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
Vvi17g436 . . . . . Bpe13g00318 . . Cmo13g01102 . . Cma11g00224 . Car11g00200 Sed08g2163 Cpe20g00090 . Bhi02g00072 Tan09g2012 Cmetu02g0670 . Hepe09g0289 . . Cla06g01526 Cam06g1683 Cec06g1745 Cco06g1743 Clacu06g1650 Cmu06g1597 Cre06g2408 . . . . Lsi02g00139 Csa01g00623 Chy12g01478 Cme12g01919 . . Bda11g01768 Bda14g00892 . Bpe15g00566 Bma03g00868 . Sed01g2281 . Cmo11g00227 Cma13g01058 . Car13g00893 . . . Bhi08g01057 Tan05g2333 Cmetu12g1433 Lac10g0185 Hepe07g2443 . . . . . . . . . Lsi06g01395 Csa01g00337 Chy02g02405 Cme02g01809
Vvi17g437 . . . . . . . . . . . . . . . Cpe20g00089 . . . . . . . . . . . . . . . . Cone16ag0224 . . Lsi02g00138 Csa01g00622 Chy12g01479 Cme12g01920 . . . Bda14g00891 . Bpe15g00567 Bma03g00867 . . . . . . . Car18g00017 Cpe09g01155 . Bhi08g01059 . . Lac10g0183 Hepe07g2444 . . Cla04g01139 Cam04g1192 Cec01g1704 Cco01g1749 Clacu04g1218 Cmu04g1197 Cre01g1496 . . . .
Vvi17g438 . . . . . . . . Cmo13g01103 . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa01g00621 Chy12g01480 Cme12g01921 . . . Bda14g00890 . Bpe15g00568 Bma03g00866 . . . . . . . Car18g00016 Cpe09g01156 . Bhi08g01062 . . Lac10g0182 . . . Cla04g01140 Cam04g1193 Cec01g1705 Cco01g1750 Clacu04g1219 Cmu04g1198 Cre01g1497 . . . .
Vvi17g439 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g440 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g441 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g442 Blo04g00799 . . . . . . . Cmo13g01106 . Cma10g00287 . Car10g00269 . Sed12g2021 Cpe20g00087 . Bhi02g00076 Tan09g2021 Cmetu02g2065 . Hepe09g0287 . . Cla06g01529 Cam06g1686 Cec06g1748 Cco06g1746 Clacu06g1653 Cmu06g1600 Cre06g2411 . . . . Lsi02g00136 . Chy12g01482 Cme12g01923 . . . Bda14g00889 . Bpe15g00570 . . Sed08g2133 Cmo10g00305 . Cma13g01061 . Car13g00897 . . Cpe18g00715 Bhi08g01066 Tan05g2341 Cmetu12g1637 Lac10g0180 Hepe07g2447 . . Cla04g01142 Cam04g1195 Cec01g1707 Cco01g1752 Clacu04g1221 Cmu04g1200 Cre01g1499 Lsi06g01399 Csa01g00339 Chy02g02403 Cme02g01811
Vvi17g443 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g444 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g445 . . Bda06g00512 Bda15g00631 . . . Bma12g00957 . . Cma10g00288 Cma11g00220 Car10g00270 Car11g00198 Sed08g0289 Cpe20g00086 Cpe04g01448 Bhi02g00080 Tan09g2022 Cmetu02g1379 . Hepe09g0286 . . Cla06g01530 Cam06g1687 Cec06g1749 Cco06g1747 Clacu06g1654 Cmu06g1601 Cre06g2413 . . . . Lsi02g00135 Csa01g00618 . . . . . . Bpe07g00746 . . Bma08g00250 . Cmo10g00306 Cmo11g00223 . . . . . Cpe18g00714 . . . . . . . . . . . . . . Lsi06g01401 Csa01g00340 Chy02g02402 Cme02g01812
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 7363540 7365999 + Bda023764.1 Bda06g00512 512
11 52516097 52517134 + Bda008688.1 Bda11g01768 1768
14 6894026 6895991 + Bda027668.1 Bda14g00889 889
14 6909384 6912478 + Bda027669.1 Bda14g00890 890
