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
Vvi18g1200 . . . . . . . . Cmo04g02535 Cmo15g00639 . . . . . . . Bhi04g02144 . . . . . . Cla08g00655 Cam08g1085 Cec08g0671 Cco08g0780 Clacu08g0789 . Cre08g0594 Cone4ag1452 Cone7ag1480 Cone17ag0802 Cone20ag0406 . . . Cme03g00421 Blo17g00225 Blo18g00225 . Bda13g01540 Bpe02g01598 Bpe14g00324 Bma01g00876 . . . . . . Car04g02333 Car15g00580 Cpe01g02095 . . . . . . . . . . . . . . . Lsi08g00515 . Chy03g00579 .
Vvi18g1201 . . . . . . . . Cmo04g02537 Cmo15g00636 . . . . Sed01g3508 . Cpe13g00661 Bhi04g01825 Tan11g1198 Cmetu03g0408 . Hepe02g2756 . Lcy10g1307 Cla08g00658 Cam08g1087 Cec08g0673 Cco08g0782 Clacu08g0793 . Cre08g0596 Cone4ag1453 Cone7ag1479 Cone17ag0801 . . . . Cme03g00418 . . . Bda13g01539 . Bpe14g00325 . Bma02g00285 . . . . . Car04g02334 Car15g00578 Cpe01g02096 . . . . . . . . . . . . . . . Lsi08g00517 . Chy03g00582 .
Vvi18g1202 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1203 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1204 Blo01g01325 . Bda01g00690 . Bpe02g00615 . . Bma01g02110 . . . Cma09g01086 . . . Cpe06g00887 . . . . . . . . . . . . . . . . Cone7ag1430 . . . . . . . . . . . . . . . . Cmo09g01095 . . . Car09g00984 . . . . . . . . . . . . . . . . . . . .
Vvi18g1205 . . . . . . . . Cmo04g02538 Cmo15g00635 . . . . Sed11g1325 . Cpe13g00662 Bhi04g01824 Tan11g1197 Cmetu03g1073 . Hepe02g2758 . Lcy10g1308 Cla08g00659 Cam08g1089 Cec08g0674 Cco08g0783 Clacu08g0794 . Cre08g0597 . Cone7ag1431 . Cone20ag0405 . . . Cme03g00408 Blo17g00224 . . Bda13g01538 . Bpe14g00326 . Bma02g00284 . . . . . Car04g02335 Car15g00577 Cpe01g02097 . . . . . . . . . . . . . . . Lsi08g00518 . Chy03g00584 .
Vvi18g1206 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1207 Blo01g01326 . Bda01g00691 . Bpe02g00614 . . Bma01g02111 Cmo04g02539 Cmo15g00634 . . . . Sed01g2883 . Cpe13g00663 Bhi04g01823 Tan11g1195 Cmetu03g0776 . Hepe02g2759 . Lcy10g1309 Cla08g00661 Cam08g1091 Cec08g0676 Cco08g0785 Clacu08g0796 . Cre08g0599 . . . . . . . Cme03g00404 . . . . . . . . . . . . . Car04g02336 Car15g00576 Cpe01g02098 . . . . . . . . . . . . . . . Lsi08g00519 . Chy03g00585 .
Vvi18g1208 . . . . . . . . . . . . Car01g00888 . . . . . . . . . . . . . . . . . . . . Cone17ag0800 Cone20ag0404 . . . . Blo17g00721 Blo18g00224 Bda08g01180 Bda13g01537 Bpe02g01599 Bpe14g00328 . Bma05g00197 Sed07g2855 Cmo01g01036 . . . . . . Cpe02g00894 Bhi09g01486 Tan01g3358 Cmetu01g1438 . Hepe03g1217 Mch11g1415 . Cla09g00911 Cam09g0963 Cec09g0968 Cco09g0974 . . Cre09g0932 . . Chy03g00638 .
