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
Vvi5g619 . . . . . Bpe14g01229 . . . . . Cma14g01782 Car06g01159 Car14g01603 . Cpe08g00311 Cpe03g01491 . . . . . . . . . . . . . . . . . . Lsi05g01676 . . Cme06g00539 Blo02g00607 . . . . . Bma02g00806 . . Cmo06g01352 Cmo14g01818 . . . . . . . . . . . . . Cla05g00482 Cam05g0525 Cec05g0538 Cco05g0538 Clacu05g0524 Cmu05g0496 Cre05g0563 . Csa03g01257 Chy06g00512 .
Vvi5g620 . . . . . Bpe14g01230 . . Cmo08g01076 Cmo17g00174 . . . . . . . . . . . . . . Cla06g00640 Cam06g0684 Cec06g0687 Cco06g0693 Clacu06g0670 Cmu06g0662 Cre06g1430 . . Cone7ag0300 Cone4ag0301 . Csa02g01086 Chy05g00348 . Blo02g00609 . . . . . . . Sed09g0705 . . Cma08g01104 Cma17g00176 Car08g00977 Car17g00158 Cpe12g00152 Cpe17g00179 Bhi12g01656 Tan06g2442 Cmetu05g0483 Lac12g2205 Hepe03g0258 . Lcy13g0344 . . . . . . . Lsi09g01259 . . Cme05g00536
Vvi5g621 . . . . . . . . . . . Cma14g01783 . Car14g01604 . . Cpe03g01492 . . . . . . . . . . . . . . . . . . Lsi05g01677 . . Cme06g00538 Blo02g00610 . . Bda13g00088 . . . . . . Cmo14g01819 . . . . . . . . . . . . . Cla05g00481 Cam05g0523 Cec05g0536 Cco05g0537 Clacu05g0523 Cmu05g0495 Cre05g0561 . Csa03g01256 Chy06g00510 .
Vvi5g622 . . . . . Bpe14g01231 . . . . . . Car06g01157 . . Cpe08g00313 . . . . . . . . . . . . . . . . Cone15ag0143 . . Lsi05g01678 . . Cme06g00537 Blo02g00611 . . Bda13g00085 . . Bma02g00804 . . Cmo06g01351 . . . . . . . . . . . . . . Cla05g00480 Cam05g0522 Cec05g0535 Cco05g0536 Clacu05g0522 Cmu05g0494 Cre05g0560 . Csa03g01255 Chy06g00509 .
Vvi5g623 . Blo12g00358 Bda03g00849 . Bpe04g00803 . Bma04g00749 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g624 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g625 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g626 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g627 Blo01g00097 . . Bda08g00268 . . . Bma05g01076 . . . . . . . . . . . . . . . . . . . . . . . . Cone15ag0144 . . . . . . . . . . Bpe05g00866 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g628 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 7358840 7360621 + Bda016839.1 Bda03g00849 849
8 2752298 2759911 + Bda024697.1 Bda08g00268 268
13 1097262 1182817 + Bda032835 Bda13g00085 85
13 1183163 1184191 - Bda000940.1 Bda13g00088 88
12 53416275 53419411 + XM_039020012.1 Bhi12g01656 1656
1 1391699 1398396 - BLOR00097 Blo01g00097 97
2 12000403 12002476 - BLOR10337 Blo02g00607 607
2 12162985 12165164 - BLOR10339 Blo02g00609 609
2 12205906 12206923 + BLOR10340 Blo02g00610 610
2 12207322 12210649 - BLOR10341 Blo02g00611 611
12 19715371 19721409 - BLOR04377 Blo12g00358 358
2 43555578 43556629 + Bma015540.1 Bma02g00804 804
2 43773568 43782452 + Bma030904 Bma02g00806 806
4 8058635 8060414 + Bma019262.1 Bma04g00749 749
5 49496952 49500787 - Bma022243.1 Bma05g01076 1076
4 5279213 5280985 + Bpe015463.1 Bpe04g00803 803
5 21860415 21865585 - Bpe018279.1 Bpe05g00866 866
14 9210481 9217543 - Bpe014590.1 Bpe14g01229 1229
14 9231119 9233291 - Bpe014591.1 Bpe14g01230 1230
14 9240923 9244039 - Bpe014592.2 Bpe14g01231 1231
5 4616932 4620920 + CaPI482276_05g005220.1 Cam05g0522 522
5 4621402 4622250 - CaPI482276_05g005230.1 Cam05g0523 523
5 4631258 4636110 + CaPI482276_05g005250.1 Cam05g0525 525
6 9185186 9187502 - CaPI482276_06g006840.1 Cam06g0684 684
6 8548503 8551501 + Carg06200-RA Car06g01157 1157
6 8556017 8559753 + Carg06198-RA Car06g01159 1159
8 6488200 6491312 + Carg10945-RA Car08g00977 977
14 12973194 12976973 - Carg16584-RA Car14g01603 1603
14 12979943 12981319 + Carg16583-RA Car14g01604 1604
17 972483 976518 + Carg10073-RA Car17g00158 158
5 4271182 4275149 + CcPI632755_05g005360.1 Cco05g0536 536
5 4275632 4276479 - CcPI632755_05g005370.1 Cco05g0537 537
5 4285303 4289021 + CcPI632755_05g005380.1 Cco05g0538 538
6 7761812 7768624 - CcPI632755_06g006930.1 Cco06g0693 693
