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
Vvi4g302 Blo01g01774 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed12g1397 Cmo01g01485 . . . . . . . Bhi09g02581 Tan01g3936 Cmetu04g0169 . . Mch11g0772 . . . . . . . . . . . Cme04g00175
Vvi4g303 . . . . . . . . . Cmo12g00210 . . . Car12g00240 Sed01g3988 Cpe07g00219 . Bhi04g00841 Tan06g0273 Cmetu03g1992 . Hepe10g0358 . Lcy13g1413 . . . . . . . . . Cone17ag1120 . . . . Cme03g01738 Blo17g00072 . . Bda13g01334 Bpe14g00514 . . . . . . . Cma12g00256 . . . . . . . . . . . Cla08g01226 Cam08g1685 Cec08g1264 Cco08g1384 Clacu08g1383 . Cre08g1168 Lsi08g01089 . Chy03g01245 .
Vvi4g304 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1119 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g305 . Blo12g00757 . . . . Bma04g00405 . . . Cma01g01434 . Car09g00562 . . . . . . . . . . . . . . . . . . . . . Cone20ag0601 Lsi04g02333 Csa03g04553 Chy04g00148 . . . . . . Bpe04g00396 . . Sed01g3987 Cmo01g01483 Cmo09g00617 Cma09g00636 . . . . Cpe02g00513 Bhi09g02582 Tan01g3937 Cmetu09g1599 . Hepe01g2223 Mch11g0774 . . . . . . . . . . . Cme04g00174
Vvi4g306 Blo01g01773 . . . Bpe02g01179 Bpe02g00171 . Bma01g02554 Cmo05g00622 . . Cma05g00596 . . . . . Bhi04g00838 . . . Hepe10g0353 . Lcy13g1408 . . . . . . . . . . Cone20ag0602 . . . Cme03g01737 . . . . . . . . . . . . . . Car05g00540 Cpe11g00522 . . . . . . . . Cla08g01227 Cam08g1686 Cec08g1265 Cco08g1385 Clacu08g1384 . Cre08g1169 Lsi08g01090 . Chy03g01243 .
Vvi4g307 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g308 . . . . . . . . . Cmo12g00211 . . . Car12g00241 Sed03g1488 Cpe07g00220 . Bhi04g00836 Tan02g2569 Cmetu03g1888 . Hepe10g0352 . Lcy13g1401 . . . . . . . . . Cone17ag1118 Cone20ag0603 . . . Cme03g01735 Blo17g00073 . . Bda13g01335 Bpe14g00513 . . . . . . . Cma12g00257 . . . . . . . . . . . Cla08g01228 Cam08g1687 Cec08g1266 Cco08g1387 Clacu08g1385 . Cre08g1170 Lsi08g01091 . Chy03g01241 .
Vvi4g309 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g310 . . . . Bpe02g01178 . . . . . . . Car09g00564 . . . Cpe06g00471 . . . . . . . . . . . . . . . . Cone17ag1154 Cone20ag0574 . Csa03g04555 Chy04g00147 . Blo17g00075 . Bda01g00933 Bda13g01336 Bpe14g00511 . . . . . Cmo09g00620 Cma09g00638 . . . . . Bhi09g02586 . . . . . . . . . . . . . . . . Cme04g00173
Vvi4g311 Blo01g01772 Blo12g00758 . Bda03g00429 . Bpe02g00172 Bma04g00404 Bma01g02553 . Cmo12g00212 . . . Car12g00242 Sed01g1273 Cpe07g00221 . Bhi04g00834 Tan02g2572 Cmetu03g1902 . Hepe10g0351 . Lcy13g1396 . . . . . . . . . Cone17ag1117 Cone20ag0604 . . . Cme03g01734 . . . . . Bpe04g00395 . . . . . . Cma12g00258 . . . . . . . . . . . Cla08g01229 Cam08g1688 Cec08g1267 Cco08g1388 Clacu08g1386 . Cre08g1171 Lsi08g01092 . Chy03g01240 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 42660768 42662562 + Bda003082.1 Bda01g00933 933
