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
Vvi18g320 . . . . . . . . Cmo04g02445 Cmo15g00720 . . . . . . . . . . . . . . . . . . . . . Cone4ag1377 Cone7ag1554 Cone17ag1264 Cone20ag0464 . . . . Blo17g00190 Blo18g00195 . Bda13g01496 Bpe02g01623 Bpe14g00370 Bma01g00837 Bma02g00235 . . . . . Car04g02258 Car15g00652 Cpe01g02027 . . . . . . . . . . . . . . . . . . .
Vvi18g321 . Blo12g00685 . Bda03g00521 . Bpe04g00475 . Bma01g02639 Cmo04g02444 Cmo15g00721 Cma01g01404 . . . . Cpe06g00646 . . . . . . . . . . . . . . . Cone4ag1376 Cone7ag1555 Cone17ag1263 Cone20ag0465 Lsi04g02372 Csa04g01823 . . Blo17g00191 Blo18g00196 Bda11g00745 Bda13g01497 Bpe02g01622 Bpe14g00369 Bma01g00838 Bma02g00236 Sed01g3035 Cmo01g01454 Cmo09g00805 . . Car04g02257 Car09g00727 Cpe01g02026 Cpe02g00538 Bhi09g02644 Tan01g3988 Cmetu09g1764 . Hepe01g2261 Mch11g0811 . Cla11g01519 Cam11g1579 Cec11g1608 Cco11g1607 Clacu11g1734 Cmu11g1552 Cre11g1971 . . Chy07g00670 Cme07g00877
Vvi18g322 . . . . Bpe02g00079 . . . Cmo04g02442 Cmo15g00723 Cma01g01405 . . . . . . . . . . . . . . . . . . . . . Cone7ag1556 . . Lsi04g02370 . . . Blo17g00192 . . Bda13g01498 . Bpe14g00368 . Bma02g00237 Sed01g3032 Cmo01g01455 . . . Car04g02253 Car15g00654 Cpe01g02025 Cpe02g00537 Bhi09g02643 Tan01g3987 Cmetu07g0205 . Hepe01g2260 Mch11g0810 . Cla11g01518 Cam11g1578 Cec11g1607 Cco11g1606 Clacu11g1733 Cmu11g1551 Cre11g1970 . . Chy07g00677 Cme07g00882
Vvi18g323 . . . . . . . . . Cmo15g00725 . . . . . . . . . . . . . . . . . . . . . Cone4ag1375 Cone7ag1557 . . . . . . Blo17g00193 . . Bda13g01499 . Bpe14g00367 . Bma02g00238 . . . . . . Car15g00655 . . . . . . . . . . . . . . . . . . . .
Vvi18g324 . . . Bda03g00519 . Bpe04g00474 . . . . Cma01g01406 . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g02369 Csa04g01828 . . . . . . . . . . Sed12g1443 Cmo01g01456 . . . . . . Cpe02g00536 Bhi09g02642 Tan01g3986 Cmetu07g0316 . Hepe01g2259 . . Cla11g01517 Cam11g1577 Cec11g1606 Cco11g1605 Clacu11g1732 Cmu11g1550 Cre11g1969 . . Chy07g00678 Cme07g00883
Vvi18g325 . . . . . . . . Cmo04g02441 Cmo15g00727 . Cma09g00664 . . . Cpe06g00519 . . . . . . . . . . . . . . . . . . Cone20ag0466 Lsi04g02366 Csa04g01830 . . Blo17g00195 Blo18g00197 . Bda13g01500 Bpe02g01621 Bpe14g00366 Bma01g00839 Bma02g00239 Sed04g0506 . Cmo09g00648 . . Car04g02252 Car09g00590 Cpe01g02024 . Bhi09g02640 Tan01g3984 Cmetu09g0993 . Hepe01g2257 Mch11g0805 . Cla11g01515 Cam11g1575 Cec11g1604 Cco11g1602 Clacu11g1730 Cmu11g1548 Cre11g1965 . . Chy07g00682 Cme07g00892
Vvi18g326 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g327 . . . . . . . . Cmo04g02438 Cmo15g00731 . . . . . . . . . . . . . . . . . . . . . Cone4ag1373 Cone7ag1558 . . . . . . Blo17g00196 Blo18g00198 . Bda13g01501 Bpe02g01620 Bpe14g00365 Bma01g00840 Bma02g00240 . . . . . Car04g02250 Car15g00658 Cpe01g02022 . . . . . . . . . . . . . . . . . . .