14 6915385 6917159 + Bda027670.1 Bda14g00891 891
14 6919759 6920931 + Bda027671.1 Bda14g00892 892
15 9445757 9453096 - Bda012475.2 Bda15g00631 631
2 1213014 1215679 - XM_039024089.1 Bhi02g00072 72
2 1256846 1259972 - XM_039023917.1 Bhi02g00076 76
2 1372577 1375876 + XM_039022940.1 Bhi02g00080 80
8 34530338 34531661 - XM_039037638.1 Bhi08g01057 1057
8 34581833 34589273 - XM_039037631.1 Bhi08g01059 1059
8 34598902 34603098 - XM_039039297.1 Bhi08g01062 1062
8 34712072 34714402 - XM_039038500.1 Bhi08g01066 1066
4 8068940 8070868 + BLOR13711 Blo04g00799 799
3 8404030 8408027 + Bma017184.1 Bma03g00866 866
3 8410947 8416003 + Bma017185.1 Bma03g00867 867
3 8419574 8420741 + Bma017186.2 Bma03g00868 868
8 3113739 3115988 - Bma027266.1 Bma08g00250 250
12 41509154 41511404 + Bma030525 Bma12g00957 957
7 13997688 14000367 + Bpe026079 Bpe07g00746 746
13 11050992 11052000 - Bpe006446.1 Bpe13g00318 318
15 16664080 16665241 - Bpe001500.1 Bpe15g00566 566
15 16678416 16689984 - Bpe001501.1 Bpe15g00567 567
15 16692832 16695877 - Bpe001502.1 Bpe15g00568 568
15 16714871 16716788 - Bpe024569 Bpe15g00570 570
4 25990888 25997027 - CaPI482276_04g011920.1 Cam04g1192 1192
4 26004192 26008106 - CaPI482276_04g011930.1 Cam04g1193 1193
4 26029081 26030943 - CaPI482276_04g011950.1 Cam04g1195 1195
6 28209725 28211198 - CaPI482276_06g016830.1 Cam06g1683 1683
6 28249332 28251981 - CaPI482276_06g016860.1 Cam06g1686 1686
6 28258485 28260867 + CaPI482276_06g016870.1 Cam06g1687 1687
10 1285595 1287436 - Carg17874-RA Car10g00269 269
10 1288557 1291055 + Carg17873-RA Car10g00270 270
11 1141442 1143816 - Carg09191-RA Car11g00198 198
11 1154975 1156111 + Carg09189-RA Car11g00200 200
13 9327725 9329402 - Carg04778-RA Car13g00893 893
13 9346612 9348556 - Carg04774-RA Car13g00897 897
18 72368 75124 - Carg22770-RA Car18g00016 16
18 76206 78760 - Carg22769-RA Car18g00017 17
1 30238044 30244142 - CcPI632755_01g017490.1 Cco01g1749 1749
1 30251519 30255380 - CcPI632755_01g017500.1 Cco01g1750 1750
1 30276749 30278612 - CcPI632755_01g017520.1 Cco01g1752 1752
6 27914110 27917180 - CcPI632755_06g017430.1 Cco06g1743 1743
6 27954822 27957475 - CcPI632755_06g017460.1 Cco06g1746 1746
6 27963746 27966796 + CcPI632755_06g017470.1 Cco06g1747 1747
1 31662116 31668296 - CePI673135_01g017040.1 Cec01g1704 1704
1 31675649 31679554 - CePI673135_01g017050.1 Cec01g1705 1705
1 31699944 31701806 - CePI673135_01g017070.1 Cec01g1707 1707
6 30966767 30968234 - CePI673135_06g017450.1 Cec06g1745 1745
6 31007465 31010119 - CePI673135_06g017480.1 Cec06g1748 1748
6 31021881 31024295 + CePI673135_06g017490.1 Cec06g1749 1749
2 27769415 27771760 - Chy2G046690.1 Chy02g02402 2402
2 27775448 27778618 + Chy2G046700.1 Chy02g02403 2403
2 27799693 27802681 + Chy2G046720.1 Chy02g02405 2405
12 18683545 18684530 - Chy12G220780.1 Chy12g01478 1478
12 18691801 18696422 - Chy12G220790.1 Chy12g01479 1479
