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
Vvi4g1242 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1243 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1244 . . . . . . . . . . Cma03g01079 Cma07g00785 Car03g00970 Car07g00772 Sed10g0487 Cpe19g00542 Cpe10g00349 Bhi03g01384 Tan03g1334 Cmetu08g1211 . Hepe04g1129 . . Cla01g01533 Cam01g1601 Cec04g1248 Cco04g1317 Clacu01g1626 Cmu01g1512 Cre04g1192 . . . . Lsi01g01132 . . Cme08g01066 . . . . . . . . . Cmo03g01069 Cmo07g00809 . . . . . . . . . . . . . . . . . . . . . Csa06g02800 Chy02g01035 .
Vvi4g1245 . . . . . . . . . . . Cma07g00786 . Car07g00773 Sed14g0002 Cpe19g00541 . Bhi03g01383 Tan03g1333 Cmetu08g0890 . Hepe04g1128 . . Cla01g01532 Cam01g1600 Cec04g1245 Cco04g1314 Clacu01g1625 Cmu01g1511 Cre04g1190 . . . . Lsi01g01133 . . Cme08g01067 . . . . . . . . . . Cmo07g00810 . . . . . . . . . . . . . . . . . . . . . Csa06g02799 Chy02g01036 .
Vvi4g1246 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1247 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1248 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1249 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1250 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1251 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 28654134 28655713 - XM_039027520.1 Bhi03g01383 1383
3 28709488 28729907 - XM_039026132.1 Bhi03g01384 1384
1 29541850 29543385 - CaPI482276_01g016000.1 Cam01g1600 1600
1 29554747 29563642 - CaPI482276_01g016010.1 Cam01g1601 1601
3 7501600 7505387 + Carg10551-RA Car03g00970 970
7 4030100 4033217 + Carg05294-RA Car07g00772 772
7 4036031 4037518 + Carg05295-RA Car07g00773 773
4 28481038 28482555 - CcPI632755_04g013140.1 Cco04g1314 1314
4 28497228 28504810 - CcPI632755_04g013170.1 Cco04g1317 1317
4 32034364 32035881 - CePI673135_04g012450.1 Cec04g1245 1245
4 32048346 32056508 - CePI673135_04g012480.1 Cec04g1248 1248
2 7053433 7060427 + Chy2G033020.1 Chy02g01035 1035
2 7068695 7070191 + Chy2G033030.1 Chy02g01036 1036
1 28335173 28336705 - ClG42_01g0162500.10 Clacu01g1625 1625
1 28348081 28356956 - ClG42_01g0162600.10 Clacu01g1626 1626
1 29880091 29881620 - ClCG01G015610.2 Cla01g01532 1532
1 29892660 29902358 - ClCG01G015640.2 Cla01g01533 1533
3 7394324 7397962 + CmaCh03G010790.1 Cma03g01079 1079
7 3549345 3553065 + CmaCh07G007850.1 Cma07g00785 785
7 3555767 3557254 + CmaCh07G007860.1 Cma07g00786 786
8 6954713 6962121 + MELO3C008035.2.1 Cme08g01066 1066
8 6972180 6973691 + MELO3C008036.2.1 Cme08g01067 1067
8 18547269 18548761 - PI0001032.1 Cmetu08g0890 890
8 18558715 18565274 - PI0003167.1 Cmetu08g1211 1211
3 7972677 7976524 + CmoCh03G010690.1 Cmo03g01069 1069
7 3729893 3733407 + CmoCh07G008090.1 Cmo07g00809 809
7 3736085 3737572 + CmoCh07G008100.1 Cmo07g00810 810
1 28683543 28685072 - CmPI595203_01g015110.1 Cmu01g1511 1511
1 28696472 28705345 - CmPI595203_01g015120.1 Cmu01g1512 1512
10 2065440 2069409 - Cp4.1LG10g03420.1 Cpe10g00349 349
19 4591273 4592517 - Cp4.1LG19g12010.1 Cpe19g00541 541
19 4595494 4599047 - Cp4.1LG19g11960.1 Cpe19g00542 542
4 30551219 30552748 - CrPI670011_04g011900.1 Cre04g1190 1190
4 30563200 30570775 - CrPI670011_04g011920.1 Cre04g1192 1192
6 24420783 24421952 - CsaV3_6G041850.1 Csa06g02799 2799
6 24429256 24437319 - CsaV3_6G041860.1 Csa06g02800 2800
4 66307782 66309335 - Hsped.04g11280.1 Hepe04g1128 1128
4 66321982 66332204 - Hsped.04g11290.1 Hepe04g1129 1129
1 9456443 9464683 + Lsi01G011320.1 Lsi01g01132 1132
1 9475120 9476619 + Lsi01G011330.1 Lsi01g01133 1133
10 3118020 3124828 + Sed0014649.1 Sed10g0487 487
14 116253 117740 - Sed0027526.1 Sed14g0002 2
3 69835733 69837274 - Tan0009936.1 Tan03g1333 1333
3 69861654 69876725 - Tan0000560.1 Tan03g1334 1334
4 21444203 21466018 + Vvi4g1242 Vvi4g1242 1242
4 21469068 21469866 + Vvi4g1243 Vvi4g1243 1243
4 21481687 21489122 + Vvi4g1244 Vvi4g1244 1244
4 21549232 21550687 + Vvi4g1245 Vvi4g1245 1245
4 21551877 21558551 + Vvi4g1246 Vvi4g1246 1246
4 21558560 21559069 + Vvi4g1247 Vvi4g1247 1247
4 21559586 21561962 - Vvi4g1248 Vvi4g1248 1248
4 21594543 21610681 - Vvi4g1249 Vvi4g1249 1249
4 21691195 21691906 + Vvi4g1250 Vvi4g1250 1250
4 21752766 21752934 + Vvi4g1251 Vvi4g1251 1251
       

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