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
Vvi5g1089 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone18ag0883 . . . . . Blo02g00422 Blo07g00080 . . . Bpe13g00744 Bma02g00995 Bma06g01412 . . . . . . . . . . . . . . . . Cla07g01497 Cam07g1596 Cec07g1692 Cco07g1655 Clacu07g1586 Cmu07g1552 Cre07g1929 . . . .
Vvi5g1090 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1091 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1092 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1093 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1094 . . . . . Bpe14g01051 . . . . . . . . . . . Bhi01g02623 . . . . . Lcy11g1238 . . . . . . . . . Cone18ag0867 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1095 . . . . . . . . . . . . . . . . . . . . . . . . Cla08g00390 Cam08g0809 Cec08g0380 Cco08g0478 Clacu08g0521 . Cre08g0349 . . Cone18ag0868 Cone11ag0640 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1096 . . . . Bpe04g00915 . . Bma05g01176 . . Cma06g01623 Cma14g01512 Car06g01379 Car14g01335 . . Cpe03g01269 Bhi01g02585 . . . Hepe05g1290 . . . . . . . . . . . . . . . . Cme07g01841 . . . . . . . . . Cmo06g01619 Cmo14g01545 . . . . . . . . . . . . . Cla07g01592 Cam07g1689 Cec07g1785 Cco07g1747 Clacu07g1672 Cmu07g1639 Cre07g2013 . . . .
Vvi5g1097 . . . . . . . . . . . Cma14g01511 . Car14g01334 . . Cpe03g01268 . . . . . . . . . . . . . . . . . Cone11ag0633 . . . Cme07g01842 . Blo07g00102 Bda11g00471 . . . . Bma06g01431 . . Cmo14g01544 . . . . . . . . . . . . . Cla07g01591 Cam07g1687 Cec07g1784 Cco07g1745 Clacu07g1671 Cmu07g1638 Cre07g2012 . . . .
Vvi5g1098 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 4961914 4965970 + Bda005210.1 Bda11g00471 471
1 63512383 63514738 + XM_039023838.1 Bhi01g02585 2585
1 64926470 64943494 + XM_039043730.1 Bhi01g02623 2623
2 5513704 5515659 + BLOR10152 Blo02g00422 422
7 1149520 1154788 + BLOR18012 Blo07g00080 80
7 1488348 1498001 + BLOR18034 Blo07g00102 102
2 50529093 50529891 - Bma015808.1 Bma02g00995 995
5 50899001 50900808 - Bma022367.1 Bma05g01176 1176
6 50864786 50867575 + Bma024527.1 Bma06g01412 1412
6 51046410 51050592 + Bma024546.1 Bma06g01431 1431
4 6111048 6112696 - Bpe015579.1 Bpe04g00915 915
13 14002990 14005770 - Bpe025240 Bpe13g00744 744
14 7862975 7877454 - Bpe014425.3 Bpe14g01051 1051
7 30639633 30642096 - CaPI482276_07g015960.1 Cam07g1596 1596
7 31569854 31572966 - CaPI482276_07g016870.1 Cam07g1687 1687
7 31584977 31587282 + CaPI482276_07g016890.1 Cam07g1689 1689
8 10419305 10430968 + CaPI482276_08g008090.1 Cam08g0809 809
6 9910029 9911100 - Carg15497-RA Car06g01379 1379
14 11279216 11282519 - Carg24805-RA Car14g01334 1334
14 11283177 11284918 + Carg24804-RA Car14g01335 1335
7 30606378 30615095 - CcPI632755_07g016550.1 Cco07g1655 1655