12 18701175 18716927 - Chy12G220800.1 Chy12g01480 1480
12 18724188 18726002 - Chy12G220820.1 Chy12g01482 1482
4 26338710 26344922 - ClG42_04g0121800.10 Clacu04g1218 1218
4 26354589 26358440 - ClG42_04g0121900.10 Clacu04g1219 1219
4 26379386 26381250 - ClG42_04g0122100.10 Clacu04g1221 1221
6 27267407 27268879 - ClG42_06g0165000.10 Clacu06g1650 1650
6 27306532 27309177 - ClG42_06g0165300.10 Clacu06g1653 1653
6 27315643 27318028 + ClG42_06g0165400.10 Clacu06g1654 1654
4 26574685 26580894 - ClCG04G011600.2 Cla04g01139 1139
4 26590560 26594413 - ClCG04G011610.2 Cla04g01140 1140
4 26615377 26617615 - ClCG04G011630.2 Cla04g01142 1142
6 28811165 28813193 - ClCG06G015470.2 Cla06g01526 1526
6 28853153 28855798 - ClCG06G015500.1 Cla06g01529 1529
6 28863541 28865926 + ClCG06G015510.2 Cla06g01530 1530
10 1276312 1280385 - CmaCh10G002870.1 Cma10g00287 287
10 1279530 1282243 + CmaCh10G002880.1 Cma10g00288 288
11 1109507 1112015 - CmaCh11G002200.1 Cma11g00220 220
11 1122547 1126819 + CmaCh11G002240.1 Cma11g00224 224
13 8032668 8037903 - CmaCh13G010580.1 Cma13g01058 1058
13 8047698 8049638 - CmaCh13G010610.1 Cma13g01061 1061
2 24864415 24866274 - MELO3C017246.2.1 Cme02g01809 1809
2 24888620 24892338 - MELO3C017244.2.1 Cme02g01811 1811
2 24896065 24898655 + MELO3C017243.2.1 Cme02g01812 1812
12 25229730 25232087 - MELO3C002051.2.1 Cme12g01919 1919
12 25234067 25239499 - MELO3C002050.2.1 Cme12g01920 1920
12 25243840 25247807 - MELO3C002049.2.1 Cme12g01921 1921
12 25265009 25267249 - MELO3C002047.2.1 Cme12g01923 1923
2 23206511 23208288 - PI0008687.1 Cmetu02g0670 670
2 23240357 23242555 + PI0009019.1 Cmetu02g1379 1379
2 23231267 23234974 - PI0025685.1 Cmetu02g2065 2065
12 919335 920684 + PI0003460.1 Cmetu12g1433 1433
12 879704 883106 + PI0006560.1 Cmetu12g1637 1637
10 1363212 1366105 - CmoCh10G003050.1 Cmo10g00305 305
10 1366269 1369598 + CmoCh10G003060.1 Cmo10g00306 306
11 1109123 1111432 - CmoCh11G002230.1 Cmo11g00223 223
11 1122330 1126191 + CmoCh11G002270.1 Cmo11g00227 227
13 9047873 9048745 - CmoCh13G011020.1 Cmo13g01102 1102
13 9050079 9053269 - CmoCh13G011030.1 Cmo13g01103 1103
13 9063058 9064972 - CmoCh13G011060.1 Cmo13g01106 1106
4 26520315 26526525 - CmPI595203_04g011970.1 Cmu04g1197 1197
4 26536181 26540037 - CmPI595203_04g011980.1 Cmu04g1198 1198
4 26561092 26562954 - CmPI595203_04g012000.1 Cmu04g1200 1200
6 27176213 27177686 - CmPI595203_06g015970.1 Cmu06g1597 1597
6 27215246 27217891 - CmPI595203_06g016000.1 Cmu06g1600 1600
6 27224357 27226742 + CmPI595203_06g016010.1 Cmu06g1601 1601
16 1634376 1640569 + Conep16aG0022800.1 Cone16ag0224 224
4 11568796 11572373 + Cp4.1LG04g14420.1 Cpe04g01448 1448
9 9833003 9835971 + Cp4.1LG09g11420.1 Cpe09g01155 1155
9 9836724 9839583 + Cp4.1LG09g11490.1 Cpe09g01156 1156
18 7039262 7042664 - Cp4.1LG18g07210.1 Cpe18g00714 714
18 7042255 7045858 + Cp4.1LG18g07100.1 Cpe18g00715 715
