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
Vvi2g502 . . . . . . Bma07g01602 . . . . Cma15g01146 . Car15g01041 . . . . . . . . . . . . . . . . . . Cone12ag0367 Cone6ag0694 . . Csa05g00399 Chy09g01114 . . Blo19g00231 . Bda09g00092 Bpe08g01437 . . . . . Cmo15g01206 . . . . . Cpe13g00222 Bhi12g00412 . . Lac11g2255 Hepe06g1655 . Lcy12g1801 . . . . . . . Lsi09g00403 . . Cme09g01644
Vvi2g503 Blo02g01052 . . Bda08g00566 Bpe05g00591 Bpe07g00162 . . . . . Cma15g01144 . . . . . Bhi11g00028 Tan01g2199 . . . Mch10g1668 . . . . . . . . . . Cone6ag0693 Cone9ag0695 . Csa05g00400 Chy09g01113 . . Blo19g00232 . Bda09g00093 Bpe08g01436 . Bma05g00773 Bma12g00153 . . . . . . Car16g01102 . . Bhi12g00413 . . Lac11g2257 Hepe06g1656 . Lcy12g1803 Cla01g00373 Cam01g0392 Cec01g0384 Cco01g0404 Clacu01g0392 Cmu01g0373 Cre09g2138 Lsi09g00404 . . Cme09g01643
Vvi2g504 . . . . . . . . Cmo06g00787 . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi07g01326 . . Cme06g02610 . . . . . . . . . . . Cma06g00767 . . Car16g01008 . . . . . . . . . . . . . . . . . . Chy06g02021 .
Vvi2g505 . . . . . Bpe07g00163 . . . Cmo16g01109 . . . . . Cpe14g00878 . . . . . . . . . . . . . . . . . . . . . . Cme06g02609 . . . . . . . Bma12g00154 . . . . Cma16g01059 Car06g00685 . . . . . . . . . . . . . . . . . . . Chy06g02022 .
Vvi2g506 . . . . . . . . . . . . . . . . . . . . . . . . Cla10g00282 Cam10g0292 Cec10g0300 Cco10g0296 Clacu10g0292 Cmu10g1131 Cre10g0539 . . . . Lsi07g01322 . . Cme06g02606 . . . . . . . . . . . . . . . Cpe08g00751 . . . . . . . . . . . . . . . . Csa03g00301 Chy06g02023 .
Vvi2g507 . Blo03g00171 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme06g02605 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy06g02024 .
Vvi2g508 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g509 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g510 . . . . . . . Bma14g00541 . . . Cma15g01142 . Car15g01038 . . . . . . . . . . . . . . . . . . . . . . Csa05g00403 Chy09g01110 . Blo03g00414 Blo19g00233 Bda07g00004 Bda09g00094 Bpe08g01435 Bpe11g00264 . . . . Cmo15g01203 . . . . . . Bhi12g00419 . . Lac11g2261 Hepe06g1658 . Lcy12g1806 Cla01g00376 Cam01g0395 Cec01g0387 Cco01g0407 Clacu01g0395 Cmu01g0376 Cre09g2135 Lsi09g00407 . . Cme09g01639
Vvi2g511 Blo02g01049 Blo03g00169 Bda06g00037 . Bpe05g00588 Bpe07g00165 . . Cmo06g00789 Cmo16g01114 . Cma15g01141 Car02g01307 Car15g01037 . Cpe14g00881 Cpe05g00242 Bhi11g00212 . . . . . . Cla10g00276 Cam10g0285 Cec10g0293 Cco10g0290 Clacu10g0286 Cmu10g1126 Cre10g0534 . . Cone6ag0690 Cone9ag0692 Lsi07g01319 . . Cme06g02601 . Blo19g00281 Bda07g00005 . . . Bma05g00770 . . . Cmo15g01200 Cma06g00769 Cma16g01066 Car06g00687 Car16g01012 Cpe08g00749 . Bhi12g00421 . . Lac11g2262 Hepe06g1148 . Lcy12g1808 . . . . . . . . Csa03g04675 . Cme09g01638