Vvi18g328 . Blo12g00687 . . Bpe02g00081 . . Bma01g02638 Cmo04g02435 Cmo15g00733 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo17g00197 Blo18g00199 Bda11g00746 Bda01g01408 Bpe02g01619 Bpe14g00364 Bma01g00841 Bma02g00241 . . . . . Car04g02247 Car15g00659 Cpe01g02021 . . . . . . . . . . . . . . . . . . .
Vvi18g329 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 49972122 49981065 + Bda003650.1 Bda01g01408 1408
3 4357026 4357529 + Bda016488.1 Bda03g00519 519
3 4365376 4367244 - Bda016490.1 Bda03g00521 521
11 7485810 7488602 + Bda005492.1 Bda11g00745 745
11 7499350 7503304 - Bda005493.1 Bda11g00746 746
13 38007048 38015639 + Bda000342.1 Bda13g01496 1496
13 38019330 38022504 + Bda000343.1 Bda13g01497 1497
13 38027175 38033761 + Bda000344.1 Bda13g01498 1498
13 38034246 38035539 - Bda000345.1 Bda13g01499 1499
13 38038976 38042326 - Bda000346.1 Bda13g01500 1500
13 38048202 38049023 - Bda000347.1 Bda13g01501 1501
9 71038915 71042205 + XM_039041148.1 Bhi09g02640 2640
9 71175186 71175917 + XM_039041554.1 Bhi09g02642 2642
9 71180617 71182763 - XM_039040687.1 Bhi09g02643 2643
9 71232836 71237992 - XM_039041747.1 Bhi09g02644 2644
12 25088274 25098185 + BLOR04704 Blo12g00685 685
12 25113978 25117025 - BLOR04706 Blo12g00687 687
17 1927789 1938999 + BLOR16011 Blo17g00190 190
17 1939023 1942203 + BLOR16012 Blo17g00191 191
17 1955464 1956927 + BLOR16013 Blo17g00192 192
17 1957340 1959012 - BLOR16014 Blo17g00193 193
17 1969855 1973171 - BLOR16016 Blo17g00195 195
17 1975340 1983517 - BLOR16017 Blo17g00196 196
17 1987384 1994296 - BLOR16018 Blo17g00197 197
18 1896298 1902715 + BLOR08683 Blo18g00195 195
18 1906785 1909884 + BLOR08684 Blo18g00196 196
18 1927631 1930913 - BLOR08685 Blo18g00197 197
18 1938239 1938982 - BLOR08686 Blo18g00198 198
18 1953006 1958640 - BLOR08687 Blo18g00199 199
1 7920131 7921203 - Bma001058.1 Bma01g00837 837
1 7924137 7927259 + Bma001059.1 Bma01g00838 838
1 7935673 7939183 - Bma001060.1 Bma01g00839 839
1 7947809 7948789 - Bma001061.1 Bma01g00840 840
1 7951419 7960174 - Bma001062.1 Bma01g00841 841
1 83891178 83895279 + Bma003523.1 Bma01g02638 2638
1 83905584 83908748 - Bma003524.1 Bma01g02639 2639
2 2467226 2479277 + Bma030861 Bma02g00235 235
2 2483051 2486198 + Bma014692.1 Bma02g00236 236
2 2496105 2497584 + Bma014693.1 Bma02g00237 237
2 2497999 2499644 - Bma030862 Bma02g00238 238
2 2504027 2507243 - Bma014694.1 Bma02g00239 239
2 2513821 2514852 - Bma014695.1 Bma02g00240 240
2 2518061 2524804 - Bma014696.1 Bma02g00241 241
2 605498 606853 + Bpe007929.1 Bpe02g00079 79
2 608986 613138 - Bpe007931.1 Bpe02g00081 81
2 19064137 19070627 + Bpe009466.1 Bpe02g01619 1619
