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
Vvi5g879 . Blo12g00123 Bda03g01118 . Bpe04g01062 . . . Cmo08g01004 . . . . . . . . . . . . . . . Cla06g00742 Cam06g0795 Cec06g0800 . Clacu06g0794 Cmu06g0767 Cre06g1548 . . . . . . Chy05g00545 . . . . . . . . . Sed09g0191 . . Cma08g01034 . . . . Cpe17g00245 Bhi12g01511 Tan06g2320 Cmetu05g0760 Lac12g2067 Hepe03g0344 . Lcy13g0450 . . . . . . . Lsi09g01157 . . Cme05g00693
Vvi5g880 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g881 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g882 . . . . . . . . . . Cma06g01259 Cma14g01914 Car06g01082 Car14g01683 . Cpe08g00386 Cpe03g01613 . . . . . . . . . . . . . . . . . . Lsi05g01820 . . . . Blo07g00297 Bda11g00660 . . . Bma02g00733 Bma06g01627 . Cmo06g01269 Cmo14g01968 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g883 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme06g00400 . . . . . . . . . . . . . . . . . . . . . . . . Cla05g00365 Cam05g0397 Cec05g0402 Cco05g0402 Clacu05g0392 Cmu05g0377 Cre05g0440 . Csa03g01118 Chy06g00386 .
Vvi5g884 Blo01g00322 . . Bda08g00027 . . Bma04g01045 Bma05g01285 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe05g01133 . . . . . . . Cma17g00113 . . Cpe12g00099 . . . . . . . . . . . . . . . . . . .
Vvi5g885 Blo01g00323 Blo12g00122 Bda03g01119 . Bpe04g01132 . Bma04g01047 . Cmo08g01003 . Cma06g01258 Cma14g01883 Car06g01081 Car14g01685 . Cpe08g00387 Cpe03g01579 . . . . . . . . . . . . . . . . Cone7ag0378 . Lsi05g01822 . Chy05g00546 Cme06g00398 . . . . . . . . . Cmo06g01268 Cmo14g01930 Cma08g01033 Cma17g00111 . . Cpe12g00098 Cpe17g00246 Bhi12g01510 . . . . . Lcy13g0451 Cla05g00363 Cam05g0395 Cec05g0400 Cco05g0400 Clacu05g0390 Cmu05g0375 Cre05g0438 Lsi09g01156 Csa03g01116 Chy06g00384 Cme05g00694
Vvi5g886 . . . . . . . . . Cmo17g00108 . . . . . . . . . . . . . . . . . . . . . . . . . . Csa02g00934 . . . . . . . . . . . . . . . . Car17g00093 . . . . . . . . . . . . . . . . . . . .
Vvi5g887 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma06g01303 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g888 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 11678910 11688259 - Bda017168.1 Bda03g01118 1118
3 11689013 11691528 - Bda017169.1 Bda03g01119 1119
8 246474 247751 - Bda024418.1 Bda08g00027 27
11 6530296 6532982 + Bda005407.1 Bda11g00660 660
12 48856537 48861857 + XM_039051146.1 Bhi12g01510 1510
12 48865873 48874733 + XM_039018757.1 Bhi12g01511 1511
1 3928283 3929559 - BLOR00322 Blo01g00322 322
1 3934373 3942382 - BLOR00323 Blo01g00323 323
7 3449040 3454270 + BLOR18229 Blo07g00297 297
12 8558691 8567050 + BLOR04141 Blo12g00122 122
12 8567582 8575569 + BLOR04142 Blo12g00123 123
2 37186986 37189468 + Bma015433.1 Bma02g00733 733
4 18978480 18979759 + Bma019672.1 Bma04g01045 1045
4 19044990 19047309 - Bma019674.1 Bma04g01047 1047
5 52191015 52192285 + Bma022475.1 Bma05g01285 1285
6 50061792 50064215 + Bma024412.1 Bma06g01303 1303
6 52385431 52388050 + Bma024742.1 Bma06g01627 1627
4 7978690 7990139 - Bpe015732.1 Bpe04g01062 1062
4 9938048 9939157 - Bpe015813.1 Bpe04g01132 1132
5 23642955 23644231 - Bpe018551.1 Bpe05g01133 1133
5 3639989 3642870 + CaPI482276_05g003950.1 Cam05g0395 395
5 3650086 3653731 - CaPI482276_05g003970.1 Cam05g0397 397
6 10831499 10848040 - CaPI482276_06g007950.1 Cam06g0795 795
6 8126556 8129605 + Carg06278-RA Car06g01081 1081
6 8130798 8134234 - Carg06277-RA Car06g01082 1082
14 13380613 13383894 + Carg16504-RA Car14g01683 1683
14 13388021 13391178 - Carg16502-RA Car14g01685 1685
17 538421 542217 - Carg10139-RA Car17g00093 93
5 3286187 3289144 + CcPI632755_05g004000.1 Cco05g0400 400
5 3296809 3300431 - CcPI632755_05g004020.1 Cco05g0402 402
5 3280716 3287388 + CePI673135_05g004000.1 Cec05g0400 400
