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
Vvi1g911 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car15g00271 Cpe13g00947 . . . . . . . . . . . . . . . . . . .
Vvi1g912 . Blo16g01116 Bda01g02158 Bda11g01216 Bpe13g01411 . . . . Cmo18g01175 . Cma18g01153 . Car18g01062 Sed08g1991 Cpe09g00177 . Bhi07g01570 Tan04g1083 Cmetu04g0016 Lac13g0316 Hepe10g1739 . . Cla05g02444 Cam05g2629 Cec05g2663 Cco05g2701 Clacu05g2633 Cmu05g2487 Cre05g2600 Cone13ag0956 . . . Lsi04g00428 Csa05g02447 Chy10g00998 Cme10g00418 . . . Bda11g01216 . . Bma01g00097 Bma06g00685 . Cmo04g02892 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g913 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone9ag0590 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g914 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo04g02894 . . . . Car15g00270 Cpe13g00948 . . . . . . . . . . . . . . . . . . .
Vvi1g915 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g916 Blo01g00426 . Bda01g02156 . . Bpe10g00871 Bma14g01644 Bma15g00158 Cmo04g01735 Cmo18g01172 . Cma18g01151 . Car18g01060 Sed08g1983 Cpe09g00179 Cpe01g01464 Bhi07g01568 Tan04g1080 Cmetu10g1577 Lac13g0318 Hepe10g1741 . . Cla05g02442 Cam05g2627 Cec05g2661 Cco05g2699 Clacu05g2631 Cmu05g2485 Cre05g2598 Cone13ag0955 Cone19ag0947 Cone6ag0584 Cone9ag0587 Lsi04g00426 Csa05g02449 Chy10g01000 Cme10g00416 Blo06g00906 Blo11g00773 Bda07g01520 . Bpe11g01642 Bpe02g02343 Bma01g00099 . . . . Cma04g01657 . Car04g01697 . . . . . . . . . . . . . . . . . . . . .
Vvi1g917 . Blo16g01115 . Bda11g01215 Bpe13g01410 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0583 Cone9ag0586 . . . . . . . Bda11g01215 . . . Bma06g00686 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g918 Blo01g00429 . Bda01g02153 . . . . . Cmo04g01736 . . . . . . . Cpe01g01465 . . . . . . . . . . . . . . . . Cone6ag0582 . Lsi04g00425 Csa05g02453 Chy10g01003 Cme10g00414 . . . . . Bpe02g02340 Bma01g00101 . . . . Cma04g01658 . Car04g01698 . . . . . . . . . . . . . . . . . . . . .
Vvi1g919 . . . . . . . . . Cmo18g01170 . Cma18g01149 . Car18g01058 . Cpe09g00181 . . . . . . . . Cla05g02440 . . . . . . . . . . . . Chy10g01005 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g920 . . . . . Bpe10g00875 . Bma15g00155 Cmo04g01738 . . . . . Sed06g0633 . Cpe01g01467 Bhi07g01564 Tan04g1076 Cmetu04g1025 Lac13g0321 Hepe10g1745 . . . . . . . . . . . . . Lsi04g00423 Csa05g02454 . Cme10g00413 . . . . . . . . . . . Cma04g01660 . Car04g01699 . Cpe13g00953 . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57471624 57473560 - Bda004487.1 Bda01g02153 2153
1 57513498 57516137 + Bda004493.2 Bda01g02156 2156
1 57520148 57521812 - Bda004495.1 Bda01g02158 2158
7 28288256 28288996 + Bda028372.1 Bda07g01520 1520
11 12514008 12517305 + Bda007722.1 Bda11g01215 1215
11 12518283 12520470 - Bda007723.1 Bda11g01216 1216
7 44724989 44726786 - XM_039037099.1 Bhi07g01564 1564
7 44856443 44859773 + XM_039036009.1 Bhi07g01568 1568
7 44948570 44952123 + XM_039035975.1 Bhi07g01570 1570
1 4835352 4837963 - BLOR00426 Blo01g00426 426
1 4851329 4858317 + BLOR00429 Blo01g00429 429