2 19073756 19074736 + Bpe009467.2 Bpe02g01620 1620
2 19078656 19082198 + Bpe009468.1 Bpe02g01621 1621
2 19088944 19092068 - Bpe009469.1 Bpe02g01622 1622
2 19095987 19102904 - Bpe009470.1 Bpe02g01623 1623
4 2994867 2995340 + Bpe015160.1 Bpe04g00474 474
4 3002766 3005950 - Bpe015161.1 Bpe04g00475 475
14 3471716 3478214 + Bpe007019.1 Bpe14g00364 364
14 3481281 3482267 + Bpe024974 Bpe14g00365 365
14 3486910 3490535 + Bpe007021.1 Bpe14g00366 366
14 3493906 3495443 + Bpe007022.1 Bpe14g00367 367
14 3495916 3496842 - Bpe007023.1 Bpe14g00368 368
14 3504533 3507705 - Bpe007024.1 Bpe14g00369 369
14 3511212 3517846 - Bpe007025.1 Bpe14g00370 370
11 28498019 28501033 + CaPI482276_11g015750.1 Cam11g1575 1575
11 28514724 28515200 + CaPI482276_11g015770.1 Cam11g1577 1577
11 28516625 28517941 - CaPI482276_11g015780.1 Cam11g1578 1578
11 28533636 28537419 - CaPI482276_11g015790.1 Cam11g1579 1579
4 18194981 18199361 + Carg18236-RA Car04g02247 2247
4 18203555 18204535 + Carg18233-RA Car04g02250 2250
4 18209258 18211488 + Carg18231-RA Car04g02252 2252
4 18212673 18214014 - Carg18230-RA Car04g02253 2253
4 18222683 18224801 - Carg18226-RA Car04g02257 2257
4 18231371 18239045 - Carg18225-RA Car04g02258 2258
9 3337129 3340494 + Carg03073-RA Car09g00590 590
9 4308582 4312687 + Carg17047-RA Car09g00727 727
15 3598111 3607579 + Carg01503-RA Car15g00652 652
15 3624688 3626251 + Carg01501-RA Car15g00654 654
15 3627463 3631880 - Carg01500-RA Car15g00655 655
15 3657191 3662223 - Carg01497-RA Car15g00658 658
15 3664044 3669039 - Carg01496-RA Car15g00659 659
11 28873764 28876778 + CcPI632755_11g016020.1 Cco11g1602 1602
11 28888873 28889349 + CcPI632755_11g016050.1 Cco11g1605 1605
11 28890784 28892160 - CcPI632755_11g016060.1 Cco11g1606 1606
11 28908428 28912212 - CcPI632755_11g016070.1 Cco11g1607 1607
11 30327135 30330145 + CePI673135_11g016040.1 Cec11g1604 1604
11 30341919 30342395 + CePI673135_11g016060.1 Cec11g1606 1606
11 30343675 30344978 - CePI673135_11g016070.1 Cec11g1607 1607
11 30359056 30364571 - CePI673135_11g016080.1 Cec11g1608 1608
7 6433003 6436693 + Chy7G135000.1 Chy07g00670 670
7 6515585 6517346 + Chy7G135070.1 Chy07g00677 677
7 6544784 6545239 - Chy7G135080.1 Chy07g00678 678
7 6605252 6608141 - Chy7G135120.1 Chy07g00682 682
11 28524267 28527279 + ClG42_11g0173000.10 Clacu11g1730 1730
11 28539948 28540424 + ClG42_11g0173200.10 Clacu11g1732 1732
11 28541862 28543170 - ClG42_11g0173300.10 Clacu11g1733 1733
11 28556689 28562218 - ClG42_11g0173400.10 Clacu11g1734 1734
11 28795757 28798769 + ClCG11G015520.1 Cla11g01515 1515
11 28813917 28814393 + ClCG11G015540.1 Cla11g01517 1517
11 28815831 28817141 - ClCG11G015550.1 Cla11g01518 1518
