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
Vvi18g1170 . . . . . . . . . Cmo12g00344 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo18g00766 . Bda01g01545 Bpe02g01741 . Bma01g00716 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1171 . . . . . . . . . . . . . . . Cpe06g00053 Cpe13g00653 Bhi04g00088 . . . . . . . . . . . . . . . . Cone20ag0415 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1172 . . . . Bpe02g00620 . . Bma01g02099 . Cmo15g00648 . . . . . . . . . . . . . . Cla08g00647 . . . . . . Cone4ag1444 . . . . . . . . . . . . . . . . . . Cma12g00384 . . Car15g00587 Cpe11g00286 . . . . . . . . . . . . . . . Lsi08g01280 . Chy03g00560 .
Vvi18g1173 . . . . . . . . Cmo04g02524 . . . . . . . . Bhi04g01837 . . . Hepe02g2102 . Lcy10g1297 . . . . . . . . . . Cone20ag0413 . . . . . . . . . . Bma01g00880 . . . . . . Car04g02324 . . . . . . . . . . . . . . . . . Lsi08g00508 . . .
Vvi18g1174 . . . . . . . . . . Cma01g01017 . Car01g00898 . . . . . . . . . . . . . . . . . . . Cone7ag1492 . . . . . . Blo17g00231 . . Bda13g01545 . Bpe14g00320 . Bma02g00289 . Cmo01g01059 . . . Car05g00806 . . . . . . . . . . . . . . . . . Lsi08g00282 . Chy03g00808 .
Vvi18g1175 . . . . . . . . Cmo04g02526 . . . Car01g01585 . . . . . . . . . . . Cla08g00648 . . . . . . Cone4ag1445 Cone7ag1489 . . Lsi04g01809 . . Cme03g00434 . . . Bda01g01381 Bpe02g01594 . . . . . . . . . . Cpe01g02090 . . . . . . . . . . . . . . . . . Chy03g00565 .
Vvi18g1176 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag0807 Cone20ag0412 . Csa03g04320 Chy04g00380 . Blo17g00230 . . Bda13g01544 . Bpe14g00321 . Bma02g00288 . . . . . . . . . . . . . . . . . . . . . . . . . . Cme04g00426
Vvi18g1177 . Blo12g01113 . Bda03g00025 . Bpe04g00016 Bma04g00023 . Cmo04g02528 Cmo15g00645 . . . . . . Cpe13g00654 Bhi04g01835 Tan11g1207 . . Hepe02g2748 . Lcy10g1301 Cla08g00651 Cam08g1078 Cec08g0664 Cco08g0775 Clacu08g0782 . Cre08g0589 . Cone7ag1488 Cone17ag0806 Cone20ag0411 . . . Cme03g00431 Blo17g00229 Blo18g00227 . Bda13g01543 Bpe02g01595 Bpe14g00322 Bma01g00879 Bma02g00287 . . . . . Car04g02327 Car15g00586 . . . . . . . . . . . . . . . . Lsi08g00510 . Chy03g00570 .
Vvi18g1178 . Blo12g00834 . Bda03g00342 . Bpe04g00302 . . Cmo04g02530 Cmo15g00644 . . . . . . Cpe13g00655 Bhi04g01834 . . . . . . . . . . . . . . . Cone17ag0805 Cone20ag0410 . . . Cme03g00430 . Blo18g00226 . Bda01g01383 Bpe02g01596 . Bma01g00878 . . . . . . Car04g02328 Car15g00585 Cpe01g02091 . . . . . . . . . . . . . . . . . Chy03g00571 .
