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
Hean1g00131	Cobi2g02290	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00132	.	Bial10g01316	.	.	Dapi20g01802	.	.	.	Amtr12g00391	.	.	Taer4g02392	Fro14g01287	Fso1g02107	Ftr2g00724	.	Fli3g00786	Stre1g04342	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00133	.	.	.	.	.	.	.	.	.	Smso1g03623	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00134	.	Bial10g01317	Bial22g00909	.	Dapi20g01806	Hetu1g00125	Hetu2g00184	Hetu3g00125	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00135	.	.	.	.	.	.	.	.	.	Smso1g03624	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00136	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00137	Cobi2g02292	Bial10g01319	Bial22g00910	.	Dapi20g01807	Hetu1g00126	Hetu2g00186	Hetu3g00126	Amtr12g00396	Smso1g03626	Smso28g00476	.	.	.	.	.	.	Stre1g04345	Mimi16g02117	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00138	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00139	Cobi2g02294	Bial10g01321	Bial22g00912	.	Dapi20g01808	.	Hetu2g00187	Hetu3g00127	Amtr12g00397	Smso1g03627	Smso28g00475	Taer4g02406	Fro14g01295	Fso1g02114	.	.	Fli3g00776	Stre1g04346	Mimi16g02118	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00140	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
12	12979296	12981501	-	AtrifAMIRv0_Chr12g0721231	Amtr12g00391	391
12	13237221	13245359	-	AtrifAMIRv0_Chr12g0721281	Amtr12g00396	396
12	13286270	13286857	-	AtrifAMIRv0_Chr12g0721291	Amtr12g00397	397
10	13090705	13092772	-	g86853.t1	Bial10g01316	1316
10	13098954	13105335	-	g86852.t1	Bial10g01317	1317
10	13139711	13145485	-	g86850.t1	Bial10g01319	1319
10	13194770	13195348	-	g86848.t1	Bial10g01321	1321
22	8663973	8671750	-	g147125.t1	Bial22g00909	909
22	8696742	8702383	-	g147124.t1	Bial22g00910	910
22	8754599	8755171	-	g147122.t1	Bial22g00912	912
2	70000995	70003298	-	h2tg000016l_1.g4956.t1	Cobi2g02290	2290
2	70128606	70133183	-	h2tg000016l_1.g4954.t1	Cobi2g02292	2292
2	70200947	70201516	-	h2tg000016l_1.g4952.t1	Cobi2g02294	2294
20	107349930	107351715	-	h1tg000169l.g129595.t1	Dapi20g01802	1802
20	107539264	107547048	-	h1tg000169l.g129591.t1	Dapi20g01806	1806
20	107595788	107602870	-	h1tg000169l.g129590.t1	Dapi20g01807	1807
20	107614449	107615039	-	h1tg000169l.g129589.t1	Dapi20g01808	1808
3	21401263	21401844	+	FliAMIRv0_Chr03g0080451	Fli3g00776	776
3	21870701	21871752	+	FliAMIRv0_Chr03g0080551	Fli3g00786	786
14	20481630	20482684	-	FroAMIRv0_Chr14g0254411	Fro14g01287	1287
14	20595150	20595722	-	FroAMIRv0_Chr14g0254491	Fro14g01295	1295
1	60704754	60706244	-	FsoAMIRv0_Chr01g0021061	Fso1g02107	2107
1	60840612	60841184	-	FsoAMIRv0_Chr01g0021131	Fso1g02114	2114
2	13592386	13593883	+	FtrAMIRv0_Chr02g0035911	Ftr2g00724	724
1	2618907	2625702	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0001471	Hean1g00131	131
1	2629327	2631405	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0001481	Hean1g00132	132
1	2684880	2692811	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0001491	Hean1g00133	133
1	2704399	2704662	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0001501	Hean1g00134	134
1	2741058	2746323	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0001511	Hean1g00135	135
1	2768017	2775993	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0001521	Hean1g00136	136
1	2871597	2879386	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0001541	Hean1g00137	137
1	2897564	2897922	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0001561	Hean1g00138	138
1	2900691	2901342	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0001571	Hean1g00139	139
1	2906153	2908818	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0001581	Hean1g00140	140
1	4735281	4740617	-	>Htub.h1tg003050l.g386.t1	Hetu1g00125	125
1	4901708	4908454	-	>Htub.h1tg003050l.g387.t1	Hetu1g00126	126
2	5728541	5733881	-	>Htub.h1tg000710l.g64.t1	Hetu2g00184	184
2	5953871	5960571	-	>Htub.h1tg000710l.g66.t1	Hetu2g00186	186
2	5962879	5963538	-	>Htub.h1tg000710l.g67.t1	Hetu2g00187	187
3	4736559	4741898	-	>Htub.h1tg000727l.g23.t1	Hetu3g00125	125
3	4888124	4893336	-	>Htub.h1tg000727l.g24.t1	Hetu3g00126	126
3	4894676	4895236	-	>Htub.h1tg000727l.g25.t1	Hetu3g00127	127
16	83566623	83575326	-	KAD3338187.1	Mimi16g02117	2117
16	83582296	83586937	-	KAD3338188.1	Mimi16g02118	2118
1	121594887	121600280	-	KAI3829586.1	Smso1g03623	3623
1	121613132	121618737	-	KAI3829587.1	Smso1g03624	3624
1	121681940	121687854	-	KAI3829589.1	Smso1g03626	3626
1	121695245	121695814	-	KAI3829590.1	Smso1g03627	3627
28	13147817	13148392	+	KAI3682755.1	Smso28g00475	475
28	13155305	13161065	+	KAI3682756.1	Smso28g00476	476
1	129661964	129663984	-	Streb.1G043420.1	Stre1g04342	4342
1	129754352	129760079	-	Streb.1G043450.1	Stre1g04345	4345
1	129761706	129762275	-	Streb.1G043460.1	Stre1g04346	4346
4	54069140	54073534	-	>KAK1428173.1	Taer4g02392	2392
4	54245633	54246214	-	>KAK1428187.1	Taer4g02406	2406

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