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
Hean1g00171	.	.	.	.	Dapi20g01824	.	.	Hetu3g00157	Amtr12g00462	.	.	Taer4g02428	Fro14g01317	Fso1g02144	Ftr2g00659	Fra18g01654	Fli3g00737	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00172	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00173	.	.	.	.	Dapi20g01825	Hetu1g00164	Hetu2g00210	Hetu3g00159	Amtr12g00470	.	.	Taer4g02431	Fro14g01318	Fso1g02146	Ftr2g00657	Fra18g01653	Fli3g00735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00174	.	.	.	.	.	.	.	Hetu3g00160	.	.	.	.	.	.	.	.	.	.	Mimi16g02130	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00175	.	.	.	.	Dapi20g01826	Hetu1g00165	Hetu2g00211	.	Amtr12g00473	.	Smso28g00468	Taer4g02432	Fro14g01319	Fso1g02149	Ftr2g00651	Fra18g01647	Fli3g00734	Stre1g04367	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00176	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00177	.	.	Bial22g00931	Dapi4g01871	.	.	.	Hetu3g00161	.	.	.	.	.	.	.	.	.	.	Mimi16g02131	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00178	.	.	Bial22g00932	Dapi4g01872	.	Hetu1g00166	Hetu2g00213	.	Amtr12g00475	Smso1g03637	Smso28g00467	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00179	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00180	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
12	15008216	15008524	-	AtrifAMIRv0_Chr12g0721941	Amtr12g00462	462
12	15065648	15065956	-	AtrifAMIRv0_Chr12g0722021	Amtr12g00470	470
12	15150976	15151281	+	AtrifAMIRv0_Chr12g0722051	Amtr12g00473	473
12	15268779	15269087	-	AtrifAMIRv0_Chr12g0722071	Amtr12g00475	475
22	8975200	8975502	-	g147103.t1	Bial22g00931	931
22	8990748	8991056	+	g147102.t1	Bial22g00932	932
4	116568008	116568316	-	h1tg000193l.g132865.t1	Dapi4g01871	1871
4	116602564	116603414	-	h1tg000193l.g132864.t1	Dapi4g01872	1872
20	108182055	108182363	-	h1tg000169l.g129573.t1	Dapi20g01824	1824
20	108191208	108191516	-	h1tg000169l.g129572.t1	Dapi20g01825	1825
20	108335226	108335534	+	h1tg000169l.g129571.t1	Dapi20g01826	1826
3	20101719	20102027	-	FliAMIRv0_Chr03g0080031	Fli3g00734	734
3	20149039	20149347	+	FliAMIRv0_Chr03g0080041	Fli3g00735	735
3	20181029	20181337	-	FliAMIRv0_Chr03g0080061	Fli3g00737	737
18	63594602	63594910	-	FraAMIRv0_Chr18g0358441	Fra18g01647	1647
18	63645533	63645841	-	FraAMIRv0_Chr18g0358501	Fra18g01653	1653
18	63648769	63649077	+	FraAMIRv0_Chr18g0358511	Fra18g01654	1654
14	20901649	20901957	+	FroAMIRv0_Chr14g0254711	Fro14g01317	1317
14	20904163	20904471	-	FroAMIRv0_Chr14g0254721	Fro14g01318	1318
14	20921491	20921799	+	FroAMIRv0_Chr14g0254731	Fro14g01319	1319
1	61695054	61695362	-	FsoAMIRv0_Chr01g0021431	Fso1g02144	2144
1	61711143	61711451	-	FsoAMIRv0_Chr01g0021451	Fso1g02146	2146
1	61731452	61731760	+	FsoAMIRv0_Chr01g0021481	Fso1g02149	2149
2	12246458	12246766	-	FtrAMIRv0_Chr02g0035181	Ftr2g00651	651
2	12323239	12323547	+	FtrAMIRv0_Chr02g0035241	Ftr2g00657	657
2	12337280	12337588	-	FtrAMIRv0_Chr02g0035261	Ftr2g00659	659
1	4271746	4272054	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0001961	Hean1g00171	171
1	4348272	4348765	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0001971	Hean1g00172	172
1	4365581	4365889	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0001981	Hean1g00173	173
1	4402891	4403199	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0001991	Hean1g00174	174
1	4455172	4455477	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0002001	Hean1g00175	175
1	4508018	4513368	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0002011	Hean1g00176	176
1	4549646	4549951	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0002021	Hean1g00177	177
1	4582208	4582729	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0002031	Hean1g00178	178
1	4590008	4591215	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0002041	Hean1g00179	179
1	4594491	4594832	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0002061	Hean1g00180	180
1	6582565	6582873	-	>Htub.h1tg003050l.g428.t1	Hetu1g00164	164
1	6734580	6735966	-	>Htub.h1tg003050l.g429.t1	Hetu1g00165	165
1	6880632	6880937	+	>Htub.h1tg003050l.g430.t1	Hetu1g00166	166
2	6822010	6822318	-	>Htub.h1tg000710l.g94.t1	Hetu2g00210	210
2	7140251	7141858	+	>Htub.h1tg000710l.g95.t1	Hetu2g00211	211
2	7172502	7172807	+	>Htub.h1tg000710l.g97.t1	Hetu2g00213	213
3	6017635	6017943	-	>Htub.h1tg000727l.g57.t1	Hetu3g00157	157
3	6233553	6234181	-	>Htub.h1tg000727l.g59.t1	Hetu3g00159	159
3	6332707	6333015	-	>Htub.h1tg000727l.g60.t1	Hetu3g00160	160
3	6489389	6489694	+	>Htub.h1tg000727l.g61.t1	Hetu3g00161	161
16	83786248	83787018	+	KAD3338200.1	Mimi16g02130	2130
16	83815174	83818733	-	KAD3338201.1	Mimi16g02131	2131
1	121901780	121902088	-	KAI3829600.1	Smso1g03637	3637
28	12664935	12665243	+	KAI3682747.1	Smso28g00467	467
28	12680038	12680346	+	KAI3682748.1	Smso28g00468	468
1	130058337	130059002	+	Streb.1G043670.1	Stre1g04367	4367
4	54616206	54616514	-	>KAK1428209.1	Taer4g02428	2428
4	54644779	54645087	-	>KAK1428212.1	Taer4g02431	2431
4	54670096	54670437	+	>KAK1428213.1	Taer4g02432	2432

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