5 3294906 3298534 - CePI673135_05g004020.1 Cec05g0402 402
6 9707131 9724223 - CePI673135_06g008000.1 Cec06g0800 800
5 5870839 5878079 - Chy5G095910.1 Chy05g00545 545
5 5881447 5884580 - Chy5G095920.1 Chy05g00546 546
6 2592912 2595753 + Chy6G109120.1 Chy06g00384 384
6 2603508 2606483 - Chy6G109140.1 Chy06g00386 386
5 3353331 3356218 + ClG42_05g0039000.10 Clacu05g0390 390
5 3363501 3367025 - ClG42_05g0039200.10 Clacu05g0392 392
6 9467514 9484150 - ClG42_06g0079400.10 Clacu06g0794 794
5 3300210 3306042 + ClCG05G003500.2 Cla05g00363 363
5 3312554 3317583 - ClCG05G003520.1 Cla05g00365 365
6 9743535 9760385 - ClCG06G007650.2 Cla06g00742 742
6 8369656 8373224 + CmaCh06G012580.1 Cma06g01258 1258
6 8374307 8378005 - CmaCh06G012590.1 Cma06g01259 1259
8 6460092 6462815 + CmaCh08G010330.1 Cma08g01033 1033
8 6463423 6473913 + CmaCh08G010340.1 Cma08g01034 1034
14 13323723 13326600 - CmaCh14G018830.1 Cma14g01883 1883
14 13512373 13519962 - CmaCh14G019140.1 Cma14g01914 1914
17 548927 551328 + CmaCh17G001110.1 Cma17g00111 111
17 552707 554145 - CmaCh17G001130.1 Cma17g00113 113
5 7998380 8007134 - MELO3C020465.2.1 Cme05g00693 693
5 8026571 8036341 - MELO3C020464.2.1 Cme05g00694 694
6 2544826 2548220 + MELO3C006328.2.1 Cme06g00398 398
6 2554511 2559042 - MELO3C006330.2.1 Cme06g00400 400
5 16767039 16775554 + PI0015181.1 Cmetu05g0760 760
6 9569193 9572628 + CmoCh06G012680.1 Cmo06g01268 1268
6 9573683 9578371 - CmoCh06G012690.1 Cmo06g01269 1269
8 6515978 6519518 + CmoCh08G010030.1 Cmo08g01003 1003
8 6520433 6528691 + CmoCh08G010040.1 Cmo08g01004 1004
14 14308522 14312228 - CmoCh14G019300.1 Cmo14g01930 1930
14 14515610 14518497 - CmoCh14G019680.1 Cmo14g01968 1968
17 580652 582249 - CmoCh17G001080.1 Cmo17g00108 108
5 3191321 3194210 + CmPI595203_05g003750.1 Cmu05g0375 375
5 3201498 3205026 - CmPI595203_05g003770.1 Cmu05g0377 377
6 9284969 9301603 - CmPI595203_06g007670.1 Cmu06g0767 767
7 1655399 1658261 - Conep07aG0038700.1 Cone7ag0378 378
3 12207029 12212301 - Cp4.1LG03g18090.1 Cpe03g01579 1579
3 12411534 12414477 - Cp4.1LG03g17720.1 Cpe03g01613 1613
8 2423159 2427691 + Cp4.1LG08g02900.1 Cpe08g00386 386
8 2428617 2432042 - Cp4.1LG08g02840.1 Cpe08g00387 387
12 595640 597854 + Cp4.1LG12g00980.1 Cpe12g00098 98
12 598873 600582 - Cp4.1LG12g01070.1 Cpe12g00099 99
17 1600140 1608642 - Cp4.1LG17g03210.1 Cpe17g00245 245
17 1609702 1613087 - Cp4.1LG17g03160.1 Cpe17g00246 246
5 3973831 3977001 + CrPI670011_05g004380.1 Cre05g0438 438
5 3984423 3988019 - CrPI670011_05g004400.1 Cre05g0440 440
6 10507507 10524006 - CrPI670011_06g015480.1 Cre06g1548 1548
2 8812145 8817260 + CsaV3_2G011500.1 Csa02g00934 934
3 8814398 8818056 + CsaV3_3G011160.1 Csa03g01116 1116
3 8825175 8827925 - CsaV3_3G011180.1 Csa03g01118 1118
3 4882014 4892022 - Hsped.03g03440.1 Hepe03g0344 344
12 37807067 37812134 + Lag0016439.1 Lac12g2067 2067
13 5310984 5324620 - Maker00023362 Lcy13g0450 450
13 5327287 5330994 - Maker00024008 Lcy13g0451 451
5 25486110 25490828 + Lsi05G018200.1 Lsi05g01820 1820
5 25498628 25502651 - Lsi05G018220.1 Lsi05g01822 1822
9 18567967 18572145 + Lsi09G011560.1 Lsi09g01156 1156
9 18575475 18590164 + Lsi09G011570.1 Lsi09g01157 1157
9 1513561 1531866 + Sed0005259.1 Sed09g0191 191
6 74474303 74490442 + Tan0000225.1 Tan06g2320 2320
5 13407869 13455264 - Vvi5g879 Vvi5g879 879
5 13494304 13495345 + Vvi5g880 Vvi5g880 880
5 13537626 13538059 + Vvi5g881 Vvi5g881 881
5 13561473 13571982 - Vvi5g882 Vvi5g882 882
5 13572013 13572375 - Vvi5g883 Vvi5g883 883
5 13597403 13599563 + Vvi5g884 Vvi5g884 884
5 13658612 13670444 + Vvi5g885 Vvi5g885 885
5 13691792 13693411 + Vvi5g886 Vvi5g886 886
5 13695061 13705253 - Vvi5g887 Vvi5g887 887
5 13705260 13706774 + Vvi5g888 Vvi5g888 888
       

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