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
Vvi3g706 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g707 . . . . . . . . . . . . . . . . . . . . . . . . Cla10g00979 Cam10g1001 Cec10g1031 Cco10g0994 Clacu10g1022 Cmu10g1805 Cre10g1179 . . Cone3ag1028 Cone10ag1044 . . . . . . . . . . . . Sed07g1261 . . . . . . Cpe14g00262 . Bhi11g01132 Tan01g0627 Cmetu07g0869 . Hepe07g0410 Mch10g0424 . . . . . . . . Lsi03g01017 . . Cme07g02192
Vvi3g708 . . . . . . . . Cmo19g00564 . . . . . . . Cpe15g00437 . . . . . . . Cla02g00683 Cam02g0717 Cec02g0730 Cco02g0752 Clacu02g0726 Cmu02g0724 Cre02g1036 Cone12ag1043 Cone8ag1076 . . Lsi03g00577 Csa07g00682 . Cme01g00122 . . . . . . . . . . . . Cma19g00550 . Car19g00408 . . . . . . . . . . . . . . . . . . Chy01g00132 .
Vvi3g709 Blo02g00927 Blo03g00071 Bda06g01200 . Bpe07g00277 . Bma05g00649 Bma12g00284 . . . . . . . . . . . . . . . . Cla10g00977 Cam10g1000 Cec10g1030 Cco10g0993 Clacu10g1021 Cmu10g1804 Cre10g1178 . . Cone3ag1029 Cone10ag1045 . . . . . . . . . Bpe05g00469 . . Sed07g1259 Cmo04g00480 Cmo16g00334 . . . . Cpe14g00261 Cpe01g00401 Bhi11g01131 Tan01g0626 Cmetu07g0597 . Hepe07g0409 Mch10g0422 . . . . . . . . Lsi03g01016 . . Cme07g02193
Vvi3g710 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1030 Cone10ag1047 Lsi03g00578 . . . . . . . . . . . Sed07g1258 Cmo04g00478 . . . . . . Cpe01g00400 Bhi11g01130 Tan01g0624 Cmetu07g1354 . Hepe07g0408 Mch10g0421 . . . . . . . . . . . .
Vvi3g711 . . . . . . . . Cmo19g00563 . . . . . . . Cpe15g00436 . . . . . . . Cla02g00685 Cam02g0718 Cec02g0731 Cco02g0753 Clacu02g0728 Cmu02g0726 Cre02g1037 . . . Cone10ag1048 Lsi03g00581 Csa07g00681 . Cme01g00123 . . . . . . . . . Cmo04g00476 . . Cma19g00549 . . . Cpe01g00398 . . . . . . . . . . . . . . . . Chy01g00133 .
Vvi3g712 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g713 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g714 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g715 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 41824581 41825846 + Bda023019.1 Bda06g01200 1200
11 32993882 32998752 - XM_039047352.1 Bhi11g01130 1130
11 33005439 33008131 - XM_039047438.1 Bhi11g01131 1131
11 33022160 33024433 + XM_039047525.1 Bhi11g01132 1132
2 35964515 35966713 + BLOR10657 Blo02g00927 927
3 2560342 2562151 + BLOR11252 Blo03g00071 71
5 38078883 38080216 + Bma021691.1 Bma05g00649 649
12 3807841 3809488 - Bma007182.3 Bma12g00284 284
5 19015017 19016713 + Bpe017889.1 Bpe05g00469 469
7 1987295 1988939 - Bpe021088.2 Bpe07g00277 277
2 8528034 8540099 - CaPI482276_02g007170.1 Cam02g0717 717
2 8550447 8562329 + CaPI482276_02g007180.1 Cam02g0718 718
10 22273155 22275386 - CaPI482276_10g010000.1 Cam10g1000 1000
10 22303248 22305164 + CaPI482276_10g010010.1 Cam10g1001 1001
19 5954437 5964290 + Carg16330-RA Car19g00408 408
2 7835524 7847647 - CcPI632755_02g007520.1 Cco02g0752 752
2 7854156 7867327 + CcPI632755_02g007530.1 Cco02g0753 753
10 21487497 21489733 - CcPI632755_10g009930.1 Cco10g0993 993
10 21522124 21524114 + CcPI632755_10g009940.1 Cco10g0994 994
2 7750449 7762293 - CePI673135_02g007300.1 Cec02g0730 730
2 7772040 7784478 + CePI673135_02g007310.1 Cec02g0731 731
10 23163946 23166179 - CePI673135_10g010300.1 Cec10g1030 1030
10 23197485 23199374 + CePI673135_10g010310.1 Cec10g1031 1031
1 874913 882675 - Chy1G001320.1 Chy01g00132 132
1 888040 893498 + Chy1G001330.1 Chy01g00133 133
2 7543670 7555846 - ClG42_02g0072600.10 Clacu02g0726 726
2 7572138 7577947 + ClG42_02g0072800.10 Clacu02g0728 728
10 21939926 21942155 - ClG42_10g0102100.10 Clacu10g1021 1021
10 21967619 21969516 + ClG42_10g0102200.10 Clacu10g1022 1022
2 7906025 7913199 - ClCG02G006830.1 Cla02g00683 683
2 7926946 7937982 + ClCG02G006850.2 Cla02g00685 685
