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
Hean1g00491	.	Bial10g01070	.	.	.	Hetu1g01820	Hetu2g01575	Hetu3g01625	.	.	.	.	.	.	.	.	.	Stre1g04068	Mimi16g01729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00492	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00493	.	Bial10g01071	.	.	.	Hetu1g01778	Hetu2g01570	Hetu3g01624	Amtr02g08984	Smso1g03325	Smso28g00653	.	.	.	.	.	.	Stre1g04069	Mimi16g01728	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00494	.	.	.	.	.	Hetu1g01777	Hetu2g01569	Hetu3g01620	.	.	.	.	.	.	.	.	.	Stre1g04070	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00495	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00496	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00497	.	Bial10g01073	.	.	.	Hetu1g01758	Hetu2g01566	Hetu3g01611	Amtr02g08989	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00498	.	.	.	.	.	.	.	.	Amtr02g08991	.	.	.	.	.	.	.	.	Stre1g04071	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00499	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00500	Cobi2g02007	Bial10g01076	.	.	.	Hetu1g01756	Hetu2g01561	Hetu3g01608	Amtr02g08993	Smso1g03326	Smso28g00650	.	.	.	.	.	.	Stre1g04072	Mimi16g01726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
2	175356448	175364075	+	AtrifAMIRv0_Chr02g0185801	Amtr02g08984	8984
2	175519289	175522286	-	AtrifAMIRv0_Chr02g0185851	Amtr02g08989	8989
2	175551767	175554911	-	AtrifAMIRv0_Chr02g0185871	Amtr02g08991	8991
2	175627922	175629610	-	AtrifAMIRv0_Chr02g0185891	Amtr02g08993	8993
10	10880186	10888776	-	g87099.t1	Bial10g01070	1070
10	10898697	10903244	+	g87098.t1	Bial10g01071	1071
10	10921091	10924016	-	g87096.t1	Bial10g01073	1073
10	10935968	10937653	+	g87093.t1	Bial10g01076	1076
2	61599663	61601463	-	h2tg000016l_1.g5239.t1	Cobi2g02007	2007
1	19644358	19652068	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005531	Hean1g00491	491
1	19647891	19648327	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005541	Hean1g00492	492
1	19658524	19663318	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005551	Hean1g00493	493
1	19721374	19723746	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005561	Hean1g00494	494
1	19779542	19781405	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005571	Hean1g00495	495
1	19780508	19780847	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005581	Hean1g00496	496
1	19783246	19787729	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005591	Hean1g00497	497
1	19848692	19856217	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005601	Hean1g00498	498
1	19855367	19856181	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005611	Hean1g00499	499
1	19882988	19886502	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005621	Hean1g00500	500
1	99700607	99704350	+	>Htub.h1tg001760l.g71.t1	Hetu1g01756	1756
1	100076554	100080714	+	>Htub.h1tg001760l.g74.t1	Hetu1g01758	1758
1	100527483	100528477	+	>Htub.h1tg001760l.g93.t1	Hetu1g01777	1777
1	100669161	100674485	-	>Htub.h1tg001760l.g94.t1	Hetu1g01778	1778
1	104323126	104335738	-	>Htub.h1tg001760l.g139.t1	Hetu1g01820	1820
2	90003996	90008823	+	>Htub.h1tg000510l.g71.t1	Hetu2g01561	1561
2	90427121	90428440	+	>Htub.h1tg000510l.g66.t1	Hetu2g01566	1566
2	91506700	91508473	+	>Htub.h1tg000510l.g63.t1	Hetu2g01569	1569
2	91588943	91590684	-	>Htub.h1tg000510l.g62.t1	Hetu2g01570	1570
2	92160852	92169755	+	>Htub.h1tg000510l.g55.t1	Hetu2g01575	1575
3	93451967	93457992	+	>Htub.h1tg000657l.g366.t1	Hetu3g01608	1608
3	93720345	93721666	+	>Htub.h1tg000657l.g369.t1	Hetu3g01611	1611
3	95609857	95611630	+	>Htub.h1tg000657l.g378.t1	Hetu3g01620	1620
3	95704817	95710372	-	>Htub.h1tg000657l.g382.t1	Hetu3g01624	1624
3	96241584	96250492	+	>Htub.h1tg000657l.g384.t1	Hetu3g01625	1625
16	76439377	76441026	+	KAD3337796.1	Mimi16g01726	1726
16	76452351	76459248	-	KAD3337798.1	Mimi16g01728	1728
16	76480058	76489008	+	KAD3337799.1	Mimi16g01729	1729
1	114744916	114760423	+	KAI3829288.1	Smso1g03325	3325
1	114765646	114767352	-	KAI3829289.1	Smso1g03326	3326
28	27321671	27323375	+	KAI3682930.1	Smso28g00650	650
28	27638292	27639262	-	KAI3682933.1	Smso28g00653	653
1	125577238	125584887	-	Streb.1G040680.1	Stre1g04068	4068
1	125617344	125624160	+	Streb.1G040690.1	Stre1g04069	4069
1	125624576	125626643	-	Streb.1G040700.1	Stre1g04070	4070
1	125628184	125629792	-	Streb.1G040710.1	Stre1g04071	4071
1	125634553	125637737	-	Streb.1G040720.1	Stre1g04072	4072

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