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
Vvi3g656 Blo02g00944 Blo03g00085 Bda06g01216 Bda08g00666 Bpe07g00262 . Bma05g00672 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1009 Cone10ag1026 . . . . . . . . . Bpe05g00488 . . . Cmo04g00496 Cmo16g00355 . . . . Cpe14g00278 Cpe01g00416 . . . . . . . . . . . . . . . . . .
Vvi3g657 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g658 Blo02g00943 Blo03g00084 Bda06g01215 Bda08g00668 Bpe07g00263 . Bma05g00671 Bma12g00268 . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1010 Cone10ag1027 . . . . . . . . . Bpe05g00487 . . . Cmo04g00495 Cmo16g00352 . . . . Cpe14g00277 Cpe01g00415 . . . . . . . . . . . . . . . . . .
Vvi3g659 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma03g01352 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g660 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g661 . . . . . Bpe12g00302 . . . Cmo11g01400 . . . . Sed06g0592 Cpe04g00310 . Bhi05g01055 Tan02g0996 Cmetu04g1635 Lac12g0194 . . . Cla02g00660 Cam02g0695 Cec02g0708 Cco02g0727 Clacu02g0701 Cmu02g0699 Cre02g1014 . . . . Lsi03g00555 Csa07g00704 . Cme01g00102 . . Bda15g00839 . . . . Bma08g00458 . . . Cma11g01715 . Car11g01126 . . . . . . . . . . . . . . . . . . . Chy01g00110 .
Vvi3g662 Blo02g00941 Blo03g00083 . Bda08g00669 . . Bma05g00670 . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1061 Cone8ag1094 . . . . . . . . . . . Bpe05g00486 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g663 . . . . . . . . . . . . . . . . . . . . . . . . Cla10g01011 Cam10g1034 Cec10g1065 Cco10g1029 Clacu10g1051 Cmu10g1836 Cre10g1207 Cone12ag1060 . . . . . . . . . . . . . . . Sed08g1334 . . . . . . . . Bhi11g01169 Tan01g0659 Cmetu04g1335 . . Mch10g0461 . . . . . . . . Lsi03g01039 . . Cme07g02163
Vvi3g664 . . Bda06g01214 . Bpe07g00264 . . Bma12g00269 . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1012 Cone10ag1029 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g665 Blo02g00940 Blo03g00082 Bda06g01212 Bda08g00670 Bpe07g00265 . Bma05g00668 Bma12g00271 . . . . . . . . . . . . . . . . Cla10g01010 Cam10g1033 Cec10g1064 Cco10g1028 Clacu10g1050 Cmu10g1834 Cre10g1206 Cone12ag1059 Cone8ag1093 Cone3ag1013 Cone10ag1030 . . . . . . . . . Bpe05g00485 . . . Cmo04g00494 Cmo16g00351 . . . . Cpe14g00276 Cpe01g00414 Bhi11g01168 Tan01g0658 . . . Mch10g0460 . . . . . . . . Lsi03g01038 . . Cme07g02166
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 42042560 42044600 - Bda023033.1 Bda06g01212 1212
6 42075700 42084371 + Bda023036.1 Bda06g01214 1214
6 42088672 42090646 - Bda023037.1 Bda06g01215 1215
6 42099996 42107517 + Bda023038.1 Bda06g01216 1216
8 6956748 6966293 - Bda029128.1 Bda08g00666 666
8 6989222 6991199 + Bda029130.1 Bda08g00668 668
8 7012735 7014175 - Bda029131.1 Bda08g00669 669
8 7037274 7039351 + Bda029132.1 Bda08g00670 670
15 12833362 12842595 - Bda012708.1 Bda15g00839 839
