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
Hean1g00481	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00482	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00483	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00484	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00485	.	Bial10g01068	.	Dapi4g01530	Dapi20g01430	.	.	.	.	.	.	.	Fro14g00984	.	.	Fra18g01353	Fli3g01147	Stre1g04065	Mimi16g01732	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00486	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00487	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00488	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00489	.	Bial10g01069	.	.	.	.	.	.	.	Smso1g03323	.	.	.	.	.	.	.	Stre1g04066	Mimi16g01731	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00490	Cobi9g01251	.	.	.	.	.	Hetu2g01582	.	.	Smso1g03324	.	.	.	.	.	.	.	Stre1g04067	Mimi16g01730	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
10	10847421	10849605	-	g87101.t1	Bial10g01068	1068
10	10877889	10879305	+	g87100.t1	Bial10g01069	1069
9	47421968	47427089	-	h2tg000008l_1.g40692.t1	Cobi9g01251	1251
4	90283981	90286034	-	h2tg000259l.g76580.t1	Dapi4g01530	1530
20	81095755	81097808	-	h1tg000190l.g132780.t1	Dapi20g01430	1430
3	44752305	44761874	+	FliAMIRv0_Chr03g0084161	Fli3g01147	1147
18	48482165	48487956	+	FraAMIRv0_Chr18g0355501	Fra18g01353	1353
14	14861679	14870181	+	FroAMIRv0_Chr14g0251381	Fro14g00984	984
1	17160572	17163773	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005371	Hean1g00481	481
1	17194460	17194905	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005381	Hean1g00482	482
1	17196295	17196986	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005391	Hean1g00483	483
1	18337299	18337880	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005411	Hean1g00484	484
1	18439674	18441334	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005421	Hean1g00485	485
1	18835323	18836070	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005471	Hean1g00486	486
1	19171648	19172877	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005481	Hean1g00487	487
1	19171673	19173531	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005491	Hean1g00488	488
1	19536470	19540954	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005501	Hean1g00489	489
1	19540849	19546201	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005511	Hean1g00490	490
2	92259182	92266029	+	>Htub.h1tg000510l.g48.t1	Hetu2g01582	1582
16	76504043	76519846	+	KAD3337800.1	Mimi16g01730	1730
16	76522846	76532215	-	KAD3337801.1	Mimi16g01731	1731
16	76537992	76539898	+	KAD3337802.1	Mimi16g01732	1732
1	114696338	114698675	+	KAI3829286.1	Smso1g03323	3323
1	114698754	114708679	-	KAI3829287.1	Smso1g03324	3324
1	125556493	125559640	-	Streb.1G040650.1	Stre1g04065	4065
1	125567669	125569841	+	Streb.1G040660.1	Stre1g04066	4066
1	125569940	125576489	-	Streb.1G040670.1	Stre1g04067	4067

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