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 329087 345896 - Bda023206.2 Bda06g00037 37
7 48102 48980 - Bda025049.1 Bda07g00004 4
7 75375 80554 + Bda025050.1 Bda07g00005 5
8 5757688 5758642 + Bda029026.1 Bda08g00566 566
9 1791880 1794834 - Bda030627.1 Bda09g00092 92
9 1803672 1804650 + Bda030628.1 Bda09g00093 93
9 1809077 1809937 - Bda030629.1 Bda09g00094 94
11 408339 410999 - XM_039049437.1 Bhi11g00028 28
11 5051206 5059961 - XM_039049345.1 Bhi11g00212 212
12 13769873 13775273 - XM_039020191.1 Bhi12g00412 412
12 13852089 13854782 + XM_039020161.1 Bhi12g00413 413
12 13915043 13916175 - XM_039018922.1 Bhi12g00419 419
12 13998862 14007509 + XM_039018899.1 Bhi12g00421 421
2 40471130 40482957 - BLOR10779 Blo02g01049 1049
2 40582557 40583556 - BLOR10782 Blo02g01052 1052
3 4269721 4276374 - BLOR11350 Blo03g00169 169
3 4328207 4330466 + BLOR11352 Blo03g00171 171
3 11874376 11875254 - BLOR11595 Blo03g00414 414
19 11482633 11486046 - BLOR09574 Blo19g00231 231
19 11523160 11524102 + BLOR09575 Blo19g00232 232
19 11583379 11584239 - BLOR09576 Blo19g00233 233
19 17096912 17101497 + BLOR09624 Blo19g00281 281
5 44545872 44553072 - Bma021869.1 Bma05g00770 770
5 44612318 44613274 - Bma021873.1 Bma05g00773 773
7 51346691 51349816 + Bma031412 Bma07g01602 1602
12 2185381 2186386 + Bma007034.1 Bma12g00153 153
12 2186705 2188696 - Bma007035.1 Bma12g00154 154
14 5889431 5890552 + Bma010969.1 Bma14g00541 541
5 19938322 19945203 - Bpe018004.5 Bpe05g00588 588
5 19965700 19966658 - Bpe018007.1 Bpe05g00591 591
7 1113995 1114721 + Bpe020972.1 Bpe07g00162 162
7 1115311 1117525 - Bpe020973.1 Bpe07g00163 163
7 1133245 1139818 + Bpe020975.1 Bpe07g00165 165
8 15105022 15105873 + Bpe023549.1 Bpe08g01435 1435
8 15113439 15114400 - Bpe023550.1 Bpe08g01436 1436
8 15121428 15124717 + Bpe023551.1 Bpe08g01437 1437
11 1917019 1917897 - Bpe003640.1 Bpe11g00264 264
1 4346169 4348009 + CaPI482276_01g003920.1 Cam01g0392 392
1 4378026 4378901 - CaPI482276_01g003950.1 Cam01g0395 395
10 4844547 4852073 - CaPI482276_10g002850.1 Cam10g0285 285
10 5052259 5056482 + CaPI482276_10g002920.1 Cam10g0292 292
2 8697873 8703333 - Carg02441-RA Car02g01307 1307
6 4072539 4076342 - Carg21597-RA Car06g00685 685
6 4109799 4116063 + Carg25162-RA Car06g00687 687
15 8155495 8161045 - Carg27917-RA Car15g01037 1037
15 8171726 8172601 + Carg27918-RA Car15g01038 1038
15 8198764 8203054 + Carg27388-RA Car15g01041 1041
16 8570435 8574635 - Carg23212-RA Car16g01008 1008
16 8614402 8621080 + Carg23216-RA Car16g01012 1012
16 9495773 9497827 + Carg26202-RA Car16g01102 1102
1 4027509 4029396 + CcPI632755_01g004040.1 Cco01g0404 404
1 4060451 4061326 - CcPI632755_01g004070.1 Cco01g0407 407
