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
Hean1g00401	.	.	.	Dapi4g02026	.	Hetu1g00385	.	.	.	.	.	Taer4g02608	Fro14g01431	Fso1g02312	Ftr2g00477	Fra18g01586	Fli3g00570	.	Mimi16g02271	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00402	.	.	.	.	.	Hetu1g00390	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00404	.	.	.	.	.	Hetu1g00391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00405	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00406	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00407	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00408	.	.	.	.	.	.	.	.	.	.	.	.	Fro14g01434	Fso1g02317	.	.	Fli3g00564	.	Mimi16g02272	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00409	.	.	.	.	.	.	Hetu2g00423	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00410	.	.	.	.	.	.	Hetu2g00422	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
4	122111217	122111519	+	h1tg000140l.g125041.t1	Dapi4g02026	2026
3	13920115	13920427	+	FliAMIRv0_Chr03g0078331	Fli3g00564	564
3	14044870	14045170	-	FliAMIRv0_Chr03g0078391	Fli3g00570	570
18	61263827	61264119	+	FraAMIRv0_Chr18g0357831	Fra18g01586	1586
14	22619051	22619339	+	FroAMIRv0_Chr14g0255851	Fro14g01431	1431
14	22650622	22650910	-	FroAMIRv0_Chr14g0255881	Fro14g01434	1434
1	64929401	64929716	+	FsoAMIRv0_Chr01g0023111	Fso1g02312	2312
1	65003720	65004009	-	FsoAMIRv0_Chr01g0023161	Fso1g02317	2317
2	7560057	7560372	-	FtrAMIRv0_Chr02g0033441	Ftr2g00477	477
1	11355272	11355967	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004491	Hean1g00401	401
1	11374115	11374832	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004501	Hean1g00402	402
1	11406659	11411784	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004511	Hean1g00403	403
1	11406805	11407288	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004521	Hean1g00404	404
1	11412416	11412710	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004531	Hean1g00405	405
1	11423123	11423748	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004541	Hean1g00406	406
1	11423190	11447840	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004551	Hean1g00407	407
1	11447334	11447999	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004561	Hean1g00408	408
1	11864500	11865983	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004581	Hean1g00409	409
1	11869829	11881047	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0004591	Hean1g00410	410
1	17142015	17142354	+	>Htub.h1tg001740l.g138.t1	Hetu1g00385	385
1	19001383	19002397	+	>Htub.h1tg001740l.g144.t1	Hetu1g00390	390
1	19152017	19152631	+	>Htub.h1tg001740l.g145.t1	Hetu1g00391	391
2	19573634	19583947	+	>Htub.h2tg000910l.g246.t1	Hetu2g00422	422
2	19590023	19591141	-	>Htub.h2tg000910l.g245.t1	Hetu2g00423	423
16	86781241	86782109	+	KAD3338341.1	Mimi16g02271	2271
16	86787465	86788026	+	KAD3338342.1	Mimi16g02272	2272
4	57109083	57109397	+	>KAK1428385.1	Taer4g02608	2608

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