hetu51g03975	3975
51	230793257	230803675	+	>Htub.h1tg000558l.g208.t1	Hetu51g03976	3976
2	1962647	1971638	-	KAD7116485.1	Mimi2g00069	69
2	1991587	1995766	+	KAD7116486.1	Mimi2g00070	70
2	2034455	2040392	+	KAD7116487.1	Mimi2g00071	71
4	17650755	17658804	-	KAI3818168.1	Smso4g01315	1315
4	17683891	17687906	+	KAI3818169.1	Smso4g01316	1316
4	17717715	17722333	+	KAI3818170.1	Smso4g01317	1317
4	17743285	17749723	-	KAI3818173.1	Smso4g01320	1320
4	17763732	17765360	+	KAI3818174.1	Smso4g01321	1321
21	13456234	13463568	-	KAI3731490.1	Smso21g01284	1284
21	13512953	13516509	+	KAI3731491.1	Smso21g01285	1285
21	13545782	13552045	+	KAI3731492.1	Smso21g01286	1286
21	13566815	13568560	-	KAI3731494.1	Smso21g01288	1288
21	13578523	13579965	+	KAI3731495.1	Smso21g01289	1289
11	3649247	3655136	-	Streb.11G001350.1	Stre11g00135	135
11	3698163	3701706	+	Streb.11G001360.1	Stre11g00136	136
11	3772060	3778311	+	Streb.11G001370.1	Stre11g00137	137
11	4108708	4113645	-	Streb.11G001400.1	Stre11g00140	140
11	4233098	4235428	+	Streb.11G001420.1	Stre11g00142	142
9	31405342	31409702	-	>KAK1413773.1	Taer9g03136	3136
9	31437289	31444020	+	>35555	Taer9g03137	3137

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