10 3374632 3381887 - CcPI632755_10g002900.1 Cco10g0290 290
10 3510037 3526831 + CcPI632755_10g002960.1 Cco10g0296 296
1 4032934 4034927 + CePI673135_01g003840.1 Cec01g0384 384
1 4064844 4065719 - CePI673135_01g003870.1 Cec01g0387 387
10 3524767 3532041 - CePI673135_10g002930.1 Cec10g0293 293
10 3690050 3695442 + CePI673135_10g003000.1 Cec10g0300 300
6 24153787 24157083 - Chy6G125490.1 Chy06g02021 2021
6 24160798 24164368 - Chy6G125500.1 Chy06g02022 2022
6 24165995 24169525 - Chy6G125510.1 Chy06g02023 2023
6 24170294 24173716 - Chy6G125520.1 Chy06g02024 2024
9 13358230 13359105 + Chy9G168260.1 Chy09g01110 1110
9 13390424 13392777 - Chy9G168290.1 Chy09g01113 1113
9 13400832 13405381 + Chy9G168300.1 Chy09g01114 1114
1 3984693 3986577 + ClG42_01g0039200.10 Clacu01g0392 392
1 4016649 4017524 - ClG42_01g0039500.10 Clacu01g0395 395
10 3657682 3664927 - ClG42_10g0028600.10 Clacu10g0286 286
10 3806674 3825998 + ClG42_10g0029200.10 Clacu10g0292 292
1 4124682 4126690 + ClCG01G003870.2 Cla01g00373 373
1 4156451 4157326 - ClCG01G003900.1 Cla01g00376 376
10 3514772 3525925 - ClCG10G002920.1 Cla10g00276 276
10 3712294 3731458 + ClCG10G002970.1 Cla10g00282 282
6 3891113 3895278 - CmaCh06G007670.1 Cma06g00767 767
6 3933269 3939827 + CmaCh06G007690.1 Cma06g00769 769
15 7251929 7258262 - CmaCh15G011410.1 Cma15g01141 1141
15 7267499 7268374 + CmaCh15G011420.1 Cma15g01142 1142
15 7279353 7280856 - CmaCh15G011440.1 Cma15g01144 1144
15 7286074 7289875 + CmaCh15G011460.1 Cma15g01146 1146
16 8113473 8117754 - CmaCh16G010590.1 Cma16g01059 1059
16 8157992 8164354 + CmaCh16G010660.1 Cma16g01066 1066
6 33199558 33207719 - MELO3C013961.2.1 Cme06g02601 2601
6 33313743 33317591 + MELO3C013964.2.1 Cme06g02605 2605
6 33318430 33322748 + MELO3C013965.2.1 Cme06g02606 2606
6 33344745 33348247 + MELO3C013966.2.1 Cme06g02609 2609
6 33348635 33352296 + MELO3C013967.2.1 Cme06g02610 2610
9 21097139 21104986 - MELO3C005554.2.1 Cme09g01638 1638
9 21132942 21133981 + MELO3C005555.2.1 Cme09g01639 1639
9 21162379 21163246 - MELO3C034000.2.1 Cme09g01643 1643
9 21171374 21176060 + MELO3C005558.2.1 Cme09g01644 1644
6 4114586 4118627 - CmoCh06G007870.1 Cmo06g00787 787
6 4161630 4167245 + CmoCh06G007890.1 Cmo06g00789 789
15 8322489 8328639 - CmoCh15G012000.1 Cmo15g01200 1200
15 8339531 8340406 + CmoCh15G012030.1 Cmo15g01203 1203
15 8360940 8364708 + CmoCh15G012060.1 Cmo15g01206 1206
16 7834107 7838487 - CmoCh16G011090.1 Cmo16g01109 1109
16 7878757 7885407 + CmoCh16G011140.1 Cmo16g01114 1114
1 3931450 3933335 + CmPI595203_01g003730.1 Cmu01g0373 373
1 3963360 3964235 - CmPI595203_01g003760.1 Cmu01g0376 376
10 3774533 3781763 - CmPI595203_10g011260.1 Cmu10g1126 1126
10 3923700 3943001 + CmPI595203_10g011310.1 Cmu10g1131 1131
