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
Vvi18g1140 . . . . . . . . Cmo05g00317 . . . . . . . . . . . . . . . . . . . . . . . . . Cone20ag0067 . . . . . . . . . Bpe05g00147 . Bma05g00171 . . . . Cma05g00316 Car05g00262 . Cpe11g00263 . . . . . . . . . . . . . . . . Csa02g02145 . .
Vvi18g1141 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1142 . . . . . . . . . . Cma01g01981 Cma09g00096 Car01g01552 . . Cpe06g00058 . . . . . . . . . . . . . . . . . Cone17ag1415 . . Csa03g04290 Chy04g00406 . . . . . . . . . . Cmo01g02039 Cmo09g00093 . . . Car09g00084 . Cpe02g00064 . . . . . . . . . . . . . . . . . .
Vvi18g1143 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1144 . . . . . . . . . Cmo12g00352 . . . Car12g00378 Sed11g1098 . Cpe07g00356 Bhi04g00131 Tan02g2840 Cmetu02g0262 . Hepe10g0165 . Lcy13g1902 Cla08g01413 Cam08g1892 Cec08g1469 Cco08g1602 Clacu08g1584 . Cre08g1367 Cone4ag1543 . Cone17ag1416 . . . . Cme03g01869 Blo17g00739 . Bda08g01211 Bda01g01538 Bpe02g01735 . . . . . . Cma12g00400 . . . . . . . . . . . . . . . . . . . Lsi08g01308 . Chy03g01373 .
Vvi18g1145 . . . . . . . . Cmo05g00320 . . . . . . . . Bhi04g00126 . . . . . . Cla08g01411 Cam08g1890 Cec08g1467 Cco08g1600 Clacu08g1582 . Cre08g1365 . . . Cone20ag0066 . . . . . . . Bda01g01539 Bpe02g01736 . . . . . . . Cma05g00317 Car05g00264 . Cpe11g00265 . . . . . . . . . . . . . . . Lsi08g01306 . . .
Vvi18g1146 Blo01g01605 . Bda01g00476 . . . . Bma01g02378 . . . Cma09g00095 . . . . . . . . . . . . . . . . . . . . Cone7ag1900 . . . . . . . . . . . . . . . . Cmo09g00092 . . . Car09g00083 . . . . . . . . . . . . . . . . . . . .
Vvi18g1147 Blo01g01606 . Bda01g00475 . Bpe02g00339 . . Bma01g02379 . Cmo12g00350 . . . . Sed02g0076 . Cpe07g00354 Bhi04g00124 Tan02g2834 Cmetu03g0402 . Hepe10g0168 . Lcy13g1898 Cla08g01409 Cam08g1889 Cec08g1466 Cco08g1599 Clacu08g1581 . Cre08g1364 Cone4ag2004 Cone7ag1901 Cone17ag1418 Cone20ag0065 . . . . . Blo18g00771 Bda08g01210 Bda01g01540 Bpe02g01737 Bpe05g00148 Bma01g00719 Bma05g00180 . . . Cma12g00399 Cma05g00318 . . Cpe11g00266 . . . . . . . . . . . . . . . Lsi08g01305 . . .
