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
Vvi1g371 . . . . Bpe13g01048 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0797 Cone19ag0802 . . . Csa05g02054 . . . . . . . . . Bma06g01092 . . Cmo15g00971 . Cma15g00931 . Car15g00875 Cpe13g00388 . Bhi12g00856 . . . Hepe02g2686 . Lcy10g1463 Cla01g00581 Cam01g0608 Cec01g0599 Cco01g0622 Clacu01g0600 Cmu01g0573 Cre09g1932 Lsi09g00631 Csa05g01229 Chy09g00883 Cme09g01416
Vvi1g372 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g373 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g374 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g375 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g376 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g377 . Blo16g00721 . Bda11g00153 Bpe13g01046 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0795 Cone19ag0800 . . . Csa05g02051 . . . . . Bda11g00153 . . . Bma06g01094 . Cmo04g02184 Cmo15g00973 Cma04g02083 Cma15g00933 Car04g02022 Car15g00877 . . Bhi12g00858 . . . Hepe02g2684 . Lcy10g1462 Cla01g00584 Cam01g0610 Cec01g0601 Cco01g0626 Clacu01g0602 Cmu01g0575 Cre09g1930 Lsi09g00633 . Chy09g00881 Cme09g01415
Vvi1g378 . . . Bda11g00154 Bpe13g01045 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0799 Cone6ag0419 Cone9ag0443 . Csa05g02050 . . . . . Bda11g00154 . . . Bma06g01095 . Cmo04g02185 . Cma04g02084 . Car04g02023 . Cpe13g00387 . Bhi12g00859 . . . Hepe02g2683 . Lcy10g1461 Cla01g00585 Cam01g0611 Cec01g0602 Cco01g0627 Clacu01g0603 Cmu01g0576 Cre09g1929 Lsi09g00634 . Chy09g00880 Cme09g01414
Vvi1g379 . . . . . . . . Cmo04g01553 Cmo18g00996 . Cma18g00989 Car04g01538 Car18g00910 Sed08g0382 Cpe09g00328 Cpe01g01321 Bhi07g01273 Tan04g0802 Cmetu02g0065 Lac13g0540 Hepe01g1156 . . Cla05g02265 Cam05g2435 Cec05g2454 Cco05g2498 Clacu05g2426 Cmu05g2292 Cre05g2409 Cone13ag0794 Cone19ag0798 . . Lsi04g00213 Csa05g02653 Chy10g01185 Cme10g00219 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g380 . Blo16g00723 . Bda11g00155 Bpe13g01043 . . . Cmo04g01551 Cmo18g00995 . Cma18g00988 Car04g01537 Car18g00909 . . . Bhi07g01267 . . . . . . . . . . . . . Cone13ag0793 Cone19ag0797 Cone6ag0418 . Lsi04g00212 Csa05g02049 Chy10g01187 Cme10g00217 . . . Bda11g00155 . . . Bma06g01099 . Cmo04g02186 Cmo15g00976 Cma04g02085 Cma15g00936 Car04g02024 Car15g00878 . . Bhi12g00861 . . . . . . Cla01g00586 Cam01g0612 Cec01g0603 Cco01g0628 Clacu01g0604 Cmu01g0577 Cre09g1928 Lsi09g00635 . Chy09g00879 Cme09g01413
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 1990778 1996312 - Bda004865.1 Bda11g00153 153
11 2005881 2009147 + Bda033010 Bda11g00154 154
11 2033174 2038576 + Bda004867.2 Bda11g00155 155
7 39322918 39331749 - XM_039036414.1 Bhi07g01267 1267
7 39339156 39352256 - XM_039036295.1 Bhi07g01273 1273
12 25931940 25935466 + XM_039019797.1 Bhi12g00856 856
12 26084186 26092710 - XM_039019633.1 Bhi12g00858 858
12 26108843 26112064 + XM_039019986.1 Bhi12g00859 859
12 26193180 26200342 + XM_039051288.1 Bhi12g00861 861
16 27941504 27948512 - BLOR21508 Blo16g00721 721
16 28092370 28098905 + BLOR21510 Blo16g00723 723
6 47739239 47741197 + Bma024186.1 Bma06g01092 1092
6 47749110 47755171 - Bma024188.1 Bma06g01094 1094
6 47758408 47761490 + Bma024189.1 Bma06g01095 1095
6 47788787 47794150 + Bma024193.2 Bma06g01099 1099
13 16095318 16100629 - Bpe010723.1 Bpe13g01043 1043
13 16124520 16127776 - Bpe025265 Bpe13g01045 1045
13 16128636 16133903 + Bpe010725.1 Bpe13g01046 1046
