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
Hean17g04451	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04452	.	Bial21g02613	Bial9g02691	.	Dapi21g00097	Hetu50g03617	Hetu51g03984	.	Amtr10g04121	Smso4g01311	Smso21g01277	Taer9g03142	Fro13g00092	Fso12g00091	.	Fra13g00735	Fli9g00091	Stre11g00124	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04453	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04454	.	.	.	.	.	Hetu50g03616	Hetu51g03983	.	.	.	.	.	.	.	.	.	.	Stre11g00125	Mimi2g00065	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04455	.	Bial21g02615	.	.	Dapi21g00099	.	.	.	Amtr10g04122	Smso4g01312	Smso21g01278	Taer9g03141	Fro13g00093	Fso12g00092	Ftr6g00066	Fra13g00734	Fli9g00092	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04456	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04457	.	Bial21g02616	.	.	Dapi21g00100	Hetu50g03615	Hetu51g03982	.	Amtr10g04124	Smso4g01373	Smso21g01279	Taer9g03140	Fro13g00094	Fso12g00093	Ftr6g00067	Fra13g00733	Fli9g00093	Stre11g00132	Mimi2g00067	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04458	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04459	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04460	.	Bial21g02621	.	.	Dapi21g00101	Hetu50g03613	Hetu51g03978	.	Amtr10g04125	Smso4g01314	Smso21g01282	Taer9g03138	Fro13g00095	Fso12g00094	Ftr6g00068	Fra13g00731	Fli9g00095	Stre11g00134	Mimi2g00068	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
10	95850915	95859459	-	AtrifAMIRv0_Chr10g0664951	Amtr10g04121	4121
10	95866747	95872321	-	AtrifAMIRv0_Chr10g0664961	Amtr10g04122	4122
10	95907046	95908164	-	AtrifAMIRv0_Chr10g0664981	Amtr10g04124	4124
10	95935817	95941476	+	AtrifAMIRv0_Chr10g0664991	Amtr10g04125	4125
9	72075995	72081745	+	g77071.t1	Bial9g02691	2691
21	69272557	69278307	+	g62381.t1	Bial21g02613	2613
21	69300812	69305201	-	g62383.t1	Bial21g02615	2615
21	69309289	69310386	-	g62384.t1	Bial21g02616	2616
21	69354983	69361132	+	g62389.t1	Bial21g02621	2621
21	2025024	2032069	-	h1tg000096l.g113465.t1	Dapi21g00097	97
21	2033384	2038064	-	h1tg000096l.g113463.t1	Dapi21g00099	99
21	2062418	2063518	-	h1tg000096l.g113462.t1	Dapi21g00100	100
21	2152654	2157297	+	h1tg000096l.g113461.t1	Dapi21g00101	101
9	1965249	1970414	-	FliAMIRv0_Chr09g0208581	Fli9g00091	91
9	1974261	1984588	-	FliAMIRv0_Chr09g0208591	Fli9g00092	92
9	2004351	2005193	-	FliAMIRv0_Chr09g0208601	Fli9g00093	93
9	2067032	2087029	+	FliAMIRv0_Chr09g0208621	Fli9g00095	95
13	34627200	34631648	-	FraAMIRv0_Chr13g0260391	Fra13g00731	731
13	34651269	34652351	+	FraAMIRv0_Chr13g0260411	Fra13g00733	733
13	34659955	34674855	+	FraAMIRv0_Chr13g0260421	Fra13g00734	734
13	34678284	34683238	+	FraAMIRv0_Chr13g0260431	Fra13g00735	735
13	1219505	1226655	-	FroAMIRv0_Chr13g0222761	Fro13g00092	92
13	1236163	1242489	-	FroAMIRv0_Chr13g0222771	Fro13g00093	93
13	1254161	1255264	-	FroAMIRv0_Chr13g0222781	Fro13g00094	94
13	1273795	1278282	+	FroAMIRv0_Chr13g0222791	Fro13g00095	95
12	1476428	1481454	-	FsoAMIRv0_Chr12g0290561	Fso12g00091	91
12	1487484	1493016	-	FsoAMIRv0_Chr12g0290571	Fso12g00092	92
12	1501050	1502132	-	FsoAMIRv0_Chr12g0290581	Fso12g00093	93
12	1521958	1526462	+	FsoAMIRv0_Chr12g0290591	Fso12g00094	94
6	785464	789178	-	FtrAMIRv0_Chr06g0162161	Ftr6g00066	66
6	798296	799378	-	FtrAMIRv0_Chr06g0162171	Ftr6g00067	67
6	813626	818045	+	FtrAMIRv0_Chr06g0162181	Ftr6g00068	68
17	191679496	191681406	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830321	Hean17g04451	4451
17	191681616	191695059	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830331	Hean17g04452	4452
17	191682138	191685007	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830341	Hean17g04453	4453
17	191699931	191700697	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830351	Hean17g04454	4454
17	191746913	191765248	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830411	Hean17g04455	4455
17	191759287	191760258	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830421	Hean17g04456	4456
17	191800799	191802125	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830431	Hean17g04457	4457
17	191803917	191804934	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830441	Hean17g04458	4458
17	191810224	191813724	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830451	Hean17g04459	4459
17	191844104	191854228	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0830461	Hean17g04460	4460
50	209636579	209641734	-	>Htub.h1tg000531l.g415.t1	Hetu50g03613	3613
50	209715938	209717029	-	>Htub.h1tg000531l.g417.t1	Hetu50g03615	3615
50	209949817	209960807	+	>Htub.h1tg000531l.g418.t1	Hetu50g03616	3616
50	209979410	209991062	+	>Htub.h1tg000531l.g419.t1	Hetu50g03617	3617
51	230807147	230812252	-	>Htub.h1tg000558l.g210.t1	Hetu51g03978	3978
51	230875207	230876316	-	>Htub.h1tg000558l.g214.t1	Hetu51g03982	3982
51	230965846	230978671	+	>Htub.h1tg000558l.g215.t1	Hetu51g03983	3983
51	230992816	231003569	+	>Htub.h1tg000558l.g216.t1	Hetu51g03984	3984
2	1833927	1856112	-	KAD7116481.1	Mimi2g00065	65
2	1884856	1885964	-	KAD7116483.1	Mimi2g00067	67
2	1948164	1957905	+	KAD7116484.1	Mimi2g00068	68
4	17592803	17598037	-	KAI3818164.1	Smso4g01311	1311
4	17607295	17614922	-	KAI3818165.1	Smso4g01312	1312
4	17643391	17648766	+	KAI3818167.1	Smso4g01314	1314
4	18636272	18636644	-	KAI3818226.1	Smso4g01373	1373
21	13391929	13400217	-	KAI3731483.1	Smso21g01277	1277
21	13402867	13408495	-	KAI3731484.1	Smso21g01278	1278
21	13411453	13412553	-	KAI3731485.1	Smso21g01279	1279
21	13448185	13453257	+	KAI3731488.1	Smso21g01282	1282
11	3451199	3456827	-	Streb.11G001240.1	Stre11g00124	124
11	3459536	3464180	-	Streb.11G001250.1	Stre11g00125	125
11	3568354	3569463	-	Streb.11G001320.1	Stre11g00132	132
11	3621118	3628022	+	Streb.11G001340.1	Stre11g00134	134
9	31444993	31449059	-	>KAK1413774.1	Taer9g03138	3138
9	31458018	31459100	+	>KAK1413775.1	Taer9g03140	3140
9	31467055	31472957	+	>KAK1413776.1	Taer9g03141	3141
9	31474705	31480356	+	>KAK1413777.1	Taer9g03142	3142

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