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
Vvi18g330 . . . . Bpe02g00082 . . Bma01g02637 Cmo04g02433 Cmo15g00734 Cma01g01407 Cma09g00662 . . . Cpe06g00518 . . . . . . . . . . . . . . . . . . . Lsi04g02363 Csa04g01832 . . Blo17g00198 Blo18g00201 Bda11g00747 Bda13g01502 Bpe02g01618 Bpe14g00363 Bma01g00845 Bma02g00242 . Cmo01g01457 Cmo09g00647 . . Car04g02246 Car15g00660 Cpe01g02020 Cpe02g00535 Bhi09g02636 . . . . . . Cla11g01513 Cam11g1573 Cec11g1602 Cco11g1600 Clacu11g1728 Cmu11g1547 Cre11g1963 . . Chy07g00685 Cme07g00893
Vvi18g331 . Blo12g00688 . Bda03g00516 Bpe02g00083 . . Bma01g02636 Cmo04g02431 Cmo15g00735 . . . . . . . . . . . . . . . . . . . . . Cone4ag1370 Cone7ag1561 . . . . . . . . Bda11g00748 . . . . . . . . . . Car04g02244 Car15g00661 Cpe01g02019 . . . . . . . . . . . . . . . . . . .
Vvi18g332 . . . . . . . . Cmo04g02429 . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1260 Cone20ag0468 . . . . Blo17g00200 . . Bda13g01503 . Bpe14g00362 . Bma02g00243 . . . . . Car04g02243 Car15g00662 Cpe01g02018 . . . . . . . . . . . . . . . . . . .
Vvi18g333 . . . Bda03g00515 . Bpe04g00471 . . Cmo04g02426 Cmo15g00736 . . . . . . . . . . . . . . . . . . . . . Cone4ag1369 Cone7ag1562 Cone17ag1257 Cone20ag0470 . . . . . . Bda11g00749 . . . . . . . . . . Car04g02241 Car15g00663 Cpe01g02016 . . . . . . . . . . . . . . . . . . .
Vvi18g334 . . . . . . . . Cmo04g02424 Cmo15g00739 . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1256 Cone20ag0471 . . . . Blo17g00201 . . Bda13g01504 . Bpe14g00360 . Bma02g00245 . . . . . Car04g02239 Car15g00666 Cpe01g02014 . . . . . . . . . . . . . . . . . . .
Vvi18g335 . Blo12g00690 . . Bpe02g00084 Bpe04g00469 . Bma01g02634 . . Cma01g01410 . . . . Cpe06g00516 . . . . . . . . Cla08g01090 Cam08g1544 Cec08g1118 Cco08g1244 Clacu08g1246 . Cre08g1027 Cone4ag1367 Cone7ag1564 . . Lsi04g02358 Csa04g01837 . Cme03g01504 . . . . . . . . Sed12g1437 Cmo01g01460 . . . . Car09g00585 . Cpe02g00534 Bhi09g02631 Tan01g3976 Cmetu07g2082 . Hepe01g2252 . . Cla11g01509 Cam11g1568 Cec11g1597 Cco11g1595 Clacu11g1724 Cmu11g1544 Cre11g1959 Lsi08g00947 . Chy07g00693 Cme07g00904
Vvi18g336 . . . . . . . . . . . . . . Sed11g1242 . Cpe07g00119 Bhi04g00709 Tan02g2360 Cmetu03g0768 . . . . Cla08g01089 Cam08g1541 Cec08g1115 Cco08g1242 Clacu08g1244 . Cre08g1025 Cone4ag1366 Cone7ag1565 . . . . . Cme03g01501 . . . . . . . . . . . Cma12g00141 . . . . . . . . . . . . . . . . . . . Lsi08g00945 . . .
Vvi18g337 . . . . . . . . . . . . . . Sed04g0120 . . Bhi04g00710 Tan02g2359 Cmetu03g1655 . . . . Cla08g01088 Cam08g1540 Cec08g1114 Cco08g1241 Clacu08g1243 . Cre08g1024 . . . . . . . Cme03g01500 Blo17g00126 Blo18g00139 . . . . Bma01g01425 . . . . Cma12g00140 . . . . . . . . . . . . . . . . . . . Lsi08g00944 . . .
