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
Hean1g00381	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00382	.	.	.	Dapi4g02023	.	Hetu1g00374	Hetu2g00330	Hetu3g00335	Amtr12g00930	.	.	.	Fro14g01428	Fso1g02308	.	Fra18g01581	Fli3g00574	.	Mimi16g02255	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00383	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00384	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00385	.	Bial10g01462	.	.	.	Hetu1g00375	.	Hetu3g00336	Amtr12g00931	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00386	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00387	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00388	.	Bial10g01464	.	Dapi4g02024	.	Hetu1g00376	Hetu2g00333	Hetu3g00337	.	.	.	Taer4g02604	.	Fso1g02309	.	Fra18g01582	Fli3g00572	.	Mimi16g02268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00389	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00390	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
12	25164966	25165684	+	AtrifAMIRv0_Chr12g0726621	Amtr12g00930	930
12	25169298	25169881	+	AtrifAMIRv0_Chr12g0726631	Amtr12g00931	931
10	14847750	14850072	+	g86707.t1	Bial10g01462	1462
10	14858166	14858489	+	g86705.t1	Bial10g01464	1464
4	122006556	122007028	+	h1tg000411l.g140572.t1	Dapi4g02023	2023
4	122013762	122014095	+	h1tg000411l.g140571.t1	Dapi4g02024	2024
3	14164488	14164833	-	FliAMIRv0_Chr03g0078411	Fli3g00572	572
3	14234705	14235051	-	FliAMIRv0_Chr03g0078431	Fli3g00574	574
18	61214126	61214428	+	FraAMIRv0_Chr18g0357781	Fra18g01581	1581
18	61229712	61230326	+	FraAMIRv0_Chr18g0357791	Fra18g01582	1582
14	22601314	22601921	+	FroAMIRv0_Chr14g0255821	Fro14g01428	1428
1	64863748	64870196	+	FsoAMIRv0_Chr01g0023071	Fso1g02308	2308
1	64889956	64890509	+	FsoAMIRv0_Chr01g0023081	Fso1g02309	2309
1	10950077	10951305	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004281	Hean1g00381	381
1	10987330	10988019	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004291	Hean1g00382	382
1	11015346	11017353	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004301	Hean1g00383	383
1	11055447	11056700	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004311	Hean1g00384	384
1	11068549	11069321	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004321	Hean1g00385	385
1	11115339	11117113	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004331	Hean1g00386	386
1	11205301	11205742	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004341	Hean1g00387	387
1	11210482	11211065	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004351	Hean1g00388	388
1	11218109	11220375	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004361	Hean1g00389	389
1	11228009	11232332	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004371	Hean1g00390	390
1	16786659	16787049	+	>Htub.h1tg001740l.g127.t1	Hetu1g00374	374
1	16841356	16846026	+	>Htub.h1tg001740l.g128.t1	Hetu1g00375	375
1	16909706	16910009	+	>Htub.h1tg001740l.g129.t1	Hetu1g00376	376
2	12844144	12844467	+	>Htub.h2tg001774l.g140.t1	Hetu2g00330	330
2	13517624	13518515	+	>Htub.h2tg001774l.g137.t1	Hetu2g00333	333
3	14037109	14037499	+	>Htub.h1tg001937l.g29.t1	Hetu3g00335	335
3	14071901	14072381	+	>Htub.h1tg001937l.g28.t1	Hetu3g00336	336
3	14092733	14093713	+	>Htub.h1tg001937l.g27.t1	Hetu3g00337	337
16	86424723	86425055	+	KAD3338325.1	Mimi16g02255	2255
16	86675887	86677709	+	KAD3338338.1	Mimi16g02268	2268
4	57058370	57058755	+	>KAK1428381.1	Taer4g02604	2604

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