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
Vvi18g1270 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda13g01438 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1271 Blo01g01757 Blo12g00764 . Bda03g00418 Bpe02g00185 Bpe04g00383 Bma04g00394 Bma01g02540 . . . Cma09g01148 Car01g00839 . . Cpe06g00928 . . . . . . . . Cla08g00750 Cam08g1177 Cec08g0767 Cco08g0875 Clacu08g0883 . Cre08g0685 . . . . . . . . . . . . . . . . Sed07g2813 . Cmo09g01241 . . . . . Cpe02g00923 Bhi09g01580 Tan01g3004 Cmetu01g2180 . . . . Cla09g00971 Cam09g1023 Cec09g1026 Cco09g1037 . . Cre09g0988 . . . Cme01g00726
Vvi18g1272 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1273 Blo01g01756 . . . . . . Bma01g02539 . . . Cma09g01150 . . . Cpe06g00927 . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g00846 . . . . . . . Cmo09g01160 . . . . . . Bhi09g01578 Tan01g3003 . . . . . Cla09g00969 Cam09g1020 Cec09g1024 Cco09g1035 . . Cre09g0986 . . . .
Vvi18g1274 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1275 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1276 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1277 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1504 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1278 . . . . . . . . Cmo04g02580 Cmo15g00607 . . . . . . Cpe13g00679 . . . . . . . Cla08g00707 Cam08g1134 Cec08g0723 Cco08g0831 Clacu08g0842 . Cre08g0643 Cone4ag1505 Cone7ag1445 Cone17ag0789 Cone20ag0384 . . . Cme03g00326 . . . . Bpe02g01112 Bpe14g00446 . . . . . . . Car04g02373 . Cpe01g02134 . . . . . . . . . . . . . . . Lsi08g00551 . . .
Vvi18g1279 . . . . . . . . . . . . . . Sed11g1345 . . Bhi04g01785 Tan11g1147 Cmetu03g0084 . Hepe02g2790 . Lcy10g1347 . . . . . . . . . . Cone20ag0385 . . . . . Blo18g00139 . . . Bpe14g00445 . . . . . . . Car04g02353 . . . . . . . . . . . . . . . . . . . Chy03g00519 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 3624903 3632812 + Bda016383.1 Bda03g00418 418
11 8339508 8342425 - Bda005597.2 Bda11g00846 846
13 37127035 37128801 + Bda000270.1 Bda13g01438 1438
4 43255205 43257783 + XM_039030328.1 Bhi04g01785 1785
9 42496760 42505881 + XM_039042590.1 Bhi09g01578 1578
9 42585445 42597112 + XM_039041480.1 Bhi09g01580 1580
1 57323474 57326853 + BLOR01756 Blo01g01756 1756
1 57330390 57337508 + BLOR01757 Blo01g01757 1757
12 25999831 26008832 - BLOR04783 Blo12g00764 764
18 1291580 1293977 - BLOR08627 Blo18g00139 139
1 83087727 83090094 + Bma003419.1 Bma01g02539 2539
1 83093329 83100036 + Bma003420.1 Bma01g02540 2540
4 3218518 3227265 + Bma018856.1 Bma04g00394 394
2 1283738 1290661 - Bpe008036.1 Bpe02g00185 185
2 14770754 14771398 - Bpe008970.2 Bpe02g01112 1112
4 2412755 2420579 + Bpe015070.1 Bpe04g00383 383
14 4072844 4084009 + Bpe007096.1 Bpe14g00445 445
14 4078724 4079359 - Bpe024981 Bpe14g00446 446
8 17679820 17680467 + CaPI482276_08g011340.1 Cam08g1134 1134
8 18124371 18127594 - CaPI482276_08g011770.1 Cam08g1177 1177
9 10612149 10618118 + CaPI482276_09g010200.1 Cam09g1020 1020
9 10641026 10649407 + CaPI482276_09g010230.1 Cam09g1023 1023
1 6622367 6626041 - Carg27969-RA Car01g00839 839
4 18925173 18926733 - Carg15787-RA Car04g02353 2353
4 19040626 19047109 - Carg15808-RA Car04g02373 2373
