Hierarchical alignments with the <em>Euptelea pleiosperma</em> genome as reference

Gene Search

Species

Gene ID

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Or, Query Sequence

Example:

Hierarchical alignments with the Euptelea pleiosperma genome as reference

Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Asteraceae genomes. We used Euptelea pleiosperma as a reference, and by comparing homologous gene locus maps and Ks values between Euptelea pleiosperma and other Asteraceae, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We constructed a 25×25,104 macro-matrices.

Query Sequence

Or, Gene ID

Species

Eupl_1	Eupl_2	Nenu_1	Nenu_2	Tesi_1	Tesi_2	Tesi_3	Tesi_4	Busi_1	Busi_2	Vivi_1	Vivi_2	Vivi_3	Nin_1	Nin_2	Nin_3	Arla_1	Arla_2	Arla_3	Arla_4	Arla_5	Arla_6	Arla_7	Arla_8	Arla_9
Eupl14g01200	Eupl8g00937	Nenu1g00465	Nenu6g00972	.	Tesi1g00795	Tesi21g00748	.	Busi12g00410	.	Vivi15g00280	.	.	.	.	.	.	Arla10g00811	Arla5g00919	.	.	.	.	.	.
Eupl14g01201	Eupl8g00939	Nenu1g00463	Nenu6g00969	.	Tesi1g00794	Tesi21g00750	.	.	.	Vivi15g00278	.	.	.	.	Nin5g00128	.	Arla11g00259	Arla5g00917	.	.	.	.	.	.
Eupl14g01202	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Eupl14g01203	Eupl8g00943	Nenu1g00458	Nenu6g00965	Tesi1g00439	Tesi1g00793	Tesi21g00751	.	.	.	Vivi15g00276	.	.	.	.	.	.	Arla10g00808	.	.	.	.	.	.	.
Eupl14g01204	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Eupl14g01205	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Eupl14g01206	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Eupl14g01207	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Eupl14g01208	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Nin5g00308	.	.	.	.	.	.	.	.	.
Eupl14g01209	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
5	24322659	24324578	-	evm.model.000083F.51	Arla5g00917	917
5	24350590	24362571	-	evm.model.000083F.49	Arla5g00919	919
10	58682731	58697057	+	evm.model.000081F.300	Arla10g00808	808
10	58769030	58774380	-	evm.model.000081F.304.1	Arla10g00811	811
11	8853111	8867208	+	evm.model.000128F.16	Arla11g00259	259
12	19283337	19290162	-	BUSI_022957-RA	Busi12g00410	410
8	26388496	26396320	+	evm.model.CTG_282.106.2	Eupl8g00937	937
8	26427504	26431994	-	evm.model.CTG_282.108	Eupl8g00939	939
8	26519627	26558592	-	evm.model.CTG_282.114.2	Eupl8g00943	943
14	26311149	26327519	-	evm.model.CTG_64.3	Eupl14g01200	1200
14	26333089	26337428	-	evm.model.CTG_64.4	Eupl14g01201	1201
14	26352344	26352904	+	evm.model.CTG_64.5	Eupl14g01202	1202
14	26388485	26407848	+	evm.model.CTG_64.6	Eupl14g01203	1203
14	26436649	26437824	+	evm.model.CTG_64.9	Eupl14g01204	1204
14	26438575	26441223	-	evm.model.CTG_64.10	Eupl14g01205	1205
14	26451476	26453293	+	evm.model.CTG_64.11	Eupl14g01206	1206
14	26469056	26490153	+	evm.model.CTG_64.14	Eupl14g01207	1207
14	26491838	26515093	-	evm.model.CTG_64.15	Eupl14g01208	1208
14	26530034	26531650	-	evm.model.CTG_64.16	Eupl14g01209	1209
1	12892420	12904676	+	OF09760.mRNA1	Nenu1g00458	458
1	12944696	12954001	+	OF09765.mRNA1	Nenu1g00463	463
1	12990558	13009622	-	OF09767.mRNA1	Nenu1g00465	465
6	34736477	34769580	+	OF11179.mRNA1	Nenu6g00965	965
6	34804474	34814385	+	OF11175.mRNA1	Nenu6g00969	969
6	34871068	34888401	-	OF11172.mRNA1	Nenu6g00972	972
5	1206492	1209585	-	NinS12941.t1	Nin5g00128	128
5	3390683	3403407	+	NinS13121.t1	Nin5g00308	308
1	8805673	8822697	-	Tesin01G0046900.1	Tesi1g00439	439
1	17507639	17515188	+	Tesin01G0083900.1	Tesi1g00793	793
1	17532333	17535810	+	Tesin01G0084000.1	Tesi1g00794	794
1	17546232	17572233	-	Tesin01G0084100.1	Tesi1g00795	795
21	16688491	16692606	+	Tesin21G0081500.1	Tesi21g00748	748
21	16702104	16713049	-	Tesin21G0081700.1	Tesi21g00750	750
21	16784929	16801140	-	Tesin21G0081900.1	Tesi21g00751	751
15	10933762	10942754	+	GSVIVT01018330001	Vivi15g00276	276
15	10984269	10987338	+	GSVIVT01018328001	Vivi15g00278	278
15	11003261	11012492	-	GSVIVT01018326001	Vivi15g00280	280

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