Vvi18g338 . . . . . . . . . . . . . Car12g00130 Sed04g0119 . Cpe07g00118 Bhi04g00711 Tan02g2357 Cmetu03g1212 . Hepe10g0529 . . Cla08g01087 Cam08g1539 Cec08g1113 Cco08g1240 Clacu08g1242 . Cre08g1023 . . . . . Csa04g01882 . Cme03g01499 . . . . . . . Bma02g00258 . . . Cma12g00139 . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g339 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 4337601 4343526 - Bda016484.1 Bda03g00515 515
3 4345343 4347188 + Bda016485.1 Bda03g00516 516
11 7505676 7508576 + Bda005494.1 Bda11g00747 747
11 7509246 7510548 - Bda033059 Bda11g00748 748
11 7511472 7514397 + Bda005495.1 Bda11g00749 749
13 38105349 38109193 + Bda000351.1 Bda13g01502 1502
13 38110393 38118800 + Bda000352.1 Bda13g01503 1503
13 38121667 38125463 - Bda000353.1 Bda13g01504 1504
4 16991364 16994395 + XM_039028761.1 Bhi04g00709 709
4 17101903 17106276 + XM_039030663.1 Bhi04g00710 710
4 17134623 17136910 + XM_039028202.1 Bhi04g00711 711
9 70896347 70900820 + XM_039043233.1 Bhi09g02631 2631
9 70950749 70957119 + XM_039043495.1 Bhi09g02636 2636
12 25119502 25132715 - BLOR04707 Blo12g00688 688
12 25135917 25138970 - BLOR04709 Blo12g00690 690
17 1161328 1163120 + BLOR15947 Blo17g00126 126
17 2000988 2004809 + BLOR16019 Blo17g00198 198
17 2016578 2017236 + BLOR16021 Blo17g00200 200
17 2020039 2023833 - BLOR16022 Blo17g00201 201
18 1291580 1293977 - BLOR08627 Blo18g00139 139
18 1968756 1972755 + BLOR08689 Blo18g00201 201
1 7992721 7996257 + Bma001066.1 Bma01g00845 845
1 24198923 24205897 - Bma001793.1 Bma01g01425 1425
1 83877737 83880064 + Bma003519.1 Bma01g02634 2634
1 83884039 83885078 + Bma003521.1 Bma01g02636 2636
1 83886250 83888692 - Bma003522.1 Bma01g02637 2637
2 2558655 2563204 + Bma014698.1 Bma02g00242 242
2 2564420 2572913 + Bma014699.1 Bma02g00243 243
2 2575487 2579205 - Bma014701.1 Bma02g00245 245
2 2724615 2727194 - Bma014714.1 Bma02g00258 258
2 615628 618565 + Bpe007932.1 Bpe02g00082 82
2 619241 620605 - Bpe007933.1 Bpe02g00083 83
2 645603 648090 - Bpe007935.1 Bpe02g00084 84
2 19047156 19051154 - Bpe009465.1 Bpe02g01618 1618
4 2971901 2974771 + Bpe015155.1 Bpe04g00469 469
4 2976987 2982837 - Bpe015157.1 Bpe04g00471 471
14 3441896 3447578 + Bpe024973 Bpe14g00360 360
14 3450469 3458880 - Bpe007017.1 Bpe14g00362 362
14 3460051 3463884 - Bpe007018.1 Bpe14g00363 363
8 21628092 21629763 - CaPI482276_08g015390.1 Cam08g1539 1539
8 21634746 21638293 - CaPI482276_08g015400.1 Cam08g1540 1540
8 21643660 21645000 - CaPI482276_08g015410.1 Cam08g1541 1541
8 21656820 21660277 + CaPI482276_08g015440.1 Cam08g1544 1544
11 28456148 28459832 + CaPI482276_11g015680.1 Cam11g1568 1568
11 28476148 28493325 + CaPI482276_11g015730.1 Cam11g1573 1573
4 18130949 18135739 + Carg18244-RA Car04g02239 2239
4 18140975 18146654 - Carg18242-RA Car04g02241 2241
4 18156284 18175669 - Carg18240-RA Car04g02243 2243
4 18176819 18182759 + Carg18239-RA Car04g02244 2244
4 18184261 18189239 - Carg18237-RA Car04g02246 2246
9 3305090 3308907 + Carg03068-RA Car09g00585 585
12 745295 748426 - Carg20555-RA Car12g00130 130
15 3674609 3678869 + Carg01495-RA Car15g00660 660
15 3679391 3683406 - Carg01494-RA Car15g00661 661
15 3683951 3701550 + Carg01493-RA Car15g00662 662
15 3702233 3707889 + Carg01492-RA Car15g00663 663
