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
Vvi5g509 . Blo12g00333 Bda03g00880 . Bpe04g00825 . Bma04g00778 . . Cmo17g00217 . . . . . . . . . . . . . . Cla06g00590 Cam06g0629 Cec06g0632 Cco06g0635 Clacu06g0615 Cmu06g0608 Cre06g1376 . . . . . . . . . . . . . . . . Sed04g1910 . . . Cma17g00228 . Car17g00207 Cpe12g00193 . Bhi12g01702 Tan06g2516 Cmetu01g0171 Lac12g2273 Hepe03g0205 . Lcy13g0288 . . . . . . . Lsi09g01313 . . Cme01g01570
Vvi5g510 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g511 . . . . . Bpe14g01189 . . . . . Cma14g01709 . Car14g01544 . . . Bhi01g00809 . . . . . Lcy11g1547 . . . . . . . . Cone10ag0051 . . . . . Cme06g00608 Blo02g00537 . . Bda13g00119 . . Bma02g00845 . . . Cmo14g01753 . . . . . . . . . . . . . . . . . . . . . Csa03g01327 Chy06g00578 .
Vvi5g512 . . . . . Bpe14g01190 . . . . Cma06g01407 . Car06g01213 . Sed12g0923 . . Bhi01g00807 Tan10g0840 Cmetu06g2304 . . . Lcy11g1548 . . . . . . . . . . . . . . Cme06g00607 . . . . . . . . . Cmo06g01410 . . . . . . . . . . . . . . Cla05g00541 Cam05g0590 Cec05g0600 Cco05g0598 Clacu05g0587 Cmu05g0557 Cre05g0626 . . . .
Vvi5g513 . . . . . . . . . . . . Car06g01212 . Sed12g0930 . . Bhi01g00805 Tan10g0838 Cmetu06g0605 . . . Lcy11g1549 . . . . . . . . . . Cone4ag0247 Lsi05g01608 . . Cme06g00606 Blo02g00536 . . Bda13g00118 . . . . . Cmo06g01409 . . . . . . . . . . . . . . Cla05g00540 Cam05g0589 Cec05g0599 . . . . . Csa03g01326 Chy06g00577 .
Vvi5g514 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g515 . . . . . Bpe14g01191 . . . . . Cma14g01710 . Car14g01545 . Cpe08g00262 Cpe03g01438 Bhi01g00803 Tan10g0836 . . . . . . . . . . . . . . Cone7ag0258 . . . . . . . . . . . Bma02g00840 . . . Cmo14g01754 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g516 . . Bda03g00879 . Bpe04g00824 . Bma04g00777 Bma05g01107 Cmo08g01114 . . Cma14g01712 Car06g01211 Car14g01547 Sed02g1308 Cpe08g00263 Cpe03g01439 Bhi01g00801 Tan10g0835 Cmetu06g0267 Lac12g2272 Hepe05g1556 . Lcy11g1550 Cla06g00591 Cam06g0630 Cec06g0633 Cco06g0636 Clacu06g0616 Cmu06g0609 Cre06g1377 . . . . Lsi05g01609 . . Cme06g00605 Blo02g00535 Blo07g00221 Bda11g00579 Bda13g00117 Bpe05g00900 Bpe13g00604 Bma02g00839 Bma06g01558 Sed04g1911 Cmo06g01408 Cmo14g01756 . Cma17g00227 Car08g01022 Car17g00203 . . Bhi12g01701 Tan06g2515 Cmetu01g1394 . . . Lcy13g0289 Cla05g00539 Cam05g0588 Cec05g0598 Cco05g0597 Clacu05g0586 Cmu05g0556 Cre05g0625 . Csa03g01324 Chy06g00575 Cme01g01571
Vvi5g517 . . . . . Bpe14g01192 . . . . . Cma14g01713 . Car14g01548 Sed12g0935 . Cpe03g01440 Bhi01g00800 Tan10g0834 Cmetu06g1819 . . . . . . . . . . . . . Cone7ag0260 Cone4ag0249 Lsi05g01610 . . Cme06g00603 . . . Bda13g00116 . . Bma02g00837 . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g01323 Chy06g00574 .
