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
Hean1g00501	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00502	.	Bial10g01080	.	.	.	.	.	.	Amtr02g09003	Smso1g03329	.	.	.	.	.	.	.	Stre1g04075	Mimi16g01811	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00503	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00504	Cobi2g02008	Bial10g01082	.	.	.	Hetu1g01753	.	Hetu3g01591	Amtr02g09008	Smso1g03332	.	.	.	.	.	.	.	Stre1g04076	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00505	.	.	.	.	.	Hetu1g01752	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00506	.	Bial10g01083	.	.	.	Hetu1g01751	.	Hetu3g01589	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00507	.	.	.	.	.	Hetu1g01749	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00508	.	.	.	.	.	.	.	Hetu3g01586	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00509	.	Bial10g01084	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00510	Cobi2g02017	Bial10g01085	.	.	.	Hetu1g01744	.	Hetu3g01585	Amtr02g09009	Smso1g03333	Smso28g00644	.	.	.	.	.	.	Stre1g04077	Mimi16g01816	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
2	175925271	175933375	+	AtrifAMIRv0_Chr02g0185991	Amtr02g09003	9003
2	176094756	176097190	+	AtrifAMIRv0_Chr02g0186041	Amtr02g09008	9008
2	176139547	176147198	-	AtrifAMIRv0_Chr02g0186051	Amtr02g09009	9009
10	10956123	10958130	+	g87089.t1	Bial10g01080	1080
10	10969603	10973179	+	g87087.t1	Bial10g01082	1082
10	10974552	10976469	-	g87086.t1	Bial10g01083	1083
10	10978557	10979502	+	g87085.t1	Bial10g01084	1084
10	10980446	10985910	-	g87084.t1	Bial10g01085	1085
2	61602555	61603707	+	h2tg000016l_1.g5238.t1	Cobi2g02008	2008
2	62132506	62137580	-	h2tg000016l_1.g5229.t1	Cobi2g02017	2017
1	20062905	20066421	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005631	Hean1g00501	501
1	20103524	20104963	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005641	Hean1g00502	502
1	20103806	20104984	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005651	Hean1g00503	503
1	20134189	20137155	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005661	Hean1g00504	504
1	20138261	20139237	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005671	Hean1g00505	505
1	20139758	20141657	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005681	Hean1g00506	506
1	20180291	20181780	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005691	Hean1g00507	507
1	20302278	20302562	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005701	Hean1g00508	508
1	20302564	20303724	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005711	Hean1g00509	509
1	20312427	20330061	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005721	Hean1g00510	510
1	98640876	98649690	+	>Htub.h1tg001760l.g59.t1	Hetu1g01744	1744
1	98660565	98661872	-	>Htub.h1tg001760l.g64.t1	Hetu1g01749	1749
1	99175064	99176115	+	>Htub.h1tg001760l.g66.t1	Hetu1g01751	1751
1	99176798	99178517	+	>Htub.h1tg001760l.g67.t1	Hetu1g01752	1752
1	99179469	99182661	-	>Htub.h1tg001760l.g68.t1	Hetu1g01753	1753
3	92047214	92056931	+	>Htub.h1tg000657l.g343.t1	Hetu3g01585	1585
3	92060663	92061932	-	>Htub.h1tg000657l.g344.t1	Hetu3g01586	1586
3	92269744	92270799	+	>Htub.h1tg000657l.g347.t1	Hetu3g01589	1589
3	92275716	92278154	-	>Htub.h1tg000657l.g349.t1	Hetu3g01591	1591
16	77861289	77873090	-	KAD3337881.1	Mimi16g01811	1811
16	77893374	77916078	-	KAD3337886.1	Mimi16g01816	1816
1	114919506	114921035	-	KAI3829292.1	Smso1g03329	3329
1	114996629	115000603	+	KAI3829295.1	Smso1g03332	3332
1	115028926	115039470	-	KAI3829296.1	Smso1g03333	3333
28	26169123	26180739	-	KAI3682924.1	Smso28g00644	644
1	125655241	125657073	-	Streb.1G040750.1	Stre1g04075	4075
1	125659226	125662242	+	Streb.1G040760.1	Stre1g04076	4076
1	125666605	125671552	-	Streb.1G040770.1	Stre1g04077	4077

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