10 22951027 22953592 - ClCG10G010250.2 Cla10g00977 977
10 22978969 22981194 + ClCG10G010270.1 Cla10g00979 979
19 6278352 6282963 - CmaCh19G005490.1 Cma19g00549 549
19 6287364 6295908 + CmaCh19G005500.1 Cma19g00550 550
1 874429 880557 - MELO3C018521.2.1 Cme01g00122 122
1 885116 890388 + MELO3C018522.2.1 Cme01g00123 123
7 26214698 26215878 - MELO3C018011.2.1 Cme07g02192 2192
7 26216820 26219771 + MELO3C018012.2.1 Cme07g02193 2193
7 396825 399914 - PI0017890.1 Cmetu07g0597 597
7 401666 403306 + PI0018624.1 Cmetu07g0869 869
7 388599 392362 - PI0019509.1 Cmetu07g1354 1354
4 2379528 2382135 - CmoCh04G004760.1 Cmo04g00476 476
4 2384534 2387358 - CmoCh04G004780.1 Cmo04g00478 478
4 2388661 2391863 - CmoCh04G004800.1 Cmo04g00480 480
16 1547103 1550310 - CmoCh16G003340.1 Cmo16g00334 334
19 6449254 6456348 - CmoCh19G005630.1 Cmo19g00563 563
19 6459063 6469214 + CmoCh19G005640.1 Cmo19g00564 564
2 7452747 7463836 - CmPI595203_02g007240.1 Cmu02g0724 724
2 7480171 7485980 + CmPI595203_02g007260.1 Cmu02g0726 726
10 22550144 22552373 - CmPI595203_10g018040.1 Cmu10g1804 1804
10 22577755 22579649 + CmPI595203_10g018050.1 Cmu10g1805 1805
3 29069291 29070126 - Conep03aG0152800.1 Cone3ag1028 1028
3 29072131 29075348 + Conep03aG0152900.1 Cone3ag1029 1029
3 29083825 29087575 + Conep03aG0153000.1 Cone3ag1030 1030
8 9737812 9742158 - Conep08aG0110700.1 Cone8ag1076 1076
10 7278099 7278869 - Conep10aG0107100.1 Cone10ag1044 1044
10 7283244 7286679 + Conep10aG0107200.1 Cone10ag1045 1045
10 7296931 7300021 + Conep10aG0107400.1 Cone10ag1047 1047
10 7303930 7308210 + Conep10aG0107500.1 Cone10ag1048 1048
12 8711651 8713877 - Conep12aG0107700.1 Cone12ag1043 1043
1 2313351 2315975 - Cp4.1LG01g02590.1 Cpe01g00398 398
1 2318299 2321208 - Cp4.1LG01g02600.1 Cpe01g00400 400
1 2322859 2326049 - Cp4.1LG01g02570.1 Cpe01g00401 401
14 1526369 1529842 - Cp4.1LG14g04520.1 Cpe14g00261 261
14 1531255 1532458 + Cp4.1LG14g04580.1 Cpe14g00262 262
15 5495882 5501401 - Cp4.1LG15g04390.1 Cpe15g00436 436
15 5504738 5513822 + Cp4.1LG15g04370.1 Cpe15g00437 437
2 8081849 8094078 - CrPI670011_02g010360.1 Cre02g1036 1036
2 8104325 8117214 + CrPI670011_02g010370.1 Cre02g1037 1037
10 24222520 24224752 - CrPI670011_10g011780.1 Cre10g1178 1178
10 24239160 24241659 + CrPI670011_10g011790.1 Cre10g1179 1179
7 4872506 4877852 - CsaV3_7G007800.1 Csa07g00681 681
7 4882370 4889127 + CsaV3_7G007810.1 Csa07g00682 682
7 4170858 4174872 - Hsped.07g04080.1 Hepe07g0408 408
7 4181561 4185247 - Hsped.07g04090.1 Hepe07g0409 409
7 4187766 4190658 + Hsped.07g04100.1 Hepe07g0410 410
3 7085616 7096153 - Lsi03G005770.1 Lsi03g00577 577
3 7103789 7111784 + Lsi03G005780.1 Lsi03g00578 578
3 7146094 7148203 + Lsi03G005810.1 Lsi03g00581 581
3 19567621 19570838 - Lsi03G010160.1 Lsi03g01016 1016
3 19573276 19575534 + Lsi03G010170.1 Lsi03g01017 1017
10 2800448 2807792 - MC10g0347 Mch10g0421 421
10 2811053 2813163 - MC10g0348 Mch10g0422 422
10 2817765 2818905 + MC10g0349 Mch10g0424 424
7 9440391 9443825 - Sed0004315.1 Sed07g1258 1258
7 9447859 9452684 - Sed0015268.1 Sed07g1259 1259
7 9455937 9458092 + Sed0016408.2 Sed07g1261 1261
1 5816484 5837073 - Tan0019274.1 Tan01g0624 624
1 5840587 5843851 - Tan0021906.2 Tan01g0626 626
1 5849272 5852053 + Tan0006029.1 Tan01g0627 627
3 7321432 7322062 + Vvi3g706 Vvi3g706 706
3 7322987 7324195 - Vvi3g707 Vvi3g707 707
3 7326028 7339940 - Vvi3g708 Vvi3g708 708
3 7342139 7357074 + Vvi3g709 Vvi3g709 709
3 7374685 7389061 + Vvi3g710 Vvi3g710 710
3 7389632 7402240 + Vvi3g711 Vvi3g711 711
3 7412392 7415825 + Vvi3g712 Vvi3g712 712
3 7415825 7415992 + Vvi3g713 Vvi3g713 713
3 7417453 7418401 - Vvi3g714 Vvi3g714 714
3 7428321 7430945 - Vvi3g715 Vvi3g715 715
       

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