13 16143718 16145595 - Bpe010727.1 Bpe13g01048 1048
1 6561955 6565558 + CaPI482276_01g006080.1 Cam01g0608 608
1 6627674 6635901 - CaPI482276_01g006100.1 Cam01g0610 610
1 6641758 6645008 + CaPI482276_01g006110.1 Cam01g0611 611
1 6670719 6676282 + CaPI482276_01g006120.1 Cam01g0612 612
5 32295802 32307505 - CaPI482276_05g024350.1 Cam05g2435 2435
4 8923689 8928597 - Carg01863-RA Car04g01537 1537
4 8931767 8942552 - Carg01862-RA Car04g01538 1538
4 16248970 16253193 - Carg27276-RA Car04g02022 2022
4 16259982 16263981 + Carg27275-RA Car04g02023 2023
4 16285915 16290413 + Carg27274-RA Car04g02024 2024
15 5176089 5178287 + Carg24919-RA Car15g00875 875
15 5190961 5199913 + Carg24917-RA Car15g00877 877
15 5227564 5231688 + Carg24916-RA Car15g00878 878
18 9891297 9896935 - Carg19035-RA Car18g00909 909
18 9903774 9914869 - Carg19036-RA Car18g00910 910
1 6288207 6293398 + CcPI632755_01g006220.1 Cco01g0622 622
1 6355884 6364146 - CcPI632755_01g006260.1 Cco01g0626 626
1 6369963 6373248 + CcPI632755_01g006270.1 Cco01g0627 627
1 6402240 6407766 + CcPI632755_01g006280.1 Cco01g0628 628
5 33353230 33364854 - CcPI632755_05g024980.1 Cco05g2498 2498
1 6344678 6348264 + CePI673135_01g005990.1 Cec01g0599 599
1 6413597 6421816 - CePI673135_01g006010.1 Cec01g0601 601
1 6427648 6430839 + CePI673135_01g006020.1 Cec01g0602 602
1 6461446 6467029 + CePI673135_01g006030.1 Cec01g0603 603
5 35703839 35715577 - CePI673135_05g024540.1 Cec05g2454 2454
9 11530059 11534723 - Chy9G165950.1 Chy09g00879 879
9 11550057 11553316 - Chy9G165960.1 Chy09g00880 880
9 11555302 11563435 + Chy9G165970.1 Chy09g00881 881
9 11608956 11611272 - Chy9G165990.1 Chy09g00883 883
10 16622748 16633688 + Chy10G183790.1 Chy10g01185 1185
10 16641461 16648949 + Chy10G183810.1 Chy10g01187 1187
1 6207776 6210806 + ClG42_01g0060000.10 Clacu01g0600 600
1 6270332 6278570 - ClG42_01g0060200.10 Clacu01g0602 602
1 6284395 6287636 + ClG42_01g0060300.10 Clacu01g0603 603
1 6313483 6319074 + ClG42_01g0060400.10 Clacu01g0604 604
5 32508698 32520433 - ClG42_05g0242600.10 Clacu05g2426 2426
1 6550969 6554142 + ClCG01G005960.1 Cla01g00581 581
1 6617662 6625900 - ClCG01G005980.2 Cla01g00584 584
1 6631140 6635398 + ClCG01G005990.2 Cla01g00585 585
1 6660810 6665540 + ClCG01G006000.2 Cla01g00586 586
5 34299135 34311124 - ClCG05G022365.1 Cla05g02265 2265
4 14416823 14428894 - CmaCh04G020830.1 Cma04g02083 2083
4 14437058 14441109 + CmaCh04G020840.1 Cma04g02084 2084
4 14459387 14466758 + CmaCh04G020850.1 Cma04g02085 2085
15 4918220 4921576 + CmaCh15G009310.1 Cma15g00931 931
15 4933478 4940432 + CmaCh15G009330.1 Cma15g00933 933
15 4968408 4973289 + CmaCh15G009360.1 Cma15g00936 936
18 8323761 8332328 - CmaCh18G009880.1 Cma18g00988 988
18 8336165 8343174 - CmaCh18G009890.1 Cma18g00989 989
9 19293211 19298508 - MELO3C005332.2.1 Cme09g01413 1413
9 19312236 19316362 - MELO3C005333.2.1 Cme09g01414 1414
9 19318278 19326951 + MELO3C005334.2.1 Cme09g01415 1415
9 19369968 19372390 - MELO3C005335.2.1 Cme09g01416 1416
10 1446609 1454472 - MELO3C012286.2.1 Cme10g00217 217
10 1459864 1474845 - MELO3C012285.2.1 Cme10g00219 219
2 22537102 22544620 - PI0025310.1 Cmetu02g0065 65
4 7933890 7939029 - CmoCh04G015510.1 Cmo04g01551 1551
4 7943030 7953481 - CmoCh04G015530.1 Cmo04g01553 1553
4 16104814 16116262 - CmoCh04G021840.1 Cmo04g02184 2184
4 16123927 16128093 + CmoCh04G021850.1 Cmo04g02185 2185
4 16145898 16152552 + CmoCh04G021860.1 Cmo04g02186 2186