Vvi5g518 . . . . . . . . . . Cma06g01402 . Car06g01210 . . Cpe08g00265 . Bhi01g00798 . . . . . . . . . . . . . Cone14ag0857 . . . Lsi05g01611 . . . . . . . . . . . . Cmo06g01406 . . . . . . . . . . . . . . Cla05g00537 . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 7608596 7609165 + Bda016870.1 Bda03g00879 879
3 7610614 7611177 + Bda016871.1 Bda03g00880 880
11 5944886 5945419 - Bda005319.1 Bda11g00579 579
13 1555154 1564347 + Bda000972.1 Bda13g00116 116
13 1593482 1594018 + Bda000974.1 Bda13g00117 117
13 1595058 1599953 - Bda000975.1 Bda13g00118 118
13 1600601 1602673 + Bda000976.1 Bda13g00119 119
1 15053312 15056045 - XM_039046344.1 Bhi01g00798 798
1 15112861 15117388 + XM_039022077.1 Bhi01g00800 800
1 15122609 15123705 + XM_039019570.1 Bhi01g00801 801
1 15126368 15131113 - XM_039041229.1 Bhi01g00803 803
1 15126368 15131113 - XM_039041238.1 Bhi01g00805 805
1 15179018 15179848 - XM_039025460.1 Bhi01g00807 807
1 15179827 15182897 + XM_039025431.1 Bhi01g00809 809
12 54921422 54923911 + XM_039050778.1 Bhi12g01701 1701
12 54940326 54942037 + XM_039020371.1 Bhi12g01702 1702
2 9016027 9016563 + BLOR10265 Blo02g00535 535
2 9017483 9020406 - BLOR10266 Blo02g00536 536
2 9054391 9056982 + BLOR10267 Blo02g00537 537
7 2769090 2780103 - BLOR18153 Blo07g00221 221
12 18978811 18981549 - BLOR04352 Blo12g00333 333
2 45377955 45381988 + Bma015589.1 Bma02g00837 837
2 45404491 45405024 + Bma015591.1 Bma02g00839 839
2 45406072 45411987 - Bma015592.1 Bma02g00840 840
2 45579586 45581722 + Bma015597.1 Bma02g00845 845
4 8484952 8485431 + Bma019301.1 Bma04g00777 777
4 8486651 8487253 + Bma019302.1 Bma04g00778 778
5 49836111 49836647 + Bma022280.1 Bma05g01107 1107
6 51890455 51890991 - Bma024676.1 Bma06g01558 1558
4 5434264 5434806 + Bpe015484.1 Bpe04g00824 824
4 5436254 5436830 + Bpe015485.1 Bpe04g00825 825
5 22044071 22044607 + Bpe018311.1 Bpe05g00900 900
13 13095130 13095663 + Bpe025231 Bpe13g00604 604
14 8898815 8900951 - Bpe014559.1 Bpe14g01189 1189
14 8901557 8902126 + Bpe025538 Bpe14g01190 1190
14 8903545 8906668 + Bpe014560.1 Bpe14g01191 1191
14 8922273 8925546 - Bpe014561.1 Bpe14g01192 1192
5 5181034 5191138 + CaPI482276_05g005880.1 Cam05g0588 588
5 5194477 5198640 - CaPI482276_05g005890.1 Cam05g0589 589
5 5200174 5200712 - CaPI482276_05g005900.1 Cam05g0590 590
6 8512911 8514336 - CaPI482276_06g006290.1 Cam06g0629 629
6 8523355 8523864 - CaPI482276_06g006300.1 Cam06g0630 630
6 8807890 8809793 - Carg17425-RA Car06g01210 1210
6 8816004 8816531 + Carg17424-RA Car06g01211 1211
6 8816727 8822323 - Carg17423-RA Car06g01212 1212
6 8823270 8823833 - Carg17422-RA Car06g01213 1213
8 6978053 6979451 + Carg15901-RA Car08g01022 1022
14 12708248 12710411 - Carg23519-RA Car14g01544 1544
14 12711021 12714964 + Carg23518-RA Car14g01545 1545
14 12717996 12718649 - Carg23516-RA Car14g01547 1547
14 12719707 12724824 - Carg23515-RA Car14g01548 1548
17 1209533 1210024 + Carg10028-RA Car17g00203 203
17 1267378 1269479 + Carg05411-RA Car17g00207 207
5 4865787 4866521 + CcPI632755_05g005970.1 Cco05g0597 597
5 4868938 4876007 - CcPI632755_05g005980.1 Cco05g0598 598
