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
Hean17g04551	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04552	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04553	Cobi5g02835	.	.	.	.	.	.	.	.	Smso4g01354	Smso21g01319	.	.	.	.	.	.	.	Mimi2g00117	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04554	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04555	Cobi5g02834	.	Bial9g02642	Dapi5g00120	Dapi21g00164	Hetu50g03503	Hetu51g03875	Hetu49g03807	Amtr10g04263	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04556	Cobi5g02833	.	Bial9g02641	Dapi5g00121	Dapi21g00165	Hetu50g03502	Hetu51g03874	Hetu49g03806	Amtr10g04264	Smso4g01353	Smso21g01317	.	.	.	.	.	.	.	Mimi2g00118	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04557	Cobi5g02832	.	Bial9g02640	Dapi5g00123	Dapi21g00166	.	.	.	Amtr10g04265	Smso4g01352	Smso21g01316	Taer9g03079	.	Fso12g00151	Ftr6g00115	Fra13g00683	Fli9g00158	Stre11g00223	Mimi2g00119	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04558	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04559	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04560	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
10	99038935	99040344	+	AtrifAMIRv0_Chr10g0666371	Amtr10g04263	4263
10	99040931	99048970	-	AtrifAMIRv0_Chr10g0666381	Amtr10g04264	4264
10	99105900	99106880	-	AtrifAMIRv0_Chr10g0666391	Amtr10g04265	4265
9	71225983	71226900	+	g77020.t1	Bial9g02640	2640
9	71247488	71260899	+	g77021.t1	Bial9g02641	2641
9	71262555	71264015	-	g77022.t1	Bial9g02642	2642
5	78949352	78950260	+	h2tg000020l_1.g9948.t1	Cobi5g02832	2832
5	78954078	78963288	+	h2tg000020l_1.g9947.t1	Cobi5g02833	2833
5	78964510	78966768	-	h2tg000020l_1.g9946.t1	Cobi5g02834	2834
5	78976275	78982261	-	h2tg000020l_1.g9945.t1	Cobi5g02835	2835
5	2722713	2725584	+	h1tg000132l.g124177.t1	Dapi5g00120	120
5	2726319	2735599	-	h1tg000132l.g124178.t1	Dapi5g00121	121
5	2744416	2745366	-	h1tg000132l.g124180.t1	Dapi5g00123	123
21	3441262	3443203	+	h1tg000096l.g113398.t1	Dapi21g00164	164
21	3443947	3453162	-	h1tg000096l.g113397.t1	Dapi21g00165	165
21	3494195	3495145	-	h1tg000096l.g113396.t1	Dapi21g00166	166
9	3326475	3327428	-	FliAMIRv0_Chr09g0209251	Fli9g00158	158
13	34037206	34038159	+	FraAMIRv0_Chr13g0259921	Fra13g00683	683
12	2357966	2358919	-	FsoAMIRv0_Chr12g0291161	Fso12g00151	151
6	1450026	1450979	-	FtrAMIRv0_Chr06g0162651	Ftr6g00115	115
17	194689822	194690895	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831601	Hean17g04551	4551
17	194694789	194696408	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831611	Hean17g04552	4552
17	194723893	194733765	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831641	Hean17g04553	4553
17	194740557	194741318	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831661	Hean17g04554	4554
17	194744687	194746664	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831671	Hean17g04555	4555
17	194747051	194758945	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831681	Hean17g04556	4556
17	194833476	194834753	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831701	Hean17g04557	4557
17	194974356	194980964	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831711	Hean17g04558	4558
17	194979871	194980882	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831721	Hean17g04559	4559
17	194982946	194983592	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831731	Hean17g04560	4560
49	219986425	219998454	+	>Htub.h1tg001001l.g537.t1	Hetu49g03806	3806
49	219999060	220000754	-	>Htub.h1tg001001l.g538.t1	Hetu49g03807	3807
50	205380340	205385409	+	>Htub.h1tg000531l.g300.t1	Hetu50g03502	3502
50	205386105	205387887	-	>Htub.h1tg000531l.g301.t1	Hetu50g03503	3503
51	226492596	226497900	+	>Htub.h1tg000558l.g104.t1	Hetu51g03874	3874
51	226498498	226500277	-	>Htub.h1tg000558l.g105.t1	Hetu51g03875	3875
2	3042412	3049814	+	KAD7116533.1	Mimi2g00117	117
2	3054172	3068061	-	KAD7116534.1	Mimi2g00118	118
2	3079257	3080204	-	KAD7116535.1	Mimi2g00119	119
4	18374173	18375120	+	KAI3818205.1	Smso4g01352	1352
4	18385382	18397068	+	KAI3818206.1	Smso4g01353	1353
4	18399398	18405616	-	KAI3818207.1	Smso4g01354	1354
21	13940641	13941558	+	KAI3731522.1	Smso21g01316	1316
21	13944465	13947004	+	KAI3731523.1	Smso21g01317	1317
21	13958971	13964624	-	KAI3731525.1	Smso21g01319	1319
11	7311885	7313548	-	Streb.11G002230.1	Stre11g00223	223
9	30971657	30972610	+	>KAK1413719.1	Taer9g03079	3079

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