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
Hean1g00631	.	.	.	.	.	Hetu1g01626	Hetu2g01397	Hetu3g01413	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00632	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00633	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00634	.	.	.	Dapi4g01654	Dapi20g01581	Hetu1g01621	Hetu2g01396	Hetu3g01411	Amtr02g08796	.	.	.	.	.	.	.	.	Stre1g04138	Mimi16g01888	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00635	.	.	Bial22g00749	.	.	Hetu1g01620	Hetu2g01394	Hetu3g01410	Amtr02g08791	.	.	.	.	.	.	.	.	.	Mimi16g01891	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00636	Cobi2g02075	Bial10g01145	Bial22g00750	Dapi4g01656	Dapi20g01582	Hetu1g01614	Hetu2g01391	Hetu3g01407	Amtr02g08786	Smso1g03430	Smso28g00592	Taer4g01899	Fro14g01089	Fso1g01723	Ftr2g01251	.	Fli3g01036	Stre1g04139	Mimi16g01892	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00637	Cobi2g02076	Bial10g01146	Bial22g00751	Dapi4g01657	Dapi20g01583	Hetu1g01613	.	Hetu3g01406	Amtr02g08785	.	Smso28g00591	.	.	.	.	.	.	Stre1g04140	Mimi16g01893	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00638	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00639	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00640	.	Bial10g01147	Bial22g00752	Dapi4g01662	Dapi20g01588	Hetu1g01612	Hetu2g01389	Hetu3g01405	Amtr02g08775	Smso1g03431	Smso28g00590	.	Fro14g01093	.	.	Fra18g01463	Fli3g01033	Stre1g04141	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
2	170825268	170839389	+	AtrifAMIRv0_Chr02g0183711	Amtr02g08775	8775
2	170993331	170996242	-	AtrifAMIRv0_Chr02g0183811	Amtr02g08785	8785
2	171000567	171001604	-	AtrifAMIRv0_Chr02g0183821	Amtr02g08786	8786
2	171151697	171152125	+	AtrifAMIRv0_Chr02g0183871	Amtr02g08791	8791
2	171226410	171226832	+	AtrifAMIRv0_Chr02g0183921	Amtr02g08796	8796
10	11440518	11441525	-	g87024.t1	Bial10g01145	1145
10	11442846	11445377	+	g87023.t1	Bial10g01146	1146
10	11454647	11466774	-	g87022.t1	Bial10g01147	1147
22	7161028	7161465	-	g147285.t1	Bial22g00749	749
22	7176436	7177443	-	g147284.t1	Bial22g00750	750
22	7178425	7182801	+	g147283.t1	Bial22g00751	751
22	7212540	7226132	-	g147282.t1	Bial22g00752	752
2	64396565	64397572	-	h2tg000016l_1.g5171.t1	Cobi2g02075	2075
2	64488772	64491352	+	h2tg000016l_1.g5170.t1	Cobi2g02076	2076
4	102399177	102399611	-	h2tg000160l.g57239.t1	Dapi4g01654	1654
4	102501993	102503021	-	h2tg000160l.g57241.t1	Dapi4g01656	1656
4	102509116	102513147	+	h2tg000160l.g57242.t1	Dapi4g01657	1657
4	102578961	102593455	-	h2tg000160l.g57247.t1	Dapi4g01662	1662
20	94101714	94102148	-	h2tg000075l.g16951.t1	Dapi20g01581	1581
20	94197520	94198548	-	h2tg000075l.g16952.t1	Dapi20g01582	1582
20	94253916	94257779	+	h2tg000075l.g16953.t1	Dapi20g01583	1583
20	94306008	94320533	-	h2tg000075l.g16958.t1	Dapi20g01588	1588
3	32448885	32465797	+	FliAMIRv0_Chr03g0083021	Fli3g01033	1033
3	32536336	32537358	+	FliAMIRv0_Chr03g0083051	Fli3g01036	1036
18	58441738	58455389	-	FraAMIRv0_Chr18g0356601	Fra18g01463	1463
14	17231519	17232532	-	FroAMIRv0_Chr14g0252431	Fro14g01089	1089