5 38133453 38138363 - XM_039032451.1 Bhi05g01055 1055
11 34007816 34010454 - XM_039049741.1 Bhi11g01168 1168
11 34037855 34038376 + XM_039050318.1 Bhi11g01169 1169
2 36464271 36466379 - BLOR10670 Blo02g00940 940
2 36548261 36549687 + BLOR10671 Blo02g00941 941
2 36694456 36696433 - BLOR10673 Blo02g00943 943
2 36717141 36722841 + BLOR10674 Blo02g00944 944
3 2740411 2742424 - BLOR11263 Blo03g00082 82
3 2768341 2791489 + BLOR11264 Blo03g00083 83
3 2817588 2819560 - BLOR11265 Blo03g00084 84
3 2836195 2842246 + BLOR11266 Blo03g00085 85
3 29185008 29187843 + Bma017884.1 Bma03g01352 1352
5 39058951 39061037 - Bma021714.1 Bma05g00668 668
5 39202851 39204339 + Bma021718.1 Bma05g00670 670
5 39243908 39245883 - Bma021720.1 Bma05g00671 671
5 39309718 39312936 + Bma021722.1 Bma05g00672 672
8 18814928 18822917 - Bma027593.1 Bma08g00458 458
12 3533752 3535730 + Bma007162.1 Bma12g00268 268
12 3559238 3562563 - Bma007164.1 Bma12g00269 269
12 3631554 3632486 + Bma007167.2 Bma12g00271 271
5 19089341 19091405 - Bpe017905.1 Bpe05g00485 485
5 19104009 19105466 + Bpe017906.1 Bpe05g00486 486
5 19106270 19108244 - Bpe017907.1 Bpe05g00487 487
5 19116348 19121492 + Bpe017908.1 Bpe05g00488 488
7 1883715 1888237 - Bpe021074.3 Bpe07g00262 262
7 1897110 1899085 + Bpe021075.1 Bpe07g00263 263
7 1904044 1909539 - Bpe021076.1 Bpe07g00264 264
7 1913833 1915887 + Bpe021077.1 Bpe07g00265 265
12 4488203 4497245 + Bpe005548.1 Bpe12g00302 302
2 8210287 8220505 + CaPI482276_02g006950.1 Cam02g0695 695
10 22743597 22745601 - CaPI482276_10g010330.1 Cam10g1033 1033
10 22784870 22785276 + CaPI482276_10g010340.1 Cam10g1034 1034
11 9002477 9007432 + Carg26991-RA Car11g01126 1126
2 7490085 7494383 + CcPI632755_02g007270.1 Cco02g0727 727
10 21957259 21959278 - CcPI632755_10g010280.1 Cco10g1028 1028
10 22004944 22005349 + CcPI632755_10g010290.1 Cco10g1029 1029
2 7422835 7427166 + CePI673135_02g007080.1 Cec02g0708 708
10 23646525 23648535 - CePI673135_10g010640.1 Cec10g1064 1064
10 23701525 23701936 + CePI673135_10g010650.1 Cec10g1065 1065
1 730313 734616 + Chy1G001100.1 Chy01g00110 110
2 7233460 7237797 + ClG42_02g0070100.10 Clacu02g0701 701
10 22387346 22389343 - ClG42_10g0105000.10 Clacu10g1050 1050
10 22432458 22432863 + ClG42_10g0105100.10 Clacu10g1051 1051
2 7575481 7582854 + ClCG02G006580.2 Cla02g00660 660
10 23421525 23423708 - ClCG10G010590.1 Cla10g01010 1010
10 23470742 23471147 + ClCG10G010600.1 Cla10g01011 1011
11 11352331 11357862 - CmaCh11G017150.1 Cma11g01715 1715
1 710092 715488 + MELO3C018502.2.1 Cme01g00102 102
7 26076528 26081332 - MELO3C017982.2.1 Cme07g02163 2163
7 26089271 26092747 + MELO3C017985.2.1 Cme07g02166 2166
4 9899420 9900907 + PI0024012.1 Cmetu04g1335 1335
4 9044288 9048792 - PI0026862.1 Cmetu04g1635 1635
4 2459958 2462474 - CmoCh04G004940.1 Cmo04g00494 494
4 2470212 2472488 - CmoCh04G004950.1 Cmo04g00495 495
