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
Hean1g00191	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00192	.	Bial10g01346	Bial22g00940	Dapi4g01878	Dapi20g01830	Hetu1g00178	Hetu2g00224	Hetu3g00170	Amtr12g00500	Smso1g03642	.	Taer4g02436	Fro14g01322	.	.	Fra18g01644	Fli3g00726	Stre1g04370	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00193	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00194	.	Bial10g01347	Bial22g00941	Dapi4g01879	Dapi20g01831	Hetu1g00181	Hetu2g00227	Hetu3g00174	Amtr12g00501	.	.	Taer4g02437	Fro14g01323	Fso1g02160	.	Fra18g01643	Fli3g00725	Stre1g04371	Mimi16g02136	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00195	.	.	.	Dapi4g01880	.	Hetu1g00182	.	.	.	.	.	.	.	.	.	.	.	Stre1g04372	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00196	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00197	.	Bial10g01349	Bial22g00943	Dapi4g01887	Dapi20g01834	.	Hetu2g00229	Hetu3g00176	.	Smso1g03644	.	.	.	.	.	.	.	Stre1g04373	Mimi16g02137	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00198	.	Bial10g01350	Bial22g00944	Dapi4g01888	Dapi20g01835	Hetu1g00183	Hetu2g00230	Hetu3g00177	Amtr12g00504	.	.	Taer4g02444	Fro14g01326	Fso1g02163	.	Fra18g01639	Fli3g00723	Stre1g04374	Mimi16g02138	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00199	.	Bial10g01351	Bial22g00945	Dapi4g01889	Dapi20g01836	Hetu1g00186	Hetu2g00231	Hetu3g00178	Amtr12g00505	Smso1g03645	.	.	.	.	.	.	.	Stre1g04376	Mimi16g02141	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00200	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
12	15798400	15802979	+	AtrifAMIRv0_Chr12g0722321	Amtr12g00500	500
12	15807234	15809210	+	AtrifAMIRv0_Chr12g0722331	Amtr12g00501	501
12	15930507	15933227	-	AtrifAMIRv0_Chr12g0722361	Amtr12g00504	504
12	15945687	15949149	+	AtrifAMIRv0_Chr12g0722371	Amtr12g00505	505
10	13483932	13488059	+	g86823.t1	Bial10g01346	1346
10	13498226	13499175	+	g86822.t1	Bial10g01347	1347
10	13506756	13513666	-	g86820.t1	Bial10g01349	1349
10	13515140	13523280	-	g86819.t1	Bial10g01350	1350
10	13528027	13531919	+	g86818.t1	Bial10g01351	1351
22	9048361	9053085	+	g147094.t1	Bial22g00940	940
22	9055283	9056228	+	g147093.t1	Bial22g00941	941
22	9067915	9076423	-	g147091.t1	Bial22g00943	943
22	9077917	9081526	-	g147090.t1	Bial22g00944	944
22	9089798	9091858	+	g147089.t1	Bial22g00945	945
4	116854665	116858995	+	h1tg000193l.g132858.t1	Dapi4g01878	1878
4	116862951	116864739	+	h1tg000193l.g132857.t1	Dapi4g01879	1879
4	116866930	116867343	-	h1tg000193l.g132856.t1	Dapi4g01880	1880
4	116927515	116935354	-	h1tg000193l.g132849.t1	Dapi4g01887	1887
4	116936883	116940745	-	h1tg000193l.g132848.t1	Dapi4g01888	1888
4	116979748	116983423	+	h1tg000193l.g132847.t1	Dapi4g01889	1889
20	108503763	108508103	+	h1tg000169l.g129567.t1	Dapi20g01830	1830
20	108514485	108516025	+	h1tg000169l.g129566.t1	Dapi20g01831	1831
20	108538812	108546616	-	h1tg000169l.g129563.t1	Dapi20g01834	1834
20	108548156	108552262	-	h1tg000169l.g129562.t1	Dapi20g01835	1835
20	108629547	108633241	+	h1tg000169l.g129561.t1	Dapi20g01836	1836
3	19774766	19777537	+	FliAMIRv0_Chr03g0079921	Fli3g00723	723
3	19863716	19864923	-	FliAMIRv0_Chr03g0079941	Fli3g00725	725
3	19867076	19872405	-	FliAMIRv0_Chr03g0079951	Fli3g00726	726
18	63421536	63424259	+	FraAMIRv0_Chr18g0358361	Fra18g01639	1639