Vvi18g1209 Blo01g01327 . Bda01g00692 . . . . Bma01g02112 . . Cma01g00999 . . . . . . . . . . . . . . . . . . . . Cone4ag1522 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 34052606 34054027 - Bda032913 Bda01g00690 690
1 34054324 34062678 + Bda002727.1 Bda01g00691 691
1 34093205 34095760 + Bda002729.2 Bda01g00692 692
8 47362611 47365643 - Bda030129.1 Bda08g01180 1180
13 38607656 38609463 + Bda000391.1 Bda13g01537 1537
13 38620291 38624083 + Bda000393.1 Bda13g01538 1538
13 38626706 38628220 + Bda000394.2 Bda13g01539 1539
13 38631724 38636676 + Bda000395.1 Bda13g01540 1540
4 44731632 44742202 - XM_039029561.1 Bhi04g01823 1823
4 44769966 44773077 + XM_039028334.1 Bhi04g01824 1824
4 44842103 44846292 + XM_039028098.1 Bhi04g01825 1825
4 58002999 58015000 - XM_039030715.1 Bhi04g02144 2144
9 38560180 38562420 + XM_039040612.1 Bhi09g01486 1486
1 50632316 50633572 - BLOR01325 Blo01g01325 1325
1 50652923 50661439 + BLOR01326 Blo01g01326 1326
1 50692004 50700301 + BLOR01327 Blo01g01327 1327
17 2307739 2316821 + BLOR16045 Blo17g00224 224
17 2321508 2325752 + BLOR16046 Blo17g00225 225
17 21375177 21387057 - BLOR08267 Blo17g00721 721
18 2198768 2200726 + BLOR08712 Blo18g00224 224
18 2207489 2212669 + BLOR08713 Blo18g00225 225
1 8235440 8240428 + Bma001098.2 Bma01g00876 876
1 77254585 77255797 - Bma002937.1 Bma01g02110 2110
1 77273243 77281548 + Bma002939.1 Bma01g02111 2111
1 77283287 77285635 + Bma002940.1 Bma01g02112 2112
2 3293422 3297221 + Bma030872 Bma02g00284 284
2 3299762 3301287 + Bma014737.1 Bma02g00285 285
5 5452839 5455098 + Bma020930.1 Bma05g00197 197
2 3998397 4006709 - Bpe008453.1 Bpe02g00614 614
2 4011755 4012957 + Bpe008454.1 Bpe02g00615 615
2 18881124 18886445 - Bpe009444.1 Bpe02g01598 1598
2 18891026 18903165 - Bpe009445.2 Bpe02g01599 1599
14 3175490 3180367 - Bpe006976.1 Bpe14g00324 324
14 3183962 3185319 - Bpe006977.1 Bpe14g00325 325
14 3188464 3192258 - Bpe006978.1 Bpe14g00326 326
14 3202693 3207105 - Bpe006980.2 Bpe14g00328 328
8 17211941 17218224 - CaPI482276_08g010850.1 Cam08g1085 1085
8 17247341 17250155 - CaPI482276_08g010870.1 Cam08g1087 1087
8 17267922 17271572 - CaPI482276_08g010890.1 Cam08g1089 1089
8 17297670 17299905 + CaPI482276_08g010910.1 Cam08g1091 1091
9 9978257 9980174 + CaPI482276_09g009630.1 Cam09g0963 963
1 8162698 8164390 - Carg25051-RA Car01g00888 888
4 18779618 18786700 - Carg15767-RA Car04g02333 2333
4 18796207 18798535 - Carg15768-RA Car04g02334 2334
4 18803730 18807806 - Carg15769-RA Car04g02335 2335
4 18808583 18815158 + Carg15770-RA Car04g02336 2336
9 6318400 6322251 + Carg27256-RA Car09g00984 984
15 3179698 3187355 - Carg01579-RA Car15g00576 576
15 3189140 3192132 + Carg01578-RA Car15g00577 577
15 3198737 3200501 + Carg01577-RA Car15g00578 578
15 3208516 3215066 + Carg01575-RA Car15g00580 580
