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
Vvi17g36 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g37 . . . . . Bpe13g00187 . . Cmo13g00858 Cmo18g00237 Cma10g00029 . Car10g00020 . . Cpe20g00290 . Bhi02g00636 . . . . . . Cla06g01775 Cam06g1968 Cec06g2019 Cco06g2026 Clacu06g1926 Cmu06g1866 Cre06g2679 . . . . Lsi02g00525 Csa01g00988 . Cme12g01565 . . Bda11g01582 . . . Bma03g01225 . Sed08g2410 Cmo10g00026 . Cma13g00828 Cma18g00297 Car13g00670 Car18g00247 Cpe09g00944 Cpe18g00931 Bhi08g01535 Tan05g3008 Cmetu02g1873 Lac10g0610 Hepe07g2084 . . Cla03g00376 Cam03g0396 Cec03g0382 Cco03g0397 Clacu03g0395 Cmu03g1000 Cre03g0692 Lsi06g01672 Csa01g00019 Chy02g02693 .
Vvi17g38 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g39 . Blo16g00287 . . . Bpe13g00188 Bma06g00280 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01583 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g40 . . Bda06g00712 Bda15g00693 Bpe12g00463 . . . . . Cma10g00030 Cma11g00009 Car10g00021 Car11g00009 . . Cpe04g01637 . . . . . . . Cla06g01774 Cam06g1966 Cec06g2017 Cco06g2024 Clacu06g1924 Cmu06g1865 Cre06g2678 . . Cone13ag0251 Cone19ag0234 . . . . . . . . Bpe07g00905 . . Bma08g00276 . Cmo10g00027 Cmo11g00008 . . . . . Cpe18g00930 . . . . . . . . . . . . . . . . Chy02g02692 Cme02g02100
Vvi17g41 . . Bda06g00713 Bda15g00692 . . . Bma12g01093 . . Cma10g00031 Cma11g00010 Car10g00023 Car11g00010 . . Cpe04g01636 . . . . . . . Cla06g01772 Cam06g1965 Cec06g2016 Cco06g2023 Clacu06g1923 Cmu06g1864 Cre06g2677 . . . Cone19ag0233 . . . . . Blo15g00193 . . Bpe07g00904 . . Bma08g00275 . Cmo10g00028 Cmo11g00009 . . . . . Cpe18g00929 . . . . . . . . . . . . . . Lsi06g01670 Csa01g00020 . Cme02g02099
Vvi17g42 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g43 . . . Bda15g00690 Bpe12g00464 . . . . Cmo18g00236 . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0250 Cone19ag0232 . . . . . Blo15g00195 . . . . . Bma08g00274 . . . . Cma18g00298 . Car18g00246 Cpe09g00945 . . . . . . . . . . . . . . . . . . .
Vvi17g44 . . Bda06g00714 Bda15g00689 . . . Bma12g01092 . . Cma10g00033 . . . Sed09g1602 . . Bhi02g00642 Tan09g2421 Cmetu02g0260 . . . . . . . . . . . . . . Cone19ag0231 . . . . . . . . Bpe07g00903 . . . . Cmo10g00029 . . . . . . Cpe18g00927 . . . . . . . . . . . . . . Lsi06g01669 Csa01g00022 Chy02g02691 Cme02g02098
Vvi17g45 . . . Bda15g00688 Bpe12g00465 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma08g00273 . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 9776885 9777802 + Bda024011.1 Bda06g00712 712
6 9778467 9782250 - Bda024012.1 Bda06g00713 713
6 9784245 9785241 - Bda024013.1 Bda06g00714 714
11 49101555 49102822 + Bda008454.1 Bda11g01582 1582
11 49129978 49134267 + Bda008455.1 Bda11g01583 1583
15 10309233 10312243 + Bda012540.1 Bda15g00688 688
15 10317107 10318135 + Bda012541.1 Bda15g00689 689
15 10337815 10339467 - Bda012543.1 Bda15g00690 690
15 10351100 10351558 + Bda012546.1 Bda15g00692 692
15 10355634 10356569 - Bda012547.1 Bda15g00693 693
2 12346843 12348677 - XM_039023096.1 Bhi02g00636 636
2 12372403 12373463 - XM_039024160.1 Bhi02g00642 642
8 44068362 44070784 - XM_039037916.1 Bhi08g01535 1535
15 1986576 1990189 - BLOR06587 Blo15g00193 193