18	63461360	63462576	-	FraAMIRv0_Chr18g0358401	Fra18g01643	1643
18	63465480	63471019	-	FraAMIRv0_Chr18g0358411	Fra18g01644	1644
14	21011864	21016950	+	FroAMIRv0_Chr14g0254761	Fro14g01322	1322
14	21018783	21019969	+	FroAMIRv0_Chr14g0254771	Fro14g01323	1323
14	21046854	21049653	-	FroAMIRv0_Chr14g0254801	Fro14g01326	1326
1	61937977	61939199	+	FsoAMIRv0_Chr01g0021591	Fso1g02160	2160
1	61978970	61981987	-	FsoAMIRv0_Chr01g0021621	Fso1g02163	2163
1	4880861	4881956	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0002201	Hean1g00191	191
1	4884036	4892072	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0002211	Hean1g00192	192
1	5062304	5067354	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0002231	Hean1g00193	193
1	5071016	5074360	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0002241	Hean1g00194	194
1	5080614	5081039	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0002251	Hean1g00195	195
1	5091199	5093941	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0002261	Hean1g00196	196
1	5098449	5109171	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0002271	Hean1g00197	197
1	5113976	5118951	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0002281	Hean1g00198	198
1	5148208	5155428	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0002291	Hean1g00199	199
1	5325139	5325672	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0002301	Hean1g00200	200
1	7176121	7183108	+	>Htub.h1tg003050l.g443.t1	Hetu1g00178	178
1	7282379	7285036	+	>Htub.h1tg003050l.g446.t1	Hetu1g00181	181
1	7316949	7317368	-	>Htub.h1tg003050l.g447.t1	Hetu1g00182	182
1	7348406	7353957	-	>Htub.h1tg003050l.g449.t1	Hetu1g00183	183
1	7402349	7408266	+	>Htub.h1tg003050l.g452.t1	Hetu1g00186	186
2	7545606	7551203	+	>Htub.h1tg000710l.g110.t1	Hetu2g00224	224
2	7668566	7671466	+	>Htub.h1tg000710l.g113.t1	Hetu2g00227	227
2	7737734	7747962	-	>Htub.h1tg000710l.g115.t1	Hetu2g00229	229
2	7748666	7754113	-	>Htub.h1tg000710l.g116.t1	Hetu2g00230	230
2	7791650	7798129	+	>Htub.h1tg000710l.g117.t1	Hetu2g00231	231
3	7011309	7018168	+	>Htub.h1tg000727l.g70.t1	Hetu3g00170	170
3	7129672	7133821	+	>Htub.h1tg000727l.g74.t1	Hetu3g00174	174
3	7145850	7158857	-	>Htub.h1tg000727l.g76.t1	Hetu3g00176	176
3	7159145	7167357	-	>Htub.h1tg000727l.g77.t1	Hetu3g00177	177
3	7211223	7216864	+	>Htub.h1tg000727l.g78.t1	Hetu3g00178	178
16	83927353	83938050	+	KAD3338206.1	Mimi16g02136	2136
16	83993264	84013692	-	KAD3338207.1	Mimi16g02137	2137
16	84016961	84020299	-	KAD3338208.1	Mimi16g02138	2138
16	84046412	84052042	+	KAD3338211.1	Mimi16g02141	2141
1	122066539	122071939	+	KAI3829605.1	Smso1g03642	3642
1	122103052	122111557	-	KAI3829607.1	Smso1g03644	3644
1	122159303	122163204	+	KAI3829608.1	Smso1g03645	3645
1	130166833	130173380	+	Streb.1G043700.1	Stre1g04370	4370
1	130174976	130177436	+	Streb.1G043710.1	Stre1g04371	4371
1	130186243	130187132	-	Streb.1G043720.1	Stre1g04372	4372
1	130198747	130206854	-	Streb.1G043730.1	Stre1g04373	4373
1	130207446	130210124	-	Streb.1G043740.1	Stre1g04374	4374
1	130243134	130247343	+	Streb.1G043760.1	Stre1g04376	4376
4	54692599	54696454	+	>KAK1428217.1	Taer4g02436	2436
4	54697773	54699965	+	>KAK1428218.1	Taer4g02437	2437
4	54765578	54768013	-	>KAK1428225.1	Taer4g02444	2444

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