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
Vvi17g596 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone2ag0824 . . . Lsi02g00093 Csa01g00574 Chy12g01522 Cme12g01969 . . . . . . . . . . . . . . . . . Bhi08g01133 Tan05g2415 Cmetu12g1066 Lac10g0122 . . . Cla04g01179 Cam04g1235 Cec01g1746 Cco01g1792 Clacu04g1263 Cmu04g1242 Cre01g1536 . . . .
Vvi17g597 . . . . . . . . . . Cma10g00210 . Car10g00197 . . . . Bhi02g00288 . . . . . . Cla06g01567 Cam06g1733 Cec06g1793 Cco06g1793 Clacu06g1700 Cmu06g1646 Cre06g2457 . . . . . . . . . . . Bda14g00863 . Bpe15g00592 Bma03g00841 . . Cmo10g00228 . . . . . . Cpe18g00779 . . . . . . . . . . . . . . Lsi06g01442 Csa01g00263 Chy02g02470 Cme02g01858
Vvi17g598 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g599 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g600 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g601 . . . Bda15g00614 Bpe12g00532 . . . . . Cma10g00211 . Car10g00198 . . . . Bhi02g00285 . . . . . . Cla06g01566 . . . . . . Cone2ag0823 . Cone13ag0052 . . . . . . . . . . . . . . . . . . . . . Cpe18g00778 . . . . . . . . . . . . . . Lsi06g01441 Csa01g00264 Chy02g02469 Cme02g01857
Vvi17g602 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g603 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g604 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g605 Blo04g00783 . . . . . . . . . Cma10g00213 Cma11g00120 Car10g00199 . Sed08g0273 . . Bhi02g00098 Tan09g2046 Cmetu02g0607 . . . . Cla06g01565 Cam06g1729 Cec06g1790 Cco06g1790 Clacu06g1697 Cmu06g1643 Cre06g2454 . . Cone13ag0051 Cone19ag0056 Lsi02g00094 . . . . . . Bda14g00864 . Bpe15g00591 . . Sed08g2093 Cmo10g00229 Cmo11g00192 . . . . . Cpe18g00776 Bhi08g01132 Tan05g2414 . Lac10g0123 Hepe07g2487 . . . . . . . . . Lsi06g01440 Csa01g00265 Chy02g02468 Cme02g01855
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
14 6647729 6649897 + Bda027638.1 Bda14g00863 863
14 6654806 6655389 + Bda027639.1 Bda14g00864 864
15 9322600 9325663 + Bda012457.1 Bda15g00614 614
2 1900642 1904484 - XM_039022451.1 Bhi02g00098 98
2 5368763 5372909 - XM_039024750.1 Bhi02g00285 285
2 5423018 5426536 - XM_039022483.1 Bhi02g00288 288
8 35891041 35891852 - XM_039039289.1 Bhi08g01132 1132
8 35898739 35900843 + XM_039039479.1 Bhi08g01133 1133
4 7774546 7775215 + BLOR13695 Blo04g00783 783
3 8040398 8042390 + Bma017156.1 Bma03g00841 841
12 11216312 11219059 - Bpe005798.1 Bpe12g00532 532
15 16841405 16841934 - Bpe001525.1 Bpe15g00591 591
15 16844700 16846868 - Bpe001526.1 Bpe15g00592 592
4 26370771 26372440 + CaPI482276_04g012350.1 Cam04g1235 1235
6 28593615 28594141 - CaPI482276_06g017290.1 Cam06g1729 1729
6 28617665 28625915 - CaPI482276_06g017330.1 Cam06g1733 1733
10 955792 957693 + Carg17946-RA Car10g00197 197
10 962190 965897 + Carg17945-RA Car10g00198 198
10 970411 971105 + Carg17944-RA Car10g00199 199
1 30625508 30627310 + CcPI632755_01g017920.1 Cco01g1792 1792
6 28299108 28299635 - CcPI632755_06g017900.1 Cco06g1790 1790
6 28323254 28331560 - CcPI632755_06g017930.1 Cco06g1793 1793
1 32048802 32050473 + CePI673135_01g017460.1 Cec01g1746 1746
6 31368972 31369498 - CePI673135_06g017900.1 Cec06g1790 1790
6 31397355 31406930 - CePI673135_06g017930.1 Cec06g1793 1793
2 28258579 28259124 - Chy2G047350.1 Chy02g02468 2468
2 28273477 28276953 - Chy2G047360.1 Chy02g02469 2469
2 28284734 28286681 - Chy2G047370.1 Chy02g02470 2470
