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
Hean1g00541	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00542	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00543	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00544	Cobi2g02034	Bial10g01105	.	Dapi4g01572	Dapi20g01485	Hetu1g01699	Hetu2g01492	Hetu3g01525	Amtr02g09079	.	Smso28g00627	.	Fro14g01000	Fso1g01515	.	.	Fli3g01125	Stre1g04097	Mimi16g01835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00545	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00546	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00547	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00548	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00549	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean1g00550	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
2	178843124	178855788	-	AtrifAMIRv0_Chr02g0186751	Amtr02g09079	9079
10	11126508	11137067	-	g87064.t1	Bial10g01105	1105
2	63078316	63082170	-	h2tg000016l_1.g5212.t1	Cobi2g02034	2034
4	95055961	95059869	-	h2tg000160l.g57157.t1	Dapi4g01572	1572
20	86969705	86981300	-	h2tg000075l.g16855.t1	Dapi20g01485	1485
3	40639826	40643755	+	FliAMIRv0_Chr03g0083941	Fli3g01125	1125
14	15177193	15181185	-	FroAMIRv0_Chr14g0251541	Fro14g01000	1000
1	40894539	40895822	-	FsoAMIRv0_Chr01g0015141	Fso1g01515	1515
1	24960573	24961261	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006071	Hean1g00541	541
1	25161068	25162370	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006091	Hean1g00542	542
1	26612982	26617919	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006111	Hean1g00543	543
1	26901016	26915221	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006121	Hean1g00544	544
1	26902128	26903734	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006131	Hean1g00545	545
1	27186092	27190013	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006141	Hean1g00546	546
1	27289920	27296641	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006151	Hean1g00547	547
1	27299199	27299525	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006161	Hean1g00548	548
1	27307020	27308311	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006171	Hean1g00549	549
1	27553923	27554350	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr01g0006201	Hean1g00550	550
1	94129775	94134403	+	>Htub.h1tg003037l.g331.t1	Hetu1g01699	1699
2	84141647	84145897	+	>Htub.h1tg000510l.g143.t1	Hetu2g01492	1492
3	86801315	86805565	+	>Htub.h1tg003659l.g273.t1	Hetu3g01525	1525
16	78253360	78257277	-	KAD3337905.1	Mimi16g01835	1835
28	23682620	23687270	+	KAI3682907.1	Smso28g00627	627
1	125962610	125969336	-	Streb.1G040970.1	Stre1g04097	4097

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