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
Vvi17g126 . . Bda06g00733 . Bpe12g00487 . . . Cmo13g00832 . . . . . . Cpe20g00310 . . . . . . . . . . . . . . . Cone2ag0968 . . Cone19ag0203 Lsi02g00499 Csa01g00959 . . . Blo15g00077 . . Bpe07g00884 . . . . . . Cma13g00801 . Car13g00649 Car18g00225 . . Bhi08g01473 . . . . . . . . . . . . . . . . .
Vvi17g127 . . . . . . . . . . . . . . . Cpe20g00311 . . . . . . . . . . . . . . . . . Cone13ag0212 Cone19ag0201 . . . . . . . Bda14g01370 . Bpe15g00213 Bma03g01260 . . . . . . Car13g00648 . . . . . . . . . . . . . . . . . . . . .
Vvi17g128 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g129 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g130 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g131 . . . . . . . . . . . Cma11g00320 . Car11g00295 . . . . . . . . . . . . . . . . . Cone2ag0777 . . . . . . . . . . . . . . . . . Cmo11g00325 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g132 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g133 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g134 . . Bda06g00735 . Bpe12g00494 . . Bma12g01078 . . Cma10g00335 Cma11g00041 Car10g00318 Car11g00037 Sed08g1476 . Cpe04g01609 Bhi02g00531 Tan09g2361 Cmetu09g1801 . Hepe09g0057 . . Cla06g01734 Cam06g1925 Cec06g1975 Cco06g1979 Clacu06g1881 Cmu06g1823 Cre06g2638 Cone2ag0967 Cone16ag0022 . . . . . . . Blo15g00213 . . . . . . . Cmo10g00363 Cmo11g00042 . . . . . . . . . . . . . . . . . . . . Lsi06g01634 Csa01g00065 . Cme02g02057
Vvi17g135 . . . . . . . . . . Cma10g00071 Cma11g00042 Car10g00058 Car11g00038 Sed08g0040 . Cpe04g01607 Bhi02g00533 Tan09g2359 Cmetu02g0049 . Hepe09g0058 . . Cla06g01733 Cam06g1924 Cec06g1974 Cco06g1978 Clacu06g1880 Cmu06g1822 Cre06g2637 . . . . . . . . . . . . . . . . . Cmo10g00066 Cmo11g00043 . . . . . . . . . . . . . . . . . . . . Lsi06g01633 Csa01g00066 Chy02g02654 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 9973979 9985277 + Bda024036.1 Bda06g00733 733
6 9998022 9998444 + Bda024038.1 Bda06g00735 735
14 16070711 16075431 + Bda011070.1 Bda14g01370 1370
2 10126053 10126813 - XM_039023850.1 Bhi02g00531 531
2 10132959 10149985 - XM_039023104.1 Bhi02g00533 533
8 43081125 43094228 - XM_039038092.1 Bhi08g01473 1473
15 670165 672063 + BLOR06471 Blo15g00077 77
15 2173917 2183822 + BLOR06607 Blo15g00213 213
3 21339865 21344605 + Bma017727.1 Bma03g01260 1260
12 43080335 43080757 + Bma008425.1 Bma12g01078 1078
7 14929705 14947281 - Bpe021727.2 Bpe07g00884 884
12 10672388 10682452 + Bpe005750.2 Bpe12g00487 487
12 10742412 10742639 - Bpe005757.1 Bpe12g00494 494
15 13234415 13239113 - Bpe001150.1 Bpe15g00213 213
6 30196157 30207866 + CaPI482276_06g019240.1 Cam06g1924 1924
6 30212261 30212689 + CaPI482276_06g019250.1 Cam06g1925 1925
10 255729 264169 - Carg10290-RA Car10g00058 58
10 1567166 1570558 + Carg15185-RA Car10g00318 318
11 190940 191365 - Carg20175-RA Car11g00037 37
11 192227 203000 - Carg20176-RA Car11g00038 38
11 1610706 1612928 + Carg09094-RA Car11g00295 295
13 8036489 8042967 - Carg07598-RA Car13g00648 648
13 8043751 8057276 - Carg07599-RA Car13g00649 649
18 1278709 1290789 - Carg06792-RA Car18g00225 225
6 29934223 29945774 + CcPI632755_06g019780.1 Cco06g1978 1978
