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
Vvi4g282 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g283 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone10ag1327 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g284 . . . . . . . . . . . . . Car12g00232 . . . Bhi04g00858 . . . . . . . . . . . . . . . . . . . . . . . . . Bpe14g00520 . . Bma02g00084 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g285 . . . . . . . . . Cmo12g00200 . . . Car12g00233 . Cpe07g00211 . . . . . . . . . . . . . . . . . . . . . . Cme03g01749 Blo17g00065 . . Bda13g01328 . . . . . . . . Cma12g00248 . . . . . . . . . . . Cla08g01218 Cam08g1677 Cec08g1255 Cco08g1375 Clacu08g1375 . Cre08g1160 Lsi08g01081 . Chy03g01253 .
Vvi4g286 . . . . . . . . . Cmo12g00201 . . . Car12g00234 . Cpe07g00212 . Bhi04g00856 . . . . . . . . . . . . . . . Cone17ag1127 Cone20ag0595 . . . Cme03g01748 Blo17g00066 . . Bda13g01329 Bpe14g00519 . . . . . . . Cma12g00249 . . . . . . . . . . . Cla08g01219 Cam08g1678 Cec08g1256 Cco08g1376 Clacu08g1376 . Cre08g1161 Lsi08g01082 . Chy03g01252 .
Vvi4g287 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g288 . . . . Bpe02g01184 Bpe02g00248 . . Cmo05g00616 Cmo12g00203 . Cma05g00591 . Car12g00235 Sed01g1263 Cpe07g00213 . Bhi04g00855 Tan02g2557 Cmetu03g1871 . Hepe10g0368 . Lcy13g1418 . . . . . . . . . Cone17ag1126 Cone20ag0596 . . . Cme03g01747 Blo17g00067 . Bda01g00938 Bda13g01330 Bpe14g00518 . Bma01g01343 . . . . . Cma12g00250 . Car05g00535 Cpe11g00517 . . . . . . . . Cla08g01220 Cam08g1679 Cec08g1257 Cco08g1377 Clacu08g1377 . Cre08g1162 Lsi08g01083 . Chy03g01251 .
Vvi4g289 Blo01g01776 . . . . Bpe02g00168 . Bma01g02556 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g290 . . . . . . . . Cmo05g00617 . . Cma05g00592 . . . . . Bhi04g00849 . . . . . Lcy13g1417 . . . . . . . . . Cone17ag1125 Cone20ag0597 . . . Cme03g01745 Blo17g00068 . . Bda13g01331 Bpe14g00517 . . . . . . . . . Car05g00536 Cpe11g00518 . . . . . . . . Cla08g01221 Cam08g1680 Cec08g1258 Cco08g1378 Clacu08g1378 . Cre08g1163 Lsi08g01084 . Chy03g01250 .
Vvi4g291 . . . . Bpe02g01183 . . . Cmo05g00618 Cmo12g00204 . Cma05g00593 . Car12g00236 Sed01g1266 Cpe07g00215 . Bhi04g00847 Tan02g2560 Cmetu03g0018 . Hepe10g0365 . Lcy13g1416 . . . . . . . . . Cone17ag1124 Cone20ag0598 . . . Cme03g01744 Blo17g00069 . . . . . . . . . . . Cma12g00252 . Car05g00537 Cpe11g00519 . . . . . . . . Cla08g01222 Cam08g1681 Cec08g1259 Cco08g1379 Clacu08g1379 . Cre08g1164 Lsi08g01085 . Chy03g01249 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 42772377 42777157 + Bda003089.1 Bda01g00938 938
13 35547716 35549919 + Bda000139.1 Bda13g01328 1328
13 35550576 35556239 + Bda000140.1 Bda13g01329 1329
13 35556936 35561465 - Bda000141.1 Bda13g01330 1330
13 35562602 35572203 + Bda000142.1 Bda13g01331 1331
4 21509929 21513775 + XM_039029493.1 Bhi04g00847 847
4 21512902 21520038 - XM_039029496.1 Bhi04g00849 849
4 21598759 21604143 + XM_039029027.1 Bhi04g00855 855
4 21605337 21611889 - XM_039029753.1 Bhi04g00856 856
4 21648474 21651602 - XM_039029359.1 Bhi04g00858 858
1 57477720 57481419 - BLOR01776 Blo01g01776 1776
17 484447 486646 + BLOR15886 Blo17g00065 65
17 488493 494045 + BLOR15887 Blo17g00066 66
