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
Hean17g04511	Cobi5g02849	.	.	Dapi5g00100	Dapi21g00148	.	.	.	Amtr10g04225	.	.	.	.	.	.	.	.	Stre11g00194	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04512	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04513	.	Bial18g00162	Bial9g02663	Dapi5g00101	Dapi21g00149	Hetu50g03533	Hetu51g03895	Hetu49g03836	Amtr10g04227	Smso4g01381	Smso21g01344	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04514	Cobi5g02848	.	Bial9g02662	Dapi5g00102	Dapi21g00150	Hetu50g03532	Hetu51g03894	Hetu49g03835	Amtr10g04228	Smso4g01382	Smso21g01345	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04515	Cobi5g00114	.	Bial9g02659	Dapi5g00103	Dapi21g00151	Hetu50g03531	Hetu51g03893	Hetu49g03833	Amtr10g04229	Smso4g01383	Smso21g01346	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04516	Cobi5g02845	.	Bial9g02658	Dapi5g00104	Dapi21g00152	Hetu50g03529	Hetu51g03892	Hetu49g03832	Amtr10g04231	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04517	Cobi5g02844	.	Bial9g02657	Dapi5g00109	Dapi21g00153	Hetu50g03528	Hetu51g03891	Hetu49g03831	Amtr10g04232	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04518	.	.	.	.	.	Hetu50g03527	Hetu51g03890	Hetu49g03830	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04519	Cobi5g02843	.	Bial9g02651	Dapi5g00110	Dapi21g00154	.	.	.	Amtr10g04235	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04520	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
10	98313655	98314144	+	AtrifAMIRv0_Chr10g0665991	Amtr10g04225	4225
10	98410802	98412487	+	AtrifAMIRv0_Chr10g0666011	Amtr10g04227	4227
10	98414375	98418744	-	AtrifAMIRv0_Chr10g0666021	Amtr10g04228	4228
10	98456144	98461086	+	AtrifAMIRv0_Chr10g0666031	Amtr10g04229	4229
10	98505495	98507608	+	AtrifAMIRv0_Chr10g0666051	Amtr10g04231	4231
10	98508869	98524287	+	AtrifAMIRv0_Chr10g0666061	Amtr10g04232	4232
10	98561314	98562797	+	AtrifAMIRv0_Chr10g0666091	Amtr10g04235	4235
9	71376954	71378411	-	g77031.t1	Bial9g02651	2651
9	71427025	71429339	-	g77037.t1	Bial9g02657	2657
9	71432533	71435871	-	g77038.t1	Bial9g02658	2658
9	71435942	71447359	-	g77039.t1	Bial9g02659	2659
9	71458498	71461533	+	g77042.t1	Bial9g02662	2662
9	71462724	71466461	-	g77043.t1	Bial9g02663	2663
18	2468336	2469745	-	g121554.t1	Bial18g00162	162
5	1928078	1937486	-	h2tg000038l_1.g23772.t1	Cobi5g00114	114
5	79086925	79087823	-	h2tg000020l_1.g9937.t1	Cobi5g02843	2843
5	79109003	79111037	-	h2tg000020l_1.g9936.t1	Cobi5g02844	2844
5	79113485	79116224	-	h2tg000020l_1.g9935.t1	Cobi5g02845	2845
5	79130104	79133037	+	h2tg000020l_1.g9932.t1	Cobi5g02848	2848
5	79134257	79135196	-	h2tg000020l_1.g9931.t1	Cobi5g02849	2849
5	2369184	2370010	+	h1tg000132l.g124157.t1	Dapi5g00100	100
5	2387399	2389187	+	h1tg000132l.g124158.t1	Dapi5g00101	101
5	2393759	2397588	-	h1tg000132l.g124159.t1	Dapi5g00102	102
5	2408690	2414420	+	h1tg000132l.g124160.t1	Dapi5g00103	103
5	2428073	2430557	+	h1tg000132l.g124161.t1	Dapi5g00104	104
5	2448920	2451083	+	h1tg000132l.g124166.t1	Dapi5g00109	109
5	2454691	2455605	+	h1tg000132l.g124167.t1	Dapi5g00110	110