15 3713107 3717901 - Carg01489-RA Car15g00666 666
8 24190880 24192564 - CcPI632755_08g012400.1 Cco08g1240 1240
8 24197638 24201274 - CcPI632755_08g012410.1 Cco08g1241 1241
8 24207246 24208583 - CcPI632755_08g012420.1 Cco08g1242 1242
8 24220251 24223650 + CcPI632755_08g012440.1 Cco08g1244 1244
11 28826107 28829856 + CcPI632755_11g015950.1 Cco11g1595 1595
11 28859298 28865050 + CcPI632755_11g016000.1 Cco11g1600 1600
8 23038349 23040034 - CePI673135_08g011130.1 Cec08g1113 1113
8 23045001 23048623 - CePI673135_08g011140.1 Cec08g1114 1114
8 23054259 23055599 - CePI673135_08g011150.1 Cec08g1115 1115
8 23067297 23070715 + CePI673135_08g011180.1 Cec08g1118 1118
11 30285371 30289115 + CePI673135_11g015970.1 Cec11g1597 1597
11 30310938 30321835 + CePI673135_11g016020.1 Cec11g1602 1602
7 6654926 6659801 - Chy7G135150.1 Chy07g00685 685
7 6709070 6712789 - Chy7G135230.1 Chy07g00693 693
8 22396046 22397731 - ClG42_08g0124200.10 Clacu08g1242 1242
8 22402708 22406198 - ClG42_08g0124300.10 Clacu08g1243 1243
8 22411616 22412953 - ClG42_08g0124400.10 Clacu08g1244 1244
8 22427389 22430791 + ClG42_08g0124600.10 Clacu08g1246 1246
11 28482326 28486091 + ClG42_11g0172400.10 Clacu11g1724 1724
11 28502458 28515786 + ClG42_11g0172800.10 Clacu11g1728 1728
8 23625256 23627268 - ClCG08G010900.1 Cla08g01087 1087
8 23631944 23635901 - ClCG08G010910.1 Cla08g01088 1088
8 23641067 23644047 - ClCG08G010920.2 Cla08g01089 1089
8 23656473 23660380 + ClCG08G010930.1 Cla08g01090 1090
11 28752101 28756319 + ClCG11G015460.2 Cla11g01509 1509
11 28780723 28786944 + ClCG11G015500.1 Cla11g01513 1513
1 9947283 9951797 - CmaCh01G014070.1 Cma01g01407 1407
1 9959422 9963924 - CmaCh01G014100.1 Cma01g01410 1410
9 3137498 3141840 + CmaCh09G006620.1 Cma09g00662 662
12 606135 609212 - CmaCh12G001390.1 Cma12g00139 139
12 610877 613604 - CmaCh12G001400.1 Cma12g00140 140
12 614875 616221 - CmaCh12G001410.1 Cma12g00141 141
3 24221630 24223746 - MELO3C011373.2.1 Cme03g01499 1499
3 24227557 24231136 - MELO3C011372.2.1 Cme03g01500 1500
3 24234776 24237844 - MELO3C011371.2.1 Cme03g01501 1501
3 24276211 24279997 + MELO3C011369.2.1 Cme03g01504 1504
7 9311081 9317138 - MELO3C010439.2.1 Cme07g00893 893
7 9422045 9426535 - MELO3C010434.2.1 Cme07g00904 904
3 5139948 5143309 + PI0028918.1 Cmetu03g0768 768
3 5155033 5157131 + PI0024205.1 Cmetu03g1212 1212
3 5149308 5152974 + PI0006388.2 Cmetu03g1655 1655
7 19287458 19291883 + PI0011003.1 Cmetu07g2082 2082
1 11356758 11360764 - CmoCh01G014570.1 Cmo01g01457 1457
1 11368827 11374001 - CmoCh01G014600.1 Cmo01g01460 1460
4 18006448 18011181 + CmoCh04G024240.1 Cmo04g02424 2424
4 18016868 18021951 - CmoCh04G024260.1 Cmo04g02426 2426
4 18032803 18053643 - CmoCh04G024290.1 Cmo04g02429 2429
4 18055288 18060308 + CmoCh04G024310.1 Cmo04g02431 2431
4 18061483 18066674 - CmoCh04G024330.1 Cmo04g02433 2433
9 3228940 3233413 + CmoCh09G006470.1 Cmo09g00647 647
15 3593474 3598194 + CmoCh15G007340.1 Cmo15g00734 734
15 3598749 3602054 - CmoCh15G007350.1 Cmo15g00735 735
15 3602594 3626812 + CmoCh15G007360.1 Cmo15g00736 736
15 3631849 3636622 - CmoCh15G007390.1 Cmo15g00739 739
11 27734678 27738443 + CmPI595203_11g015440.1 Cmu11g1544 1544
11 27749389 27773163 + CmPI595203_11g015470.1 Cmu11g1547 1547
