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
Vvi2g302 . . . . . . Bma07g01666 . . . Cma02g01441 . Car02g01208 . . . Cpe05g00346 . . . . . . . . . . . . . . Cone8ag0292 Cone12ag0298 . . . Csa05g00269 Chy09g01240 . . . . Bda09g00031 . . . . . Cmo02g01477 Cmo15g01300 . . . . . Cpe13g00149 Bhi12g00279 . . Lac11g2075 Hepe06g1533 . Lcy12g1636 Cla01g00252 Cam01g0258 Cec01g0250 Cco01g0263 Clacu01g0256 Cmu01g0245 Cre09g2264 Lsi09g00243 . . Cme09g01774
Vvi2g303 . . . . . . . . . Cmo16g00645 . . . . . . . . . . . . . . Cla07g00774 Cam07g0832 Cec07g0887 Cco07g0864 Clacu07g0809 Cmu07g0815 Cre07g1169 Cone8ag0293 Cone12ag0299 . . . . . Cme07g01631 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy07g01217 .
Vvi2g304 . . . . . . . Bma14g00702 . . Cma02g01442 . Car02g01209 . . . Cpe05g00345 . . . . . . . . . . . . . . Cone8ag0294 Cone12ag0300 . . . Csa05g00270 Chy09g01239 . Blo03g00341 . Bda07g00482 . . . . . . Cmo02g01478 . . . . . . . Bhi12g00278 . . Lac11g2076 Hepe06g1534 . Lcy12g1637 Cla01g00253 Cam01g0259 Cec01g0251 Cco01g0264 Clacu01g0257 Cmu01g0246 Cre09g2263 Lsi09g00244 . . Cme09g01773
Vvi2g305 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0301 . . . . . . . . . . . . . . . . . . . . . . Cpe13g00150 Bhi12g00277 . . Lac11g2077 Hepe06g1535 . Lcy12g1638 . . . . . . . Lsi09g00245 . . Cme09g01772
Vvi2g306 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g307 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g308 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g309 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi12g00492 . . . . . . . . . . . . . . . . .
Vvi2g310 Blo02g01124 Blo03g00227 . Bda08g00502 Bpe05g00662 . . . . Cmo16g00644 . Cma15g01280 . Car15g01154 . Cpe14g00505 . . . . . . . . Cla07g00772 Cam07g0831 Cec07g0886 Cco07g0863 Clacu07g0808 Cmu07g0814 Cre07g1168 Cone8ag0615 . . Cone9ag0789 . Csa05g00120 Chy09g01373 Cme07g01630 . . . . . . Bma05g00836 . . . . . . . . . . Bhi12g00031 . . Lac11g0044 . . Lcy12g0041 Cla01g00106 Cam01g0105 Cec01g0106 Cco01g0107 Clacu01g0103 Cmu01g0104 Cre09g2402 Lsi09g00092 Csa04g00593 . Cme09g01920
Vvi2g311 Blo02g01123 Blo03g00226 Bda06g00122 Bda08g00503 Bpe05g00661 Bpe07g00094 . . . . . Cma15g01235 . . . . . . . . . . . . . . . . . . . Cone8ag0296 . Cone6ag0785 . . . Chy09g01237 . . . . . . . Bma05g00835 Bma12g00064 . . Cmo15g01298 . . . . . Cpe13g00151 Bhi12g00276 . . Lac11g2078 Hepe06g1536 . Lcy12g1639 Cla01g00255 Cam01g0261 Cec01g0253 Cco01g0266 Clacu01g0259 Cmu01g0248 Cre09g2261 Lsi09g00247 . . Cme09g01771
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 1914445 1915781 + Bda023317.1 Bda06g00122 122
7 6062971 6064407 - Bda025584.1 Bda07g00482 482
8 5097685 5100128 - Bda024953.2 Bda08g00502 502
8 5105350 5106787 - Bda024954.1 Bda08g00503 503
9 455935 459019 - Bda030550.4 Bda09g00031 31
12 600356 605918 + XM_039020197.1 Bhi12g00031 31
12 8092411 8095054 + XM_039019776.1 Bhi12g00276 276
12 8097065 8098969 - XM_039020373.1 Bhi12g00277 277
12 8116410 8118144 - XM_039020375.1 Bhi12g00278 278
12 8119937 8128801 - XM_039018665.1 Bhi12g00279 279
12 15573403 15580360 - XM_039051354.1 Bhi12g00492 492
2 42493006 42494487 + BLOR10853 Blo02g01123 1123
2 42519464 42527642 + BLOR10854 Blo02g01124 1124
3 5084808 5086572 + BLOR11407 Blo03g00226 226
3 5088903 5091044 + BLOR11408 Blo03g00227 227
3 7369926 7371344 - BLOR11522 Blo03g00341 341
5 45726737 45728176 + Bma021945.1 Bma05g00835 835
