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
Vvi2g432 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0338 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g433 Blo02g01077 . . . Bpe05g00616 . . . Cmo06g00757 . . . . . Sed03g1293 . . Bhi11g00230 Tan01g1957 Cmetu06g0126 . Hepe06g1192 Mch10g1486 . Cla10g00319 Cam10g0334 Cec10g0348 Cco10g0340 Clacu10g0331 Cmu10g1171 Cre10g0581 . . Cone6ag0732 Cone9ag0736 Lsi07g01368 . . Cme06g02653 . . . . . . Bma05g00795 . . . . Cma06g00733 . Car06g00653 . Cpe08g00785 . . . . . . . . . . . . . . . . . Chy06g01983 .
Vvi2g434 . . . . . . . . . Cmo16g01045 Cma02g01498 . Car02g01261 . . . Cpe05g00291 . . . . . . . . . . . . . . Cone8ag0344 . . . . Csa05g00344 Chy09g01163 . . . Bda07g00509 . . . . . . Cmo02g01539 . . . . . . . Bhi12g00343 . . . Hepe06g1605 . Lcy12g1726 . . . . . . . Lsi09g00337 . . Cme09g01695
Vvi2g435 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe11g00696 . . . . . . . . . . . . . . . . . . Cla01g00326 Cam01g0337 Cec01g0331 Cco01g0344 Clacu01g0341 Cmu01g0321 Cre09g2189 Lsi09g00341 . . .
Vvi2g436 . . . . . . . . . Cmo16g01025 . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy09g01159 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi09g00343 . . .
Vvi2g437 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00348 Chy09g01158 . . . . . . . . . . . . . . . . . . Bhi12g00346 . . . . . Lcy12g1729 . . . . . . . Lsi09g00345 . . Cme09g01692
Vvi2g438 . Blo03g00183 Bda06g00061 . . Bpe07g00137 . . . . . . . . . . . Bhi11g00229 . . . . . . Cla10g00318 Cam10g0333 Cec10g0347 Cco10g0339 Clacu10g0330 Cmu10g1170 Cre10g0580 . . Cone6ag0730 Cone9ag0734 Lsi07g01367 . . Cme06g02652 . . . . . . . Bma12g00113 . . . Cma06g00735 . Car06g00654 . Cpe08g00784 . . . . . . . . . . . . . . . . Csa03g00341 Chy06g01984 .
Vvi2g439 . . . . . . . . . . . Cma15g01181 . . . . . . . . . . . . . . . . . . . Cone8ag0345 Cone12ag0339 . . . . . . . Blo19g00291 . . Bpe08g01456 . . . . . Cmo15g01243 . . . . . Cpe13g00192 . . . . . . . Cla01g00327 Cam01g0339 Cec01g0333 Cco01g0346 Clacu01g0343 Cmu01g0323 Cre09g2187 . . . .
Vvi2g440 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g441 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 638677 640438 - Bda023232.1 Bda06g00061 61
7 6502406 6504634 - Bda025618.1 Bda07g00509 509
11 5529164 5534462 - XM_039050496.1 Bhi11g00229 229
11 5535824 5538321 - XM_039047412.1 Bhi11g00230 230
12 10722852 10725932 - XM_039020159.1 Bhi12g00343 343
12 10803699 10805939 + XM_039050524.1 Bhi12g00346 346
2 41128674 41131388 - BLOR10807 Blo02g01077 1077
3 4488143 4490904 - BLOR11364 Blo03g00183 183
19 18377194 18385405 + BLOR09634 Blo19g00291 291
5 44951146 44952195 - Bma021896.1 Bma05g00795 795
12 1758067 1759803 + Bma006987.1 Bma12g00113 113
5 20090067 20091587 - Bpe018032.1 Bpe05g00616 616
7 973881 975629 + Bpe026041 Bpe07g00137 137
8 15286083 15287994 + Bpe023568.1 Bpe08g01456 1456
11 5355501 5357729 - Bpe004052.1 Bpe11g00696 696
1 3794803 3797124 - CaPI482276_01g003370.1 Cam01g0337 337
1 3803999 3806579 - CaPI482276_01g003390.1 Cam01g0339 339
10 5475196 5479923 - CaPI482276_10g003330.1 Cam10g0333 333
10 5482315 5486911 - CaPI482276_10g003340.1 Cam10g0334 334
2 8478096 8480504 - Carg02487-RA Car02g01261 1261
6 3911260 3913800 + Carg21629-RA Car06g00653 653
6 3914172 3917781 + Carg21628-RA Car06g00654 654
1 3453942 3456263 - CcPI632755_01g003440.1 Cco01g0344 344
1 3463085 3465576 - CcPI632755_01g003460.1 Cco01g0346 346
10 3959090 3963820 - CcPI632755_10g003390.1 Cco10g0339 339
10 3971110 3973135 - CcPI632755_10g003400.1 Cco10g0340 340
1 3444936 3447257 - CePI673135_01g003310.1 Cec01g0331 331
1 3454235 3458560 - CePI673135_01g003330.1 Cec01g0333 333
10 4135765 4140488 - CePI673135_10g003470.1 Cec10g0347 347
10 4142111 4144122 - CePI673135_10g003480.1 Cec10g0348 348
6 23827198 23829592 + Chy6G125110.1 Chy06g01983 1983
