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
Hean1g00331	.	.	.	.	.	Hetu1g00297	Hetu2g00288	Hetu3g00277	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00332	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00333	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00334	.	.	.	.	.	.	.	.	Amtr12g00869	Smso1g03746	Smso28g00405	.	.	.	.	.	.	Stre1g04467	Mimi16g02207	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00335	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00336	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00337	Cobi2g02443	Bial10g01434	.	Dapi4g01989	.	Hetu1g00301	.	Hetu3g00285	Amtr12g00872	Smso1g03747	Smso28g00404	Taer4g02562	.	Fso1g02266	.	.	Fli3g00612	Stre1g04468	Mimi16g02209	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00338	Cobi2g02444	.	.	Dapi4g01990	.	.	.	.	Amtr12g00873	.	.	.	.	.	.	.	.	Stre1g04469	Mimi16g02214	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00339	.	.	.	.	.	.	.	.	Amtr12g00878	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00340	.	.	.	.	.	Hetu1g00312	Hetu2g00293	Hetu3g00290	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
12	24183183	24186236	-	AtrifAMIRv0_Chr12g0726011	Amtr12g00869	869
12	24222014	24222610	-	AtrifAMIRv0_Chr12g0726041	Amtr12g00872	872
12	24224844	24225101	+	AtrifAMIRv0_Chr12g0726051	Amtr12g00873	873
12	24268824	24269249	-	AtrifAMIRv0_Chr12g0726101	Amtr12g00878	878
10	14513137	14513721	-	g86735.t1	Bial10g01434	1434
2	73503042	73505587	-	h2tg000016l_1.g4803.t1	Cobi2g02443	2443
2	73507622	73509731	+	h2tg000016l_1.g4802.t1	Cobi2g02444	2444
4	120472719	120473321	-	h1tg000121l.g120127.t1	Dapi4g01989	1989
4	120477981	120480080	+	h1tg000121l.g120126.t1	Dapi4g01990	1990
3	15707741	15708331	+	FliAMIRv0_Chr03g0078811	Fli3g00612	612
1	64068518	64068790	-	FsoAMIRv0_Chr01g0022651	Fso1g02266	2266
1	8975159	8978182	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0003721	Hean1g00331	331
1	9059574	9063033	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0003731	Hean1g00332	332
1	9080917	9083919	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0003741	Hean1g00333	333
1	9084341	9087391	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0003751	Hean1g00334	334
1	9220879	9221489	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0003761	Hean1g00335	335
1	9270240	9272940	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0003771	Hean1g00336	336
1	9276332	9278564	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0003781	Hean1g00337	337
1	9281153	9295532	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0003791	Hean1g00338	338
1	9418142	9418567	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0003801	Hean1g00339	339
1	9475116	9475882	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0003811	Hean1g00340	340
1	11590984	11595077	+	>Htub.h1tg000484l.g215.t1	Hetu1g00297	297
1	11877998	11878597	-	>Htub.h1tg000484l.g211.t1	Hetu1g00301	301
1	13085972	13086453	+	>Htub.h1tg000484l.g200.t1	Hetu1g00312	312
2	10384926	10386221	+	>Htub.h2tg002734l.g192.t1	Hetu2g00288	288
2	10917910	10919373	+	>Htub.h2tg001440l.g146.t1	Hetu2g00293	293
3	11595768	11597208	+	>Htub.h1tg003572l.g266.t1	Hetu3g00277	277
3	11926059	11926652	-	>Htub.h1tg003572l.g258.t1	Hetu3g00285	285
3	12108963	12109648	+	>Htub.h1tg001937l.g75.t1	Hetu3g00290	290
16	85555755	85558817	-	KAD3338277.1	Mimi16g02207	2207
16	85604418	85606744	-	KAD3338279.1	Mimi16g02209	2209
16	85674482	85679752	+	KAD3338284.1	Mimi16g02214	2214
1	124491622	124494666	-	KAI3829709.1	Smso1g03746	3746
1	124575280	124575873	-	KAI3829710.1	Smso1g03747	3747
28	10604002	10604595	+	KAI3682684.1	Smso28g00404	404
28	10634775	10637804	+	KAI3682685.1	Smso28g00405	405
1	132056925	132060335	-	Streb.1G044670.1	Stre1g04467	4467
1	132090693	132092939	-	Streb.1G044680.1	Stre1g04468	4468
1	132094966	132106213	+	Streb.1G044690.1	Stre1g04469	4469
4	56509173	56509760	-	>KAK1428339.1	Taer4g02562	2562

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