3 3699708 3706575 - Bda016395.1 Bda03g00429 429
13 35622513 35623545 - Bda000145.1 Bda13g01334 1334
13 35625183 35629215 - Bda000146.1 Bda13g01335 1335
13 35635130 35636929 - Bda000147.1 Bda13g01336 1336
4 21078859 21086562 - XM_039029165.1 Bhi04g00834 834
4 21137831 21147147 + XM_039029053.1 Bhi04g00836 836
4 21181814 21184931 - XM_039029724.1 Bhi04g00838 838
4 21240017 21241445 + XM_039029279.1 Bhi04g00841 841
9 70196486 70197560 + XM_039041345.1 Bhi09g02581 2581
9 70197616 70200931 - XM_039041344.1 Bhi09g02582 2582
9 70204034 70207863 - XM_039042674.1 Bhi09g02586 2586
1 57439915 57447246 - BLOR01772 Blo01g01772 1772
1 57449275 57456988 + BLOR01773 Blo01g01773 1773
1 57457600 57458985 - BLOR01774 Blo01g01774 1774
12 25909556 25913375 - BLOR04776 Blo12g00757 757
12 25916935 25926560 + BLOR04777 Blo12g00758 758
17 548820 549836 - BLOR15893 Blo17g00072 72
17 551806 556956 - BLOR15894 Blo17g00073 73
17 559838 561380 - BLOR15896 Blo17g00075 75
1 83186417 83191327 - Bma003435.1 Bma01g02553 2553
1 83195100 83197367 + Bma003436.1 Bma01g02554 2554
4 3288791 3296892 - Bma018867.1 Bma04g00404 404
4 3300293 3302421 + Bma018868.1 Bma04g00405 405
2 1182493 1195633 - Bpe008022.1 Bpe02g00171 171
2 1196986 1204144 + Bpe008023.1 Bpe02g00172 172
2 15450904 15452730 + Bpe009039.1 Bpe02g01178 1178
2 15470820 15472627 - Bpe009040.1 Bpe02g01179 1179
4 2474018 2482113 - Bpe015079.1 Bpe04g00395 395
4 2485467 2487550 + Bpe015080.1 Bpe04g00396 396
14 4518687 4520492 + Bpe007161.1 Bpe14g00511 511
14 4522829 4527775 + Bpe007163.2 Bpe14g00513 513
14 4529349 4530373 + Bpe007164.1 Bpe14g00514 514
8 23122376 23123496 - CaPI482276_08g016850.1 Cam08g1685 1685
8 23131679 23135562 + CaPI482276_08g016860.1 Cam08g1686 1686
8 23137417 23146376 - CaPI482276_08g016870.1 Cam08g1687 1687
8 23148576 23157760 + CaPI482276_08g016880.1 Cam08g1688 1688
5 3153472 3162062 + Carg08283-RA Car05g00540 540
9 3189085 3192707 - Carg03044-RA Car09g00562 562
9 3194768 3198407 - Carg03046-RA Car09g00564 564
12 1610548 1612181 - Carg03847-RA Car12g00240 240
12 1613900 1623078 - Carg03848-RA Car12g00241 241
12 1625823 1630021 + Carg03849-RA Car12g00242 242
8 25750245 25751360 - CcPI632755_08g013840.1 Cco08g1384 1384
8 25760727 25763289 + CcPI632755_08g013850.1 Cco08g1385 1385
8 25767395 25775268 - CcPI632755_08g013870.1 Cco08g1387 1387
8 25779368 25786060 + CcPI632755_08g013880.1 Cco08g1388 1388
8 24605311 24606426 - CePI673135_08g012640.1 Cec08g1264 1264
8 24614571 24620357 + CePI673135_08g012650.1 Cec08g1265 1265
8 24621298 24628651 - CePI673135_08g012660.1 Cec08g1266 1266
