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
Hean1g00371	.	.	.	Dapi4g02015	.	Hetu1g00367	.	.	Amtr12g00927	.	Smso28g00384	.	.	.	.	.	.	.	.	Hean11g02464	.	Bial12g02667	Bial24g02507	.	Dapi31g01994	.	Hetu31g02073	.	Amtr07g04469	.	Smso20g01645	.	.	.	.	.	.	.	.
Hean1g00372	Cobi9g01286	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00373	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00374	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00375	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00376	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00377	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00378	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00379	Cobi2g02466	.	.	.	.	.	Hetu2g00322	.	.	.	.	.	Fro14g01424	.	Ftr2g00482	Fra18g01579	Fli3g00577	Stre1g04494	Mimi16g02249	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00380	.	Bial10g01461	.	Dapi4g02022	.	Hetu1g00373	Hetu2g00323	Hetu3g00334	Amtr12g00929	.	.	Taer4g02603	Fro14g01425	Fso1g02307	.	Fra18g01580	Fli3g00575	Stre1g04495	Mimi16g02250	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
7	93160672	93165392	-	AtrifAMIRv0_Chr07g0496161	Amtr07g04469	4469
12	25121111	25124992	+	AtrifAMIRv0_Chr12g0726591	Amtr12g00927	927
12	25144057	25144420	+	AtrifAMIRv0_Chr12g0726611	Amtr12g00929	929
10	14841473	14841829	+	g86708.t1	Bial10g01461	1461
12	56913266	56919025	+	g35866.t1	Bial12g02667	2667
24	55923899	55929656	+	g68173.t1	Bial24g02507	2507
2	73935332	73935665	+	h2tg000016l_1.g4780.t1	Cobi2g02466	2466
9	49150816	49155164	-	h2tg000008l_1.g40727.t1	Cobi9g01286	1286
4	121655144	121659472	+	h1tg000121l.g120101.t1	Dapi4g02015	2015
4	121999427	121999760	+	h1tg000411l.g140573.t1	Dapi4g02022	2022
31	98332592	98337411	-	h2tg000063l.g12079.t1	Dapi31g01994	1994
3	14333306	14333600	-	FliAMIRv0_Chr03g0078441	Fli3g00575	575
3	14411514	14411812	-	FliAMIRv0_Chr03g0078461	Fli3g00577	577
18	61190792	61191086	+	FraAMIRv0_Chr18g0357761	Fra18g01579	1579
18	61202196	61202511	+	FraAMIRv0_Chr18g0357771	Fra18g01580	1580
14	22556920	22557214	+	FroAMIRv0_Chr14g0255781	Fro14g01424	1424
14	22565239	22565563	+	FroAMIRv0_Chr14g0255791	Fro14g01425	1425
1	64855826	64856141	+	FsoAMIRv0_Chr01g0023061	Fso1g02307	2307
2	7647994	7648294	-	FtrAMIRv0_Chr02g0033491	Ftr2g00482	482
1	10715726	10722657	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004151	Hean1g00371	371
1	10781560	10784544	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004161	Hean1g00372	372
1	10785564	10787751	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004171	Hean1g00373	373
1	10795046	10798798	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004181	Hean1g00374	374
1	10811076	10811300	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004191	Hean1g00375	375
1	10826536	10828173	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004201	Hean1g00376	376
1	10829837	10831379	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004221	Hean1g00377	377
1	10831381	10832441	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004231	Hean1g00378	378
1	10889034	10889666	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004261	Hean1g00379	379
1	10927207	10927830	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004271	Hean1g00380	380
11	107409501	107413849	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr11g0495341	Hean11g02464	2464
1	16348089	16354211	-	>Htub.h1tg001740l.g120.t1	Hetu1g00367	367
1	16678537	16678840	+	>Htub.h1tg001740l.g126.t1	Hetu1g00373	373
2	12617873	12618176	+	>Htub.h2tg001774l.g148.t1	Hetu2g00322	322
2	12671378	12671584	+	>Htub.h2tg001774l.g147.t1	Hetu2g00323	323
3	13985609	13985936	+	>Htub.h1tg001937l.g30.t1	Hetu3g00334	334
31	117889261	117894625	-	>Htub.h1tg001293l.g148.t1	Hetu31g02073	2073
16	86358562	86360626	+	KAD3338319.1	Mimi16g02249	2249
16	86366327	86366887	+	KAD3338320.1	Mimi16g02250	2250
20	54971514	54978096	+	KAI3742641.1	Smso20g01645	1645
28	9922377	9925698	-	KAI3682664.1	Smso28g00384	384
1	132619222	132620216	+	Streb.1G044940.1	Stre1g04494	4494
1	132631281	132631897	+	Streb.1G044950.1	Stre1g04495	4495
4	57030692	57031114	-	>KAK1428380.1	Taer4g02603	2603

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