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
Vvi5g759 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g760 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g761 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00687 Cam06g0738 Cec06g0745 Cco06g0756 Clacu06g0729 Cmu06g0713 Cre06g1488 Cone14ag0171 Cone15ag0178 . . . Csa02g01038 Chy05g00302 . . . . . Bpe05g01103 . . . . . . . . . . . . Bhi12g01577 . . . . . . . . . . . . . Lsi09g01206 . . Cme05g00600
Vvi5g762 Blo01g00299 Blo12g00140 Bda03g01091 . Bpe04g00987 . Bma04g01016 Bma05g01250 Cmo08g01037 Cmo17g00147 . . . . . . . . . . . . . . Cla06g00688 Cam06g0739 Cec06g0746 Cco06g0757 Clacu06g0730 Cmu06g0714 Cre06g1489 . . Cone7ag0342 Cone4ag0355 . Csa02g01037 Chy05g00300 . . . . . Bpe05g01104 . . . Sed09g0643 . . Cma08g01068 Cma17g00148 Car08g00943 Car17g00130 Cpe12g00125 Cpe17g00209 Bhi12g01574 Tan06g2380 Cmetu05g0543 Lac12g2130 Hepe03g0304 . Lcy13g0400 . . . . . . . Lsi09g01204 . . Cme05g00604
Vvi5g763 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g764 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g765 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g766 . . . . . . . . Cmo08g01036 . . . . . . . . . . . . . . . Cla06g00689 Cam06g0740 Cec06g0747 Cco06g0758 Clacu06g0731 Cmu06g0715 Cre06g1490 . . . . . . Chy05g00299 . . . . . . . . . Sed09g0641 . . Cma08g01067 . Car08g00942 . . Cpe17g00210 Bhi12g01573 Tan06g2379 Cmetu05g0044 Lac12g2129 Hepe03g0305 . Lcy13g0401 . . . . . . . Lsi09g01203 . . Cme05g00605
Vvi5g767 . . . . . . . . . . . Cma14g01836 . Car14g01644 . . Cpe03g01537 Bhi01g00111 . . . . . . . . . . . . . . . . . Lsi05g01761 . . . . . Bda11g00645 . . Bpe13g00541 . . . . . . . . . . . . . . . . . . Cla05g00418 Cam05g0456 Cec05g0463 Cco05g0465 Clacu05g0453 Cmu05g0431 Cre05g0492 . . Chy06g00442 .
Vvi5g768 . . . . . Bpe14g01274 . . . . . Cma14g01837 . Car14g01645 . . . Bhi01g00686 Tan10g0647 . . Hepe05g1684 . Lcy11g1697 . . . . . . . . . Cone7ag0343 . Lsi05g01762 . . Cme06g00459 Blo02g00768 . . Bda13g00044 . . Bma02g00755 . . . Cmo14g01878 . . . . . . . . . . . . . Cla05g00417 Cam05g0455 Cec05g0462 Cco05g0464 Clacu05g0452 Cmu05g0430 Cre05g0491 . Csa03g01179 Chy06g00441 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 10971785 10974313 + Bda017135.1 Bda03g01091 1091
11 6419375 6419810 - Bda005391.1 Bda11g00645 645
13 654161 656445 - Bda000886.1 Bda13g00044 44
1 2310727 2312691 - XM_039050636.1 Bhi01g00111 111
1 12804203 12807880 - XM_039027923.1 Bhi01g00686 686
12 50984439 50987775 - XM_039018616.1 Bhi12g01573 1573
12 50989691 50992218 + XM_039018384.1 Bhi12g01574 1574
12 51059923 51068959 + XM_039020132.1 Bhi12g01577 1577
1 3709694 3714819 + BLOR00299 Blo01g00299 299
2 25797009 25803270 + BLOR10498 Blo02g00768 768
12 9830426 9832971 - BLOR04159 Blo12g00140 140
2 38870314 38872618 - Bma015460.2 Bma02g00755 755
