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
Hean17g04531	Cobi5g00143	Bial18g00187	Bial9g02645	Dapi5g00117	Dapi21g00161	Hetu50g03513	Hetu51g03884	Hetu49g03822	Amtr10g04256	Smso4g01357	.	Taer9g03084	.	.	Ftr6g00111	.	Fli9g00157	.	Mimi2g00115	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04532	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04533	Cobi5g02836	.	Bial9g02644	Dapi5g00118	Dapi21g00162	Hetu50g03508	Hetu51g03882	Hetu49g03821	Amtr10g04258	Smso4g01355	Smso21g01320	.	.	.	.	.	.	.	Mimi2g00116	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04534	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04535	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04536	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04537	.	.	.	.	.	.	Hetu51g03880	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04538	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04539	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
10	98957708	98961285	-	AtrifAMIRv0_Chr10g0666301	Amtr10g04256	4256
10	98982974	98998655	+	AtrifAMIRv0_Chr10g0666321	Amtr10g04258	4258
9	71279091	71284810	-	g77024.t1	Bial9g02644	2644
9	71295598	71298549	+	g77025.t1	Bial9g02645	2645
18	2814429	2816615	-	g121529.t1	Bial18g00187	187
5	2148732	2152170	-	h2tg000038l_1.g23743.t1	Cobi5g00143	143
5	78984292	78990346	-	h2tg000020l_1.g9944.t1	Cobi5g02836	2836
5	2637285	2641130	-	h1tg000132l.g124174.t1	Dapi5g00117	117
5	2688390	2693983	+	h1tg000132l.g124175.t1	Dapi5g00118	118
21	3385825	3393773	-	h1tg000096l.g113401.t1	Dapi21g00161	161
21	3397758	3403385	+	h1tg000096l.g113400.t1	Dapi21g00162	162
9	3235838	3239606	-	FliAMIRv0_Chr09g0209241	Fli9g00157	157
6	1394784	1399036	-	FtrAMIRv0_Chr06g0162611	Ftr6g00111	111
17	194260036	194266409	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831391	Hean17g04531	4531
17	194282759	194286602	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831401	Hean17g04532	4532
17	194288596	194310113	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831421	Hean17g04533	4533
17	194294801	194298694	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831431	Hean17g04534	4534
17	194315135	194315597	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831441	Hean17g04535	4535
17	194317074	194318530	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831451	Hean17g04536	4536
17	194318547	194318825	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831461	Hean17g04537	4537
17	194395363	194399033	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831471	Hean17g04538	4538
17	194402481	194403356	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831481	Hean17g04539	4539
17	194426682	194426996	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831491	Hean17g04540	4540
49	220938911	220951118	-	>Htub.h1tg001001l.g552.t1	Hetu49g03821	3821
49	220961032	220965379	+	>Htub.h1tg001001l.g553.t1	Hetu49g03822	3822
50	205775090	205790329	-	>Htub.h1tg000531l.g306.t1	Hetu50g03508	3508
50	206005429	206010787	+	>Htub.h1tg000531l.g311.t1	Hetu50g03513	3513
51	226917421	226938461	-	>Htub.h1tg000558l.g110.t1	Hetu51g03880	3880
51	227108248	227114965	-	>Htub.h1tg000558l.g112.t1	Hetu51g03882	3882
51	227277320	227281803	+	>Htub.h1tg000558l.g114.t1	Hetu51g03884	3884
2	3001925	3005791	-	KAD7116531.1	Mimi2g00115	115
2	3030793	3039937	+	KAD7116532.1	Mimi2g00116	116
4	18412681	18418907	-	KAI3818208.1	Smso4g01355	1355
4	18428668	18445613	+	KAI3818210.1	Smso4g01357	1357
21	13966449	13973377	-	KAI3731526.1	Smso21g01320	1320
9	31015503	31020541	+	>KAK1413724.1	Taer9g03084	3084

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