5 45739126 45741580 + Bma021946.1 Bma05g00836 836
7 52235690 52241864 + Bma026963.1 Bma07g01666 1666
12 1219290 1220615 - Bma006935.1 Bma12g00064 64
14 7657809 7659233 - Bma011157.1 Bma14g00702 702
5 20348895 20350331 + Bpe018074.1 Bpe05g00661 661
5 20351107 20357456 + Bpe018075.1 Bpe05g00662 662
7 682472 683826 - Bpe020908.1 Bpe07g00094 94
1 1355379 1359890 + CaPI482276_01g001050.1 Cam01g0105 105
1 2891605 2899985 + CaPI482276_01g002580.1 Cam01g0258 258
1 2902792 2904213 + CaPI482276_01g002590.1 Cam01g0259 259
1 2912432 2914966 - CaPI482276_01g002610.1 Cam01g0261 261
7 20772580 20775508 + CaPI482276_07g008310.1 Cam07g0831 831
7 20776719 20778826 - CaPI482276_07g008320.1 Cam07g0832 832
2 8205105 8211636 + Carg02540-RA Car02g01208 1208
2 8212369 8213487 + Carg02539-RA Car02g01209 1209
15 9074619 9077004 + Carg21278-RA Car15g01154 1154
1 890501 895055 + CcPI632755_01g001070.1 Cco01g0107 107
1 2520213 2528554 + CcPI632755_01g002630.1 Cco01g0263 263
1 2531354 2532775 + CcPI632755_01g002640.1 Cco01g0264 264
1 2541294 2543722 - CcPI632755_01g002660.1 Cco01g0266 266
7 20006364 20016404 + CcPI632755_07g008630.1 Cco07g0863 863
7 20017618 20019737 - CcPI632755_07g008640.1 Cco07g0864 864
1 914713 926249 + CePI673135_01g001060.1 Cec01g0106 106
1 2496778 2505194 + CePI673135_01g002500.1 Cec01g0250 250
1 2508148 2509569 + CePI673135_01g002510.1 Cec01g0251 251
1 2518083 2520547 - CePI673135_01g002530.1 Cec01g0253 253
7 21891767 21900967 + CePI673135_07g008860.1 Cec07g0886 886
7 21902181 21904282 - CePI673135_07g008870.1 Cec07g0887 887
7 16967169 16969322 - Chy7G140470.1 Chy07g01217 1217
9 14434288 14435998 + Chy9G169530.1 Chy09g01237 1237
9 14444097 14445524 - Chy9G169550.1 Chy09g01239 1239
9 14446389 14455048 - Chy9G169560.1 Chy09g01240 1240
9 15537496 15541012 - Chy9G170890.1 Chy09g01373 1373
1 958462 969865 + ClG42_01g0010300.10 Clacu01g0103 103
1 2509833 2518203 + ClG42_01g0025600.10 Clacu01g0256 256
1 2520265 2522354 + ClG42_01g0025700.10 Clacu01g0257 257
1 2530915 2533470 - ClG42_01g0025900.10 Clacu01g0259 259
7 20475310 20485457 + ClG42_07g0080800.10 Clacu07g0808 808
7 20486668 20488776 - ClG42_07g0080900.10 Clacu07g0809 809
1 925278 940791 + ClCG01G001080.2 Cla01g00106 106
1 2565353 2573711 + ClCG01G002580.2 Cla01g00252 252
1 2576441 2577862 + ClCG01G002590.1 Cla01g00253 253
1 2586172 2589248 - ClCG01G002610.1 Cla01g00255 255
7 21591133 21604465 + ClCG07G008100.1 Cla07g00772 772
7 21604934 21607548 - ClCG07G008110.1 Cla07g00774 774
2 8293028 8299410 + CmaCh02G014410.1 Cma02g01441 1441
2 8300028 8301446 + CmaCh02G014420.1 Cma02g01442 1442
15 7826897 7828790 + CmaCh15G012350.1 Cma15g01235 1235
15 8115488 8118429 + CmaCh15G012800.1 Cma15g01280 1280
7 22054195 22060245 + MELO3C016354.2.1 Cme07g01630 1630
7 22060798 22063444 - MELO3C016355.2.1 Cme07g01631 1631
9 22174537 22176868 + MELO3C005685.2.1 Cme09g01771 1771
9 22177392 22179127 - MELO3C005686.2.1 Cme09g01772 1772
9 22183047 22184920 - MELO3C005687.2.1 Cme09g01773 1773
9 22185488 22194688 - MELO3C005688.2.1 Cme09g01774 1774
9 23301248 23305093 - MELO3C005826.2.1 Cme09g01920 1920
2 8653951 8660380 + CmoCh02G014770.1 Cmo02g01477 1477
2 8661058 8662476 + CmoCh02G014780.1 Cmo02g01478 1478
15 8913115 8914745 + CmoCh15G012980.1 Cmo15g01298 1298
15 8921812 8930047 - CmoCh15G013000.1 Cmo15g01300 1300
16 3175325 3180576 + CmoCh16G006440.1 Cmo16g00644 644