12 18988286 18989104 + Chy12G221220.1 Chy12g01522 1522
4 26726896 26728536 + ClG42_04g0126300.10 Clacu04g1263 1263
6 27652646 27653172 - ClG42_06g0169700.10 Clacu06g1697 1697
6 27675215 27684855 - ClG42_06g0170000.10 Clacu06g1700 1700
4 26967722 26969362 + ClCG04G012040.1 Cla04g01179 1179
6 29206037 29207136 - ClCG06G015900.1 Cla06g01565 1565
6 29215387 29218856 - ClCG06G015910.2 Cla06g01566 1566
6 29229821 29242356 - ClCG06G015920.2 Cla06g01567 1567
10 943752 946149 + CmaCh10G002100.1 Cma10g00210 210
10 950082 954382 + CmaCh10G002110.1 Cma10g00211 211
10 958152 958893 + CmaCh10G002130.1 Cma10g00213 213
11 644678 645283 - CmaCh11G001200.1 Cma11g00120 120
2 25202550 25203470 - MELO3C017201.2.1 Cme02g01855 1855
2 25211219 25215461 - MELO3C017200.2.1 Cme02g01857 1857
2 25223208 25226351 - MELO3C017199.2.1 Cme02g01858 1858
12 25527518 25528327 + MELO3C002004.2.1 Cme12g01969 1969
2 23349022 23351815 - PI0005731.1 Cmetu02g0607 607
12 595158 597731 - PI0017299.1 Cmetu12g1066 1066
10 1003093 1014231 + CmoCh10G002280.1 Cmo10g00228 228
10 1019043 1019573 + CmoCh10G002290.1 Cmo10g00229 229
11 939714 940450 + CmoCh11G001920.1 Cmo11g00192 192
4 26908799 26910439 + CmPI595203_04g012420.1 Cmu04g1242 1242
6 27561231 27561757 - CmPI595203_06g016430.1 Cmu06g1643 1643
6 27583819 27593457 - CmPI595203_06g016460.1 Cmu06g1646 1646
2 34230417 34233842 - Conep02aG0185100.1 Cone2ag0823 823
2 34248197 34249610 + Conep02aG0185200.1 Cone2ag0824 824
13 324344 324942 - Conep13aG0005400.1 Cone13ag0051 51
13 329681 332854 - Conep13aG0005500.1 Cone13ag0052 52
19 359304 359812 - Conep19aG0006000.1 Cone19ag0056 56
18 7374548 7378745 - Cp4.1LG18g07700.1 Cpe18g00776 776
18 7379495 7383615 - Cp4.1LG18g07710.1 Cpe18g00778 778
18 7387974 7391333 - Cp4.1LG18g07740.1 Cpe18g00779 779
1 28571338 28573004 + CrPI670011_01g015360.1 Cre01g1536 1536
6 32356184 32356710 - CrPI670011_06g024540.1 Cre06g2454 2454
6 32378349 32388627 - CrPI670011_06g024570.1 Cre06g2457 2457
1 1644571 1646516 + CsaV3_1G002630.1 Csa01g00263 263
1 1653204 1657278 + CsaV3_1G002640.1 Csa01g00264 264
1 1665078 1666427 + CsaV3_1G002650.1 Csa01g00265 265
1 3693768 3694904 - CsaV3_1G005740.1 Csa01g00574 574
7 69192797 69193278 - Hsped.07g24870.1 Hepe07g2487 2487
10 928537 929953 - Lag0024167.1 Lac10g0122 122
10 934183 934921 + Lag0024168.1 Lac10g0123 123
2 786202 788541 - Lsi02G000930.1 Lsi02g00093 93
2 793042 794129 + Lsi02G000940.1 Lsi02g00094 94
6 24927204 24928373 - Lsi06G014400.1 Lsi06g01440 1440
6 24936447 24940412 - Lsi06G014410.1 Lsi06g01441 1441
6 24953095 24961859 - Lsi06G014420.1 Lsi06g01442 1442
8 1593661 1596795 + Sed0020095.5 Sed08g0273 273
8 35059199 35061240 + Sed0016148.1 Sed08g2093 2093
5 75310595 75312028 - Tan0002712.2 Tan05g2414 2414
5 75315801 75317099 + Tan0013596.1 Tan05g2415 2415
9 70960850 70964297 - Tan0000161.1 Tan09g2046 2046
17 7231478 7234983 - Vvi17g596 Vvi17g596 596
17 7239171 7243130 + Vvi17g597 Vvi17g597 597
17 7243745 7246234 - Vvi17g598 Vvi17g598 598
17 7253254 7253956 - Vvi17g599 Vvi17g599 599
17 7286221 7292038 + Vvi17g600 Vvi17g600 600
17 7307382 7310961 + Vvi17g601 Vvi17g601 601
17 7311469 7311955 - Vvi17g602 Vvi17g602 602
17 7311995 7316054 + Vvi17g603 Vvi17g603 603
17 7317399 7320708 + Vvi17g604 Vvi17g604 604
17 7320788 7323760 + Vvi17g605 Vvi17g605 605
       

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