Vvi18g1148 Blo01g01607 . Bda01g00474 . . . . Bma01g02380 . . Cma01g01983 Cma09g00094 Car01g01554 . . Cpe06g00056 . . . . . . . . . . . . . . . . . . . . Csa03g04293 Chy04g00403 . . . . . . . . . Sed01g2488 Cmo01g02041 Cmo09g00091 . . . Car09g00081 . Cpe02g00062 Bhi09g02073 Tan01g5039 Cmetu04g2094 . Hepe01g1603 Mch11g0102 . . . . . . . . . . . Cme04g00456
Vvi18g1149 . . . . . . . . Cmo04g02508 Cmo15g00658 . . . . . . Cpe13g00644 Bhi04g01860 . . . . . Lcy10g1259 Cla08g00627 . . . . . . . . Cone17ag0817 Cone20ag0422 . . . . . . . . . . . . . . . . . Car04g02316 . Cpe01g02077 . . . . . . . . . . . . . . . Lsi08g00467 . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 31814890 31826636 - Bda002476.1 Bda01g00474 474
1 31828017 31829654 - Bda002477.1 Bda01g00475 475
1 31830555 31837347 - Bda002478.2 Bda01g00476 476
1 51317026 51321131 - Bda003803.1 Bda01g01538 1538
1 51323261 51325338 - Bda003804.1 Bda01g01539 1539
1 51327942 51329742 + Bda003805.1 Bda01g01540 1540
8 49620039 49621702 - Bda034044 Bda08g01210 1210
8 49655382 49659451 + Bda030191.4 Bda08g01211 1211
4 3171806 3174908 - XM_039030290.1 Bhi04g00124 124
4 3194846 3199317 + XM_039030353.1 Bhi04g00126 126
4 3298165 3302707 + XM_039029760.1 Bhi04g00131 131
4 46930876 46934648 - XM_039029490.1 Bhi04g01860 1860
9 59155051 59163716 - XM_039042074.1 Bhi09g02073 2073
1 55923490 55928809 + BLOR01605 Blo01g01605 1605
1 55941341 55947541 + BLOR01606 Blo01g01606 1606
1 55957021 55964341 + BLOR01607 Blo01g01607 1607
17 22816172 22820308 + BLOR08285 Blo17g00739 739
18 21755109 21757181 - BLOR09259 Blo18g00771 771
1 6577026 6578776 - Bma030201 Bma01g00719 719
1 81405532 81410519 + Bma003249.1 Bma01g02378 2378
1 81411545 81419514 + Bma003250.1 Bma01g02379 2379
1 81420867 81430737 + Bma003251.1 Bma01g02380 2380
5 4832301 4836432 - Bma031170 Bma05g00171 171
5 5108450 5110103 + Bma020906.1 Bma05g00180 180
2 2219872 2221578 - Bpe008180.1 Bpe02g00339 339
2 19774156 19778260 - Bpe009567.1 Bpe02g01735 1735
2 19780368 19782423 - Bpe009568.2 Bpe02g01736 1736
2 19784919 19786715 + Bpe025176 Bpe02g01737 1737
5 4250415 4254508 - Bpe017534.2 Bpe05g00147 147
5 4263628 4265285 + Bpe017535.1 Bpe05g00148 148
8 24868491 24871007 - CaPI482276_08g018890.1 Cam08g1889 1889
8 24876438 24881318 + CaPI482276_08g018900.1 Cam08g1890 1890
8 24896832 24900702 + CaPI482276_08g018920.1 Cam08g1892 1892
1 12971729 12975221 - Carg17207-RA Car01g01552 1552
1 12979446 12988396 + Carg17209-RA Car01g01554 1554
4 18659144 18662593 + Carg15750-RA Car04g02316 2316
5 1456369 1459777 - Carg09397-RA Car05g00262 262
5 1465492 1468578 - Carg09395-RA Car05g00264 264
9 408759 417392 - Carg08664-RA Car09g00081 81
9 422282 423610 - Carg08666-RA Car09g00083 83