6 32332284 32335818 - BLOR17489 Blo06g00906 906
11 11141863 11150852 - BLOR03649 Blo11g00773 773
16 39641576 39644907 + BLOR21902 Blo16g01115 1115
16 39645882 39654247 - BLOR21903 Blo16g01116 1116
1 1045311 1047991 + Bma000262.1 Bma01g00097 97
1 1051882 1054598 - Bma000264.1 Bma01g00099 99
1 1065696 1067627 + Bma000266.1 Bma01g00101 101
6 36756969 36759368 + Bma023662.1 Bma06g00685 685
6 36760524 36763853 - Bma023663.1 Bma06g00686 686
14 34761088 34764445 - Bma012362.1 Bma14g01644 1644
15 1648579 1650329 - Bma013136.1 Bma15g00155 155
15 1664058 1666412 + Bma013138.1 Bma15g00158 158
2 23937497 23939402 - Bpe010157.1 Bpe02g02340 2340
2 23950707 23953173 + Bpe010160.1 Bpe02g02343 2343
10 14539854 14542607 - Bpe003175.2 Bpe10g00871 871
10 14554289 14555346 + Bpe003179.1 Bpe10g00875 875
11 12540446 12554080 - Bpe004955.1 Bpe11g01642 1642
13 19353238 19356676 + Bpe011073.1 Bpe13g01410 1410
13 19357826 19361007 - Bpe011074.1 Bpe13g01411 1411
5 33783337 33786015 + CaPI482276_05g026270.1 Cam05g2627 2627
5 33794990 33797304 + CaPI482276_05g026290.1 Cam05g2629 2629
4 9738335 9742225 - Carg01702-RA Car04g01697 1697
4 9744531 9746539 + Carg01701-RA Car04g01698 1698
4 9750788 9753650 + Carg01700-RA Car04g01699 1699
15 1466885 1470846 + Carg02251-RA Car15g00270 270
15 1473282 1474330 - Carg02252-RA Car15g00271 271
18 10811940 10813736 - Carg17272-RA Car18g01058 1058
18 10818495 10822162 + Carg17270-RA Car18g01060 1060
18 10827370 10830348 + Carg17268-RA Car18g01062 1062
5 34907404 34910081 + CcPI632755_05g026990.1 Cco05g2699 2699
5 34919670 34922560 + CcPI632755_05g027010.1 Cco05g2701 2701
5 37229035 37231668 + CePI673135_05g026610.1 Cec05g2661 2661
5 37240947 37243828 + CePI673135_05g026630.1 Cec05g2663 2663
10 15437782 15439739 - Chy10G181920.1 Chy10g00998 998
10 15447060 15449800 - Chy10G181940.1 Chy10g01000 1000
10 15456661 15462282 + Chy10G181970.1 Chy10g01003 1003
10 15465211 15467025 + Chy10G181990.1 Chy10g01005 1005
5 33993166 33995838 + ClG42_05g0263100.10 Clacu05g2631 2631
5 34005109 34007423 + ClG42_05g0263300.10 Clacu05g2633 2633
5 35862331 35864919 - ClCG05G024240.1 Cla05g02440 2440
5 35877776 35881037 + ClCG05G024280.2 Cla05g02442 2442
5 35888338 35894509 + ClCG05G024300.2 Cla05g02444 2444
4 8349479 8352733 - CmaCh04G016570.1 Cma04g01657 1657
4 8354370 8356443 + CmaCh04G016580.1 Cma04g01658 1658
4 8361173 8362247 + CmaCh04G016600.1 Cma04g01660 1660
18 9245799 9247683 - CmaCh18G011490.1 Cma18g01149 1149
18 9251784 9255785 + CmaCh18G011510.1 Cma18g01151 1151
18 9261427 9264514 + CmaCh18G011530.1 Cma18g01153 1153
10 2624471 2626613 - MELO3C012099.2.1 Cme10g00413 413
10 2627835 2629427 - MELO3C012098.2.1 Cme10g00414 414
10 2635549 2638541 + MELO3C012095.2.1 Cme10g00416 416
10 2644462 2648348 + MELO3C012093.2.1 Cme10g00418 418
4 8746111 8751558 + PI0022322.1 Cmetu04g0016 16
4 8530970 8532989 - PI0024720.1 Cmetu04g1025 1025
10 19378759 19382239 - PI0007356.3 Cmetu10g1577 1577
4 8785286 8788942 - CmoCh04G017350.1 Cmo04g01735 1735
4 8790922 8793128 + CmoCh04G017360.1 Cmo04g01736 1736
4 8798529 8799544 + CmoCh04G017380.1 Cmo04g01738 1738