6 7023149 7024479 - CcPI632755_06g006350.1 Cco06g0635 635
6 7036087 7036596 - CcPI632755_06g006360.1 Cco06g0636 636
5 4878227 4890688 + CePI673135_05g005980.1 Cec05g0598 598
5 4896257 4899493 - CePI673135_05g005990.1 Cec05g0599 599
5 4900482 4903151 - CePI673135_05g006000.1 Cec05g0600 600
6 7068768 7070093 - CePI673135_06g006320.1 Cec06g0632 632
6 7081707 7082216 - CePI673135_06g006330.1 Cec06g0633 633
6 3907540 3912358 + Chy6G111020.1 Chy06g00574 574
6 3915965 3916817 + Chy6G111030.1 Chy06g00575 575
6 3919901 3929826 - Chy6G111050.1 Chy06g00577 577
6 3930186 3932388 + Chy6G111060.1 Chy06g00578 578
5 4905863 4906597 + ClG42_05g0058600.10 Clacu05g0586 586
5 4909216 4916224 - ClG42_05g0058700.10 Clacu05g0587 587
6 7073591 7074919 - ClG42_06g0061500.10 Clacu06g0615 615
6 7083715 7084224 - ClG42_06g0061600.10 Clacu06g0616 616
5 4936028 4938507 - ClCG05G005100.1 Cla05g00537 537
5 4949957 4950691 + ClCG05G005125.1 Cla05g00539 539
5 4953126 4958250 - ClCG05G005130.1 Cla05g00540 540
5 4957607 4960724 - ClCG05G005150.2 Cla05g00541 541
6 7179710 7181072 - ClCG06G006265.1 Cla06g00590 590
6 7189724 7190233 - ClCG06G006270.1 Cla06g00591 591
6 9057700 9060542 - CmaCh06G014020.1 Cma06g01402 1402
6 9077529 9078376 - CmaCh06G014070.1 Cma06g01407 1407
14 12635886 12638021 - CmaCh14G017090.1 Cma14g01709 1709
14 12638478 12642656 + CmaCh14G017100.1 Cma14g01710 1710
14 12645534 12646187 - CmaCh14G017120.1 Cma14g01712 1712
14 12647067 12651586 - CmaCh14G017130.1 Cma14g01713 1713
17 1156704 1163408 + CmaCh17G002270.1 Cma17g00227 227
17 1164229 1166142 + CmaCh17G002280.1 Cma17g00228 228
1 20827630 20829216 - MELO3C012654.2.1 Cme01g01570 1570
1 20832290 20833248 - MELO3C012655.2.1 Cme01g01571 1571
6 3867302 3872049 + MELO3C006526.2.1 Cme06g00603 603
6 3875103 3876325 + MELO3C006527.2.1 Cme06g00605 605
6 3878356 3883901 - MELO3C006528.2.1 Cme06g00606 606
6 3884256 3885476 - MELO3C031694.2.1 Cme06g00607 607
6 3885818 3888025 + MELO3C006529.2.1 Cme06g00608 608
1 7787426 7789014 - PI0008545.1 Cmetu01g0171 171
1 7792013 7793069 - PI0017548.1 Cmetu01g1394 1394
6 4113494 4115118 + PI0023601.1 Cmetu06g0267 267
6 4116871 4122269 - PI0003291.3 Cmetu06g0605 605
6 4105577 4110552 + PI0011724.1 Cmetu06g1819 1819
6 4124519 4125048 - PI0026558.1 Cmetu06g2304 2304
6 10272948 10275422 - CmoCh06G014060.1 Cmo06g01406 1406
6 10280168 10280695 + CmoCh06G014080.1 Cmo06g01408 1408
6 10282724 10285153 - CmoCh06G014090.1 Cmo06g01409 1409
6 10286266 10288127 - CmoCh06G014100.1 Cmo06g01410 1410
8 7115980 7116462 + CmoCh08G011140.1 Cmo08g01114 1114
14 13606212 13608376 - CmoCh14G017530.1 Cmo14g01753 1753
14 13608794 13612759 + CmoCh14G017540.1 Cmo14g01754 1754
14 13616832 13617485 - CmoCh14G017560.1 Cmo14g01756 1756
17 1276194 1278451 + CmoCh17G002170.1 Cmo17g00217 217
5 4749515 4750249 + CmPI595203_05g005560.1 Cmu05g0556 556
5 4752861 4759869 - CmPI595203_05g005570.1 Cmu05g0557 557
6 6879883 6881211 - CmPI595203_06g006080.1 Cmu06g0608 608
6 6890002 6890511 - CmPI595203_06g006090.1 Cmu06g0609 609
4 1115529 1118488 + Conep04aG0025600.1 Cone4ag0247 247