17 496040 500314 - BLOR15888 Blo17g00067 67
17 502988 508997 + BLOR15889 Blo17g00068 68
17 506817 508032 - BLOR15890 Blo17g00069 69
1 18839867 18843745 - Bma001665.1 Bma01g01343 1343
1 83230618 83231709 - Bma003438.1 Bma01g02556 2556
2 702368 703960 + Bma014540.1 Bma02g00084 84
2 1160706 1161797 + Bpe008019.1 Bpe02g00168 168
2 1692157 1694044 + Bpe008093.1 Bpe02g00248 248
2 15526874 15529443 + Bpe009044.1 Bpe02g01183 1183
2 15531871 15536639 + Bpe009045.1 Bpe02g01184 1184
14 4549398 4556837 - Bpe024983 Bpe14g00517 517
14 4558045 4562590 + Bpe007168.1 Bpe14g00518 518
14 4563254 4568895 - Bpe007169.1 Bpe14g00519 519
14 4570930 4573137 - Bpe007170.1 Bpe14g00520 520
8 22999391 23004287 + CaPI482276_08g016770.1 Cam08g1677 1677
8 23006247 23014119 + CaPI482276_08g016780.1 Cam08g1678 1678
8 23014237 23019072 - CaPI482276_08g016790.1 Cam08g1679 1679
8 23026674 23031052 + CaPI482276_08g016800.1 Cam08g1680 1680
8 23032570 23036336 - CaPI482276_08g016810.1 Cam08g1681 1681
5 3105147 3110051 - Carg08278-RA Car05g00535 535
5 3111919 3116391 + Carg08279-RA Car05g00536 536
5 3117390 3120812 - Carg08280-RA Car05g00537 537
12 1550148 1550792 + Carg03839-RA Car12g00232 232
12 1551988 1553989 + Carg03840-RA Car12g00233 233
12 1555282 1562342 + Carg03841-RA Car12g00234 234
12 1563151 1568066 - Carg03842-RA Car12g00235 235
12 1574995 1577981 - Carg03843-RA Car12g00236 236
8 25647516 25650222 + CcPI632755_08g013750.1 Cco08g1375 1375
8 25652303 25659609 + CcPI632755_08g013760.1 Cco08g1376 1376
8 25660336 25665190 - CcPI632755_08g013770.1 Cco08g1377 1377
8 25672712 25677057 + CcPI632755_08g013780.1 Cco08g1378 1378
8 25678574 25682442 - CcPI632755_08g013790.1 Cco08g1379 1379
8 24480739 24486345 + CePI673135_08g012550.1 Cec08g1255 1255
8 24487783 24493726 + CePI673135_08g012560.1 Cec08g1256 1256
8 24495818 24500672 - CePI673135_08g012570.1 Cec08g1257 1257
8 24508336 24512691 + CePI673135_08g012580.1 Cec08g1258 1258
8 24514185 24517969 - CePI673135_08g012590.1 Cec08g1259 1259
3 15588308 15591809 + Chy3G062290.1 Chy03g01249 1249
3 15593375 15599042 - Chy3G062300.1 Chy03g01250 1250
3 15603847 15608470 + Chy3G062310.1 Chy03g01251 1251
3 15610436 15616332 - Chy3G062320.1 Chy03g01252 1252
3 15617544 15621801 - Chy3G062330.1 Chy03g01253 1253
8 23772242 23777146 + ClG42_08g0137500.10 Clacu08g1375 1375
8 23779105 23787068 + ClG42_08g0137600.10 Clacu08g1376 1376
8 23787183 23792035 - ClG42_08g0137700.10 Clacu08g1377 1377
8 23799525 23803861 + ClG42_08g0137800.10 Clacu08g1378 1378
8 23805383 23809177 - ClG42_08g0137900.10 Clacu08g1379 1379
8 25060127 25064423 + ClCG08G012200.2 Cla08g01218 1218
8 25065079 25074977 + ClCG08G012210.2 Cla08g01219 1219
8 25076157 25081547 - ClCG08G012220.2 Cla08g01220 1220
8 25088946 25093644 + ClCG08G012230.1 Cla08g01221 1221
8 25094802 25098596 - ClCG08G012240.1 Cla08g01222 1222
5 2923820 2928770 - CmaCh05G005910.1 Cma05g00591 591
5 2930659 2935210 + CmaCh05G005920.1 Cma05g00592 592
5 2935895 2939657 - CmaCh05G005930.1 Cma05g00593 593
12 1242446 1245612 + CmaCh12G002480.1 Cma12g00248 248
12 1246547 1253120 + CmaCh12G002490.1 Cma12g00249 249
12 1254009 1259531 - CmaCh12G002500.1 Cma12g00250 250
12 1265328 1268282 - CmaCh12G002520.1 Cma12g00252 252
