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
Vvi2g92 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g93 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda07g01915 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g94 Blo02g01135 Blo03g00240 Bda06g00135 Bda08g00489 Bpe05g00675 Bpe07g00081 . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0260 Cone12ag0266 . . . . . . . . . . . . Bma05g00848 Bma12g00600 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g95 . . . . . . . . . . Cma02g00951 . Car02g00700 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda07g01916 . . . . . . Cmo02g00959 Cmo15g01105 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g96 . . . . . . . . Cmo06g01064 . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0830 . . . . . . . . . . . . . . . . Cma06g01037 . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g97 Blo02g01136 . . Bda08g00488 Bpe05g00676 . . . . Cmo16g00612 . . . . . Cpe14g00477 . . . . . . . . Cla07g01406 Cam07g1507 Cec07g1604 Cco07g1561 Clacu07g1497 Cmu07g1467 Cre07g1843 . . . . . . . Cme07g01587 . . . . . . Bma05g00849 . . . . Cma06g01035 Cma16g00563 . . . . . . . . . . . . . . . . . . . Csa04g00635 Chy07g01178 .
Vvi2g98 . . . . . . Bma07g01678 . . . Cma02g01404 Cma15g01263 Car02g01181 Car15g01139 . . Cpe05g00620 . . . . . . . . . . . . . . . . . . . Csa05g00223 Chy09g01277 . . . . Bda09g00021 Bpe08g01513 . . . . Cmo02g01122 Cmo15g01332 . . . . . Cpe13g00125 Bhi12g00167 . . . . . Lcy12g1591 Cla01g00205 . . . . . . Lsi09g00194 . . Cme09g01821
Vvi2g99 Blo02g01137 . . Bda08g00487 Bpe05g00677 . . . . . . . Car02g01180 . . . Cpe05g00618 . . . . . . . . . . . . . . . Cone12ag0264 Cone6ag0831 Cone9ag0830 . Csa05g00222 Chy09g01278 . . . Bda07g01917 . . . Bma05g00850 . . Cmo02g01437 . . . . . . Cpe13g00124 Bhi12g00166 . . Lac11g2026 Hepe06g1497 . Lcy12g1590 . . . . . . . Lsi09g00193 . . Cme09g01822
Vvi2g100 Blo02g01139 Blo03g00241 . Bda08g00485 Bpe05g00679 . . . . Cmo16g00610 . . . . . . . . . . . . . . Cla07g01409 Cam07g1509 Cec07g1606 Cco07g1564 Clacu07g1499 Cmu07g1469 Cre07g1846 . . Cone6ag0833 Cone9ag0832 . . . Cme07g01585 . . . . . . Bma05g00852 . . . . . Cma16g00561 . . . . . . . . . . . . . . . . . . . Csa04g00638 Chy07g01173 .
Vvi2g101 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 2050534 2052182 - Bda023332.1 Bda06g00135 135
7 36601765 36607599 - Bda028891.3 Bda07g01915 1915
7 36613706 36615488 + Bda028892.1 Bda07g01916 1916
7 36617496 36619733 + Bda028893.1 Bda07g01917 1917
8 4990724 4991863 + Bda024936.1 Bda08g00485 485
8 4998068 5000086 - Bda024938.1 Bda08g00487 487
8 5001058 5002806 - Bda024939.1 Bda08g00488 488
8 5005017 5007290 + Bda024940.1 Bda08g00489 489
9 334378 336384 - Bda030539.1 Bda09g00021 21
12 4855974 4862345 - XM_039018912.1 Bhi12g00166 166
12 4866851 4870400 - XM_039019472.1 Bhi12g00167 167
2 42740776 42742794 - BLOR10865 Blo02g01135 1135
2 42762297 42764049 + BLOR10866 Blo02g01136 1136
2 42764944 42766940 + BLOR10867 Blo02g01137 1137
2 42774570 42775300 - BLOR10869 Blo02g01139 1139
3 5210447 5217420 - BLOR11421 Blo03g00240 240
3 5233822 5242797 - BLOR11422 Blo03g00241 241
5 46031662 46033680 - Bma031211 Bma05g00848 848
5 46035904 46037659 + Bma021964.3 Bma05g00849 849
5 46045097 46047014 + Bma021965.2 Bma05g00850 850
5 46067172 46068260 - Bma021968.1 Bma05g00852 852
7 52362916 52364449 + Bma026975.1 Bma07g01678 1678
12 27319223 27322824 - Bma030506 Bma12g00600 600
5 20422414 20424136 - Bpe018088.1 Bpe05g00675 675
5 20426022 20427778 + Bpe018089.1 Bpe05g00676 676
5 20428798 20431018 + Bpe018090.1 Bpe05g00677 677
5 20440783 20441872 - Bpe018092.1 Bpe05g00679 679
7 597875 600029 + Bpe020894.1 Bpe07g00081 81
8 15802651 15804669 + Bpe023624.2 Bpe08g01513 1513
7 29696616 29699854 + CaPI482276_07g015070.1 Cam07g1507 1507
7 29724342 29725207 - CaPI482276_07g015090.1 Cam07g1509 1509
2 5185294 5189794 - Carg08523-RA Car02g00700 700
