Hierarchical alignments with the <em>Arctium lappa</em> genome as reference

Gene Search

Species

Gene ID

Example:

Or, Query Sequence

Example:

Hierarchical alignments with the Arctium lappa genome as reference

Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Asteraceae genomes. We used Arctium lappa as a reference, and by comparing homologous gene locus maps and Ks values between Arctium lappa and other Asteraceae, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We constructed a 74×31,441 macro-matrices.

Query Sequence

Or, Gene ID

Species

Armi_1	Sain_1	Ceso_1	Cati_1	Ccar_1	Cien_1	Cich_1	Lssa_1	Laca_1	Tako_1	Tamo_1	Pslu_1	Lomi_1	Lomi_2	Enbr_1	Ecan_1	Soca_1	Glco_1	Artr_1	Aary_1	Aary_2	Aann_1	Chma_1	Chmo_1	Chmo_2	Chmo_3	Chla_1	Chna_1	Cind_1	Pdy_1	Cobi_1	Hean_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	Cobi_2	Hean_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
.	Sain12g00254	.	.	Ccar2g02120	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
.	Sain12g00256	.	Cati3g00303	Ccar2g02119	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Armi1g00269	Sain12g00257	.	Cati3g00304	.	.	.	.	.	.	.	.	.	Lomi2g04088	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Armi1g00270	Sain12g00258	Ceso2g03347	Cati3g00305	Ccar2g02118	.	.	.	.	.	.	Pslu1g06610	Lomi1g00540	Lomi2g04087	.	.	.	.	.	.	.	.	.	Chmo13g01399	Chmo14g01252	Chmo15g01229	.	Chna2g01210	Cind3g00565	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Armi1g00271	Sain12g00259	.	Cati3g00306	Ccar2g02117	.	.	.	.	.	.	Pslu1g06611	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Chna2g01211	Cind3g00566	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Chmo13g01400	Chmo14g01253	Chmo15g01230	.	Chna2g01212	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Armi1g00273	Sain12g00262	.	Cati3g00308	.	Cien5g03416	Cich4g04709	Lssa7g03671	Laca7g02982	Tako4g03656	.	Pslu1g20978	.	.	.	Ecan3g02327	Soca5g02273	Glco3g01355	Artr3g11129	.	.	Aann4g00936	Chma7g07771	Chmo13g00948	Chmo14g00900	Chmo15g00838	Chla6g05568	Chna2g00801	Cind3g05598	Pdy4g00712	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Chna2g00800	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
4	55182383	55184084	-	chr4g0771041	Aann4g00936	936
1	4826607	4827670	+	AmiAMIRv0_Chr01g0002691	Armi1g00269	269
1	4831686	4832813	+	AmiAMIRv0_Chr01g0002701	Armi1g00270	270
1	4833809	4834123	-	AmiAMIRv0_Chr01g0002711	Armi1g00271	271
1	4850603	4850947	-	AmiAMIRv0_Chr01g0002731	Armi1g00273	273
3	375655510	375655866	-	AtridAMIRv0_Chr03g0418651	Artr3g11129	11129
3	2443620	2445568	-	CtAH03T0020500.1	Cati3g00303	303
3	2447872	2448318	+	CtAH03T0020600.1	Cati3g00304	304
3	2451489	2455832	+	CtAH03T0020700.1	Cati3g00305	305
3	2455982	2456335	-	CtAH03T0020800.1	Cati3g00306	306
3	2471342	2471686	-	CtAH03T0021000.1	Cati3g00308	308
