Doc-Alignment

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Cucurbitales genomes. We used V.vinifera as a reference, and by comparing homologous gene locus maps and Ks values between V.vinifera and other Cucurbitales, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We created a hierarchical lists of homologous genes using V.vinifera as a reference.
  The relevant gene ids can be obtained from the Cucurbitales blast and match under the Tools module. This link is Cucurbitales blast and match.

Orthogroup analysis platform
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Select Vvi1 Blo1 Blo2 Bda1 Bda2 Bpe1 Bpe2 Bma1 Bma2 Cmo1 Cmo2 Cma1 Cma2 Car1 Car2 Sed1 Cpe1 Cpe2 Bhi1 Tan1 Cmetu1 Lac1 Hepe1 Mch1 Lcy1 Cla1 Cam1 Cec1 Cco1 Clacu1 Cmu1 Cre1 Cone1 Cone2 Cone3 Cone4 Lsi1 Csa1 Chy1 Cme1 Blo3 Blo4 Bda3 Bda4 Bpe3 Bpe4 Bma3 Bma4 Sed2 Cmo3 Cmo4 Cma3 Cma4 Car3 Car4 Cpe3 Cpe4 Bhi2 Tan2 Cmetu2 Lac2 Hepe2 Mch2 Lcy2 Cla2 Cam2 Cec2 Cco2 Clacu2 Cmu2 Cre2 Lsi2 Csa2 Chy2 Cme2
Vvi1g1391 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0632 Cone15ag0641 . . . . . . . . . . Bpe14g00837 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1392 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1393 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1394 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0631 Cone15ag0640 . . . . Chy11g01844 Cme11g02381 . . . . . . . . . . . . . . . Cpe17g00951 . . . . . . . . . . . . . . . Lsi09g01779 . . .
Vvi1g1395 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00149 Cam06g0065 Cec06g0165 Cco06g0159 Clacu06g0160 Cmu06g0157 Cre06g0931 . . . . . . Chy11g01847 . . . . . . . . . Sed09g0354 . . . . . . . . Bhi12g02377 Tan06g1429 Cmetu11g2072 . . . . . . . . . . . . . . .
Vvi1g1396 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1397 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0630 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1398 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1399 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0629 Cone15ag0638 . . . . . . . . . . . . . Bma06g01297 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1 . . . Bda08g00515 . Bpe07g00104 . Bma14g00608 . Cmo16g00658 Cma02g01438 . Car02g01208 . . . Cpe05g00646 . . . . . . . Cla07g00786 Cam07g0848 Cec07g0901 Cco07g0883 Clacu07g0823 Cmu07g0826 Cre07g1184 . . . . . Csa05g00266 . . . . Bda07g00484 . . Bpe11g00661 . Bma12g00073 . Cmo02g01473 Cmo15g01132 . Cma16g00602 Car06g00910 . . Cpe13g00146 Bhi12g00184 . . . . . . Cla01g00250 Cam01g0255 Cec01g0247 Cco01g0261 Clacu01g0253 Cmu01g0243 Cre09g2266 Lsi09g00241 . Chy07g01225 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 6070542 6077369 - Bda025586.1 Bda07g00484 484
8 5197591 5200662 - Bda024970.2 Bda08g00515 515
12 5530775 5566045 + XM_039051110.1 Bhi12g00184 184
12 75049755 75055120 - XM_039050781.1 Bhi12g02377 2377
6 50011055 50019521 - Bma031327 Bma06g01297 1297
12 1284561 1287701 - Bma006943.1 Bma12g00073 73
14 6613933 6615363 + Bma011048.1 Bma14g00608 608
7 744519 746203 + Bpe020918.2 Bpe07g00104 104
11 5077561 5082605 + Bpe004018.2 Bpe11g00661 661
14 6289978 6292065 - Bpe014214.1 Bpe14g00837 837