11 28830724 28837171 - ClCG11G015560.2 Cla11g01519 1519
1 9933775 9937833 + CmaCh01G014040.1 Cma01g01404 1404
1 9943074 9944174 + CmaCh01G014050.1 Cma01g01405 1405
1 9945430 9945903 - CmaCh01G014060.1 Cma01g01406 1406
9 3143282 3146465 + CmaCh09G006640.1 Cma09g00664 664
7 8795980 8800831 + MELO3C010456.2.1 Cme07g00877 877
7 8849061 8851149 + MELO3C032636.2.1 Cme07g00882 882
7 8891356 8892075 - MELO3C010454.2.1 Cme07g00883 883
7 9089573 9092706 - MELO3C010444.2.1 Cme07g00892 892
7 19426066 19427840 - PI0024099.1 Cmetu07g0205 205
7 19411478 19412531 + PI0019609.1 Cmetu07g0316 316
9 13779147 13782726 + PI0028836.1 Cmetu09g0993 993
9 13983207 13986352 - PI0011715.1 Cmetu09g1764 1764
1 11342708 11347232 + CmoCh01G014540.1 Cmo01g01454 1454
1 11352770 11353880 + CmoCh01G014550.1 Cmo01g01455 1455
1 11354914 11355387 - CmoCh01G014560.1 Cmo01g01456 1456
4 18073433 18078923 + CmoCh04G024350.1 Cmo04g02435 2435
4 18083761 18084741 + CmoCh04G024380.1 Cmo04g02438 2438
4 18089704 18092005 + CmoCh04G024410.1 Cmo04g02441 2441
4 18092925 18094603 - CmoCh04G024420.1 Cmo04g02442 2442
4 18101666 18105316 - CmoCh04G024440.1 Cmo04g02444 2444
4 18112176 18120382 - CmoCh04G024450.1 Cmo04g02445 2445
9 3235211 3238354 + CmoCh09G006480.1 Cmo09g00648 648
9 4121256 4125169 + CmoCh09G008050.1 Cmo09g00805 805
15 3503276 3513449 + CmoCh15G007200.1 Cmo15g00720 720
15 3520575 3524089 + CmoCh15G007210.1 Cmo15g00721 721
15 3531267 3532831 + CmoCh15G007230.1 Cmo15g00723 723
15 3537178 3538122 - CmoCh15G007250.1 Cmo15g00725 725
15 3549157 3552290 + CmoCh15G007270.1 Cmo15g00727 727
15 3576487 3577482 - CmoCh15G007310.1 Cmo15g00731 731
15 3583896 3588366 - CmoCh15G007330.1 Cmo15g00733 733
11 27776678 27779690 + CmPI595203_11g015480.1 Cmu11g1548 1548
11 27792319 27792795 + CmPI595203_11g015500.1 Cmu11g1550 1550
11 27794238 27795548 - CmPI595203_11g015510.1 Cmu11g1551 1551
11 27808952 27814451 - CmPI595203_11g015520.1 Cmu11g1552 1552
4 11139049 11141234 + Conep04aG0142200.1 Cone4ag1373 1373
4 11145964 11147094 + Conep04aG0142400.1 Cone4ag1375 1375
4 11162535 11166701 - Conep04aG0142500.1 Cone4ag1376 1376
4 11171824 11173412 - Conep04aG0142600.1 Cone4ag1377 1377
7 10691928 10693245 + Conep07aG0160000.1 Cone7ag1554 1554
7 10695384 10699403 + Conep07aG0160100.1 Cone7ag1555 1555
7 10706329 10708559 + Conep07aG0160200.1 Cone7ag1556 1556
7 10709549 10711282 - Conep07aG0160300.1 Cone7ag1557 1557
7 10713396 10715572 - Conep07aG0160400.1 Cone7ag1558 1558
17 9100578 9104423 - Conep17aG0129400.1 Cone17ag1263 1263
17 9107629 9114948 - Conep17aG0129500.1 Cone17ag1264 1264
20 2407934 2415736 + Conep20aG0047900.1 Cone20ag0464 464
