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
Vvi2g522 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g523 . Blo03g00166 Bda06g00032 . . Bpe07g00171 . . Cmo06g00797 . . . . . . . . Bhi11g00202 . . . Hepe06g1138 Mch10g1557 . Cla10g00263 Cam10g0270 Cec10g0277 Cco10g0274 Clacu10g0270 Cmu10g1113 Cre10g0521 . . Cone6ag0677 Cone9ag0682 Lsi07g01308 . . Cme06g02577 . . . . . . . Bma12g00639 . . . Cma06g00777 . Car06g00691 . Cpe08g00745 . . . . . . . . . . . . . . . . Csa03g00282 Chy06g02040 .
Vvi2g524 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g525 . . . . . . Bma07g01599 . . . . Cma15g01127 . Car15g01032 . . . . . . . . . . . . . . . . . Cone8ag0393 . Cone6ag0676 Cone9ag0681 . Csa05g00416 Chy09g01093 . . Blo19g00255 . Bda09g00097 Bpe08g00875 . . . . . Cmo15g01186 . . . . . Cpe13g00229 Bhi12g00436 . . Lac11g2279 . . Lcy12g1824 Cla09g01215 Cam09g1280 Cec09g1296 Cco09g1326 . . Cre09g1240 . . . Cme09g01622
Vvi2g526 . . . . . . . . Cmo06g00799 Cmo16g01195 . . . . Sed07g1687 Cpe14g00948 . Bhi11g00199 Tan01g2024 Cmetu06g2197 . Hepe06g1136 Mch10g1820 . Cla10g00261 Cam10g0267 Cec10g0274 Cco10g0272 Clacu10g0268 Cmu10g1111 Cre10g0519 . . . . Lsi07g01305 . . Cme06g02576 . . Bda07g00131 . . Bpe11g00361 . . . . . Cma06g00779 Cma16g01144 Car06g00693 Car16g01082 Cpe08g00744 . . . . . . . . . . . . . . . . Csa03g00280 Chy06g02042 .
Vvi2g527 . . . . . . Bma07g01598 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda09g00098 Bpe08g01431 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g528 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g529 . . . . . . Bma07g01597 . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0378 . . . Csa05g00417 Chy09g01092 . . Blo19g00254 . Bda09g00099 Bpe08g01430 . . . . . . . . . . . . Bhi12g00440 . . Lac11g2280 Hepe06g1668 . Lcy12g1825 Cla01g00393 Cam01g0410 . . Clacu01g0411 Cmu01g0392 Cre09g2118 Lsi09g00419 . . Cme09g01621
Vvi2g530 . Blo03g00163 Bda06g00030 . . Bpe07g00174 . . . . . Cma15g01126 . Car15g01031 . . . . . . . . . . . . . . . . . . Cone12ag0379 . . . Csa05g00418 Chy09g01091 . . . . . . . . Bma12g00641 . . . . . . . . Cpe13g00230 Bhi12g00442 . . . . . Lcy12g1826 Cla01g00394 Cam01g0411 Cec01g0402 Cco01g0423 Clacu01g0412 Cmu01g0393 . . . . Cme09g01620
Vvi2g531 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 281246 281920 - Bda023198.1 Bda06g00030 30
6 292597 295988 - Bda023201.1 Bda06g00032 32
7 1670854 1671961 + Bda025196.1 Bda07g00131 131
9 1842203 1843850 + Bda030632.1 Bda09g00097 97
9 1858528 1860795 - Bda030633.1 Bda09g00098 98
9 1862042 1866880 + Bda030634.3 Bda09g00099 99
11 4324483 4327906 - XM_039048130.1 Bhi11g00199 199
11 4458267 4464335 - XM_039047538.1 Bhi11g00202 202
12 14598081 14601142 - XM_039020404.1 Bhi12g00436 436
12 14670665 14683453 + XM_039018578.1 Bhi12g00440 440
12 14743585 14745632 + XM_039018782.1 Bhi12g00442 442
3 4181251 4181922 - BLOR11344 Blo03g00163 163
3 4217643 4220768 - BLOR11347 Blo03g00166 166
