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
Hean1g00601	Cobi2g02049	Bial10g01131	Bial22g00732	Dapi4g01637	Dapi20g01559	Hetu1g01649	Hetu2g01433	Hetu3g01454	Amtr02g08839	Smso1g03412	Smso28g00599	.	.	.	.	.	.	Stre1g04123	Mimi16g01876	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00602	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00603	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00604	.	Bial10g01132	.	.	.	Hetu1g01646	Hetu2g01431	Hetu3g01448	.	.	Smso28g00598	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00605	Cobi2g02050	Bial10g01136	Bial22g00735	Dapi4g01639	Dapi20g01561	Hetu1g01641	Hetu2g01420	Hetu3g01440	Amtr02g08836	Smso1g03414	.	.	Fro14g01062	Fso1g01681	.	.	Fli3g01061	Stre1g04125	Mimi16g01878	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00606	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00607	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00608	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00609	Cobi2g02051	Bial10g01137	Bial22g00736	Dapi4g01640	Dapi20g01562	Hetu1g01640	Hetu2g01419	Hetu3g01439	Amtr02g08834	Smso1g03415	.	.	Fro14g01065	Fso1g01684	Ftr2g01323	.	Fli3g01059	Stre1g04127	Mimi16g01879	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00610	Cobi2g02052	Bial10g01138	Bial22g00737	Dapi4g01641	Dapi20g01563	Hetu1g01638	Hetu2g01417	Hetu3g01437	Amtr02g08833	Smso1g03416	.	.	Fro14g01066	Fso1g01685	Ftr2g01318	Fra18g01427	Fli3g01058	Stre1g04128	Mimi16g01880	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
2	171858207	171861756	-	AtrifAMIRv0_Chr02g0184291	Amtr02g08833	8833
2	171864365	171868833	-	AtrifAMIRv0_Chr02g0184301	Amtr02g08834	8834
2	171968495	171971689	-	AtrifAMIRv0_Chr02g0184321	Amtr02g08836	8836
2	172065280	172070348	+	AtrifAMIRv0_Chr02g0184351	Amtr02g08839	8839
10	11329669	11331398	-	g87038.t1	Bial10g01131	1131
10	11332810	11334984	+	g87037.t1	Bial10g01132	1132
10	11352788	11355246	+	g87033.t1	Bial10g01136	1136
10	11357288	11361936	+	g87032.t1	Bial10g01137	1137
10	11363368	11365857	+	g87031.t1	Bial10g01138	1138
22	7058573	7063281	-	g147302.t1	Bial22g00732	732
22	7076639	7080165	+	g147299.t1	Bial22g00735	735
22	7084197	7088526	+	g147298.t1	Bial22g00736	736
22	7088726	7093187	+	g147297.t1	Bial22g00737	737
2	63872184	63874697	-	h2tg000016l_1.g5197.t1	Cobi2g02049	2049
2	63889332	63891241	+	h2tg000016l_1.g5196.t1	Cobi2g02050	2050
2	63923042	63927905	+	h2tg000016l_1.g5195.t1	Cobi2g02051	2051
2	63940370	63942701	+	h2tg000016l_1.g5194.t1	Cobi2g02052	2052
4	101089951	101101072	-	h2tg000160l.g57222.t1	Dapi4g01637	1637
4	101159001	101162391	+	h2tg000160l.g57224.t1	Dapi4g01639	1639
4	101226815	101231326	+	h2tg000160l.g57225.t1	Dapi4g01640	1640
4	101282977	101286749	-	h2tg000160l.g57226.t1	Dapi4g01641	1641
20	92793723	92797735	-	h2tg000075l.g16929.t1	Dapi20g01559	1559
20	92847377	92850749	+	h2tg000075l.g16931.t1	Dapi20g01561	1561
20	92885429	92890005	+	h2tg000075l.g16932.t1	Dapi20g01562	1562
20	92952366	92956137	-	h2tg000075l.g16933.t1	Dapi20g01563	1563
3	34641030	34644378	-	FliAMIRv0_Chr03g0083271	Fli3g01058	1058
3	34699758	34701150	-	FliAMIRv0_Chr03g0083281	Fli3g01059	1059
3	34892747	34895073	-	FliAMIRv0_Chr03g0083301	Fli3g01061	1061
18	54627458	54630333	-	FraAMIRv0_Chr18g0356241	Fra18g01427	1427