8 19601603 19607878 - CcPI632755_08g007800.1 Cco08g0780 780
8 19639069 19642526 - CcPI632755_08g007820.1 Cco08g0782 782
8 19660519 19664185 - CcPI632755_08g007830.1 Cco08g0783 783
8 19684595 19686799 + CcPI632755_08g007850.1 Cco08g0785 785
9 9231455 9233348 + CcPI632755_09g009740.1 Cco09g0974 974
8 18418847 18427837 - CePI673135_08g006710.1 Cec08g0671 671
8 18456366 18459701 - CePI673135_08g006730.1 Cec08g0673 673
8 18477487 18481133 - CePI673135_08g006740.1 Cec08g0674 674
8 18508869 18511102 + CePI673135_08g006760.1 Cec08g0676 676
9 9267941 9269855 + CePI673135_09g009680.1 Cec09g0968 968
3 8283731 8290612 - Chy3G055590.1 Chy03g00579 579
3 8330514 8333646 - Chy3G055620.1 Chy03g00582 582
3 8373121 8375965 - Chy3G055640.1 Chy03g00584 584
3 8386255 8394879 + Chy3G055650.1 Chy03g00585 585
3 8893358 8897108 - Chy3G056180.1 Chy03g00638 638
8 17934020 17943078 - ClG42_08g0078900.10 Clacu08g0789 789
8 17983676 17987050 - ClG42_08g0079300.10 Clacu08g0793 793
8 18004394 18008044 - ClG42_08g0079400.10 Clacu08g0794 794
8 18034829 18037033 + ClG42_08g0079600.10 Clacu08g0796 796
8 18793469 18800763 - ClCG08G006370.2 Cla08g00655 655
8 18843126 18848278 - ClCG08G006400.1 Cla08g00658 658
8 18865284 18869120 - ClCG08G006410.2 Cla08g00659 659
8 18881486 18900394 + ClCG08G006430.2 Cla08g00661 661
9 9509336 9511509 + ClCG09G009760.1 Cla09g00911 911
1 7236942 7240772 - CmaCh01G009990.1 Cma01g00999 999
9 5839000 5842810 + CmaCh09G010860.1 Cma09g01086 1086
3 5620181 5629954 - MELO3C008414.2.1 Cme03g00404 404
3 5689170 5692391 + MELO3C008415.2.1 Cme03g00408 408
3 5750612 5754348 + MELO3C008417.2.1 Cme03g00418 418
3 5822509 5830936 + MELO3C008420.2.1 Cme03g00421 421
1 17915807 17918002 - PI0023307.1 Cmetu01g1438 1438
3 10211157 10215313 + PI0009576.1 Cmetu03g0408 408
3 10125706 10135626 - PI0004812.1 Cmetu03g0776 776
3 10177717 10180853 + PI0012031.1 Cmetu03g1073 1073
1 8116082 8118127 - CmoCh01G010360.1 Cmo01g01036 1036
4 18611539 18618239 - CmoCh04G025350.1 Cmo04g02535 2535
4 18627274 18629784 - CmoCh04G025370.1 Cmo04g02537 2537
4 18635502 18639391 - CmoCh04G025380.1 Cmo04g02538 2538
4 18640122 18650094 + CmoCh04G025390.1 Cmo04g02539 2539
9 6065856 6069703 + CmoCh09G010950.1 Cmo09g01095 1095
15 3063254 3074901 - CmoCh15G006340.1 Cmo15g00634 634
15 3076734 3079791 + CmoCh15G006350.1 Cmo15g00635 635
15 3086110 3087783 + CmoCh15G006360.1 Cmo15g00636 636
15 3096562 3102876 + CmoCh15G006390.1 Cmo15g00639 639
4 11511786 11516733 - Conep04aG0150400.1 Cone4ag1452 1452
4 11517533 11519850 - Conep04aG0150500.1 Cone4ag1453 1453
4 11786266 11789024 - Conep04aG0157400.1 Cone4ag1522 1522
7 10165185 10166792 - Conep07aG0147200.1 Cone7ag1430 1430
7 10167232 10169693 - Conep07aG0147300.1 Cone7ag1431 1431
7 10389410 10391551 + Conep07aG0152100.1 Cone7ag1479 1479