Vvi18g1179 . . . . . . Bma04g00302 . . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag1487 . . . . . . Blo17g00228 . . Bda13g01542 . Bpe14g00323 . Bma02g00286 . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 49666073 49674449 + Bda003621.1 Bda01g01381 1381
1 49717568 49730380 - Bda003624.1 Bda01g01383 1383
1 51349774 51350841 + Bda003810.1 Bda01g01545 1545
3 445212 446682 + Bda015958.1 Bda03g00025 25
3 2893279 2898192 - Bda016303.1 Bda03g00342 342
13 38653409 38659130 + Bda000398.1 Bda13g01542 1542
13 38662186 38663642 - Bda000399.2 Bda13g01543 1543
13 38665106 38669280 - Bda000400.1 Bda13g01544 1544
13 38672009 38674305 - Bda000401.1 Bda13g01545 1545
4 2319736 2322585 - XM_039028839.1 Bhi04g00088 88
4 45240464 45244856 + XM_039028826.1 Bhi04g01834 1834
4 45245047 45249774 - XM_039028828.1 Bhi04g01835 1835
4 45259840 45263519 - XM_039028823.1 Bhi04g01837 1837
12 26640297 26652460 + BLOR04853 Blo12g00834 834
12 28796481 28798032 - BLOR05132 Blo12g01113 1113
17 2336938 2342670 + BLOR16049 Blo17g00228 228
17 2343159 2344885 - BLOR16050 Blo17g00229 229
17 2345996 2351055 - BLOR16051 Blo17g00230 230
17 2360557 2364020 - BLOR16052 Blo17g00231 231
18 2226215 2229983 + BLOR08714 Blo18g00226 226
18 2237870 2244055 - BLOR08715 Blo18g00227 227
18 21496711 21497676 - BLOR09254 Blo18g00766 766
1 6548686 6549636 - Bma000926.1 Bma01g00716 716
1 8249397 8252309 + Bma001100.2 Bma01g00878 878
1 8252568 8254406 - Bma030209 Bma01g00879 879
1 8255810 8263052 - Bma001101.1 Bma01g00880 880
1 77039814 77041907 + Bma002921.1 Bma01g02099 2099
2 3318575 3324283 + Bma014738.1 Bma02g00286 286
2 3324753 3326304 - Bma030873 Bma02g00287 287
2 3327664 3330308 - Bma014739.1 Bma02g00288 288
2 3332892 3335185 - Bma014740.1 Bma02g00289 289
4 304387 305858 + Bma018474.1 Bma04g00023 23
4 2397562 2401023 - Bma018756.1 Bma04g00302 302
2 4039041 4041134 - Bpe008461.2 Bpe02g00620 620
2 18861195 18868433 + Bpe009441.1 Bpe02g01594 1594
2 18870171 18872426 + Bpe025157 Bpe02g01595 1595
2 18872701 18875598 - Bpe009442.3 Bpe02g01596 1596
2 19808818 19809921 + Bpe009572.1 Bpe02g01741 1741
4 171750 173233 + Bpe014743.1 Bpe04g00016 16
4 1934256 1947232 - Bpe015003.1 Bpe04g00302 302
14 3140773 3143608 + Bpe006972.1 Bpe14g00320 320
14 3146113 3148894 + Bpe006973.1 Bpe14g00321 321
14 3150201 3151808 + Bpe006974.1 Bpe14g00322 322
14 3152878 3158591 - Bpe006975.1 Bpe14g00323 323
8 17135342 17139025 + CaPI482276_08g010780.1 Cam08g1078 1078
1 8475832 8478717 - Carg26863-RA Car01g00898 898
1 13138239 13140634 - Carg21370-RA Car01g01585 1585
4 18742727 18744631 + Carg15758-RA Car04g02324 2324
4 18756330 18759684 + Carg15761-RA Car04g02327 2327
4 18760396 18763476 - Carg15762-RA Car04g02328 2328
5 7587203 7591696 - Carg26434-RA Car05g00806 806
15 3230268 3233138 + Carg01570-RA Car15g00585 585
15 3234335 3238206 - Carg01569-RA Car15g00586 586
15 3241138 3246169 - Carg01568-RA Car15g00587 587
8 19535006 19538866 + CcPI632755_08g007750.1 Cco08g0775 775
8 18358995 18362685 + CePI673135_08g006640.1 Cec08g0664 664
3 8036438 8038531 + Chy3G055400.1 Chy03g00560 560
3 8099580 8106825 + Chy3G055450.1 Chy03g00565 565
3 8135293 8139074 + Chy3G055500.1 Chy03g00570 570
3 8141145 8144090 - Chy3G055510.1 Chy03g00571 571
3 11209603 11219405 + Chy3G057880.1 Chy03g00808 808
4 3363601 3365709 + Chy4G070980.1 Chy04g00380 380
8 17861633 17865322 + ClG42_08g0078200.10 Clacu08g0782 782
