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
Hean17g04491	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04492	Cobi5g02863	.	Bial9g02681	Dapi5g00089	Dapi21g00136	Hetu50g03567	Hetu51g03933	Hetu49g03860	Amtr10g04195	Smso4g01365	Smso21g01329	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04493	Cobi5g02861	.	Bial9g02679	Dapi5g00091	.	.	Hetu51g03931	.	Amtr10g04197	Smso4g01367	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04494	.	.	.	Dapi5g00092	Dapi21g00139	Hetu50g03565	Hetu51g03929	.	Amtr10g04198	Smso4g01368	Smso21g01332	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04495	Cobi5g02860	.	Bial9g02678	Dapi5g00093	Dapi21g00140	Hetu50g03550	Hetu51g03918	Hetu49g03852	Amtr10g04199	Smso4g01369	Smso21g01333	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04496	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04497	Cobi5g02859	.	Bial9g02677	Dapi5g00094	Dapi21g00141	Hetu50g03547	Hetu51g03913	Hetu49g03851	Amtr10g04200	Smso4g01370	Smso21g01334	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04498	.	.	.	.	.	Hetu50g03546	Hetu51g03910	Hetu49g03850	Amtr10g04202	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04499	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04500	Cobi5g02858	.	Bial9g02671	Dapi5g00095	Dapi21g00142	.	.	.	Amtr10g04205	Smso4g01371	Smso21g01336	Taer9g03102	Fro13g00125	Fso12g00124	Ftr6g00094	Fra13g00703	Fli9g00134	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
10	97675986	97676288	-	AtrifAMIRv0_Chr10g0665691	Amtr10g04195	4195
10	97695025	97695474	-	AtrifAMIRv0_Chr10g0665711	Amtr10g04197	4197
10	97702268	97703460	-	AtrifAMIRv0_Chr10g0665721	Amtr10g04198	4198
10	97709180	97714588	-	AtrifAMIRv0_Chr10g0665731	Amtr10g04199	4199
10	97716706	97720158	-	AtrifAMIRv0_Chr10g0665741	Amtr10g04200	4200
10	97796672	97800675	+	AtrifAMIRv0_Chr10g0665761	Amtr10g04202	4202
10	97869177	97874195	-	AtrifAMIRv0_Chr10g0665791	Amtr10g04205	4205
9	71670182	71676582	+	g77051.t1	Bial9g02671	2671
9	71783166	71786451	+	g77057.t1	Bial9g02677	2677
9	71788000	71792316	+	g77058.t1	Bial9g02678	2678
9	71804082	71804675	+	g77059.t1	Bial9g02679	2679
9	71809861	71810163	+	g77061.t1	Bial9g02681	2681
5	79247759	79255337	+	h2tg000020l_1.g9922.t1	Cobi5g02858	2858
5	79272567	79276310	+	h2tg000020l_1.g9921.t1	Cobi5g02859	2859
5	79277330	79281545	+	h2tg000020l_1.g9920.t1	Cobi5g02860	2860
5	79290654	79291241	+	h2tg000020l_1.g9919.t1	Cobi5g02861	2861
5	79296624	79296926	+	h2tg000020l_1.g9917.t1	Cobi5g02863	2863
5	2116817	2121619	-	h1tg000132l.g124146.t1	Dapi5g00089	89
5	2133049	2133555	-	h1tg000132l.g124148.t1	Dapi5g00091	91
5	2134905	2136086	-	h1tg000132l.g124149.t1	Dapi5g00092	92
5	2138895	2141660	-	h1tg000132l.g124150.t1	Dapi5g00093	93
5	2142719	2146495	-	h1tg000132l.g124151.t1	Dapi5g00094	94
5	2201682	2206740	+	h1tg000132l.g124152.t1	Dapi5g00095	95
21	2816060	2816362	-	h1tg000096l.g113426.t1	Dapi21g00136	136
21	2830612	2833119	-	h1tg000096l.g113423.t1	Dapi21g00139	139
21	2839933	2842745	-	h1tg000096l.g113422.t1	Dapi21g00140	140
21	2844349	2849862	-	h1tg000096l.g113421.t1	Dapi21g00141	141