15 2016138 2022102 + BLOR06589 Blo15g00195 195
16 6837215 6841787 - BLOR07535 Blo16g00287 287
3 19434382 19436616 + Bma017664.1 Bma03g01225 1225
6 3911829 3912728 - Bma022915.1 Bma06g00280 280
8 3705290 3709396 + Bma027293.1 Bma08g00273 273
8 3755903 3757555 - Bma027295.1 Bma08g00274 274
8 3764609 3765364 + Bma027296.1 Bma08g00275 275
8 3772362 3773291 - Bma027297.1 Bma08g00276 276
12 43210990 43211976 + Bma008437.1 Bma12g01092 1092
12 43214675 43218279 + Bma008438.1 Bma12g01093 1093
7 15033951 15034876 + Bpe021744.1 Bpe07g00903 903
7 15041835 15045383 + Bpe021745.1 Bpe07g00904 904
7 15045964 15046866 - Bpe021746.1 Bpe07g00905 905
12 10364750 10365688 + Bpe005723.1 Bpe12g00463 463
12 10371471 10373123 + Bpe005724.2 Bpe12g00464 464
12 10386934 10389872 - Bpe005725.1 Bpe12g00465 465
13 9819148 9820404 + Bpe006307.1 Bpe13g00187 187
13 9832028 9836267 + Bpe006308.1 Bpe13g00188 188
3 5088370 5090213 - CaPI482276_03g003960.1 Cam03g0396 396
6 30488684 30492580 + CaPI482276_06g019650.1 Cam06g1965 1965
6 30493915 30494823 - CaPI482276_06g019660.1 Cam06g1966 1966
6 30501636 30502945 - CaPI482276_06g019680.1 Cam06g1968 1968
10 102908 104318 + Carg10252-RA Car10g00020 20
10 106723 107646 + Carg10253-RA Car10g00021 21
10 108942 113601 - Carg10255-RA Car10g00023 23
11 45156 46094 + Carg24559-RA Car11g00009 9
11 47170 50699 - Carg24558-RA Car11g00010 10
13 8171756 8172753 - Carg07620-RA Car13g00670 670
18 1424209 1425864 - Carg06813-RA Car18g00246 246
18 1434555 1437115 - Carg06814-RA Car18g00247 247
3 4315485 4317266 - CcPI632755_03g003970.1 Cco03g0397 397
6 30238013 30241904 + CcPI632755_06g020230.1 Cco06g2023 2023
6 30243210 30244118 - CcPI632755_06g020240.1 Cco06g2024 2024
6 30250933 30252197 - CcPI632755_06g020260.1 Cco06g2026 2026
3 4272660 4274391 - CePI673135_03g003820.1 Cec03g0382 382
6 33316063 33319973 + CePI673135_06g020160.1 Cec06g2016 2016
6 33321306 33322214 - CePI673135_06g020170.1 Cec06g2017 2017
6 33329021 33330306 - CePI673135_06g020190.1 Cec06g2019 2019
2 29804352 29813409 + Chy2G049580.1 Chy02g02691 2691
2 29814957 29815871 - Chy2G049590.1 Chy02g02692 2692
2 29819597 29821135 - Chy2G049600.1 Chy02g02693 2693
3 4404117 4405944 - ClG42_03g0039500.10 Clacu03g0395 395
6 29530194 29534090 + ClG42_06g0192300.10 Clacu06g1923 1923
6 29535427 29536335 - ClG42_06g0192400.10 Clacu06g1924 1924
6 29543167 29544444 - ClG42_06g0192600.10 Clacu06g1926 1926
3 4364060 4365887 - ClCG03G003990.2 Cla03g00376 376
6 31186620 31195269 + ClCG06G018210.2 Cla06g01772 1772
6 31195922 31197281 - ClCG06G018240.2 Cla06g01774 1774
6 31204841 31206645 - ClCG06G018250.2 Cla06g01775 1775
10 106370 107979 + CmaCh10G000290.1 Cma10g00029 29
10 110368 111306 + CmaCh10G000300.1 Cma10g00030 30
10 112268 116628 - CmaCh10G000310.1 Cma10g00031 31
10 118583 119633 - CmaCh10G000330.1 Cma10g00033 33
11 49188 50336 + CmaCh11G000090.1 Cma11g00009 9
11 51212 55515 - CmaCh11G000100.1 Cma11g00010 10
13 6927496 6929598 - CmaCh13G008280.1 Cma13g00828 828
18 1577245 1579874 + CmaCh18G002970.1 Cma18g00297 297
18 1588793 1590448 + CmaCh18G002980.1 Cma18g00298 298
2 26796694 26797827 + MELO3C026176.2.1 Cme02g02098 2098
2 26799498 26806046 + MELO3C026175.2.1 Cme02g02099 2099