8 18665376 18668472 + ClCG08G006260.1 Cla08g00647 647
8 18679207 18694007 + ClCG08G006270.1 Cla08g00648 648
8 18717876 18722443 + ClCG08G006300.1 Cla08g00651 651
1 7463516 7466238 - CmaCh01G010170.1 Cma01g01017 1017
12 1985504 1987636 + CmaCh12G003840.1 Cma12g00384 384
3 5990139 5995681 + MELO3C008428.2.1 Cme03g00430 430
3 5999698 6004572 - MELO3C008429.2.1 Cme03g00431 431
3 6082409 6089192 - MELO3C008431.2.1 Cme03g00434 434
4 3369336 3372144 + MELO3C003714.2.1 Cme04g00426 426
1 8505927 8508892 - CmoCh01G010590.1 Cmo01g01059 1059
4 18574582 18576486 + CmoCh04G025240.1 Cmo04g02524 2524
4 18577828 18583552 + CmoCh04G025260.1 Cmo04g02526 2526
4 18589206 18590644 + CmoCh04G025280.1 Cmo04g02528 2528
4 18591952 18595009 - CmoCh04G025300.1 Cmo04g02530 2530
12 2140361 2141380 + CmoCh12G003440.1 Cmo12g00344 344
15 3127366 3130856 + CmoCh15G006440.1 Cmo15g00644 644
15 3131902 3135443 - CmoCh15G006450.1 Cmo15g00645 645
15 3141955 3144048 - CmoCh15G006480.1 Cmo15g00648 648
4 11466972 11471254 + Conep04aG0149600.1 Cone4ag1444 1444
4 11471892 11474968 + Conep04aG0149700.1 Cone4ag1445 1445
7 10428834 10432971 + Conep07aG0153000.1 Cone7ag1487 1487
7 10433019 10435566 - Conep07aG0153100.1 Cone7ag1488 1488
7 10436979 10439861 - Conep07aG0153200.1 Cone7ag1489 1489
7 10442520 10445050 - Conep07aG0153500.1 Cone7ag1492 1492
17 6367797 6370716 + Conep17aG0082400.1 Cone17ag0805 805
17 6371063 6374202 - Conep17aG0082500.1 Cone17ag0806 806
17 6378764 6381804 - Conep17aG0082600.1 Cone17ag0807 807
20 1988766 1991407 + Conep20aG0042400.1 Cone20ag0410 410
20 1991655 1994721 - Conep20aG0042500.1 Cone20ag0411 411
20 1998928 2000946 - Conep20aG0042600.1 Cone20ag0412 412
20 2006919 2009309 - Conep20aG0042700.1 Cone20ag0413 413
20 2017608 2020503 + Conep20aG0042900.1 Cone20ag0415 415
1 17701846 17715389 + Cp4.1LG01g20920.1 Cpe01g02090 2090
1 17715313 17719019 - Cp4.1LG01g21010.1 Cpe01g02091 2091
6 263370 265301 + Cp4.1LG06g00450.1 Cpe06g00053 53
11 1550190 1553772 - Cp4.1LG11g02900.1 Cpe11g00286 286
13 6191627 6196371 + Cp4.1LG13g04380.1 Cpe13g00653 653
13 6199654 6205547 + Cp4.1LG13g04340.1 Cpe13g00654 654
13 6205348 6209161 - Cp4.1LG13g04290.1 Cpe13g00655 655
8 18805811 18809467 + CrPI670011_08g005890.1 Cre08g0589 589
3 37783214 37785696 - CsaV3_3G046260.1 Csa03g04320 4320
2 54967442 54969442 - Hsped.02g21020.1 Hepe02g2102 2102
2 76002579 76009253 + Hsped.02g27480.1 Hepe02g2748 2748
10 35842953 35844857 + Maker00008625 Lcy10g1297 1297
10 35895776 35901758 + Maker00008529 Lcy10g1301 1301
4 25327852 25331257 - Lsi04G018090.1 Lsi04g01809 1809
8 7110301 7121541 + Lsi08G002820.1 Lsi08g00282 282
8 13009108 13011003 + Lsi08G005080.1 Lsi08g00508 508
8 13020976 13024913 + Lsi08G005100.1 Lsi08g00510 510
8 21203936 21209148 + Lsi08G012800.1 Lsi08g01280 1280
11 10004507 10009350 - Tan0009795.1 Tan11g1207 1207
18 12959803 12961382 + Vvi18g1170 Vvi18g1170 1170
18 12964007 12971832 - Vvi18g1171 Vvi18g1171 1171
18 12980372 12985434 + Vvi18g1172 Vvi18g1172 1172
18 12985918 12989790 + Vvi18g1173 Vvi18g1173 1173
18 12992479 12996865 + Vvi18g1174 Vvi18g1174 1174
18 12997416 13013502 + Vvi18g1175 Vvi18g1175 1175
18 13029893 13036147 + Vvi18g1176 Vvi18g1176 1176
18 13037310 13042345 + Vvi18g1177 Vvi18g1177 1177
18 13043155 13050653 - Vvi18g1178 Vvi18g1178 1178
18 13055733 13072493 - Vvi18g1179 Vvi18g1179 1179
       

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