19 14461448 14470900 - BLOR09597 Blo19g00254 254
19 14516125 14518191 - BLOR09598 Blo19g00255 255
7 51236371 51251141 - Bma026892.1 Bma07g01597 1597
7 51252495 51254759 + Bma026893.1 Bma07g01598 1598
7 51263008 51264719 - Bma026894.2 Bma07g01599 1599
12 27628236 27631182 + Bma007817.1 Bma12g00639 639
12 27638996 27639670 + Bma007819.1 Bma12g00641 641
7 1165439 1173012 + Bpe026044 Bpe07g00171 171
7 1181881 1182555 + Bpe020983.1 Bpe07g00174 174
8 11134949 11137762 + Bpe022997.1 Bpe08g00875 875
8 15049717 15055549 - Bpe023544.3 Bpe08g01430 1430
8 15060280 15062544 + Bpe023545.1 Bpe08g01431 1431
11 2722618 2725075 + Bpe003735.1 Bpe11g00361 361
1 4536649 4543946 + CaPI482276_01g004100.1 Cam01g0410 410
1 4547057 4548118 + CaPI482276_01g004110.1 Cam01g0411 411
9 15365306 15369197 - CaPI482276_09g012800.1 Cam09g1280 1280
10 4551672 4554169 - CaPI482276_10g002670.1 Cam10g0267 267
10 4630231 4635501 - CaPI482276_10g002700.1 Cam10g0270 270
6 4178614 4184994 + Carg25166-RA Car06g00691 691
6 4205860 4208181 + Carg25168-RA Car06g00693 693
15 8041875 8043230 - Carg23208-RA Car15g01031 1031
15 8044632 8047379 + Carg23209-RA Car15g01032 1032
16 9296213 9298035 - Carg26182-RA Car16g01082 1082
1 4231942 4242760 + CcPI632755_01g004230.1 Cco01g0423 423
9 15401609 15405618 - CcPI632755_09g013260.1 Cco09g1326 1326
10 3029320 3031808 - CcPI632755_10g002720.1 Cco10g0272 272
10 3113985 3119418 - CcPI632755_10g002740.1 Cco10g0274 274
1 4235287 4246354 + CePI673135_01g004020.1 Cec01g0402 402
9 15665552 15669672 - CePI673135_09g012960.1 Cec09g1296 1296
10 3139801 3142684 - CePI673135_10g002740.1 Cec10g0274 274
10 3268511 3273965 - CePI673135_10g002770.1 Cec10g0277 277
6 24590521 24595081 + Chy6G125680.1 Chy06g02040 2040
6 24626542 24628662 + Chy6G125700.1 Chy06g02042 2042
9 13211974 13213408 - Chy9G168070.1 Chy09g01091 1091
9 13213888 13220610 - Chy9G168080.1 Chy09g01092 1092
9 13226313 13228085 + Chy9G168090.1 Chy09g01093 1093
1 4177185 4183694 + ClG42_01g0041100.10 Clacu01g0411 411
1 4188937 4190377 + ClG42_01g0041200.10 Clacu01g0412 412
10 3322667 3325009 - ClG42_10g0026800.10 Clacu10g0268 268
10 3414082 3419338 - ClG42_10g0027000.10 Clacu10g0270 270
1 4337188 4346749 + ClCG01G003990.2 Cla01g00393 393
1 4351113 4353250 + ClCG01G004000.1 Cla01g00394 394
9 15423308 15427603 - ClCG09G012750.1 Cla09g01215 1215
10 3189905 3192247 - ClCG10G002760.1 Cla10g00261 261
10 3284811 3290626 - ClCG10G002780.2 Cla10g00263 263
6 4015733 4020876 + CmaCh06G007770.1 Cma06g00777 777
6 4039432 4041747 + CmaCh06G007790.1 Cma06g00779 779
15 7169636 7172261 - CmaCh15G011260.1 Cma15g01126 1126
15 7174104 7177058 + CmaCh15G011270.1 Cma15g01127 1127
16 8784996 8787179 - CmaCh16G011440.1 Cma16g01144 1144
6 32776191 32778739 - MELO3C013947.2.1 Cme06g02576 2576
6 32814497 32819890 - MELO3C013948.2.1 Cme06g02577 2577
9 20969602 20971799 - MELO3C005537.2.1 Cme09g01620 1620
9 20974540 20979904 - MELO3C033998.2.1 Cme09g01621 1621
9 20983984 20986156 + MELO3C005538.2.1 Cme09g01622 1622