2 26806337 26808334 - MELO3C026174.2.1 Cme02g02100 2100
12 23037307 23039499 + MELO3C002383.2.1 Cme12g01565 1565
2 25123769 25124317 + PI0027562.1 Cmetu02g0260 260
2 25138362 25140350 - PI0022142.1 Cmetu02g1873 1873
10 144859 146093 + CmoCh10G000260.1 Cmo10g00026 26
10 148811 149749 + CmoCh10G000270.1 Cmo10g00027 27
10 150791 155680 - CmoCh10G000280.1 Cmo10g00028 28
10 156780 157749 - CmoCh10G000290.1 Cmo10g00029 29
11 43144 44052 + CmoCh11G000080.1 Cmo11g00008 8
11 44721 50407 - CmoCh11G000090.1 Cmo11g00009 9
13 7861441 7864216 - CmoCh13G008580.1 Cmo13g00858 858
18 1547437 1549581 - CmoCh18G002360.1 Cmo18g00236 236
18 1559926 1562454 - CmoCh18G002370.1 Cmo18g00237 237
3 4618220 4620048 - CmPI595203_03g010000.1 Cmu03g1000 1000
6 29440729 29444625 + CmPI595203_06g018640.1 Cmu06g1864 1864
6 29445962 29446870 - CmPI595203_06g018650.1 Cmu06g1865 1865
6 29453668 29454938 - CmPI595203_06g018660.1 Cmu06g1866 1866
13 1706730 1708762 - Conep13aG0026100.1 Cone13ag0250 250
13 1712360 1713818 - Conep13aG0026200.1 Cone13ag0251 251
19 1500505 1501291 + Conep19aG0023800.1 Cone19ag0231 231
19 1502290 1504322 - Conep19aG0023900.1 Cone19ag0232 232
19 1512498 1516957 + Conep19aG0024000.1 Cone19ag0233 233
19 1517776 1519223 - Conep19aG0024100.1 Cone19ag0234 234
4 12646892 12654388 + Cp4.1LG04g16230.1 Cpe04g01636 1636
4 12652828 12653766 - Cp4.1LG04g16330.1 Cpe04g01637 1637
9 8454037 8457750 + Cp4.1LG09g09490.1 Cpe09g00944 944
9 8468524 8470179 + Cp4.1LG09g09440.1 Cpe09g00945 945
18 8214769 8215923 + Cp4.1LG18g09260.1 Cpe18g00927 927
18 8221041 8230152 + Cp4.1LG18g09270.1 Cpe18g00929 929
18 8227177 8228115 - Cp4.1LG18g09370.1 Cpe18g00930 930
18 8230223 8231813 - Cp4.1LG18g09440.1 Cpe18g00931 931
20 1619873 1621903 + Cp4.1LG20g02900.1 Cpe20g00290 290
3 5832425 5834242 - CrPI670011_03g006920.1 Cre03g0692 692
6 34273786 34277681 + CrPI670011_06g026770.1 Cre06g2677 2677
6 34279018 34279926 - CrPI670011_06g026780.1 Cre06g2678 2678
6 34286817 34287688 - CrPI670011_06g026790.1 Cre06g2679 2679
1 132006 133915 + CsaV3_1G000190.1 Csa01g00019 19
1 137679 146865 - CsaV3_1G000200.1 Csa01g00020 20
1 148053 149750 - CsaV3_1G000220.1 Csa01g00022 22
1 6153304 6155828 - CsaV3_1G009880.1 Csa01g00988 988
7 65134691 65136837 + Hsped.07g20840.1 Hepe07g2084 2084
10 4683919 4685543 - Lag0024655.1 Lac10g0610 610
2 4541496 4544088 - Lsi02G005250.1 Lsi02g00525 525
6 26942183 26942752 + Lsi06G016690.1 Lsi06g01669 1669
6 26946250 26951580 + Lsi06G016700.1 Lsi06g01670 1670
6 26959007 26961121 - Lsi06G016720.1 Lsi06g01672 1672
8 37207905 37209739 + Sed0013200.1 Sed08g2410 2410
9 39503307 39506499 - Sed0001710.1 Sed09g1602 1602
5 81996318 81998481 - Tan0012321.2 Tan05g3008 3008
9 73810267 73811289 + Tan0014405.1 Tan09g2421 2421
17 294341 299620 - Vvi17g36 Vvi17g36 36
17 299664 302297 + Vvi17g37 Vvi17g37 37
17 309493 318858 - Vvi17g38 Vvi17g38 38
17 321602 329954 + Vvi17g39 Vvi17g39 39
17 333606 334551 + Vvi17g40 Vvi17g40 40
17 337603 343588 - Vvi17g41 Vvi17g41 41
17 344952 353431 - Vvi17g42 Vvi17g42 42
17 359708 361734 + Vvi17g43 Vvi17g43 43
17 364770 366466 - Vvi17g44 Vvi17g44 44
17 369676 378037 - Vvi17g45 Vvi17g45 45
       

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