2 8033689 8038490 - Carg02568-RA Car02g01180 1180
2 8039599 8042521 - Carg02567-RA Car02g01181 1181
15 8984359 8990228 + Carg21263-RA Car15g01139 1139
7 29634222 29638327 + CcPI632755_07g015610.1 Cco07g1561 1561
7 29662880 29663769 - CcPI632755_07g015640.1 Cco07g1564 1564
7 31554190 31558303 + CePI673135_07g016040.1 Cec07g1604 1604
7 31582505 31583398 - CePI673135_07g016060.1 Cec07g1606 1606
7 16599442 16600828 + Chy7G140030.1 Chy07g01173 1173
7 16626002 16629100 - Chy7G140080.1 Chy07g01178 1178
9 14792785 14795278 + Chy9G169930.1 Chy09g01277 1277
9 14798335 14803293 + Chy9G169940.1 Chy09g01278 1278
7 29554551 29557777 + ClG42_07g0149700.10 Clacu07g1497 1497
7 29582396 29583257 - ClG42_07g0149900.10 Clacu07g1499 1499
1 2033852 2047038 - ClCG01G002090.2 Cla01g00205 205
7 31255098 31259520 + ClCG07G014830.2 Cla07g01406 1406
7 31283498 31285052 - ClCG07G014850.2 Cla07g01409 1409
2 5653050 5657664 - CmaCh02G009510.1 Cma02g00951 951
2 8128944 8137427 - CmaCh02G014040.1 Cma02g01404 1404
6 6972375 6974513 - CmaCh06G010350.1 Cma06g01035 1035
6 6979799 6985594 - CmaCh06G010370.1 Cma06g01037 1037
15 8026674 8037258 + CmaCh15G012630.1 Cma15g01263 1263
16 2870690 2871581 + CmaCh16G005610.1 Cma16g00561 561
16 2879056 2883193 - CmaCh16G005630.1 Cma16g00563 563
7 21655527 21657063 + MELO3C016312.2.1 Cme07g01585 1585
7 21688472 21692905 - MELO3C016314.2.1 Cme07g01587 1587
9 22530090 22533630 + MELO3C005732.2.1 Cme09g01821 1821
9 22536861 22542327 + MELO3C005733.2.1 Cme09g01822 1822
2 5878412 5882984 - CmoCh02G009590.1 Cmo02g00959 959
2 6813662 6817655 - CmoCh02G011220.1 Cmo02g01122 1122
2 8475644 8480526 - CmoCh02G014370.1 Cmo02g01437 1437
6 8264306 8268973 + CmoCh06G010640.1 Cmo06g01064 1064
15 7411580 7416248 - CmoCh15G011050.1 Cmo15g01105 1105
15 9137087 9146807 + CmoCh15G013320.1 Cmo15g01332 1332
16 2977914 2978586 + CmoCh16G006100.1 Cmo16g00610 610
16 2986147 2990415 - CmoCh16G006120.1 Cmo16g00612 612
7 29806261 29809487 + CmPI595203_07g014670.1 Cmu07g1467 1467
7 29834203 29835064 - CmPI595203_07g014690.1 Cmu07g1469 1469
6 4251309 4253816 + Conep06aG0085600.1 Cone6ag0830 830
6 4254766 4256950 + Conep06aG0085700.1 Cone6ag0831 831
6 4264025 4264697 - Conep06aG0085900.1 Cone6ag0833 833
8 1504354 1507405 + Conep08aG0027100.1 Cone8ag0260 260
9 4054886 4056782 + Conep09aG0085000.1 Cone9ag0830 830
9 4071452 4072142 - Conep09aG0085200.1 Cone9ag0832 832
12 1401205 1407098 - Conep12aG0027000.1 Cone12ag0264 264
12 1413403 1416264 + Conep12aG0027200.1 Cone12ag0266 266
5 3756610 3759744 - Cp4.1LG05g06190.1 Cpe05g00618 618
5 3765216 3769481 + Cp4.1LG05g06100.1 Cpe05g00620 620
13 866864 875712 - Cp4.1LG13g01170.1 Cpe13g00124 124
13 876777 880507 - Cp4.1LG13g01150.1 Cpe13g00125 125
14 2998798 3003942 - Cp4.1LG14g02350.1 Cpe14g00477 477
7 33801308 33805407 + CrPI670011_07g018430.1 Cre07g1843 1843
7 33830314 33831183 - CrPI670011_07g018460.1 Cre07g1846 1846
4 4244509 4249209 + CsaV3_4G006350.1 Csa04g00635 635
4 4269193 4270379 - CsaV3_4G006380.1 Csa04g00638 638
5 1325359 1332231 - CsaV3_5G002220.1 Csa05g00222 222
5 1334228 1338522 - CsaV3_5G002230.1 Csa05g00223 223
6 65549281 65555610 - Hsped.06g14970.1 Hepe06g1497 1497
11 35802263 35812143 - Lag0032664.1 Lac11g2026 2026
12 35981710 35986433 - Maker00029318 Lcy12g1590 1590
12 35990174 35994286 - Maker00029364 Lcy12g1591 1591
9 2006813 2013420 - Lsi09G001930.1 Lsi09g00193 193
9 2018164 2021922 - Lsi09G001940.1 Lsi09g00194 194
2 933099 947137 - Vvi2g92 Vvi2g92 92
2 952857 960480 - Vvi2g93 Vvi2g93 93
2 970123 974084 - Vvi2g94 Vvi2g94 94
2 978399 986946 + Vvi2g95 Vvi2g95 95
2 990819 996189 + Vvi2g96 Vvi2g96 96
2 1000292 1003016 + Vvi2g97 Vvi2g97 97
2 1009739 1014911 + Vvi2g98 Vvi2g98 98
2 1020200 1030408 + Vvi2g99 Vvi2g99 99
2 1047975 1048904 - Vvi2g100 Vvi2g100 100
2 1050409 1052639 + Vvi2g101 Vvi2g101 101
       

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