6 28599796 28602989 + PI0010794.1 Cmetu06g2197 2197
6 4247410 4254056 + CmoCh06G007970.1 Cmo06g00797 797
6 4278969 4281302 + CmoCh06G007990.1 Cmo06g00799 799
15 8235637 8238431 + CmoCh15G011860.1 Cmo15g01186 1186
16 8521675 8523864 - CmoCh16G011950.1 Cmo16g01195 1195
1 4123934 4130440 + CmPI595203_01g003920.1 Cmu01g0392 392
1 4135760 4137200 + CmPI595203_01g003930.1 Cmu01g0393 393
10 3462541 3465032 - CmPI595203_10g011110.1 Cmu10g1111 1111
10 3554838 3560093 - CmPI595203_10g011130.1 Cmu10g1113 1113
6 3427206 3429207 + Conep06aG0069800.1 Cone6ag0676 676
6 3431430 3434313 - Conep06aG0069900.1 Cone6ag0677 677
8 2429145 2430220 - Conep08aG0040900.1 Cone8ag0393 393
9 3244998 3247036 + Conep09aG0069800.1 Cone9ag0681 681
9 3249607 3252305 - Conep09aG0069900.1 Cone9ag0682 682
12 2176245 2180514 + Conep12aG0039300.1 Cone12ag0378 378
12 2181360 2182001 + Conep12aG0039400.1 Cone12ag0379 379
8 5898341 5900689 - Cp4.1LG08g07440.1 Cpe08g00744 744
8 5927944 5930599 - Cp4.1LG08g07470.1 Cpe08g00745 745
13 1801570 1804605 - Cp4.1LG13g02370.1 Cpe13g00229 229
13 1806345 1808841 + Cp4.1LG13g02320.1 Cpe13g00230 230
14 7988889 7991078 - Cp4.1LG14g09530.1 Cpe14g00948 948
9 15582692 15586772 - CrPI670011_09g012400.1 Cre09g1240 1240
9 40163613 40174769 - CrPI670011_09g021180.1 Cre09g2118 2118
10 4433417 4436294 - CrPI670011_10g005190.1 Cre10g0519 519
10 4530090 4535543 - CrPI670011_10g005210.1 Cre10g0521 521
3 2263515 2268337 - CsaV3_3G002800.1 Csa03g00280 280
3 2295833 2301371 - CsaV3_3G002820.1 Csa03g00282 282
5 2760959 2763818 - CsaV3_5G004160.1 Csa05g00416 416
5 2768574 2773783 + CsaV3_5G004170.1 Csa05g00417 417
5 2775585 2776853 + CsaV3_5G004180.1 Csa05g00418 418
6 60381166 60384461 - Hsped.06g11360.1 Hepe06g1136 1136
6 60451280 60463607 - Hsped.06g11380.1 Hepe06g1138 1138
6 67717659 67727516 + Hsped.06g16680.1 Hepe06g1668 1668
11 38864832 38866647 - Lag0032917.1 Lac11g2279 2279
11 38874070 38887089 + Lag0032918.1 Lac11g2280 2280
12 39360833 39364005 - Maker00038126 Lcy12g1824 1824
12 39375916 39382647 + Maker00038120 Lcy12g1825 1825
12 39384019 39386644 + Maker00038247 Lcy12g1826 1826
7 19027646 19030122 - Lsi07G013050.1 Lsi07g01305 1305
7 19104174 19108288 - Lsi07G013080.1 Lsi07g01308 1308
9 4454969 4465298 + Lsi09G004190.1 Lsi09g00419 419
10 15661205 15668001 + MC10g1233 Mch10g1557 1557
10 17846582 17847034 + MC10g1462 Mch10g1820 1820
7 15118360 15120197 - Sed0013118.1 Sed07g1687 1687
1 23091558 23094882 + Tan0007525.1 Tan01g2024 2024
2 5166428 5166605 + Vvi2g522 Vvi2g522 522
2 5167368 5172416 + Vvi2g523 Vvi2g523 523
2 5173995 5175801 - Vvi2g524 Vvi2g524 524
2 5185046 5189256 - Vvi2g525 Vvi2g525 525
2 5202973 5204512 + Vvi2g526 Vvi2g526 526
2 5221959 5224224 - Vvi2g527 Vvi2g527 527
2 5224809 5228573 + Vvi2g528 Vvi2g528 528
2 5231387 5241248 + Vvi2g529 Vvi2g529 529
2 5241334 5245744 + Vvi2g530 Vvi2g530 530
2 5245991 5247909 + Vvi2g531 Vvi2g531 531
       

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