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
Hean1g00551	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00552	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00553	Cobi2g02040	Bial10g01114	.	Dapi4g01593	Dapi20g01508	Hetu1g01695	Hetu2g01475	Hetu3g01487	Amtr02g09125	Smso1g03379	Smso28g00619	.	Fro14g01018	Fso1g01582	Ftr2g01379	.	Fli3g01110	Stre1g04106	Mimi16g01857	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00554	.	Bial10g01116	.	Dapi4g01603	Dapi20g01516	Hetu1g01694	Hetu2g01467	Hetu3g01486	Amtr02g09130	Smso1g03381	Smso28g00618	.	.	.	.	.	.	Stre1g04108	Mimi16g01859	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00555	.	Bial10g01117	.	Dapi4g01604	Dapi20g01517	.	.	.	.	Smso1g03382	Smso28g00617	.	.	.	.	.	.	Stre1g04109	Mimi16g01860	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00556	.	.	.	Dapi4g01612	.	.	.	.	.	Smso1g03383	Smso28g00616	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00557	.	.	.	.	.	.	.	Hetu3g01483	.	.	.	.	.	.	.	.	.	Stre1g04110	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00558	.	.	.	.	Dapi20g01525	.	.	.	.	.	.	.	.	.	.	.	Fli3g01087	.	Mimi16g01861	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00559	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00560	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
2	180852528	180855279	-	AtrifAMIRv0_Chr02g0187211	Amtr02g09125	9125
2	180994659	180998218	-	AtrifAMIRv0_Chr02g0187261	Amtr02g09130	9130
10	11207723	11210123	-	g87055.t1	Bial10g01114	1114
10	11220964	11222219	-	g87053.t1	Bial10g01116	1116
10	11227337	11228643	+	g87052.t1	Bial10g01117	1117
2	63461098	63463918	+	h2tg000016l_1.g5206.t1	Cobi2g02040	2040
4	97021514	97024110	-	h2tg000160l.g57178.t1	Dapi4g01593	1593
4	97658018	97659834	-	h2tg000160l.g57188.t1	Dapi4g01603	1603
4	97693737	97695581	+	h2tg000160l.g57189.t1	Dapi4g01604	1604
4	98365423	98392878	-	h2tg000160l.g57197.t1	Dapi4g01612	1612
20	89152443	89155038	-	h2tg000075l.g16878.t1	Dapi20g01508	1508
20	89718975	89720825	-	h2tg000075l.g16886.t1	Dapi20g01516	1516
20	89759953	89761799	+	h2tg000075l.g16887.t1	Dapi20g01517	1517
20	90435016	90470605	-	h2tg000075l.g16895.t1	Dapi20g01525	1525
3	36924795	36941779	-	FliAMIRv0_Chr03g0083561	Fli3g01087	1087
3	38631924	38632628	+	FliAMIRv0_Chr03g0083791	Fli3g01110	1110
14	15668121	15670093	-	FroAMIRv0_Chr14g0251721	Fro14g01018	1018
1	45241713	45243741	-	FsoAMIRv0_Chr01g0015811	Fso1g01582	1582
2	40682936	40684939	-	FtrAMIRv0_Chr02g0042461	Ftr2g01379	1379
1	27580109	27580533	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006211	Hean1g00551	551
1	27712981	27715723	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006231	Hean1g00552	552
1	28022004	28024913	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006271	Hean1g00553	553
1	28094122	28097465	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006281	Hean1g00554	554
1	28286795	28289095	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006291	Hean1g00555	555
1	28566906	28572104	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006301	Hean1g00556	556
1	28578130	28578306	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006311	Hean1g00557	557
1	28579684	28579896	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006321	Hean1g00558	558
1	28830670	28831477	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006341	Hean1g00559	559
1	28897374	28898165	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006361	Hean1g00560	560
1	93630529	93631528	+	>Htub.h1tg001922l.g425.t1	Hetu1g01694	1694
1	93683219	93685922	+	>Htub.h1tg001922l.g426.t1	Hetu1g01695	1695
2	83265333	83267772	+	>Htub.h1tg000330l.g295.t1	Hetu2g01467	1467
2	83343963	83344817	+	>Htub.h1tg000330l.g286.t1	Hetu2g01475	1475
3	80675792	80678680	+	>Htub.h1tg000150l.g6.t1	Hetu3g01483	1483
3	80732497	80737034	+	>Htub.h1tg000150l.g3.t1	Hetu3g01486	1486
3	80806016	80808432	+	>Htub.h1tg000150l.g1.t1	Hetu3g01487	1487
16	78697243	78699245	-	KAD3337927.1	Mimi16g01857	1857
16	78716991	78719239	-	KAD3337929.1	Mimi16g01859	1859
16	78724351	78727003	+	KAD3337930.1	Mimi16g01860	1860
16	78732316	78746713	-	KAD3337931.1	Mimi16g01861	1861
1	116202595	116204676	-	KAI3829342.1	Smso1g03379	3379
1	116249323	116252948	-	KAI3829344.1	Smso1g03381	3381
1	116287829	116288599	+	KAI3829345.1	Smso1g03382	3382
1	116295237	116303109	-	KAI3829346.1	Smso1g03383	3383
28	21972365	21982808	+	KAI3682896.1	Smso28g00616	616
28	21985841	21986323	-	KAI3682897.1	Smso28g00617	617
28	21988358	21990396	+	KAI3682898.1	Smso28g00618	618
28	22258135	22260241	+	KAI3682899.1	Smso28g00619	619
1	126051668	126053699	-	Streb.1G041060.1	Stre1g04106	4106
1	126076324	126078997	-	Streb.1G041080.1	Stre1g04108	4108
1	126080369	126082280	+	Streb.1G041090.1	Stre1g04109	4109
1	126084576	126098404	-	Streb.1G041100.1	Stre1g04110	4110

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