2	68431627	68431953	+	gnl\|WGS:LEKV\|Ccrd_011166.mRNA.1_mrna	Ccar2g02117	2117
2	68432740	68442194	-	gnl\|WGS:LEKV\|Ccrd_011167.mRNA.1_mrna	Ccar2g02118	2118
2	68441141	68443675	+	gnl\|WGS:LEKV\|Ccrd_011168.mRNA.1_mrna	Ccar2g02119	2119
2	68448969	68449611	+	gnl\|WGS:LEKV\|Ccrd_011169.mRNA.1_mrna	Ccar2g02120	2120
2	83340931	83343001	+	>KAJ9562753.1	Ceso2g03347	3347
6	220121399	220121704	-	ClaG1_Chr06g0428151	Chla6g05568	5568
7	266184021	266184371	-	CmaNakai_Chr07g0700731	Chma7g07771	7771
13	49490616	49490966	+	evm.model.scaffold_191.209	Chmo13g00948	948
13	72724278	72726322	+	evm.model.scaffold_10346.66	Chmo13g01399	1399
13	72768698	72770905	+	evm.model.scaffold_10346.64	Chmo13g01400	1400
14	43790435	43790785	+	evm.model.scaffold_25.278	Chmo14g00900	900
14	65567742	65569859	+	evm.model.scaffold_1182.173	Chmo14g01252	1252
14	65625196	65627415	+	evm.model.scaffold_1182.176	Chmo14g01253	1253
15	48129515	48129865	+	evm.model.scaffold_1806.396	Chmo15g00838	838
15	71005277	71006528	+	evm.model.scaffold_969.245	Chmo15g01229	1229
15	71118868	71121088	+	evm.model.scaffold_969.243	Chmo15g01230	1230
2	60756744	60760348	-	Cn0026160	Chna2g00800	800
2	60982314	60982664	+	Cn0026180	Chna2g00801	801
2	98235331	98236701	+	Cn0678140	Chna2g01210	1210
2	98237529	98237864	-	Cn0678130	Chna2g01211	1211
2	98254818	98256896	+	Cn0678120	Chna2g01212	1212
4	135357460	135360004	+	KAI3753844.1	Cich4g04709	4709
5	80086664	80089160	+	KAI3509936.1	Cien5g03416	3416
3	293476248	293477069	-	D.indicum_Contig13_G00176.t1	Cind3g00565	565
3	293474749	293475204	+	D.indicum_Contig13_G00177.t1	Cind3g00566	566
3	319934928	319935269	-	D.indicum_Contig84_G00030.t1	Cind3g05598	5598
3	33940873	33941434	+	XM_043766208.1	Ecan3g02327	2327
3	86168659	86169021	+	GcoAMIRv0_Chr03g0169841	Glco3g01355	1355
7	142236802	142237170	-	CAI9295176.1	Laca7g02982	2982
1	5117099	5118403	+	LmiAMIRv0_Chr01g0005401	Lomi1g00540	540
2	46557353	46558649	-	LmiAMIRv0_Chr02g0086201	Lomi2g04087	4087
2	46563367	46564090	-	LmiAMIRv0_Chr02g0086221	Lomi2g04088	4088
7	193677751	193678113	+	>KAJ0195757.1	Lssa7g03671	3671
4	12987647	12988003	+	PdyAMIRv0_Chr04g0155191	Pdy4g00712	712
1	45212919	45214128	+	PluAMIRv0_Chr01g0065861	Pslu1g06610	6610
1	45215250	45215555	-	PluAMIRv0_Chr01g0065871	Pslu1g06611	6611
1	151070770	151071123	-	PluAMIRv0_Chr01g0208861	Pslu1g20978	20978
12	4518690	4519148	-	SinAMIRv0_Chr12g0358191	Sain12g00254	254
12	4598515	4599229	-	SinAMIRv0_Chr12g0358211	Sain12g00256	256
12	4599811	4600556	+	SinAMIRv0_Chr12g0358221	Sain12g00257	257
12	4604098	4610906	+	SinAMIRv0_Chr12g0358231	Sain12g00258	258
12	4611897	4612220	-	SinAMIRv0_Chr12g0358241	Sain12g00259	259
12	4667740	4668084	-	SinAMIRv0_Chr12g0358271	Sain12g00262	262
5	24327293	24332394	-	augustus16532.t01	Soca5g02273	2273
4	81526941	81527590	-	TkA04G322820.1	Tako4g03656	3656

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