6 23830954 23834101 + Chy6G125120.1 Chy06g01984 1984
9 13808660 13810924 - Chy9G168740.1 Chy09g01158 1158
9 13815579 13817782 - Chy9G168750.1 Chy09g01159 1159
9 13834431 13835907 + Chy9G168790.1 Chy09g01163 1163
1 3436487 3438808 - ClG42_01g0034100.10 Clacu01g0341 341
1 3445545 3448135 - ClG42_01g0034300.10 Clacu01g0343 343
10 4237975 4242678 - ClG42_10g0033000.10 Clacu10g0330 330
10 4245026 4247032 - ClG42_10g0033100.10 Clacu10g0331 331
1 3538905 3541421 - ClCG01G003380.2 Cla01g00326 326
1 3542573 3552951 - ClCG01G003390.1 Cla01g00327 327
10 4182855 4187855 - ClCG10G003380.2 Cla10g00318 318
10 4189835 4192389 - ClCG10G003390.1 Cla10g00319 319
2 8558222 8565908 - CmaCh02G014980.1 Cma02g01498 1498
6 3713848 3716131 + CmaCh06G007330.1 Cma06g00733 733
6 3716765 3720888 + CmaCh06G007350.1 Cma06g00735 735
15 7472044 7475675 + CmaCh15G011810.1 Cma15g01181 1181
6 33681877 33685813 - MELO3C014007.2.1 Cme06g02652 2652
6 33686621 33689553 - MELO3C014008.2.1 Cme06g02653 2653
9 21572971 21575263 - MELO3C005605.2.1 Cme09g01692 1692
9 21593972 21596209 + MELO3C005609.2.1 Cme09g01695 1695
6 27973362 27976401 + PI0011954.1 Cmetu06g0126 126
2 8934923 8937139 - CmoCh02G015390.1 Cmo02g01539 1539
6 3930697 3937632 + CmoCh06G007570.1 Cmo06g00757 757
15 8541899 8545541 + CmoCh15G012430.1 Cmo15g01243 1243
16 7118362 7122383 - CmoCh16G010250.1 Cmo16g01025 1025
16 7296692 7312413 + CmoCh16G010450.1 Cmo16g01045 1045
1 3381248 3383569 - CmPI595203_01g003210.1 Cmu01g0321 321
1 3391297 3393767 - CmPI595203_01g003230.1 Cmu01g0323 323
10 4380486 4385190 - CmPI595203_10g011700.1 Cmu10g1170 1170
10 4387539 4389545 - CmPI595203_10g011710.1 Cmu10g1171 1171
6 3677513 3679277 - Conep06aG0075300.1 Cone6ag0730 730
6 3683099 3684028 - Conep06aG0075500.1 Cone6ag0732 732
8 1974723 1977074 - Conep08aG0036000.1 Cone8ag0344 344
8 1978138 1980268 - Conep08aG0036100.1 Cone8ag0345 345
9 3495118 3497357 - Conep09aG0075100.1 Cone9ag0734 734
9 3499572 3502197 - Conep09aG0075300.1 Cone9ag0736 736
12 1847941 1851008 + Conep12aG0035300.1 Cone12ag0338 338
12 1852318 1854812 - Conep12aG0035400.1 Cone12ag0339 339
5 1636417 1639607 + Cp4.1LG05g03970.1 Cpe05g00291 291
8 6239723 6243844 - Cp4.1LG08g07900.1 Cpe08g00784 784
8 6244004 6246802 - Cp4.1LG08g07920.1 Cpe08g00785 785
13 1499025 1502419 - Cp4.1LG13g02030.1 Cpe13g00192 192
9 40914817 40917437 + CrPI670011_09g021870.1 Cre09g2187 2187
9 40924359 40926680 + CrPI670011_09g021890.1 Cre09g2189 2189
10 5307629 5312600 - CrPI670011_10g005800.1 Cre10g0580 580
10 5313895 5318469 - CrPI670011_10g005810.1 Cre10g0581 581
3 2831528 2835234 - CsaV3_3G003410.1 Csa03g00341 341
5 2210324 2212561 - CsaV3_5G003440.1 Csa05g00344 344
5 2230560 2232853 + CsaV3_5G003480.1 Csa05g00348 348
6 61432026 61434823 - Hsped.06g11920.1 Hepe06g1192 1192
6 66938643 66941048 - Hsped.06g16050.1 Hepe06g1605 1605
12 37985057 37987321 - Maker00003072 Lcy12g1726 1726
12 38013485 38015713 + Maker00003093 Lcy12g1729 1729
7 19864738 19869384 - Lsi07G013670.1 Lsi07g01367 1367
7 19870561 19873400 - Lsi07G013680.1 Lsi07g01368 1368
9 3521105 3523342 - Lsi09G003370.1 Lsi09g00337 337
9 3541767 3543381 + Lsi09G003410.1 Lsi09g00341 341
9 3549223 3556534 + Lsi09G003430.1 Lsi09g00343 343
9 3588571 3590829 + Lsi09G003450.1 Lsi09g00345 345
10 14832103 14839425 + MC10g1171 Mch10g1486 1486
3 8251160 8255200 - Sed0023863.3 Sed03g1293 1293
1 21687967 21697864 + Tan0018379.1 Tan01g1957 1957
2 4307377 4323174 + Vvi2g432 Vvi2g432 432
2 4323522 4327771 + Vvi2g433 Vvi2g433 433
2 4329209 4331242 - Vvi2g434 Vvi2g434 434
2 4333157 4334766 - Vvi2g435 Vvi2g435 435
2 4337076 4339299 - Vvi2g436 Vvi2g436 436
2 4339351 4356199 - Vvi2g437 Vvi2g437 437
2 4357334 4364368 + Vvi2g438 Vvi2g438 438
2 4365044 4369553 - Vvi2g439 Vvi2g439 439
2 4381265 4389110 - Vvi2g440 Vvi2g440 440
2 4398445 4399315 + Vvi2g441 Vvi2g441 441
       

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