15 5095772 5098621 + CmoCh15G009710.1 Cmo15g00971 971
15 5111094 5117769 + CmoCh15G009730.1 Cmo15g00973 973
15 5144423 5150656 + CmoCh15G009760.1 Cmo15g00976 976
18 10863877 10872116 - CmoCh18G009950.1 Cmo18g00995 995
18 10877440 10888473 - CmoCh18G009960.1 Cmo18g00996 996
1 6164427 6167463 + CmPI595203_01g005730.1 Cmu01g0573 573
1 6226989 6235228 - CmPI595203_01g005750.1 Cmu01g0575 575
1 6241047 6244288 + CmPI595203_01g005760.1 Cmu01g0576 576
1 6270146 6275735 + CmPI595203_01g005770.1 Cmu01g0577 577
5 32246657 32258393 - CmPI595203_05g022920.1 Cmu05g2292 2292
6 2025380 2031553 - Conep06aG0042800.1 Cone6ag0418 418
6 2034940 2037733 + Conep06aG0042900.1 Cone6ag0419 419
9 2048604 2051326 + Conep09aG0045300.1 Cone9ag0443 443
13 7363320 7368761 - Conep13aG0081800.1 Cone13ag0793 793
13 7370496 7375811 - Conep13aG0081900.1 Cone13ag0794 794
13 7376405 7381391 + Conep13aG0082000.1 Cone13ag0795 795
13 7387829 7389360 - Conep13aG0082300.1 Cone13ag0797 797
19 6419220 6424517 - Conep19aG0081900.1 Cone19ag0797 797
19 6425135 6433317 - Conep19aG0082000.1 Cone19ag0798 798
19 6433581 6434221 - Conep19aG0082100.1 Cone19ag0799 799
19 6437278 6441918 + Conep19aG0082200.1 Cone19ag0800 800
19 6446452 6447831 - Conep19aG0082500.1 Cone19ag0802 802
1 7948447 7960341 - Cp4.1LG01g13830.1 Cpe01g01321 1321
9 1974411 1986309 + Cp4.1LG09g03220.1 Cpe09g00328 328
13 4229983 4233826 + Cp4.1LG13g06960.1 Cpe13g00387 387
13 4242845 4246021 - Cp4.1LG13g06850.1 Cpe13g00388 388
5 35574260 35585967 - CrPI670011_05g024090.1 Cre05g2409 2409
9 38037840 38043427 - CrPI670011_09g019280.1 Cre09g1928 1928
9 38076851 38080123 - CrPI670011_09g019290.1 Cre09g1929 1929
9 38086141 38094337 + CrPI670011_09g019300.1 Cre09g1930 1930
9 38167718 38171687 - CrPI670011_09g019320.1 Cre09g1932 1932
5 12915450 12926425 - CsaV3_5G015530.1 Csa05g01229 1229
5 23796738 23804235 - CsaV3_5G028680.1 Csa05g02049 2049
5 23814914 23819169 - CsaV3_5G028690.1 Csa05g02050 2050
5 23820431 23830355 + CsaV3_5G028700.1 Csa05g02051 2051
5 23862912 23866616 - CsaV3_5G028730.1 Csa05g02054 2054
5 27531154 27544227 + CsaV3_5G034720.1 Csa05g02653 2653
1 76663946 76676691 - Hsped.01g11560.1 Hepe01g1156 1156
2 74544719 74548515 - Hsped.02g26830.1 Hepe02g2683 2683
2 74557060 74565837 + Hsped.02g26840.1 Hepe02g2684 2684
2 74610364 74614518 - Hsped.02g26860.1 Hepe02g2686 2686
13 3963364 3977057 + Lag0040336.1 Lac13g0540 540
10 38444519 38446944 - Maker00006927 Lcy10g1461 1461
10 38458851 38469125 + Maker00006932 Lcy10g1462 1462
10 38557505 38561227 - Maker00006968 Lcy10g1463 1463
4 2221987 2226572 - Lsi04G002120.1 Lsi04g00212 212
4 2233831 2247936 - Lsi04G002130.1 Lsi04g00213 213
9 6929308 6933135 + Lsi09G006310.1 Lsi09g00631 631
9 6987036 6996655 - Lsi09G006330.1 Lsi09g00633 633
9 7003898 7007456 + Lsi09G006340.1 Lsi09g00634 634
9 7034981 7042764 + Lsi09G006350.1 Lsi09g00635 635
8 2309288 2318564 + Sed0006886.1 Sed08g0382 382
4 6777384 6792938 - Tan0003020.1 Tan04g0802 802
1 3858748 3861883 + Vvi1g371 Vvi1g371 371
1 3874210 3875347 + Vvi1g372 Vvi1g372 372
1 3875425 3876784 - Vvi1g373 Vvi1g373 373
1 3887164 3889989 - Vvi1g374 Vvi1g374 374
1 3891702 3907393 - Vvi1g375 Vvi1g375 375
1 3907608 3908170 - Vvi1g376 Vvi1g376 376
1 3909007 3915680 - Vvi1g377 Vvi1g377 377
1 3939295 3943923 + Vvi1g378 Vvi1g378 378
1 3945265 3976762 + Vvi1g379 Vvi1g379 379
1 3981901 3993615 + Vvi1g380 Vvi1g380 380
       

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