20 2425262 2429807 + Conep20aG0048000.1 Cone20ag0465 465
20 2440144 2444199 - Conep20aG0048100.1 Cone20ag0466 466
1 17213329 17218668 + Cp4.1LG01g20200.1 Cpe01g02021 2021
1 17219910 17223680 + Cp4.1LG01g20240.1 Cpe01g02022 2022
1 17228582 17230921 + Cp4.1LG01g20220.1 Cpe01g02024 2024
1 17231969 17233547 - Cp4.1LG01g20260.1 Cpe01g02025 2025
1 17240522 17244833 - Cp4.1LG01g20290.1 Cpe01g02026 2026
1 17251190 17259160 - Cp4.1LG01g20280.1 Cpe01g02027 2027
2 3182671 3183144 + Cp4.1LG02g03370.1 Cpe02g00536 536
2 3184265 3185521 - Cp4.1LG02g03330.1 Cpe02g00537 537
2 3190427 3195236 - Cp4.1LG02g03300.1 Cpe02g00538 538
6 3100083 3104069 + Cp4.1LG06g05180.1 Cpe06g00519 519
6 3996830 4001464 + Cp4.1LG06g06480.1 Cpe06g00646 646
11 31423620 31426632 + CrPI670011_11g019650.1 Cre11g1965 1965
11 31438095 31438571 + CrPI670011_11g019690.1 Cre11g1969 1969
11 31439996 31441426 - CrPI670011_11g019700.1 Cre11g1970 1970
11 31456082 31461587 - CrPI670011_11g019710.1 Cre11g1971 1971
4 17860259 17866723 + CsaV3_4G028490.1 Csa04g01823 1823
4 17930673 17931878 - CsaV3_4G028540.1 Csa04g01828 1828
4 17957732 17961707 - CsaV3_4G028560.1 Csa04g01830 1830
1 87210185 87213867 + Hsped.01g22570.1 Hepe01g2257 2257
1 87226044 87226517 + Hsped.01g22590.1 Hepe01g2259 2259
1 87229154 87230332 - Hsped.01g22600.1 Hepe01g2260 2260
1 87246967 87252215 - Hsped.01g22610.1 Hepe01g2261 2261
4 30810134 30812218 + Lsi04G023660.1 Lsi04g02366 2366
4 30828042 30828521 + Lsi04G023690.1 Lsi04g02369 2369
4 30830465 30831643 - Lsi04G023700.1 Lsi04g02370 2370
4 30848515 30853290 - Lsi04G023720.1 Lsi04g02372 2372
11 5414020 5417434 + MC11g0680 Mch11g0805 805
11 5461795 5462974 - MC11g0682 Mch11g0810 810
11 5472444 5478186 - MC11g0683 Mch11g0811 811
1 33213251 33214881 - Sed0027932.1 Sed01g3032 3032
1 33357053 33361207 - Sed0012969.1 Sed01g3035 3035
4 3787345 3791073 - Sed0022627.1 Sed04g0506 506
12 12278927 12279400 + Sed0011944.1 Sed12g1443 1443
1 104649703 104653741 + Tan0000932.1 Tan01g3984 3984
1 104703949 104704731 + Tan0015113.1 Tan01g3986 3986
1 104708851 104710103 - Tan0017360.1 Tan01g3987 3987
1 104736306 104741761 - Tan0002616.1 Tan01g3988 3988
18 3515279 3530530 + Vvi18g320 Vvi18g320 320
18 3536801 3542239 + Vvi18g321 Vvi18g321 321
18 3555521 3560233 + Vvi18g322 Vvi18g322 322
18 3562457 3563622 - Vvi18g323 Vvi18g323 323
18 3564129 3567538 - Vvi18g324 Vvi18g324 324
18 3577961 3582206 - Vvi18g325 Vvi18g325 325
18 3586979 3587379 + Vvi18g326 Vvi18g326 326
18 3587964 3594834 - Vvi18g327 Vvi18g327 327
18 3594892 3606331 - Vvi18g328 Vvi18g328 328
18 3638734 3639936 + Vvi18g329 Vvi18g329 329
       

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