4 20587467 20595377 - CmoCh04G028920.1 Cmo04g02892 2892
4 20602294 20602584 - CmoCh04G028940.1 Cmo04g02894 2894
18 11830524 11832609 - CmoCh18G011700.1 Cmo18g01170 1170
18 11837026 11839428 + CmoCh18G011720.1 Cmo18g01172 1172
18 11846219 11850272 + CmoCh18G011750.1 Cmo18g01175 1175
5 33731301 33733973 + CmPI595203_05g024850.1 Cmu05g2485 2485
5 33743240 33745554 + CmPI595203_05g024870.1 Cmu05g2487 2487
6 2856884 2858384 - Conep06aG0059500.1 Cone6ag0582 582
6 2860965 2864472 + Conep06aG0059600.1 Cone6ag0583 583
6 2869089 2872027 + Conep06aG0059700.1 Cone6ag0584 584
9 2769989 2773493 + Conep09aG0059600.1 Cone9ag0586 586
9 2774049 2776813 + Conep09aG0059700.1 Cone9ag0587 587
9 2785129 2788949 - Conep09aG0060000.1 Cone9ag0590 590
13 8198879 8202308 + Conep13aG0098300.1 Cone13ag0955 955
13 8203823 8207274 + Conep13aG0098400.1 Cone13ag0956 956
19 7238402 7241557 + Conep19aG0097500.1 Cone19ag0947 947
1 8766008 8770299 - Cp4.1LG01g12440.1 Cpe01g01464 1464
1 8771797 8774998 + Cp4.1LG01g12520.1 Cpe01g01465 1465
1 8779549 8780778 + Cp4.1LG01g12540.1 Cpe01g01467 1467
9 1031701 1034499 - Cp4.1LG09g01840.1 Cpe09g00177 177
9 1039886 1045267 - Cp4.1LG09g01820.1 Cpe09g00179 179
9 1049168 1050408 + Cp4.1LG09g01750.1 Cpe09g00181 181
13 7971245 7972466 + Cp4.1LG13g08460.1 Cpe13g00947 947
13 7974800 7975090 - Cp4.1LG13g08420.1 Cpe13g00948 948
13 7986033 7987100 + Cp4.1LG13g08500.1 Cpe13g00953 953
5 37091122 37093789 + CrPI670011_05g025980.1 Cre05g2598 2598
5 37103428 37106484 + CrPI670011_05g026000.1 Cre05g2600 2600
5 26400430 26402846 - CsaV3_5G032660.1 Csa05g02447 2447
5 26408726 26412347 - CsaV3_5G032680.1 Csa05g02449 2449
5 26417828 26419618 + CsaV3_5G032720.1 Csa05g02453 2453
5 26420804 26425248 + CsaV3_5G032730.1 Csa05g02454 2454
10 54212211 54214776 - Hsped.10g17390.1 Hepe10g1739 1739
10 54232295 54234966 - Hsped.10g17410.1 Hepe10g1741 1741
10 54267030 54268594 + Hsped.10g17450.1 Hepe10g1745 1745
13 2267691 2270008 - Lag0040112.1 Lac13g0316 316
13 2279219 2283355 - Lag0040114.1 Lac13g0318 318
13 2310704 2311668 + Lag0040117.1 Lac13g0321 321
4 4053694 4055514 - Lsi04G004230.1 Lsi04g00423 423
4 4068219 4070530 - Lsi04G004250.1 Lsi04g00425 425
4 4074080 4077678 + Lsi04G004260.1 Lsi04g00426 426
4 4087934 4090323 + Lsi04G004280.1 Lsi04g00428 428
6 5952916 5954568 + Sed0005369.1 Sed06g0633 633
8 34195331 34200243 - Sed0013891.2 Sed08g1983 1983
8 34270818 34273927 + Sed0020884.1 Sed08g1991 1991
4 9642846 9645009 - Tan0010713.1 Tan04g1076 1076
4 9702029 9705320 + Tan0021480.2 Tan04g1080 1080
4 9718756 9721396 + Tan0015531.2 Tan04g1083 1083
1 11978785 11983285 - Vvi1g911 Vvi1g911 911
1 11986694 11993881 - Vvi1g912 Vvi1g912 912
1 12006748 12014396 + Vvi1g913 Vvi1g913 913
1 12038069 12043051 + Vvi1g914 Vvi1g914 914
1 12043064 12043439 + Vvi1g915 Vvi1g915 915
1 12066060 12085003 - Vvi1g916 Vvi1g916 916
1 12090745 12106439 - Vvi1g917 Vvi1g917 917
1 12125591 12127646 + Vvi1g918 Vvi1g918 918
1 12128654 12130442 + Vvi1g919 Vvi1g919 919
1 12137414 12138997 + Vvi1g920 Vvi1g920 920
       

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