21	2876574	2881326	+	h1tg000096l.g113420.t1	Dapi21g00142	142
9	2911613	2916857	+	FliAMIRv0_Chr09g0209011	Fli9g00134	134
13	34267863	34278169	-	FraAMIRv0_Chr13g0260111	Fra13g00703	703
13	1654946	1661384	+	FroAMIRv0_Chr13g0223091	Fro13g00125	125
12	2000692	2004060	+	FsoAMIRv0_Chr12g0290891	Fso12g00124	124
6	1220057	1225477	+	FtrAMIRv0_Chr06g0162441	Ftr6g00094	94
17	193072350	193073791	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830861	Hean17g04491	4491
17	193108626	193109787	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830871	Hean17g04492	4492
17	193114291	193115061	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830881	Hean17g04493	4493
17	193119511	193122579	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830891	Hean17g04494	4494
17	193136274	193138724	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830901	Hean17g04495	4495
17	193139545	193139871	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830911	Hean17g04496	4496
17	193140841	193144329	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830921	Hean17g04497	4497
17	193170174	193174398	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830931	Hean17g04498	4498
17	193170239	193170980	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830941	Hean17g04499	4499
17	193262356	193268851	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830961	Hean17g04500	4500
49	222336497	222337916	-	>Htub.h1tg001001l.g582.t1	Hetu49g03850	3850
49	222415394	222419946	+	>Htub.h1tg001001l.g583.t1	Hetu49g03851	3851
49	222423892	222425592	+	>Htub.h1tg001001l.g584.t1	Hetu49g03852	3852
49	222654242	222654544	+	>Htub.h1tg001001l.g593.t1	Hetu49g03860	3860
50	207031791	207041063	-	>Htub.h1tg000531l.g346.t1	Hetu50g03546	3546
50	207061938	207065085	+	>Htub.h1tg000531l.g347.t1	Hetu50g03547	3547
50	207089002	207096231	+	>Htub.h1tg000531l.g350.t1	Hetu50g03550	3550
50	207728030	207730725	+	>Htub.h1tg000531l.g366.t1	Hetu50g03565	3565
50	207747311	207748373	+	>Htub.h1tg000531l.g368.t1	Hetu50g03567	3567
51	228597659	228599920	-	>Htub.h1tg000558l.g141.t1	Hetu51g03910	3910
51	228655030	228668779	+	>Htub.h1tg000558l.g144.t1	Hetu51g03913	3913
51	228751341	228752988	+	>Htub.h1tg000558l.g149.t1	Hetu51g03918	3918
51	229208843	229211530	+	>Htub.h1tg000558l.g160.t1	Hetu51g03929	3929
51	229219947	229220411	+	>Htub.h1tg000558l.g162.t1	Hetu51g03931	3931
51	229225270	229225728	+	>Htub.h1tg000558l.g164.t1	Hetu51g03933	3933
4	18530425	18530859	-	KAI3818218.1	Smso4g01365	1365
4	18539361	18539819	-	KAI3818220.1	Smso4g01367	1367
4	18546406	18549437	-	KAI3818221.1	Smso4g01368	1368
4	18549658	18552778	-	KAI3818222.1	Smso4g01369	1369
4	18553991	18558915	-	KAI3818223.1	Smso4g01370	1370
4	18583589	18588757	-	KAI3818224.1	Smso4g01371	1371
21	14080725	14081027	-	KAI3731535.1	Smso21g01329	1329
21	14117353	14119619	-	KAI3731538.1	Smso21g01332	1332
21	14120965	14123218	-	KAI3731539.1	Smso21g01333	1333
21	14125295	14129771	-	KAI3731540.1	Smso21g01334	1334
21	14164671	14169021	-	KAI3731542.1	Smso21g01336	1336
9	31131536	31134346	-	>KAK1413740.1	Taer9g03102	3102

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