8 20149500 20150144 + CcPI632755_08g008310.1 Cco08g0831 831
8 20611279 20615308 - CcPI632755_08g008750.1 Cco08g0875 875
9 9920645 9926296 + CcPI632755_09g010350.1 Cco09g1035 1035
9 9946208 9955514 + CcPI632755_09g010370.1 Cco09g1037 1037
8 18952660 18953307 + CePI673135_08g007230.1 Cec08g0723 723
8 19401479 19404664 - CePI673135_08g007670.1 Cec08g0767 767
9 9923098 9929006 + CePI673135_09g010240.1 Cec09g1024 1024
9 9946144 9956288 + CePI673135_09g010260.1 Cec09g1026 1026
3 7178412 7180220 + Chy3G054990.1 Chy03g00519 519
8 18461279 18461926 + ClG42_08g0084200.10 Clacu08g0842 842
8 18912922 18916144 - ClG42_08g0088300.10 Clacu08g0883 883
8 19341799 19342446 + ClCG08G006940.1 Cla08g00707 707
8 19811127 19814976 - ClCG08G007390.1 Cla08g00750 750
9 10183010 10189615 + ClCG09G010370.2 Cla09g00969 969
9 10206646 10218504 + ClCG09G010390.2 Cla09g00971 971
9 6565016 6573063 - CmaCh09G011480.1 Cma09g01148 1148
9 6592103 6601729 - CmaCh09G011500.1 Cma09g01150 1150
1 7047210 7058815 - MELO3C023672.2.1 Cme01g00726 726
3 4245196 4246173 - MELO3C008350.2.1 Cme03g00326 326
1 15550443 15560946 - PI0007860.1 Cmetu01g2180 2180
3 8875937 8877779 + PI0027152.1 Cmetu03g0084 84
4 18877131 18886260 - CmoCh04G025800.1 Cmo04g02580 2580
9 7325057 7337632 - CmoCh09G011600.1 Cmo09g01160 1160
9 10664889 10671245 + CmoCh09G012410.1 Cmo09g01241 1241
15 2949497 2950135 - CmoCh15G006070.1 Cmo15g00607 607
4 11694928 11701008 + Conep04aG0155600.1 Cone4ag1504 1504
4 11702118 11702777 - Conep04aG0155700.1 Cone4ag1505 1505
7 10230273 10230932 + Conep07aG0148700.1 Cone7ag1445 1445
17 6104243 6105070 - Conep17aG0080700.1 Cone17ag0789 789
20 1797722 1798408 - Conep20aG0039800.1 Cone20ag0384 384
20 1803649 1807292 + Conep20aG0039900.1 Cone20ag0385 385
1 17996928 18003614 - Cp4.1LG01g21290.1 Cpe01g02134 2134
2 7428310 7432872 + Cp4.1LG02g09200.1 Cpe02g00923 923
6 6835787 6845879 + Cp4.1LG06g09200.1 Cpe06g00927 927
6 6868845 6877767 + Cp4.1LG06g09170.1 Cpe06g00928 928
13 6371430 6372068 + Cp4.1LG13g04000.1 Cpe13g00679 679
8 19375151 19375798 + CrPI670011_08g006430.1 Cre08g0643 643
8 19819946 19823598 - CrPI670011_08g006850.1 Cre08g0685 685
9 10132167 10137833 + CrPI670011_09g009860.1 Cre09g0986 986
9 10154371 10164673 + CrPI670011_09g009880.1 Cre09g0988 988
2 76820424 76822658 - Hsped.02g27900.1 Hepe02g2790 2790
10 36623456 36625637 - Maker00008815 Lcy10g1347 1347
8 13677376 13678029 + Lsi08G005510.1 Lsi08g00551 551
7 42977382 42989197 + Sed0011272.2 Sed07g2813 2813
11 29504717 29508203 - Sed0019060.1 Sed11g1345 1345
1 73637286 73658328 + Tan0006000.2 Tan01g3003 3003
1 73942605 73955046 + Tan0008109.1 Tan01g3004 3004
11 9086250 9089343 + Tan0015405.1 Tan11g1147 1147
18 15923473 15926074 - Vvi18g1270 Vvi18g1270 1270
18 15967401 15986153 - Vvi18g1271 Vvi18g1271 1271
18 15986160 15987116 - Vvi18g1272 Vvi18g1272 1272
18 16025494 16053846 - Vvi18g1273 Vvi18g1273 1273
18 16093376 16093805 - Vvi18g1274 Vvi18g1274 1274
18 16137226 16137823 - Vvi18g1275 Vvi18g1275 1275
18 16148679 16149243 + Vvi18g1276 Vvi18g1276 1276
18 16149268 16162689 + Vvi18g1277 Vvi18g1277 1277
18 16184240 16187178 - Vvi18g1278 Vvi18g1278 1278
18 16209618 16218061 + Vvi18g1279 Vvi18g1279 1279
       

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