4 17863476 17865985 + Bma019632.1 Bma04g01016 1016
5 51839078 51841625 + Bma022441.1 Bma05g01250 1250
4 6848812 6851309 - Bpe015654.1 Bpe04g00987 987
5 23425959 23433170 + Bpe018519.1 Bpe05g01103 1103
5 23434403 23436995 + Bpe018520.1 Bpe05g01104 1104
13 12713349 12713787 + Bpe010245.1 Bpe13g00541 541
14 9632514 9634786 + Bpe014631.4 Bpe14g01274 1274
5 4074990 4078668 - CaPI482276_05g004550.1 Cam05g0455 455
5 4083610 4084626 + CaPI482276_05g004560.1 Cam05g0456 456
6 10013230 10031440 + CaPI482276_06g007380.1 Cam06g0738 738
6 10033734 10035864 - CaPI482276_06g007390.1 Cam06g0739 739
6 10038702 10039829 + CaPI482276_06g007400.1 Cam06g0740 740
8 6294245 6295567 - Carg10981-RA Car08g00942 942
8 6295908 6300476 + Carg10980-RA Car08g00943 943
14 13171900 13173238 - Carg16543-RA Car14g01644 1644
14 13174183 13177484 + Carg16542-RA Car14g01645 1645
17 782085 783778 + Carg10102-RA Car17g00130 130
5 3734020 3736733 - CcPI632755_05g004640.1 Cco05g0464 464
5 3741696 3742693 + CcPI632755_05g004650.1 Cco05g0465 465
6 8701012 8721908 + CcPI632755_06g007560.1 Cco06g0756 756
6 8724231 8726384 - CcPI632755_06g007570.1 Cco06g0757 757
6 8726426 8730439 + CcPI632755_06g007580.1 Cco06g0758 758
5 3726495 3729137 - CePI673135_05g004620.1 Cec05g0462 462
5 3734002 3735018 + CePI673135_05g004630.1 Cec05g0463 463
6 8738396 8757271 + CePI673135_06g007450.1 Cec06g0745 745
6 8759579 8761697 - CePI673135_06g007460.1 Cec06g0746 746
6 8761975 8765714 + CePI673135_06g007470.1 Cec06g0747 747
5 2893141 2894191 - Chy5G093450.1 Chy05g00299 299
5 2896595 2898698 + Chy5G093460.1 Chy05g00300 300
5 2918194 2927690 - Chy5G093480.1 Chy05g00302 302
6 2966263 2968981 - Chy6G109690.1 Chy06g00441 441
6 2972239 2973222 + Chy6G109700.1 Chy06g00442 442
5 3784169 3786881 - ClG42_05g0045200.10 Clacu05g0452 452
5 3791839 3792855 + ClG42_05g0045300.10 Clacu05g0453 453
6 8573734 8599353 + ClG42_06g0072900.10 Clacu06g0729 729
6 8601626 8603683 - ClG42_06g0073000.10 Clacu06g0730 730
6 8606579 8607705 + ClG42_06g0073100.10 Clacu06g0731 731
5 3753717 3758092 - ClCG05G004070.1 Cla05g00417 417
5 3763551 3765149 + ClCG05G004080.1 Cla05g00418 418
6 8794060 8813335 + ClCG06G007180.1 Cla06g00687 687
6 8813931 8817471 - ClCG06G007190.1 Cla06g00688 688
6 8822766 8823932 + ClCG06G007200.2 Cla06g00689 689
8 6655497 6656623 - CmaCh08G010670.1 Cma08g01067 1067
8 6657577 6659884 + CmaCh08G010680.1 Cma08g01068 1068
14 13106273 13107973 - CmaCh14G018360.1 Cma14g01836 1836
14 13108405 13111953 + CmaCh14G018370.1 Cma14g01837 1837
17 726965 730456 + CmaCh17G001480.1 Cma17g00148 148
5 6195148 6198979 - MELO3C023030.2.1 Cme05g00600 600
5 6246317 6249802 - MELO3C023033.2.1 Cme05g00604 604
5 6251396 6253016 + MELO3C023034.2.1 Cme05g00605 605
6 2910026 2913745 - MELO3C006386.2.1 Cme06g00459 459
5 17843691 17845531 - PI0010177.1 Cmetu05g0044 44
5 17847284 17850319 + PI0003972.1 Cmetu05g0543 543
