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
Hean1g00531	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00532	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00533	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00534	.	.	.	.	.	.	Hetu2g01538	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Stre1g04094	Mimi16g01832	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00536	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00537	.	Bial10g01100	.	Dapi4g01566	Dapi20g01476	Hetu1g01718	Hetu2g01520	.	Amtr02g09063	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00538	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00539	.	.	.	.	.	.	Hetu2g01517	Hetu3g01550	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
2	178048510	178053284	+	AtrifAMIRv0_Chr02g0186591	Amtr02g09063	9063
10	11088099	11092977	+	g87069.t1	Bial10g01100	1100
4	94572667	94578124	+	h2tg000160l.g57151.t1	Dapi4g01566	1566
20	86530531	86537706	+	h2tg000075l.g16846.t1	Dapi20g01476	1476
1	22455106	22456161	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005951	Hean1g00531	531
1	24237353	24238576	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005981	Hean1g00532	532
1	24238701	24241254	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005991	Hean1g00533	533
1	24269298	24269987	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006001	Hean1g00534	534
1	24270028	24270990	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006011	Hean1g00535	535
1	24495220	24495525	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006021	Hean1g00536	536
1	24903556	24908408	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006031	Hean1g00537	537
1	24908589	24908863	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006041	Hean1g00538	538
1	24949565	24956305	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006051	Hean1g00539	539
1	24959429	24959935	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006061	Hean1g00540	540
1	95779275	95782188	-	>Htub.h1tg001760l.g31.t1	Hetu1g01718	1718
2	87097461	87103295	+	>Htub.h1tg000510l.g117.t1	Hetu2g01517	1517
2	87257021	87259406	+	>Htub.h1tg000510l.g113.t1	Hetu2g01520	1520
2	87770269	87771960	+	>Htub.h1tg000510l.g94.t1	Hetu2g01538	1538
3	88865345	88866707	-	>Htub.h1tg003659l.g247.t1	Hetu3g01550	1550
16	78220654	78226874	+	KAD3337902.1	Mimi16g01832	1832
1	125948756	125950660	+	Streb.1G040940.1	Stre1g04094	4094

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