14	16844920	16847348	+	FroAMIRv0_Chr14g0252161	Fro14g01062	1062
14	16884267	16887972	+	FroAMIRv0_Chr14g0252191	Fro14g01065	1065
14	16906428	16910043	+	FroAMIRv0_Chr14g0252201	Fro14g01066	1066
1	48631235	48633576	+	FsoAMIRv0_Chr01g0016801	Fso1g01681	1681
1	48709013	48712771	+	FsoAMIRv0_Chr01g0016831	Fso1g01684	1684
1	48736899	48740517	+	FsoAMIRv0_Chr01g0016841	Fso1g01685	1685
2	36697756	36698403	-	FtrAMIRv0_Chr02g0041851	Ftr2g01318	1318
2	36897994	36901667	-	FtrAMIRv0_Chr02g0041901	Ftr2g01323	1323
1	31078370	31084535	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006791	Hean1g00601	601
1	31140395	31140901	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006801	Hean1g00602	602
1	31174374	31176631	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006811	Hean1g00603	603
1	31215029	31223543	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006821	Hean1g00604	604
1	31389676	31392833	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006831	Hean1g00605	605
1	31396841	31397104	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006851	Hean1g00606	606
1	31397509	31398288	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006861	Hean1g00607	607
1	31398735	31399052	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006871	Hean1g00608	608
1	31516628	31522321	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006891	Hean1g00609	609
1	31553404	31557139	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006901	Hean1g00610	610
1	89821491	89824356	-	>Htub.h1tg001922l.g364.t1	Hetu1g01638	1638
1	89922248	89924114	-	>Htub.h1tg001922l.g366.t1	Hetu1g01640	1640
1	90044690	90046909	-	>Htub.h1tg001922l.g367.t1	Hetu1g01641	1641
1	90331689	90336692	+	>Htub.h1tg001922l.g373.t1	Hetu1g01646	1646
1	90742564	90747995	+	>Htub.h1tg001922l.g376.t1	Hetu1g01649	1649
2	80310529	80314032	-	>Htub.h1tg000330l.g349.t1	Hetu2g01417	1417
2	80540876	80547811	-	>Htub.h1tg000330l.g347.t1	Hetu2g01419	1419
2	80605347	80607626	-	>Htub.h1tg000330l.g345.t1	Hetu2g01420	1420
2	81062070	81067016	+	>Htub.h1tg000330l.g333.t1	Hetu2g01431	1431
2	81416150	81421636	-	>Htub.h1tg000330l.g331.t1	Hetu2g01433	1433
3	78135217	78139230	-	>Htub.h1tg000150l.g54.t1	Hetu3g01437	1437
3	78354839	78361551	-	>Htub.h1tg000150l.g52.t1	Hetu3g01439	1439
3	78426664	78428941	-	>Htub.h1tg000150l.g50.t1	Hetu3g01440	1440
3	78821781	78826716	+	>Htub.h1tg000150l.g41.t1	Hetu3g01448	1448
3	79063692	79071934	-	>Htub.h1tg000150l.g35.t1	Hetu3g01454	1454
16	79033179	79045222	-	KAD3337946.1	Mimi16g01876	1876
16	79083331	79087281	+	KAD3337948.1	Mimi16g01878	1878
16	79092409	79099817	+	KAD3337949.1	Mimi16g01879	1879
16	79106739	79111118	+	KAD3337950.1	Mimi16g01880	1880
1	116973803	116979294	-	KAI3829375.1	Smso1g03412	3412
1	117005714	117012586	+	KAI3829377.1	Smso1g03414	3414
1	117042739	117047761	+	KAI3829378.1	Smso1g03415	3415
1	117067241	117071244	+	KAI3829379.1	Smso1g03416	3416
28	20493760	20499110	+	KAI3682878.1	Smso28g00598	598
28	20525945	20531983	-	KAI3682879.1	Smso28g00599	599
1	126303746	126310279	-	Streb.1G041230.1	Stre1g04123	4123
1	126323993	126327084	+	Streb.1G041250.1	Stre1g04125	4125
1	126385675	126391203	+	Streb.1G041270.1	Stre1g04127	4127
1	126393993	126397297	+	Streb.1G041280.1	Stre1g04128	4128

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