8 6724328 6726657 - CmoCh08G010360.1 Cmo08g01036 1036
8 6727187 6729385 + CmoCh08G010370.1 Cmo08g01037 1037
14 14088504 14092069 + CmoCh14G018780.1 Cmo14g01878 1878
17 820878 824272 + CmoCh17G001470.1 Cmo17g00147 147
5 3619312 3622979 - CmPI595203_05g004300.1 Cmu05g0430 430
5 3627933 3628949 + CmPI595203_05g004310.1 Cmu05g0431 431
6 8399342 8417723 + CmPI595203_06g007130.1 Cmu06g0713 713
6 8419996 8422053 - CmPI595203_06g007140.1 Cmu06g0714 714
6 8424948 8426074 + CmPI595203_06g007150.1 Cmu06g0715 715
4 1623389 1626390 - Conep04aG0036700.1 Cone4ag0355 355
7 1492843 1495818 - Conep07aG0035000.1 Cone7ag0342 342
7 1499025 1504157 + Conep07aG0035100.1 Cone7ag0343 343
14 806370 807881 + Conep14aG0017500.1 Cone14ag0171 171
15 855199 860687 + Conep15aG0018200.1 Cone15ag0178 178
3 11984244 11986016 - Cp4.1LG03g09710.1 Cpe03g01537 1537
12 780999 784576 + Cp4.1LG12g01260.1 Cpe12g00125 125
17 1361155 1364443 - Cp4.1LG17g02210.1 Cpe17g00209 209
17 1365472 1366863 + Cp4.1LG17g02090.1 Cpe17g00210 210
5 4411184 4414911 - CrPI670011_05g004910.1 Cre05g0491 491
5 4420375 4421390 + CrPI670011_05g004920.1 Cre05g0492 492
6 9540213 9560596 + CrPI670011_06g014880.1 Cre06g1488 1488
6 9562903 9565034 - CrPI670011_06g014890.1 Cre06g1489 1489
6 9567986 9569111 + CrPI670011_06g014900.1 Cre06g1490 1490
2 10022583 10026604 + CsaV3_2G012530.1 Csa02g01037 1037
2 10026792 10038249 - CsaV3_2G012540.1 Csa02g01038 1038
3 9159593 9163408 - CsaV3_3G011790.1 Csa03g01179 1179
3 4214349 4217893 - Hsped.03g03040.1 Hepe03g0304 304
3 4222707 4224009 + Hsped.03g03050.1 Hepe03g0305 305
5 66768977 66772342 + Hsped.05g16840.1 Hepe05g1684 1684
12 38421403 38422534 - Lag0016501.1 Lac12g2129 2129
12 38427516 38428660 + Lag0016502.1 Lac12g2130 2130
11 40861501 40864785 + Maker00031371 Lcy11g1697 1697
13 4676499 4680336 - Maker00023981 Lcy13g0400 400
13 4683948 4685705 + Maker00024038 Lcy13g0401 401
5 24979386 24981296 - Lsi05G017610.1 Lsi05g01761 1761
5 24985350 24989035 + Lsi05G017620.1 Lsi05g01762 1762
9 19255655 19256945 - Lsi09G012030.1 Lsi09g01203 1203
9 19259669 19263122 + Lsi09G012040.1 Lsi09g01204 1204
9 19288985 19298351 - Lsi09G012060.1 Lsi09g01206 1206
9 8080614 8082815 - Sed0022466.1 Sed09g0641 641
9 8095589 8101207 + Sed0012588.2 Sed09g0643 643
6 75825526 75826815 - Tan0018243.1 Tan06g2379 2379
6 75830180 75833585 + Tan0005456.1 Tan06g2380 2380
10 5214118 5218120 - Tan0004556.2 Tan10g0647 647
5 9051146 9055240 + Vvi5g759 Vvi5g759 759
5 9075797 9076764 + Vvi5g760 Vvi5g760 760
5 9095909 9110102 + Vvi5g761 Vvi5g761 761
5 9110995 9114911 - Vvi5g762 Vvi5g762 762
5 9136220 9137303 + Vvi5g763 Vvi5g763 763
5 9142828 9143017 + Vvi5g764 Vvi5g764 764
5 9144320 9145180 - Vvi5g765 Vvi5g765 765
5 9167985 9170443 + Vvi5g766 Vvi5g766 766
5 9170577 9176581 - Vvi5g767 Vvi5g767 767
5 9178945 9184983 + Vvi5g768 Vvi5g768 768
       

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