20 461896 463428 - Cp4.1LG20g00910.1 Cpe20g00086 86
20 466393 470117 + Cp4.1LG20g00720.1 Cpe20g00087 87
20 477882 481111 + Cp4.1LG20g00760.1 Cpe20g00089 89
20 481830 483797 + Cp4.1LG20g00730.1 Cpe20g00090 90
1 28185534 28191775 - CrPI670011_01g014960.1 Cre01g1496 1496
1 28199248 28203157 - CrPI670011_01g014970.1 Cre01g1497 1497
1 28224148 28226010 - CrPI670011_01g014990.1 Cre01g1499 1499
6 31973723 31975191 - CrPI670011_06g024080.1 Cre06g2408 2408
6 32010742 32013398 - CrPI670011_06g024110.1 Cre06g2411 2411
6 32019750 32022136 + CrPI670011_06g024130.1 Cre06g2413 2413
1 2100296 2102313 - CsaV3_1G003370.1 Csa01g00337 337
1 2121775 2128426 - CsaV3_1G003390.1 Csa01g00339 339
1 2128397 2130907 + CsaV3_1G003400.1 Csa01g00340 340
1 3946497 3948404 - CsaV3_1G006180.1 Csa01g00618 618
1 3970082 3974493 + CsaV3_1G006210.1 Csa01g00621 621
1 3977607 3984044 + CsaV3_1G006220.1 Csa01g00622 622
1 3985747 3989827 + CsaV3_1G006230.1 Csa01g00623 623
7 68770582 68772601 - Hsped.07g24430.1 Hepe07g2443 2443
7 68775594 68783373 - Hsped.07g24440.1 Hepe07g2444 2444
7 68817450 68819743 - Hsped.07g24470.1 Hepe07g2447 2447
9 2451841 2455032 - Hsped.09g02860.1 Hepe09g0286 286
9 2458625 2462195 + Hsped.09g02870.1 Hepe09g0287 287
9 2490635 2493008 + Hsped.09g02890.1 Hepe09g0289 289
10 1377062 1378945 + Lag0024225.1 Lac10g0180 180
10 1400970 1405012 + Lag0024227.1 Lac10g0182 182
10 1412884 1418261 + Lag0024228.1 Lac10g0183 183
10 1432061 1433294 + Lag0024230.1 Lac10g0185 185
2 1100186 1103738 - Lsi02G001350.1 Lsi02g00135 135
2 1109788 1112245 + Lsi02G001360.1 Lsi02g00136 136
2 1135478 1140427 + Lsi02G001380.1 Lsi02g00138 138
2 1157903 1159231 + Lsi02G001390.1 Lsi02g00139 139
6 24522479 24524659 - Lsi06G013950.1 Lsi06g01395 1395
6 24555640 24562280 - Lsi06G013990.1 Lsi06g01399 1399
6 24569403 24572592 + Lsi06G014010.1 Lsi06g01401 1401
1 17220818 17222328 - Sed0006060.1 Sed01g2281 2281
8 1710521 1713753 - Sed0017468.1 Sed08g0289 289
8 35317551 35320288 + Sed0006387.1 Sed08g2133 2133
8 35549073 35552353 + Sed0025711.1 Sed08g2163 2163
12 31069455 31072373 + Sed0026471.1 Sed12g2021 2021
5 74762551 74763766 - Tan0018489.1 Tan05g2333 2333
5 74827566 74829919 - Tan0021591.1 Tan05g2341 2341
9 70792307 70794126 - Tan0006319.1 Tan09g2012 2012
9 70824643 70826873 - Tan0016323.1 Tan09g2021 2021
9 70831783 70834572 + Tan0007131.1 Tan09g2022 2022
17 5431007 5432328 - Vvi17g436 Vvi17g436 436
17 5434019 5452793 - Vvi17g437 Vvi17g437 437
17 5457737 5464643 - Vvi17g438 Vvi17g438 438
17 5482656 5494676 - Vvi17g439 Vvi17g439 439
17 5506359 5512212 + Vvi17g440 Vvi17g440 440
17 5512214 5513288 + Vvi17g441 Vvi17g441 441
17 5513954 5516946 - Vvi17g442 Vvi17g442 442
17 5521944 5526410 + Vvi17g443 Vvi17g443 443
17 5528193 5529185 + Vvi17g444 Vvi17g444 444
17 5529704 5544382 + Vvi17g445 Vvi17g445 445
       

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