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
Hean1g00441	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00442	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00443	.	Bial10g02031	Bial22g01568	.	.	Hetu1g01895	.	Hetu3g01666	.	Smso1g03310	.	.	.	.	.	.	.	.	Mimi16g01783	Hean11g02986	Cobi6g00890	Bial12g02886	Bial24g02723	.	.	Hetu32g02555	Hetu31g02544	Hetu33g02459	.	.	Smso29g01632	.	.	.	.	.	.	.	Mimi16g01748
Hean1g00444	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00445	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00446	.	.	.	.	.	Hetu1g01892	.	Hetu3g01664	.	.	.	.	.	.	.	.	.	Stre1g04047	Mimi16g01781	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00448	.	Bial10g02028	Bial22g01564	.	.	Hetu1g01891	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00449	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00450	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
10	21697033	21700161	-	g86141.t1	Bial10g02028	2028
10	21720329	21721836	-	g86138.t1	Bial10g02031	2031
12	58913493	58917174	+	g36085.t1	Bial12g02886	2886
22	16778840	16781941	-	g112799.t1	Bial22g01564	1564
22	16804231	16805738	-	g112795.t1	Bial22g01568	1568
24	57911285	57913944	+	g68389.t1	Bial24g02723	2723
6	7243834	7247672	-	h2tg000031l_1.g19203.t1	Cobi6g00890	890
1	12945731	12948340	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004911	Hean1g00441	441
1	12957260	12957462	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004921	Hean1g00442	442
1	12958576	12961999	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004931	Hean1g00443	443
1	13117827	13121093	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004951	Hean1g00444	444
1	13121095	13124822	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004961	Hean1g00445	445
1	13131079	13133068	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004971	Hean1g00446	446
1	13132579	13133850	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004981	Hean1g00447	447
1	13133361	13133847	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004991	Hean1g00448	448
1	13532570	13538397	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005001	Hean1g00449	449
1	13547128	13549665	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0005011	Hean1g00450	450
11	140541053	140545944	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr11g0501861	Hean11g02986	2986
1	113750068	113750850	-	>Htub.h1tg001853l.g202.t1	Hetu1g01891	1891
1	113751086	113752737	-	>Htub.h1tg001853l.g203.t1	Hetu1g01892	1892
1	113930475	113932746	-	>Htub.h1tg001853l.g207.t1	Hetu1g01895	1895
3	101149837	101151920	-	>Htub.h1tg002641l.g76.t1	Hetu3g01664	1664
3	101436678	101438906	-	>Htub.h1tg002641l.g79.t1	Hetu3g01666	1666
31	147277614	147281771	+	>Htub.h1tg000896l.g760.t1	Hetu31g02544	2544
32	149178623	149182958	+	>Htub.h1tg002137l.g89.t1	Hetu32g02555	2555
33	140070378	140075123	+	>Htub.h1tg002022l.g391.t1	Hetu33g02459	2459
16	76819390	76826727	+	KAD3337818.1	Mimi16g01748	1748
16	77249135	77254478	-	KAD3337851.1	Mimi16g01781	1781
16	77317984	77325324	-	KAD3337853.1	Mimi16g01783	1783
1	114337270	114338949	+	KAI3829273.1	Smso1g03310	3310
29	43466756	43471636	-	KAI3676626.1	Smso29g01632	1632
1	125385305	125388052	-	Streb.1G040470.1	Stre1g04047	4047

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