21	3005471	3006266	+	h1tg000096l.g113414.t1	Dapi21g00148	148
21	3056964	3059847	+	h1tg000096l.g113413.t1	Dapi21g00149	149
21	3065425	3069204	-	h1tg000096l.g113412.t1	Dapi21g00150	150
21	3077919	3087141	+	h1tg000096l.g113411.t1	Dapi21g00151	151
21	3087212	3089689	+	h1tg000096l.g113410.t1	Dapi21g00152	152
21	3098675	3100787	+	h1tg000096l.g113409.t1	Dapi21g00153	153
21	3104323	3105237	+	h1tg000096l.g113408.t1	Dapi21g00154	154
17	193658274	193660058	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831151	Hean17g04511	4511
17	193696461	193706657	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831161	Hean17g04512	4512
17	193705358	193707497	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831171	Hean17g04513	4513
17	193710187	193715340	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831181	Hean17g04514	4514
17	193719960	193725006	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831191	Hean17g04515	4515
17	193728461	193734999	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831201	Hean17g04516	4516
17	193737842	193740050	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831211	Hean17g04517	4517
17	193763896	193768863	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831221	Hean17g04518	4518
17	193807935	193811285	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831251	Hean17g04519	4519
17	193813616	193814802	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831261	Hean17g04520	4520
49	221444394	221445732	-	>Htub.h1tg001001l.g561.t1	Hetu49g03830	3830
49	221450018	221452110	-	>Htub.h1tg001001l.g562.t1	Hetu49g03831	3831
49	221453733	221456849	-	>Htub.h1tg001001l.g563.t1	Hetu49g03832	3832
49	221461281	221464343	-	>Htub.h1tg001001l.g564.t1	Hetu49g03833	3833
49	221472922	221477187	+	>Htub.h1tg001001l.g566.t1	Hetu49g03835	3835
49	221479251	221481352	-	>Htub.h1tg001001l.g567.t1	Hetu49g03836	3836
50	206398449	206399752	-	>Htub.h1tg000531l.g325.t1	Hetu50g03527	3527
50	206404564	206406695	-	>Htub.h1tg000531l.g326.t1	Hetu50g03528	3528
50	206408589	206411647	-	>Htub.h1tg000531l.g327.t1	Hetu50g03529	3529
50	206417460	206423713	-	>Htub.h1tg000531l.g329.t1	Hetu50g03531	3531
50	206426846	206431583	+	>Htub.h1tg000531l.g330.t1	Hetu50g03532	3532
50	206436051	206437711	-	>Htub.h1tg000531l.g331.t1	Hetu50g03533	3533
51	227805486	227806792	-	>Htub.h1tg000558l.g120.t1	Hetu51g03890	3890
51	227811616	227813776	-	>Htub.h1tg000558l.g121.t1	Hetu51g03891	3891
51	227815034	227818060	-	>Htub.h1tg000558l.g122.t1	Hetu51g03892	3892
51	227825810	227828870	-	>Htub.h1tg000558l.g123.t1	Hetu51g03893	3893
51	227840565	227845323	+	>Htub.h1tg000558l.g124.t1	Hetu51g03894	3894
51	227848322	227850375	-	>Htub.h1tg000558l.g125.t1	Hetu51g03895	3895
4	18854838	18856781	+	KAI3818234.1	Smso4g01381	1381
4	18870290	18874424	-	KAI3818235.1	Smso4g01382	1382
4	18877423	18883669	+	KAI3818236.1	Smso4g01383	1383
21	14318752	14321067	+	KAI3731550.1	Smso21g01344	1344
21	14322576	14327012	-	KAI3731551.1	Smso21g01345	1345
21	14368213	14373864	+	KAI3731552.1	Smso21g01346	1346
11	6162725	6163771	-	Streb.11G001940.1	Stre11g00194	194

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