9 426464 429446 + Carg08667-RA Car09g00084 84
12 2409471 2413545 + Carg03985-RA Car12g00378 378
8 27533831 27536334 - CcPI632755_08g015990.1 Cco08g1599 1599
8 27543332 27546686 + CcPI632755_08g016000.1 Cco08g1600 1600
8 27562163 27566023 + CcPI632755_08g016020.1 Cco08g1602 1602
8 26396495 26398994 - CePI673135_08g014660.1 Cec08g1466 1466
8 26404929 26409444 + CePI673135_08g014670.1 Cec08g1467 1467
8 26424761 26428620 + CePI673135_08g014690.1 Cec08g1469 1469
3 16571272 16575190 + Chy3G063530.1 Chy03g01373 1373
4 3579881 3599267 - Chy4G071210.1 Chy04g00403 403
4 3632517 3636810 + Chy4G071240.1 Chy04g00406 406
8 25615820 25618128 - ClG42_08g0158100.10 Clacu08g1581 1581
8 25623507 25628392 + ClG42_08g0158200.10 Clacu08g1582 1582
8 25642660 25646529 + ClG42_08g0158400.10 Clacu08g1584 1584
8 18303997 18307916 + ClCG08G006040.1 Cla08g00627 627
8 26972204 26974963 - ClCG08G014150.2 Cla08g01409 1409
8 26980603 26984794 + ClCG08G014170.2 Cla08g01411 1411
8 26999547 27003729 + ClCG08G014200.1 Cla08g01413 1413
1 12745016 12748796 - CmaCh01G019810.1 Cma01g01981 1981
1 12752618 12762087 + CmaCh01G019830.1 Cma01g01983 1983
5 1367244 1371409 - CmaCh05G003160.1 Cma05g00316 316
5 1376221 1379607 - CmaCh05G003170.1 Cma05g00317 317
5 1381482 1384880 + CmaCh05G003180.1 Cma05g00318 318
9 409189 418284 - CmaCh09G000940.1 Cma09g00094 94
9 418372 424716 - CmaCh09G000950.1 Cma09g00095 95
9 426714 430213 + CmaCh09G000960.1 Cma09g00096 96
12 2056290 2059433 - CmaCh12G003990.1 Cma12g00399 399
12 2064885 2069512 + CmaCh12G004000.1 Cma12g00400 400
3 26921041 26925752 + MELO3C011022.2.1 Cme03g01869 1869
4 3606294 3623138 - MELO3C003740.2.1 Cme04g00456 456
2 5932706 5936405 + PI0011073.1 Cmetu02g0262 262
3 4991001 4994158 - PI0001469.1 Cmetu03g0402 402
4 29750084 29759718 + PI0029127.1 Cmetu04g2094 2094
1 14285614 14289262 - CmoCh01G020390.1 Cmo01g02039 2039
1 14293800 14302742 + CmoCh01G020410.1 Cmo01g02041 2041
4 18481789 18485223 + CmoCh04G025080.1 Cmo04g02508 2508
5 1408159 1410216 - CmoCh05G003170.1 Cmo05g00317 317
5 1419305 1422830 - CmoCh05G003200.1 Cmo05g00320 320
9 419432 437410 - CmoCh09G000910.1 Cmo09g00091 91
9 438438 443470 - CmoCh09G000920.1 Cmo09g00092 92
9 446395 449446 + CmoCh09G000930.1 Cmo09g00093 93
12 2165845 2168957 - CmoCh12G003500.1 Cmo12g00350 350
12 2174534 2179029 + CmoCh12G003520.1 Cmo12g00352 352
15 3185027 3188672 - CmoCh15G006580.1 Cmo15g00658 658
4 11909302 11911369 - Conep04aG0159500.1 Cone4ag1543 1543
4 13981446 13983382 - Conep04aG0206900.1 Cone4ag2004 2004
7 12180404 12184889 + Conep07aG0195700.1 Cone7ag1900 1900
7 12185778 12187013 + Conep07aG0195800.1 Cone7ag1901 1901
17 6507785 6511598 - Conep17aG0083600.1 Cone17ag0817 817
17 9711716 9715131 - Conep17aG0145200.1 Cone17ag1415 1415