8 24634430 24641117 + CePI673135_08g012670.1 Cec08g1267 1267
3 15480112 15487274 + Chy3G062200.1 Chy03g01240 1240
3 15488212 15495290 + Chy3G062210.1 Chy03g01241 1241
3 15508330 15510868 - Chy3G062230.1 Chy03g01243 1243
3 15524638 15525754 + Chy3G062250.1 Chy03g01245 1245
4 1324076 1327169 + Chy4G068650.1 Chy04g00147 147
4 1327845 1333025 + Chy4G068660.1 Chy04g00148 148
8 23876761 23877881 - ClG42_08g0138300.10 Clacu08g1383 1383
8 23885486 23889655 + ClG42_08g0138400.10 Clacu08g1384 1384
8 23891492 23900416 - ClG42_08g0138500.10 Clacu08g1385 1385
8 23905202 23911926 + ClG42_08g0138600.10 Clacu08g1386 1386
8 25167953 25169515 - ClCG08G012280.2 Cla08g01226 1226
8 25178189 25181256 + ClCG08G012290.1 Cla08g01227 1227
8 25183815 25191993 - ClCG08G012300.2 Cla08g01228 1228
8 25196496 25203719 + ClCG08G012310.1 Cla08g01229 1229
1 10094776 10096913 + CmaCh01G014340.1 Cma01g01434 1434
5 2974866 2983364 + CmaCh05G005960.1 Cma05g00596 596
9 3004470 3008549 - CmaCh09G006360.1 Cma09g00636 636
9 3010369 3014043 - CmaCh09G006380.1 Cma09g00638 638
12 1299988 1301475 - CmaCh12G002560.1 Cma12g00256 256
12 1303002 1313127 - CmaCh12G002570.1 Cma12g00257 257
12 1314054 1320086 + CmaCh12G002580.1 Cma12g00258 258
3 25923795 25931476 + MELO3C011151.2.1 Cme03g01734 1734
3 25932029 25939929 + MELO3C011150.2.1 Cme03g01735 1735
3 25946992 25950234 - MELO3C011148.2.1 Cme03g01737 1737
3 25963205 25965078 + MELO3C011146.2.1 Cme03g01738 1738
4 1300359 1307398 + MELO3C003459.2.1 Cme04g00173 173
4 1307787 1310895 + MELO3C003460.2.1 Cme04g00174 174
4 1310169 1310609 - MELO3C003461.2.1 Cme04g00175 175
3 3498570 3505209 - PI0023264.1 Cmetu03g1888 1888
3 3505898 3513595 - PI0016237.1 Cmetu03g1902 1902
3 3478179 3479293 - PI0025776.1 Cmetu03g1992 1992
4 32108712 32109296 + PI0028129.1 Cmetu04g0169 169
9 3251461 3254335 + PI0018865.1 Cmetu09g1599 1599
1 11508164 11510687 + CmoCh01G014830.1 Cmo01g01483 1483
1 11510877 11512283 - CmoCh01G014850.1 Cmo01g01485 1485
5 3122214 3125752 + CmoCh05G006220.1 Cmo05g00622 622
9 3084770 3091533 - CmoCh09G006170.1 Cmo09g00617 617
9 3093952 3097015 - CmoCh09G006200.1 Cmo09g00620 620
12 1376613 1377684 - CmoCh12G002100.1 Cmo12g00210 210
12 1379162 1388503 - CmoCh12G002110.1 Cmo12g00211 211
12 1390153 1396243 + CmoCh12G002120.1 Cmo12g00212 212
17 8287205 8292548 - Conep17aG0114600.1 Cone17ag1117 1117
17 8293263 8297421 + Conep17aG0114700.1 Cone17ag1118 1118
17 8297862 8301370 - Conep17aG0114800.1 Cone17ag1119 1119
17 8302366 8303273 + Conep17aG0114900.1 Cone17ag1120 1120
17 8524709 8527337 + Conep17aG0118300.1 Cone17ag1154 1154
20 3281919 3284672 - Conep20aG0059100.1 Cone20ag0574 574
20 3521031 3523216 - Conep20aG0061800.1 Cone20ag0601 601