6 3486789 3490404 - Conep06aG0071200.1 Cone6ag0690 690
6 3503554 3504594 - Conep06aG0071500.1 Cone6ag0693 693
6 3506545 3509181 + Conep06aG0071600.1 Cone6ag0694 694
9 3316604 3320016 - Conep09aG0070900.1 Cone9ag0692 692
9 3338531 3339533 - Conep09aG0071200.1 Cone9ag0695 695
12 2100464 2105877 + Conep12aG0038200.1 Cone12ag0367 367
5 1375105 1381288 + Cp4.1LG05g02340.1 Cpe05g00242 242
8 6011359 6018040 - Cp4.1LG08g07570.1 Cpe08g00749 749
8 6050729 6055112 + Cp4.1LG08g07490.1 Cpe08g00751 751
13 1679233 1683606 - Cp4.1LG13g02150.1 Cpe13g00222 222
14 7248094 7252649 - Cp4.1LG14g08820.1 Cpe14g00878 878
14 7292929 7299804 + Cp4.1LG14g08810.1 Cpe14g00881 881
9 40333348 40334223 + CrPI670011_09g021350.1 Cre09g2135 2135
9 40365377 40367439 - CrPI670011_09g021380.1 Cre09g2138 2138
10 4761338 4768573 - CrPI670011_10g005340.1 Cre10g0534 534
10 4903151 4908846 + CrPI670011_10g005390.1 Cre10g0539 539
3 2546039 2563471 + CsaV3_3G003010.1 Csa03g00301 301
3 40664396 40666530 + CsaV3_3G049810.1 Csa03g04675 4675
5 2593967 2599602 - CsaV3_5G003990.1 Csa05g00399 399
5 2606992 2609507 + CsaV3_5G004000.1 Csa05g00400 400
5 2635203 2637092 - CsaV3_5G004030.1 Csa05g00403 403
6 60708847 60717564 - Hsped.06g11480.1 Hepe06g1148 1148
6 67445543 67450399 - Hsped.06g16550.1 Hepe06g1655 1655
6 67463511 67465656 + Hsped.06g16560.1 Hepe06g1656 1656
6 67493750 67494958 - Hsped.06g16580.1 Hepe06g1658 1658
11 38592982 38598027 - Lag0032893.1 Lac11g2255 2255
11 38633858 38636121 + Lag0032895.1 Lac11g2257 2257
11 38669947 38670807 - Lag0032899.1 Lac11g2261 2261
11 38705747 38712204 + Lag0032900.1 Lac11g2262 2262
12 39064792 39070575 - Maker00038213 Lcy12g1801 1801
12 39114059 39116373 + Maker00037949 Lcy12g1803 1803
12 39148952 39149812 - Maker00038228 Lcy12g1806 1806
12 39202246 39211195 + Maker00037891 Lcy12g1808 1808
7 19321813 19332193 - Lsi07G013190.1 Lsi07g01319 1319
7 19419291 19423185 + Lsi07G013220.1 Lsi07g01322 1322
7 19438941 19443917 + Lsi07G013260.1 Lsi07g01326 1326
9 4242194 4243907 - Lsi09G004030.1 Lsi09g00403 403
9 4257550 4261465 + Lsi09G004040.1 Lsi09g00404 404
9 4297045 4297923 - Lsi09G004070.1 Lsi09g00407 407
10 16778350 16780897 + MC10g1325 Mch10g1668 1668
1 26087445 26090110 + Tan0013003.2 Tan01g2199 2199
2 4923751 4935337 - Vvi2g502 Vvi2g502 502
2 4948963 4950534 + Vvi2g503 Vvi2g503 503
2 4951820 4956004 - Vvi2g504 Vvi2g504 504
2 4957740 4960852 - Vvi2g505 Vvi2g505 505
2 4962611 4965728 - Vvi2g506 Vvi2g506 506
2 4974656 4978139 - Vvi2g507 Vvi2g507 507
2 4983355 4986675 + Vvi2g508 Vvi2g508 508
2 4989460 4989778 + Vvi2g509 Vvi2g509 509
2 5025233 5026199 - Vvi2g510 Vvi2g510 510
2 5062530 5074048 + Vvi2g511 Vvi2g511 511
       

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