4 11104946 11107738 - Conep04aG0141500.1 Cone4ag1366 1366
4 11109090 11112030 + Conep04aG0141600.1 Cone4ag1367 1367
4 11120228 11123840 - Conep04aG0141800.1 Cone4ag1369 1369
4 11124045 11126683 + Conep04aG0141900.1 Cone4ag1370 1370
7 10730781 10733484 - Conep07aG0160700.1 Cone7ag1561 1561
7 10733882 10736222 + Conep07aG0160800.1 Cone7ag1562 1562
7 10740700 10744052 - Conep07aG0161000.1 Cone7ag1564 1564
7 10746232 10747099 + Conep07aG0161100.1 Cone7ag1565 1565
17 9046833 9049829 + Conep17aG0128700.1 Cone17ag1256 1256
17 9051917 9055417 - Conep17aG0128800.1 Cone17ag1257 1257
17 9066778 9075195 - Conep17aG0129100.1 Cone17ag1260 1260
20 2459873 2468215 + Conep20aG0048300.1 Cone20ag0468 468
20 2477098 2480493 + Conep20aG0048500.1 Cone20ag0470 470
20 2486748 2489608 - Conep20aG0048600.1 Cone20ag0471 471
1 17151608 17156456 + Cp4.1LG01g20050.1 Cpe01g02014 2014
1 17161629 17167046 - Cp4.1LG01g20150.1 Cpe01g02016 2016
1 17174767 17193976 - Cp4.1LG01g20170.1 Cpe01g02018 2018
1 17195724 17201208 + Cp4.1LG01g20060.1 Cpe01g02019 2019
1 17202950 17208760 - Cp4.1LG01g20310.1 Cpe01g02020 2020
2 3163262 3168382 + Cp4.1LG02g03400.1 Cpe02g00534 534
2 3175397 3181466 + Cp4.1LG02g03380.1 Cpe02g00535 535
6 3071079 3075156 + Cp4.1LG06g05000.1 Cpe06g00516 516
6 3093652 3098169 + Cp4.1LG06g05220.1 Cpe06g00518 518
7 659616 667476 - Cp4.1LG07g01180.1 Cpe07g00118 118
7 668781 671351 - Cp4.1LG07g01200.1 Cpe07g00119 119
8 23395752 23397437 - CrPI670011_08g010230.1 Cre08g1023 1023
8 23401708 23405398 - CrPI670011_08g010240.1 Cre08g1024 1024
8 23411267 23412607 - CrPI670011_08g010250.1 Cre08g1025 1025
8 23424187 23427580 + CrPI670011_08g010270.1 Cre08g1027 1027
11 31381931 31385691 + CrPI670011_11g019590.1 Cre11g1959 1959
11 31401820 31415119 + CrPI670011_11g019630.1 Cre11g1963 1963
4 17973440 17977861 - CsaV3_4G028580.1 Csa04g01832 1832
4 18004601 18008883 - CsaV3_4G028630.1 Csa04g01837 1837
4 18605148 18608860 + CsaV3_4G029080.1 Csa04g01882 1882
1 87171805 87176624 + Hsped.01g22520.1 Hepe01g2252 2252
10 6139320 6142705 + Hsped.10g05290.1 Hepe10g0529 529
4 30767448 30770261 + Lsi04G023580.1 Lsi04g02358 2358
4 30793765 30800084 + Lsi04G023630.1 Lsi04g02363 2363
8 17909532 17918565 - Lsi08G009440.1 Lsi08g00944 944
8 17924831 17926177 - Lsi08G009450.1 Lsi08g00945 945
8 17936468 17940541 + Lsi08G009470.1 Lsi08g00947 947
4 745254 749390 - Sed0015738.1 Sed04g0119 119
4 751296 754947 - Sed0017908.1 Sed04g0120 120
11 28214091 28220661 + Sed0016020.1 Sed11g1242 1242
12 11991446 11998060 + Sed0022783.1 Sed12g1437 1437
1 104599949 104604452 + Tan0016729.1 Tan01g3976 3976
2 92240027 92243050 - Tan0016356.1 Tan02g2357 2357
2 92249434 92253330 - Tan0013108.1 Tan02g2359 2359
2 92265546 92266886 - Tan0018022.1 Tan02g2360 2360
18 3639935 3646238 + Vvi18g330 Vvi18g330 330
18 3648245 3660889 - Vvi18g331 Vvi18g331 331
18 3668327 3697476 + Vvi18g332 Vvi18g332 332
18 3700490 3718099 + Vvi18g333 Vvi18g333 333
18 3725279 3732386 - Vvi18g334 Vvi18g334 334
18 3732845 3738423 - Vvi18g335 Vvi18g335 335
18 3741184 3745653 + Vvi18g336 Vvi18g336 336
18 3748755 3757534 + Vvi18g337 Vvi18g337 337
18 3759264 3763554 + Vvi18g338 Vvi18g338 338
18 3798809 3803646 - Vvi18g339 Vvi18g339 339
       

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