20 3524858 3526964 + Conep20aG0061900.1 Cone20ag0602 602
20 3529059 3530825 - Conep20aG0062000.1 Cone20ag0603 603
20 3536013 3541578 + Conep20aG0062100.1 Cone20ag0604 604
2 3026173 3031082 - Cp4.1LG02g03610.1 Cpe02g00513 513
6 2780044 2783784 - Cp4.1LG06g03880.1 Cpe06g00471 471
7 1415743 1417143 - Cp4.1LG07g02270.1 Cpe07g00219 219
7 1419677 1429454 - Cp4.1LG07g02280.1 Cpe07g00220 220
7 1430865 1438210 + Cp4.1LG07g02360.1 Cpe07g00221 221
11 3071959 3084532 + Cp4.1LG11g05140.1 Cpe11g00522 522
8 24914205 24915321 - CrPI670011_08g011680.1 Cre08g1168 1168
8 24923117 24927304 + CrPI670011_08g011690.1 Cre08g1169 1169
8 24929592 24939587 - CrPI670011_08g011700.1 Cre08g1170 1170
8 24944293 24951020 + CrPI670011_08g011710.1 Cre08g1171 1171
3 39668988 39671377 - CsaV3_3G048590.1 Csa03g04553 4553
3 39674836 39677876 - CsaV3_3G048610.1 Csa03g04555 4555
1 86919337 86922105 - Hsped.01g22230.1 Hepe01g2223 2223
10 3839962 3847409 - Hsped.10g03510.1 Hepe10g0351 351
10 3850219 3861884 + Hsped.10g03520.1 Hepe10g0352 352
10 3863911 3868613 - Hsped.10g03530.1 Hepe10g0353 353
10 3917491 3918592 + Hsped.10g03580.1 Hepe10g0358 358
13 32234092 32244406 - Maker00025766 Lcy13g1396 1396
13 32302322 32309081 + Maker00025762 Lcy13g1401 1401
13 32419083 32428439 + Maker00025665 Lcy13g1408 1408
13 32482233 32485478 + Maker00025632 Lcy13g1413 1413
4 30543474 30553447 - Lsi04G023330.1 Lsi04g02333 2333
8 19491710 19493129 - Lsi08G010890.1 Lsi08g01089 1089
8 19503100 19507458 + Lsi08G010900.1 Lsi08g01090 1090
8 19509276 19517307 - Lsi08G010910.1 Lsi08g01091 1091
8 19521696 19529348 + Lsi08G010920.1 Lsi08g01092 1092
11 5211388 5213034 + MC11g0650 Mch11g0772 772
11 5215228 5217987 - MC11g0651 Mch11g0774 774
1 9503844 9511415 + Sed0024259.2 Sed01g1273 1273
1 68965324 68968471 - Sed0013197.1 Sed01g3987 3987
1 68982161 68985521 - Sed0005733.1 Sed01g3988 3988
3 9507338 9518509 - Sed0007027.1 Sed03g1488 1488
12 11473431 11482165 + Sed0000497.1 Sed12g1397 1397
1 104262982 104265821 + Tan0021395.1 Tan01g3936 3936
1 104267771 104270209 - Tan0009185.1 Tan01g3937 3937
2 94258973 94287639 - Tan0000996.2 Tan02g2569 2569
2 94290873 94298642 + Tan0005104.1 Tan02g2572 2572
6 2170720 2172878 - Tan0004598.1 Tan06g0273 273
4 2897024 2898371 + Vvi4g302 Vvi4g302 302
4 2903930 2905762 - Vvi4g303 Vvi4g303 303
4 2911562 2917396 + Vvi4g304 Vvi4g304 304
4 2917396 2920694 - Vvi4g305 Vvi4g305 305
4 2926995 2934108 + Vvi4g306 Vvi4g306 306
4 2935958 2937695 - Vvi4g307 Vvi4g307 307
4 2939876 2952804 - Vvi4g308 Vvi4g308 308
4 2957071 2958231 - Vvi4g309 Vvi4g309 309
4 2958241 2971785 - Vvi4g310 Vvi4g310 310
4 2974862 2984519 + Vvi4g311 Vvi4g311 311
       

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