6 29950241 29950669 + CcPI632755_06g019790.1 Cco06g1979 1979
6 33010444 33022134 + CePI673135_06g019740.1 Cec06g1974 1974
6 33026493 33026921 + CePI673135_06g019750.1 Cec06g1975 1975
2 29570673 29585286 + Chy2G049210.1 Chy02g02654 2654
6 29246920 29258626 + ClG42_06g0188000.10 Clacu06g1880 1880
6 29263021 29263449 + ClG42_06g0188100.10 Clacu06g1881 1881
6 30884184 30899918 + ClCG06G017790.2 Cla06g01733 1733
6 30905379 30905807 + ClCG06G017800.1 Cla06g01734 1734
10 273170 282654 - CmaCh10G000710.1 Cma10g00071 71
10 1555617 1558979 + CmaCh10G003350.1 Cma10g00335 335
11 181220 181645 - CmaCh11G000410.1 Cma11g00041 41
11 182386 188298 - CmaCh11G000420.1 Cma11g00042 42
11 1587033 1601317 + CmaCh11G003200.1 Cma11g00320 320
13 6793733 6814722 - CmaCh13G008010.1 Cma13g00801 801
2 26578798 26579521 + MELO3C026214.2.1 Cme02g02057 2057
2 24869364 24880311 + PI0015533.1 Cmetu02g0049 49
9 5004178 5005221 - PI0022801.1 Cmetu09g1801 1801
10 301666 310711 - CmoCh10G000660.1 Cmo10g00066 66
10 1647651 1651524 + CmoCh10G003630.1 Cmo10g00363 363
11 176647 177072 - CmoCh11G000420.1 Cmo11g00042 42
11 177786 189046 - CmoCh11G000430.1 Cmo11g00043 43
11 1574165 1590170 + CmoCh11G003250.1 Cmo11g00325 325
13 7722307 7743891 - CmoCh13G008320.1 Cmo13g00832 832
6 29150176 29161924 + CmPI595203_06g018220.1 Cmu06g1822 1822
6 29166302 29166730 + CmPI595203_06g018230.1 Cmu06g1823 1823
2 33756899 33759781 - Conep02aG0180400.1 Cone2ag0777 777
2 35212098 35212857 + Conep02aG0200100.1 Cone2ag0967 967
2 35213306 35222035 - Conep02aG0200200.1 Cone2ag0968 968
13 1368959 1374548 - Conep13aG0021700.1 Cone13ag0212 212
16 152840 153659 - Conep16aG0002200.1 Cone16ag0022 22
19 1255365 1261146 - Conep19aG0020700.1 Cone19ag0201 201
19 1277344 1294101 - Conep19aG0020900.1 Cone19ag0203 203
4 12505583 12517842 + Cp4.1LG04g16060.1 Cpe04g01607 1607
4 12518798 12519223 + Cp4.1LG04g16040.1 Cpe04g01609 1609
20 1743519 1756814 + Cp4.1LG20g03070.1 Cpe20g00310 310
20 1757952 1765008 + Cp4.1LG20g03060.1 Cpe20g00311 311
6 33976822 33988559 + CrPI670011_06g026370.1 Cre06g2637 2637
6 33993006 33993434 + CrPI670011_06g026380.1 Cre06g2638 2638
1 374744 378031 - CsaV3_1G000650.1 Csa01g00065 65
1 378802 389948 - CsaV3_1G000660.1 Csa01g00066 66
1 5941976 5955452 - CsaV3_1G009590.1 Csa01g00959 959
9 474103 475067 - Hsped.09g00570.1 Hepe09g0057 57
9 477649 489418 - Hsped.09g00580.1 Hepe09g0058 58
2 4219975 4240106 - Lsi02G004990.1 Lsi02g00499 499
6 26632587 26646532 + Lsi06G016330.1 Lsi06g01633 1633
6 26650893 26651318 + Lsi06G016340.1 Lsi06g01634 1634
8 187381 198166 - Sed0018235.1 Sed08g0040 40
8 29259214 29259724 + Sed0017027.1 Sed08g1476 1476
9 73336686 73348277 + Tan0002817.2 Tan09g2359 2359
9 73354367 73355400 + Tan0007343.1 Tan09g2361 2361
17 1100350 1115997 + Vvi17g126 Vvi17g126 126
17 1116768 1128710 + Vvi17g127 Vvi17g127 127
17 1129227 1136881 + Vvi17g128 Vvi17g128 128
17 1137077 1137550 + Vvi17g129 Vvi17g129 129
17 1138001 1138926 - Vvi17g130 Vvi17g130 130
17 1152188 1164212 - Vvi17g131 Vvi17g131 131
17 1164923 1190012 - Vvi17g132 Vvi17g132 132
17 1190772 1197806 - Vvi17g133 Vvi17g133 133
17 1200419 1200851 - Vvi17g134 Vvi17g134 134
17 1201557 1215948 - Vvi17g135 Vvi17g135 135
       

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