5 4271851 4275841 + CePI673135_05g005350.1 Cec05g0535 535
5 4276332 4277180 - CePI673135_05g005360.1 Cec05g0536 536
5 4286103 4290363 + CePI673135_05g005380.1 Cec05g0538 538
6 7778516 7780963 - CePI673135_06g006870.1 Cec06g0687 687
5 3595665 3598565 + Chy5G093940.1 Chy05g00348 348
6 3434680 3438689 + Chy6G110370.1 Chy06g00509 509
6 3439240 3440077 - Chy6G110380.1 Chy06g00510 510
6 3448630 3451893 + Chy6G110400.1 Chy06g00512 512
5 4324742 4328714 + ClG42_05g0052200.10 Clacu05g0522 522
5 4329201 4330044 - ClG42_05g0052300.10 Clacu05g0523 523
5 4338970 4342679 + ClG42_05g0052400.10 Clacu05g0524 524
6 7738138 7740452 - ClG42_06g0067000.10 Clacu06g0670 670
5 4340122 4344094 + ClCG05G004570.2 Cla05g00480 480
5 4344316 4345691 - ClCG05G004580.1 Cla05g00481 481
5 4354773 4359101 + ClCG05G004590.2 Cla05g00482 482
6 7896577 7903487 - ClCG06G006750.2 Cla06g00640 640
8 6849356 6858374 + CmaCh08G011040.1 Cma08g01104 1104
14 12897482 12902030 - CmaCh14G017820.1 Cma14g01782 1782
14 12904601 12905903 + CmaCh14G017830.1 Cma14g01783 1783
17 916067 918953 + CmaCh17G001760.1 Cma17g00176 176
5 5182265 5185556 - MELO3C026782.2.1 Cme05g00536 536
6 3364714 3369373 + MELO3C006466.2.1 Cme06g00537 537
6 3369725 3370404 - MELO3C006467.2.1 Cme06g00538 538
6 3378251 3382471 + MELO3C006468.2.1 Cme06g00539 539
5 18678769 18681673 + PI0000580.1 Cmetu05g0483 483
6 10005728 10008524 + CmoCh06G013510.1 Cmo06g01351 1351
6 10012564 10024238 + CmoCh06G013520.1 Cmo06g01352 1352
8 6931946 6936523 + CmoCh08G010760.1 Cmo08g01076 1076
14 13880047 13884581 - CmoCh14G018180.1 Cmo14g01818 1818
14 13887842 13888863 + CmoCh14G018190.1 Cmo14g01819 1819
17 1018721 1030362 + CmoCh17G001740.1 Cmo17g00174 174
5 4168241 4172214 + CmPI595203_05g004940.1 Cmu05g0494 494
5 4172701 4173543 - CmPI595203_05g004950.1 Cmu05g0495 495
5 4182465 4187338 + CmPI595203_05g004960.1 Cmu05g0496 496
6 7543839 7546153 - CmPI595203_06g006620.1 Cmu06g0662 662
4 1374783 1377149 - Conep04aG0031300.1 Cone4ag0301 301
7 1296615 1299192 - Conep07aG0030800.1 Cone7ag0300 300
15 674818 677526 - Conep15aG0014600.1 Cone15ag0143 143
15 678126 682021 + Conep15aG0014700.1 Cone15ag0144 144
3 11780187 11784329 - Cp4.1LG03g10220.1 Cpe03g01491 1491
3 11786880 11788687 + Cp4.1LG03g10050.1 Cpe03g01492 1492
8 1980914 1986763 - Cp4.1LG08g03730.1 Cpe08g00311 311
8 1989329 1992720 - Cp4.1LG08g03450.1 Cpe08g00313 313
12 975594 979657 + Cp4.1LG12g01430.1 Cpe12g00152 152
17 1156434 1159421 - Cp4.1LG17g01870.1 Cpe17g00179 179
5 4961592 4965586 + CrPI670011_05g005600.1 Cre05g0560 560
5 4966070 4966918 - CrPI670011_05g005610.1 Cre05g0561 561
5 4975673 4981049 + CrPI670011_05g005630.1 Cre05g0563 563
6 8642237 8644553 - CrPI670011_06g014300.1 Cre06g1430 1430
2 10581382 10586243 + CsaV3_2G013020.1 Csa02g01086 1086
3 9598059 9602067 + CsaV3_3G012550.1 Csa03g01255 1255
3 9602326 9603496 - CsaV3_3G012560.1 Csa03g01256 1256
3 9611320 9616020 + CsaV3_3G012570.1 Csa03g01257 1257
3 3379935 3383748 - Hsped.03g02580.1 Hepe03g0258 258
12 39178197 39180106 + Lag0016577.1 Lac12g2205 2205
13 3840119 3845070 - Maker00023857 Lcy13g0344 344
5 24362731 24367148 - Lsi05G016760.1 Lsi05g01676 1676
5 24376848 24378250 + Lsi05G016770.1 Lsi05g01677 1677
5 24377524 24381923 - Lsi05G016780.1 Lsi05g01678 1678
9 20253282 20256181 + Lsi09G012590.1 Lsi09g01259 1259
9 10694299 10702975 + Sed0009235.1 Sed09g0705 705
6 76892667 76896036 + Tan0001129.1 Tan06g2442 2442
5 6714619 6724790 - Vvi5g619 Vvi5g619 619
5 6744586 6749194 - Vvi5g620 Vvi5g620 620
5 6754913 6756137 + Vvi5g621 Vvi5g621 621
5 6756406 6766369 - Vvi5g622 Vvi5g622 622
5 6777135 6780522 + Vvi5g623 Vvi5g623 623
5 6782084 6784040 - Vvi5g624 Vvi5g624 624
5 6784988 6797069 - Vvi5g625 Vvi5g625 625
5 6800300 6804756 + Vvi5g626 Vvi5g626 626
5 6821635 6835674 - Vvi5g627 Vvi5g627 627
5 6846823 6849103 - Vvi5g628 Vvi5g628 628
       

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