14	17273113	17291494	-	FroAMIRv0_Chr14g0252471	Fro14g01093	1093
1	49940741	49941508	-	FsoAMIRv0_Chr01g0017221	Fso1g01723	1723
2	33187863	33188186	+	FtrAMIRv0_Chr02g0041181	Ftr2g01251	1251
1	32326890	32329372	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0007131	Hean1g00631	631
1	32326950	32329358	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0007141	Hean1g00632	632
1	32412343	32412867	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0007151	Hean1g00633	633
1	32446463	32446903	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0007161	Hean1g00634	634
1	32533388	32533825	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0007171	Hean1g00635	635
1	32648631	32650010	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0007181	Hean1g00636	636
1	32652430	32656163	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0007191	Hean1g00637	637
1	32668263	32669236	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0007211	Hean1g00638	638
1	32707694	32727987	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0007221	Hean1g00639	639
1	32719333	32738231	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0007231	Hean1g00640	640
1	87481687	87497705	+	>Htub.h1tg001922l.g336.t1	Hetu1g01612	1612
1	87731246	87734672	-	>Htub.h1tg001922l.g337.t1	Hetu1g01613	1613
1	87786096	87787100	+	>Htub.h1tg001922l.g338.t1	Hetu1g01614	1614
1	88028487	88028924	+	>Htub.h1tg001922l.g344.t1	Hetu1g01620	1620
1	88219973	88220413	+	>Htub.h1tg001922l.g346.t1	Hetu1g01621	1621
1	88455657	88456595	+	>Htub.h1tg001922l.g351.t1	Hetu1g01626	1626
2	78017357	78033377	+	>Htub.h1tg000330l.g380.t1	Hetu2g01389	1389
2	78261058	78262724	+	>Htub.h1tg000330l.g377.t1	Hetu2g01391	1391
2	78532821	78533258	+	>Htub.h1tg000330l.g374.t1	Hetu2g01394	1394
2	78721605	78722045	+	>Htub.h1tg000330l.g371.t1	Hetu2g01396	1396
2	79015017	79015955	+	>Htub.h1tg000330l.g370.t1	Hetu2g01397	1397
3	76621649	76636854	+	>Htub.h1tg000150l.g87.t1	Hetu3g01405	1405
3	76733467	76736103	-	>Htub.h1tg000150l.g86.t1	Hetu3g01406	1406
3	76738855	76740030	+	>Htub.h1tg000150l.g85.t1	Hetu3g01407	1407
3	76814747	76815139	+	>Htub.h1tg000150l.g82.t1	Hetu3g01410	1410
3	77211338	77211736	+	>Htub.h1tg000150l.g81.t1	Hetu3g01411	1411
3	77233609	77237575	+	>Htub.h1tg000150l.g79.t1	Hetu3g01413	1413
16	79212643	79218699	-	KAD3337958.1	Mimi16g01888	1888
16	79261307	79261828	-	KAD3337961.1	Mimi16g01891	1891
16	79272235	79273161	-	KAD3337962.1	Mimi16g01892	1892
16	79275467	79277629	+	KAD3337963.1	Mimi16g01893	1893
1	117395413	117396630	-	KAI3829393.1	Smso1g03430	3430
1	117421245	117436200	-	KAI3829394.1	Smso1g03431	3431
28	19963287	19975635	+	KAI3682870.1	Smso28g00590	590
28	19994359	20002795	-	KAI3682871.1	Smso28g00591	591
28	20004470	20005480	+	KAI3682872.1	Smso28g00592	592
1	126508005	126508442	-	Streb.1G041380.1	Stre1g04138	4138
1	126513202	126514807	-	Streb.1G041390.1	Stre1g04139	4139
1	126516483	126519507	+	Streb.1G041400.1	Stre1g04140	4140
1	126521672	126542002	-	Streb.1G041410.1	Stre1g04141	4141
4	19422190	19423176	+	>KAK1427814.1	Taer4g01899	1899

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