3 26021587 26025164 + MELO3C011142.2.1 Cme03g01744 1744
3 26026357 26032211 - MELO3C011141.2.1 Cme03g01745 1745
3 26036656 26041960 + MELO3C011140.2.1 Cme03g01747 1747
3 26043422 26049539 - MELO3C011139.2.1 Cme03g01748 1748
3 26050355 26053451 - MELO3C011138.2.1 Cme03g01749 1749
3 3410712 3414189 - PI0019110.1 Cmetu03g0018 18
3 3393362 3398498 - PI0018970.1 Cmetu03g1871 1871
5 3070481 3075394 - CmoCh05G006160.1 Cmo05g00616 616
5 3077178 3081902 + CmoCh05G006170.1 Cmo05g00617 617
5 3082399 3087453 - CmoCh05G006180.1 Cmo05g00618 618
12 1306455 1318585 + CmoCh12G002000.1 Cmo12g00200 200
12 1319472 1326425 + CmoCh12G002010.1 Cmo12g00201 201
12 1327583 1332551 - CmoCh12G002030.1 Cmo12g00203 203
12 1340192 1343166 - CmoCh12G002040.1 Cmo12g00204 204
10 10347494 10349514 + Conep10aG0136900.1 Cone10ag1327 1327
17 8336125 8339021 + Conep17aG0115300.1 Cone17ag1124 1124
17 8339173 8341086 - Conep17aG0115400.1 Cone17ag1125 1125
17 8342521 8346781 + Conep17aG0115500.1 Cone17ag1126 1126
17 8347052 8352155 - Conep17aG0115600.1 Cone17ag1127 1127
20 3434250 3439506 + Conep20aG0061200.1 Cone20ag0595 595
20 3448439 3452550 - Conep20aG0061300.1 Cone20ag0596 596
20 3456005 3457660 + Conep20aG0061400.1 Cone20ag0597 597
20 3457952 3461377 - Conep20aG0061500.1 Cone20ag0598 598
7 1352910 1357030 + Cp4.1LG07g02490.1 Cpe07g00211 211
7 1357844 1365289 + Cp4.1LG07g02480.1 Cpe07g00212 212
7 1365934 1371406 - Cp4.1LG07g02240.1 Cpe07g00213 213
7 1377936 1380859 - Cp4.1LG07g02310.1 Cpe07g00215 215
11 3023402 3030412 - Cp4.1LG11g05150.1 Cpe11g00517 517
11 3030406 3035024 + Cp4.1LG11g05100.1 Cpe11g00518 518
11 3036224 3039624 - Cp4.1LG11g05170.1 Cpe11g00519 519
8 24807987 24813646 + CrPI670011_08g011600.1 Cre08g1160 1160
8 24815058 24822358 + CrPI670011_08g011610.1 Cre08g1161 1161
8 24823079 24827931 - CrPI670011_08g011620.1 Cre08g1162 1162
8 24835681 24840066 + CrPI670011_08g011630.1 Cre08g1163 1163
8 24841585 24845388 - CrPI670011_08g011640.1 Cre08g1164 1164
10 4026972 4031585 + Hsped.10g03650.1 Hepe10g0365 365
10 4073237 4081915 + Hsped.10g03680.1 Hepe10g0368 368
13 32578873 32582497 + Maker00034049 Lcy13g1416 1416
13 32585564 32595198 - Maker00034096 Lcy13g1417 1417
13 32604314 32610693 + Maker00033840 Lcy13g1418 1418
8 19383450 19387345 + Lsi08G010810.1 Lsi08g01081 1081
8 19387416 19395148 + Lsi08G010820.1 Lsi08g01082 1082
8 19394258 19401069 - Lsi08G010830.1 Lsi08g01083 1083
8 19408568 19414905 + Lsi08G010840.1 Lsi08g01084 1084
8 19415522 19419519 - Lsi08G010850.1 Lsi08g01085 1085
1 9372249 9377473 - Sed0004211.1 Sed01g1263 1263
1 9397011 9401029 - Sed0014536.1 Sed01g1266 1266
2 94097604 94102917 - Tan0000874.1 Tan02g2557 2557
2 94118116 94121256 - Tan0020688.2 Tan02g2560 2560
4 2748488 2749818 - Vvi4g282 Vvi4g282 282
4 2749900 2752003 - Vvi4g283 Vvi4g283 283
4 2752783 2754121 + Vvi4g284 Vvi4g284 284
4 2754157 2755987 + Vvi4g285 Vvi4g285 285
4 2757092 2765577 + Vvi4g286 Vvi4g286 286
4 2765833 2766476 - Vvi4g287 Vvi4g287 287
4 2766506 2771861 - Vvi4g288 Vvi4g288 288
4 2777824 2778904 + Vvi4g289 Vvi4g289 289
4 2781797 2785626 + Vvi4g290 Vvi4g290 290
4 2785954 2788687 - Vvi4g291 Vvi4g291 291
       

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