4 2479320 2489180 + CmoCh04G004960.1 Cmo04g00496 496
11 9846199 9851419 + CmoCh11G014000.1 Cmo11g01400 1400
16 1623095 1625832 - CmoCh16G003510.1 Cmo16g00351 351
16 1630666 1632704 - CmoCh16G003520.1 Cmo16g00352 352
16 1640025 1645344 + CmoCh16G003550.1 Cmo16g00355 355
2 7138634 7148893 + CmPI595203_02g006990.1 Cmu02g0699 699
10 23002166 23004163 - CmPI595203_10g018340.1 Cmu10g1834 1834
10 23047453 23047858 + CmPI595203_10g018360.1 Cmu10g1836 1836
3 28893546 28902683 - Conep03aG0150800.1 Cone3ag1009 1009
3 28917042 28919407 + Conep03aG0150900.1 Cone3ag1010 1010
3 28957029 28962270 - Conep03aG0151100.1 Cone3ag1012 1012
3 28976253 28979040 + Conep03aG0151200.1 Cone3ag1013 1013
8 9807217 9810368 - Conep08aG0112400.1 Cone8ag1093 1093
8 9816315 9818135 + Conep08aG0112500.1 Cone8ag1094 1094
10 7151963 7160545 - Conep10aG0105300.1 Cone10ag1026 1026
10 7169016 7171274 + Conep10aG0105400.1 Cone10ag1027 1027
10 7184912 7190534 - Conep10aG0105600.1 Cone10ag1029 1029
10 7193813 7196564 + Conep10aG0105700.1 Cone10ag1030 1030
12 8770573 8773352 - Conep12aG0109300.1 Cone12ag1059 1059
12 8779421 8780015 + Conep12aG0109400.1 Cone12ag1060 1060
12 8780227 8782414 + Conep12aG0109500.1 Cone12ag1061 1061
1 2389970 2392611 - Cp4.1LG01g02510.1 Cpe01g00414 414
1 2400593 2403146 - Cp4.1LG01g02350.1 Cpe01g00415 415
1 2411317 2422950 + Cp4.1LG01g02480.1 Cpe01g00416 416
4 3882383 3887731 + Cp4.1LG04g07700.1 Cpe04g00310 310
14 1598104 1600529 - Cp4.1LG14g04370.1 Cpe14g00276 276
14 1604903 1607416 - Cp4.1LG14g04360.1 Cpe14g00277 277
14 1612991 1624485 + Cp4.1LG14g04420.1 Cpe14g00278 278
2 7763024 7767361 + CrPI670011_02g010140.1 Cre02g1014 1014
10 24701511 24703527 - CrPI670011_10g012060.1 Cre10g1206 1206
10 24740516 24740927 + CrPI670011_10g012070.1 Cre10g1207 1207
7 5023312 5028969 - CsaV3_7G008030.1 Csa07g00704 704
12 2136970 2143266 - Lag0014566.1 Lac12g0194 194
3 6721913 6730573 + Lsi03G005550.1 Lsi03g00555 555
3 19924844 19927939 - Lsi03G010380.1 Lsi03g01038 1038
3 19955854 19956253 + Lsi03G010390.1 Lsi03g01039 1039
10 2997235 2999309 - MC10g0376 Mch10g0460 460
10 3011243 3011419 + MC10g0377 Mch10g0461 461
6 5210535 5214819 + Sed0020844.1 Sed06g0592 592
8 27782007 27783423 - Sed0021074.1 Sed08g1334 1334
1 6225423 6228767 - Tan0000706.2 Tan01g0658 658
1 6253789 6254353 + Tan0003426.1 Tan01g0659 659
2 13956476 13961368 + Tan0008087.1 Tan02g0996 996
3 6571800 6592129 - Vvi3g656 Vvi3g656 656
3 6623123 6623416 + Vvi3g657 Vvi3g657 657
3 6633678 6636058 + Vvi3g658 Vvi3g658 658
3 6642096 6659818 - Vvi3g659 Vvi3g659 659
3 6660499 6667636 - Vvi3g660 Vvi3g660 660
3 6668087 6688722 + Vvi3g661 Vvi3g661 661
3 6699290 6705616 - Vvi3g662 Vvi3g662 662
3 6715490 6716068 - Vvi3g663 Vvi3g663 663
3 6718591 6754398 - Vvi3g664 Vvi3g664 664
3 6773154 6775422 + Vvi3g665 Vvi3g665 665
       

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