4 1121100 1123149 - Conep04aG0025800.1 Cone4ag0249 249
7 1071760 1074674 + Conep07aG0026300.1 Cone7ag0258 258
7 1078605 1081791 - Conep07aG0026500.1 Cone7ag0260 260
10 313503 315287 - Conep10aG0005100.1 Cone10ag0051 51
14 5462025 5463608 + Conep14aG0087400.1 Cone14ag0857 857
3 11523719 11528226 + Cp4.1LG03g10760.1 Cpe03g01438 1438
3 11529278 11529931 - Cp4.1LG03g10690.1 Cpe03g01439 1439
3 11531392 11536500 - Cp4.1LG03g10720.1 Cpe03g01440 1440
8 1711377 1716344 + Cp4.1LG08g04160.1 Cpe08g00262 262
8 1715489 1716016 - Cp4.1LG08g04070.1 Cpe08g00263 263
8 1721130 1723647 + Cp4.1LG08g04190.1 Cpe08g00265 265
12 1233809 1241742 + Cp4.1LG12g01890.1 Cpe12g00193 193
5 5538180 5538911 + CrPI670011_05g006250.1 Cre05g0625 625
5 5541610 5548740 - CrPI670011_05g006260.1 Cre05g0626 626
6 7949797 7951115 - CrPI670011_06g013760.1 Cre06g1376 1376
6 7960494 7961003 - CrPI670011_06g013770.1 Cre06g1377 1377
3 10050519 10055891 + CsaV3_3G013230.1 Csa03g01323 1323
3 10058119 10060256 + CsaV3_3G013240.1 Csa03g01324 1324
3 10062315 10068764 - CsaV3_3G013260.1 Csa03g01326 1326
3 10069126 10071329 + CsaV3_3G013270.1 Csa03g01327 1327
3 2622307 2624276 - Hsped.03g02050.1 Hepe03g0205 205
5 65167705 65168851 - Hsped.05g15560.1 Hepe05g1556 1556
12 39858337 39858846 + Lag0016644.1 Lac12g2272 2272
12 39863792 39864927 + Lag0016645.1 Lac12g2273 2273
11 39331242 39338771 - Maker00031773 Lcy11g1547 1547
11 39337883 39338268 + Maker00032144 Lcy11g1548 1548
11 39344309 39350564 + Maker00032086 Lcy11g1549 1549
11 39353120 39353845 - Maker00031519 Lcy11g1550 1550
13 3131329 3133115 - Maker00023241 Lcy13g0288 288
13 3136206 3136715 - Maker00023938 Lcy13g0289 289
5 23774298 23786545 + Lsi05G016080.1 Lsi05g01608 1608
5 23789281 23790015 - Lsi05G016090.1 Lsi05g01609 1609
5 23793640 23798809 - Lsi05G016100.1 Lsi05g01610 1610
5 23794961 23804617 + Lsi05G016110.1 Lsi05g01611 1611
9 21011125 21012455 + Lsi09G013130.1 Lsi09g01313 1313
2 49627171 49630878 + Sed0013199.1 Sed02g1308 1308
4 33832006 33833801 - Sed0026467.1 Sed04g1910 1910
4 33837968 33838965 - Sed0025413.1 Sed04g1911 1911
12 5804034 5805467 + Sed0006923.1 Sed12g0923 923
12 5811462 5816835 + Sed0023955.5 Sed12g0930 930
12 5824086 5828654 - Sed0010969.4 Sed12g0935 935
6 77781211 77782575 + Tan0015884.1 Tan06g2515 2515
6 77788939 77790230 + Tan0009659.1 Tan06g2516 2516
10 6931197 6935711 + Tan0006438.2 Tan10g0834 834
10 6938084 6940134 + Tan0001121.1 Tan10g0835 835
10 6941566 6948267 - Tan0007967.1 Tan10g0836 836
10 6942732 6948267 - Tan0007967.3 Tan10g0838 838
10 6961099 6961621 - Tan0014495.1 Tan10g0840 840
5 5292306 5294612 - Vvi5g509 Vvi5g509 509
5 5297909 5298444 + Vvi5g510 Vvi5g510 510
5 5303086 5305764 - Vvi5g511 Vvi5g511 511
5 5307186 5307921 + Vvi5g512 Vvi5g512 512
5 5310889 5316248 + Vvi5g513 Vvi5g513 513
5 5316261 5317685 - Vvi5g514 Vvi5g514 514
5 5318273 5333813 + Vvi5g515 Vvi5g515 515
5 5336358 5337658 - Vvi5g516 Vvi5g516 516
5 5339502 5347393 - Vvi5g517 Vvi5g517 517
5 5347964 5350466 + Vvi5g518 Vvi5g518 518
       

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