17 9717503 9720950 - Conep17aG0145400.1 Cone17ag1416 1416
17 9726865 9729535 + Conep17aG0145600.1 Cone17ag1418 1418
20 310857 313399 - Conep20aG0006700.1 Cone20ag0065 65
20 314545 316794 + Conep20aG0006800.1 Cone20ag0066 66
20 322077 325207 + Conep20aG0006900.1 Cone20ag0067 67
20 2066692 2070412 - Conep20aG0043600.1 Cone20ag0422 422
1 17624119 17627579 + Cp4.1LG01g20790.1 Cpe01g02077 2077
2 320124 329203 - Cp4.1LG02g08140.1 Cpe02g00062 62
2 333563 337055 + Cp4.1LG02g08230.1 Cpe02g00064 64
6 286741 295397 - Cp4.1LG06g00720.1 Cpe06g00056 56
6 303308 306800 + Cp4.1LG06g00590.1 Cpe06g00058 58
7 2289537 2292668 - Cp4.1LG07g03590.1 Cpe07g00354 354
7 2298987 2302987 + Cp4.1LG07g03490.1 Cpe07g00356 356
11 1422756 1427521 - Cp4.1LG11g02680.1 Cpe11g00263 263
11 1432673 1435769 - Cp4.1LG11g02720.1 Cpe11g00265 265
11 1438365 1441094 + Cp4.1LG11g02620.1 Cpe11g00266 266
13 6153030 6156561 + Cp4.1LG13g04350.1 Cpe13g00644 644
8 26673252 26675760 - CrPI670011_08g013640.1 Cre08g1364 1364
8 26684846 26685787 + CrPI670011_08g013650.1 Cre08g1365 1365
8 26701376 26705025 + CrPI670011_08g013670.1 Cre08g1367 1367
2 19406220 19411036 - CsaV3_2G029640.1 Csa02g02145 2145
3 37558642 37562279 - CsaV3_3G045960.1 Csa03g04290 4290
3 37589202 37601568 + CsaV3_3G045990.1 Csa03g04293 4293
1 81305615 81314935 - Hsped.01g16030.1 Hepe01g1603 1603
10 1690930 1694882 - Hsped.10g01650.1 Hepe10g0165 165
10 1723527 1726897 + Hsped.10g01680.1 Hepe10g0168 168
10 35286296 35290197 + Maker00008449 Lcy10g1259 1259
13 37923460 37927118 - Maker00033624 Lcy13g1898 1898
13 37961553 37966843 + Maker00033749 Lcy13g1902 1902
8 12398614 12402738 + Lsi08G004670.1 Lsi08g00467 467
8 21409246 21412328 - Lsi08G013050.1 Lsi08g01305 1305
8 21418386 21423084 + Lsi08G013060.1 Lsi08g01306 1306
8 21437598 21442382 + Lsi08G013080.1 Lsi08g01308 1308
11 672417 681683 - MC11g0091 Mch11g0102 102
1 18601429 18614398 + Sed0010944.2 Sed01g2488 2488
2 9168501 9168942 + Sed0013329.1 Sed02g0076 76
11 26685623 26689955 - Sed0001294.1 Sed11g1098 1098
1 115969778 115980179 + Tan0022694.1 Tan01g5039 5039
2 96619581 96622771 - Tan0009955.1 Tan02g2834 2834
2 96670326 96674294 + Tan0021582.1 Tan02g2840 2840
18 12634520 12635198 - Vvi18g1140 Vvi18g1140 1140
18 12645228 12650755 - Vvi18g1141 Vvi18g1141 1141
18 12668322 12671744 - Vvi18g1142 Vvi18g1142 1142
18 12678959 12679433 + Vvi18g1143 Vvi18g1143 1143
18 12682734 12691905 - Vvi18g1144 Vvi18g1144 1144
18 12699749 12707465 - Vvi18g1145 Vvi18g1145 1145
18 12710694 12716741 + Vvi18g1146 Vvi18g1146 1146
18 12718754 12724364 + Vvi18g1147 Vvi18g1147 1147
18 12725143 12753122 - Vvi18g1148 Vvi18g1148 1148
18 12763410 12766861 + Vvi18g1149 Vvi18g1149 1149
       

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