16 3181069 3181945 - CmoCh16G006450.1 Cmo16g00645 645
1 903269 914747 + CmPI595203_01g001040.1 Cmu01g0104 104
1 2462768 2471113 + CmPI595203_01g002450.1 Cmu01g0245 245
1 2473175 2475266 + CmPI595203_01g002460.1 Cmu01g0246 246
1 2483825 2486380 - CmPI595203_01g002480.1 Cmu01g0248 248
7 20695469 20699459 + CmPI595203_07g008140.1 Cmu07g0814 814
7 20700670 20702778 - CmPI595203_07g008150.1 Cmu07g0815 815
6 4000558 4002159 + Conep06aG0080800.1 Cone6ag0785 785
8 1697262 1700508 + Conep08aG0030700.1 Cone8ag0292 292
8 1701644 1703831 + Conep08aG0030800.1 Cone8ag0293 293
8 1704867 1706645 + Conep08aG0030900.1 Cone8ag0294 294
8 1713588 1717952 - Conep08aG0031100.1 Cone8ag0296 296
8 5927691 5929801 - Conep08aG0063600.1 Cone8ag0615 615
9 3786302 3788787 + Conep09aG0080600.1 Cone9ag0789 789
12 1625606 1632705 + Conep12aG0031100.1 Cone12ag0298 298
12 1633274 1635680 + Conep12aG0031200.1 Cone12ag0299 299
12 1636413 1637995 + Conep12aG0031300.1 Cone12ag0300 300
12 1644993 1647169 + Conep12aG0031400.1 Cone12ag0301 301
5 1932688 1934106 - Cp4.1LG05g03320.1 Cpe05g00345 345
5 1934983 1941587 - Cp4.1LG05g03290.1 Cpe05g00346 346
13 1083150 1090652 + Cp4.1LG13g01510.1 Cpe13g00149 149
13 1093759 1095384 + Cp4.1LG13g01490.1 Cpe13g00150 150
13 1096359 1097819 - Cp4.1LG13g01550.1 Cpe13g00151 151
14 3196950 3207623 + Cp4.1LG14g02170.1 Cpe14g00505 505
7 24013976 24024042 + CrPI670011_07g011680.1 Cre07g1168 1168
7 24025254 24027369 - CrPI670011_07g011690.1 Cre07g1169 1169
9 41798059 41800498 + CrPI670011_09g022610.1 Cre09g2261 2261
9 41808918 41810339 - CrPI670011_09g022630.1 Cre09g2263 2263
9 41813130 41821526 - CrPI670011_09g022640.1 Cre09g2264 2264
9 43392826 43397780 - CrPI670011_09g024020.1 Cre09g2402 2402
4 3923424 3932357 - CsaV3_4G005940.1 Csa04g00593 593
5 607480 613022 + CsaV3_5G001200.1 Csa05g00120 120
5 1654817 1659156 + CsaV3_5G002690.1 Csa05g00269 269
5 1660141 1661571 + CsaV3_5G002700.1 Csa05g00270 270
6 66036314 66039550 + Hsped.06g15330.1 Hepe06g1533 1533
6 66041293 66043084 + Hsped.06g15340.1 Hepe06g1534 1534
6 66054091 66055993 + Hsped.06g15350.1 Hepe06g1535 1535
6 66057199 66058837 - Hsped.06g15360.1 Hepe06g1536 1536
11 376074 380427 - Lag0030682.1 Lac11g0044 44
11 36615036 36622455 + Lag0032713.1 Lac11g2075 2075
11 36624634 36626050 + Lag0032714.1 Lac11g2076 2076
11 36645245 36646885 + Lag0032715.1 Lac11g2077 2077
11 36652190 36653393 - Lag0032716.1 Lac11g2078 2078
12 662810 663832 - Maker00038776 Lcy12g0041 41
12 36708892 36717239 + Maker00029273 Lcy12g1636 1636
12 36724705 36726117 + Maker00029360 Lcy12g1637 1637
12 36741963 36743582 + Maker00029439 Lcy12g1638 1638
12 36747682 36749714 - Maker00029245 Lcy12g1639 1639
9 816008 825801 + Lsi09G000920.1 Lsi09g00092 92
9 2562878 2570606 + Lsi09G002430.1 Lsi09g00243 243
9 2574579 2576009 + Lsi09G002440.1 Lsi09g00244 244
9 2581643 2583250 + Lsi09G002450.1 Lsi09g00245 245
9 2583854 2587471 - Lsi09G002470.1 Lsi09g00247 247
2 2803899 2807681 + Vvi2g302 Vvi2g302 302
2 2809885 2813515 + Vvi2g303 Vvi2g303 303
2 2814261 2824023 + Vvi2g304 Vvi2g304 304
2 2828669 2842078 + Vvi2g305 Vvi2g305 305
2 2848086 2851168 - Vvi2g306 Vvi2g306 306
2 2851919 2853149 + Vvi2g307 Vvi2g307 307
2 2853792 2870798 + Vvi2g308 Vvi2g308 308
2 2874832 2882840 + Vvi2g309 Vvi2g309 309
2 2883746 2889066 - Vvi2g310 Vvi2g310 310
2 2890637 2893841 - Vvi2g311 Vvi2g311 311
       

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