1 2868163 2869989 + CaPI482276_01g002550.1 Cam01g0255 255
6 2505561 2516946 + CaPI482276_06g000650.1 Cam06g0065 65
7 21225194 21225675 - CaPI482276_07g008480.1 Cam07g0848 848
2 8205105 8211636 + Carg02540-RA Car02g01208 1208
6 7036743 7041396 - Carg24655-RA Car06g00910 910
1 2497384 2499210 + CcPI632755_01g002610.1 Cco01g0261 261
6 1655111 1662502 - CcPI632755_06g001590.1 Cco06g0159 159
7 20625590 20626087 - CcPI632755_07g008830.1 Cco07g0883 883
1 2473442 2475281 + CePI673135_01g002470.1 Cec01g0247 247
6 1683433 1691176 - CePI673135_06g001650.1 Cec06g0165 165
7 22419162 22419643 - CePI673135_07g009010.1 Cec07g0901 901
7 17044264 17047500 - Chy7G140550.1 Chy07g01225 1225
11 24742637 24749076 + Chy11G204240.1 Chy11g01844 1844
11 24751289 24755664 - Chy11G204270.1 Chy11g01847 1847
1 2486709 2488540 + ClG42_01g0025300.10 Clacu01g0253 253
6 1825844 1833519 - ClG42_06g0016000.10 Clacu06g0160 160
7 20906918 20907399 - ClG42_07g0082300.10 Clacu07g0823 823
1 2539726 2542081 + ClCG01G002550.2 Cla01g00250 250
6 1692446 1700985 - ClCG06G001640.2 Cla06g00149 149
7 22036398 22039216 - ClCG07G008240.2 Cla07g00786 786
2 8277306 8280138 + CmaCh02G014380.1 Cma02g01438 1438
16 3107263 3108848 - CmaCh16G006020.1 Cma16g00602 602
11 30752471 30757353 - MELO3C022370.2.1 Cme11g02381 2381
11 1303648 1307575 - PI0026745.4 Cmetu11g2072 2072
2 8643763 8644568 + CmoCh02G014730.1 Cmo02g01473 1473
15 7859006 7860805 - CmoCh15G011320.1 Cmo15g01132 1132
16 3250160 3250834 + CmoCh16G006580.1 Cmo16g00658 658
1 2439624 2441455 + CmPI595203_01g002430.1 Cmu01g0243 243
6 1621156 1635489 - CmPI595203_06g001570.1 Cmu06g0157 157
7 21120798 21121279 - CmPI595203_07g008260.1 Cmu07g0826 826
14 3159667 3162330 + Conep14aG0064300.1 Cone14ag0629 629
14 3163299 3167845 + Conep14aG0064400.1 Cone14ag0630 630
14 3168584 3171927 + Conep14aG0064500.1 Cone14ag0631 631
14 3173171 3175885 + Conep14aG0064600.1 Cone14ag0632 632
15 3342346 3345282 + Conep15aG0065100.1 Cone15ag0638 638
15 3365856 3369019 + Conep15aG0065300.1 Cone15ag0640 640
15 3369435 3371084 + Conep15aG0065400.1 Cone15ag0641 641
5 3947924 3952518 + Cp4.1LG05g06450.1 Cpe05g00646 646
13 1065851 1069602 + Cp4.1LG13g01370.1 Cpe13g00146 146
17 7288250 7297052 - Cp4.1LG17g09550.1 Cpe17g00951 951
6 2722337 2723647 - CrPI670011_06g009310.1 Cre06g0931 931
7 24720221 24720702 - CrPI670011_07g011840.1 Cre07g1184 1184
9 41843385 41845214 - CrPI670011_09g022660.1 Cre09g2266 2266
5 1629640 1632091 + CsaV3_5G002660.1 Csa05g00266 266
9 2537992 2540778 + Lsi09G002410.1 Lsi09g00241 241
9 26544333 26551745 - Lsi09G017790.1 Lsi09g01779 1779
9 3211032 3217527 + Sed0027865.3 Sed09g0354 354
6 18825843 18834904 - Tan0017802.1 Tan06g1429 1429
1 22888194 22892828 - Vvi1g1391 Vvi1g1391 1391
1 22895504 22897007 + Vvi1g1392 Vvi1g1392 1392
1 22897009 22897774 + Vvi1g1393 Vvi1g1393 1393
1 22898899 22922421 - Vvi1g1394 Vvi1g1394 1394
1 22940963 22960324 + Vvi1g1395 Vvi1g1395 1395
1 22961218 22972983 + Vvi1g1396 Vvi1g1396 1396
1 22973509 22982647 - Vvi1g1397 Vvi1g1397 1397
1 22983270 23001188 + Vvi1g1398 Vvi1g1398 1398
1 23002139 23021474 - Vvi1g1399 Vvi1g1399 1399
2 12464 13764 - Vvi2g1 Vvi2g1 1
       

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