7 31555547 31558616 - CcPI632755_07g017450.1 Cco07g1745 1745
7 31571002 31573202 + CcPI632755_07g017470.1 Cco07g1747 1747
8 12179963 12191122 + CcPI632755_08g004780.1 Cco08g0478 478
7 32512638 32521355 - CePI673135_07g016920.1 Cec07g1692 1692
7 33484423 33487528 - CePI673135_07g017840.1 Cec07g1784 1784
7 33498024 33500227 + CePI673135_07g017850.1 Cec07g1785 1785
8 10734706 10745896 + CePI673135_08g003800.1 Cec08g0380 380
7 30492390 30494850 - ClG42_07g0158600.10 Clacu07g1586 1586
7 31421063 31424172 - ClG42_07g0167100.10 Clacu07g1671 1671
7 31433186 31438272 + ClG42_07g0167200.10 Clacu07g1672 1672
8 10228715 10240378 + ClG42_08g0052100.10 Clacu08g0521 521
7 32222911 32229203 - ClCG07G015710.2 Cla07g01497 1497
7 33203013 33206430 - ClCG07G016700.1 Cla07g01591 1591
7 33219779 33222059 + ClCG07G016710.2 Cla07g01592 1592
8 10397876 10409979 + ClCG08G003770.2 Cla08g00390 390
6 10098128 10100118 - CmaCh06G016230.1 Cma06g01623 1623
14 11424646 11427450 - CmaCh14G015110.1 Cma14g01511 1511
14 11428180 11430254 + CmaCh14G015120.1 Cma14g01512 1512
7 23878791 23881494 - MELO3C017671.2.1 Cme07g01841 1841
7 23889765 23893039 + MELO3C017672.2.1 Cme07g01842 1842
6 11308243 11310343 - CmoCh06G016190.1 Cmo06g01619 1619
14 12336250 12339176 - CmoCh14G015440.1 Cmo14g01544 1544
14 12339913 12341891 + CmoCh14G015450.1 Cmo14g01545 1545
7 30740970 30746864 - CmPI595203_07g015520.1 Cmu07g1552 1552
7 31672983 31676092 - CmPI595203_07g016380.1 Cmu07g1638 1638
7 31685129 31690214 + CmPI595203_07g016390.1 Cmu07g1639 1639
11 4137614 4141793 + Conep11aG0065000.1 Cone11ag0633 633
11 4226499 4236472 - Conep11aG0065700.1 Cone11ag0640 640
18 5981459 6009906 - Conep18aG0089300.1 Cone18ag0867 867
18 6015009 6025498 + Conep18aG0089400.1 Cone18ag0868 868
18 6224857 6229916 - Conep18aG0090900.1 Cone18ag0883 883
3 10283170 10286406 - Cp4.1LG03g12440.1 Cpe03g01268 1268
3 10287007 10289051 + Cp4.1LG03g12390.1 Cpe03g01269 1269
7 34745498 34754162 - CrPI670011_07g019290.1 Cre07g1929 1929
7 35676284 35679311 - CrPI670011_07g020120.1 Cre07g2012 2012
7 35689984 35692207 + CrPI670011_07g020130.1 Cre07g2013 2013
8 11358033 11369179 + CrPI670011_08g003490.1 Cre08g0349 349
5 60728926 60731326 + Hsped.05g12900.1 Hepe05g1290 1290
11 35276193 35283551 - Maker00005131 Lcy11g1238 1238
5 19770328 19774873 + Vvi5g1089 Vvi5g1089 1089
5 19783562 19785854 + Vvi5g1090 Vvi5g1090 1090
5 19809628 19814198 + Vvi5g1091 Vvi5g1091 1091
5 19817317 19818964 + Vvi5g1092 Vvi5g1092 1092
5 19871693 19875293 - Vvi5g1093 Vvi5g1093 1093
5 19895339 19909576 + Vvi5g1094 Vvi5g1094 1094
5 19911021 19937061 - Vvi5g1095 Vvi5g1095 1095
5 19947203 19951503 - Vvi5g1096 Vvi5g1096 1096
5 19967431 19975143 + Vvi5g1097 Vvi5g1097 1097
5 19975588 19979672 - Vvi5g1098 Vvi5g1098 1098
       

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