7 10392817 10397873 + Conep07aG0152200.1 Cone7ag1480 1480
17 6280691 6283680 - Conep17aG0081800.1 Cone17ag0800 800
17 6327084 6329953 + Conep17aG0081900.1 Cone17ag0801 801
17 6346743 6354500 + Conep17aG0082000.1 Cone17ag0802 802
20 1953346 1955766 + Conep20aG0041800.1 Cone20ag0404 404
20 1958046 1967063 + Conep20aG0041900.1 Cone20ag0405 405
20 1971557 1979343 + Conep20aG0042000.1 Cone20ag0406 406
1 17732502 17740635 - Cp4.1LG01g21000.1 Cpe01g02095 2095
1 17748946 17751885 - Cp4.1LG01g20970.1 Cpe01g02096 2096
1 17758185 17762166 - Cp4.1LG01g20990.1 Cpe01g02097 2097
1 17762626 17772823 + Cp4.1LG01g20900.1 Cpe01g02098 2098
2 6418140 6420283 + Cp4.1LG02g08880.1 Cpe02g00894 894
6 5912023 5916728 + Cp4.1LG06g07670.1 Cpe06g00887 887
13 6237982 6240000 - Cp4.1LG13g04260.1 Cpe13g00661 661
13 6245875 6248898 - Cp4.1LG13g04280.1 Cpe13g00662 662
13 6249985 6263453 + Cp4.1LG13g04370.1 Cpe13g00663 663
8 18871533 18877825 - CrPI670011_08g005940.1 Cre08g0594 594
8 18906448 18910415 - CrPI670011_08g005960.1 Cre08g0596 596
8 18928675 18932334 - CrPI670011_08g005970.1 Cre08g0597 597
8 18958337 18960705 + CrPI670011_08g005990.1 Cre08g0599 599
9 9476761 9478674 + CrPI670011_09g009320.1 Cre09g0932 932
2 76145215 76147902 - Hsped.02g27560.1 Hepe02g2756 2756
2 76176527 76179930 - Hsped.02g27580.1 Hepe02g2758 2758
2 76181824 76191629 + Hsped.02g27590.1 Hepe02g2759 2759
3 66348438 66355971 - Hsped.03g12170.1 Hepe03g1217 1217
10 35985996 35989339 - Maker00008713 Lcy10g1307 1307
10 36003756 36007710 - Maker00008670 Lcy10g1308 1308
10 36011369 36026169 + Maker00008785 Lcy10g1309 1309
8 13068820 13077822 - Lsi08G005150.1 Lsi08g00515 515
8 13111223 13115561 - Lsi08G005170.1 Lsi08g00517 517
8 13136355 13139008 - Lsi08G005180.1 Lsi08g00518 518
8 13139030 13154918 + Lsi08G005190.1 Lsi08g00519 519
11 10522351 10527442 + MC11g1166 Mch11g1415 1415
1 24494958 24504483 - Sed0007773.1 Sed01g2883 2883
1 64200430 64205614 - Sed0025367.1 Sed01g3508 3508
7 43311526 43314947 - Sed0021475.4 Sed07g2855 2855
11 28997399 29001143 - Sed0020214.1 Sed11g1325 1325
1 93337875 93340565 + Tan0001751.2 Tan01g3358 3358
11 9849130 9869780 - Tan0011270.2 Tan11g1195 1195
11 9878432 9881603 + Tan0020917.2 Tan11g1197 1197
11 9896318 9899751 + Tan0021412.1 Tan11g1198 1198
18 13446198 13457203 - Vvi18g1200 Vvi18g1200 1200
18 13476397 13478606 - Vvi18g1201 Vvi18g1201 1201
18 13489002 13490580 - Vvi18g1202 Vvi18g1202 1202
18 13493088 13494429 + Vvi18g1203 Vvi18g1203 1203
18 13494964 13497893 - Vvi18g1204 Vvi18g1204 1204
18 13498400 13504533 - Vvi18g1205 Vvi18g1205 1205
18 13511610 13520058 + Vvi18g1206 Vvi18g1206 1206
18 13526073 13535704 + Vvi18g1207 Vvi18g1207 1207
18 13539022 13541804 - Vvi18g1208 Vvi18g1208 1208
18 13551372 13554376 + Vvi18g1209 Vvi18g1209 1209
       

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