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
Vvi5g299 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g300 . . . . . . . . . . Cma06g01502 . Car06g01293 . . . . . . . . . . . . . . . . . . . . . . Lsi05g01544 . . Cme06g00736 . Blo07g00171 Bda11g00523 . . Bpe13g00667 . . . Cmo06g01500 . . . . . . . . . . . . . . Cla05g00656 Cam05g0717 Cec05g0728 Cco05g0727 Clacu05g0712 Cmu05g0677 Cre05g0751 . Csa03g01470 Chy06g00708 .
Vvi5g301 . . . . . . . . . . . . . . Sed12g0842 Cpe08g00182 . Bhi01g01020 Tan10g1013 Cmetu06g1851 . Hepe05g1444 . . . . . . . . . . . . Cone4ag0148 . . . . . . . . . . . Bma06g01499 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g302 . . . . . . . . . . . . . . . . . Bhi01g01018 Tan10g1011 . . Hepe05g1445 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g303 . . . . . . . . . . . Cma14g01618 Car06g01291 Car14g01441 Sed02g1179 Cpe08g00184 Cpe03g01359 Bhi01g01015 Tan10g1009 Cmetu06g2058 . Hepe05g1446 . Lcy11g1412 . . . . . . . Cone14ag0763 . . . Lsi05g01541 . . Cme06g00735 . Blo07g00172 Bda11g00524 . . Bpe13g00666 . Bma06g01500 . Cmo06g01497 Cmo14g01655 . . . . . . . . . . . . . Cla05g00654 Cam05g0714 Cec05g0726 Cco05g0723 Clacu05g0708 Cmu05g0675 Cre05g0748 . Csa03g01466 Chy06g00706 .
Vvi5g304 . Blo12g00018 . . Bpe04g01134 . . . . Cmo17g00313 . . . . . . . . . . . . . . Cla06g00479 Cam06g0514 Cec06g0515 Cco06g0518 Clacu06g0498 Cmu06g0500 Cre06g1271 . . . . . . Chy11g01508 . . . . . . . . . Sed04g1796 . . . . . Car17g00298 Cpe12g00276 . Bhi12g02060 Tan06g2675 Cmetu11g2440 Lac11g0838 Hepe03g0103 . Lcy12g0730 . . . . . . . Lsi09g01429 . . Cme11g02010
Vvi5g305 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g306 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo02g00588 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g307 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g308 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 5540588 5543119 - Bda005258.1 Bda11g00523 523
11 5550944 5552258 + Bda005259.1 Bda11g00524 524
1 18500757 18502457 - XM_039040984.1 Bhi01g01015 1015
1 18534706 18540141 - XM_039040937.1 Bhi01g01018 1018
1 18586896 18593070 + XM_039040740.1 Bhi01g01020 1020
12 63975896 63980546 - XM_039019937.1 Bhi12g02060 2060
2 10973239 10974826 + BLOR10318 Blo02g00588 588
7 2180663 2188183 - BLOR18103 Blo07g00171 171
7 2188222 2196225 + BLOR18104 Blo07g00172 172
12 1188421 1190708 - BLOR04037 Blo12g00018 18
6 51475565 51480686 - Bma024611.2 Bma06g01499 1499
6 51495996 51497629 + Bma024613.1 Bma06g01500 1500
4 9948271 9950884 + Bpe015815.1 Bpe04g01134 1134
13 13430418 13432049 - Bpe010367.1 Bpe13g00666 666
13 13433802 13438945 + Bpe010368.1 Bpe13g00667 667
5 6253390 6254698 - CaPI482276_05g007140.1 Cam05g0714 714
5 6264038 6269165 + CaPI482276_05g007170.1 Cam05g0717 717
6 7222013 7229270 - CaPI482276_06g005140.1 Cam06g0514 514
6 9250713 9252903 - Carg17342-RA Car06g01291 1291
6 9259173 9265072 + Carg17340-RA Car06g01293 1293
14 12089619 12091600 + Carg20105-RA Car14g01441 1441
17 1856922 1861044 + Carg05504-RA Car17g00298 298
5 5960057 5961366 - CcPI632755_05g007230.1 Cco05g0723 723
5 5970658 5975810 + CcPI632755_05g007270.1 Cco05g0727 727
6 5647226 5654557 - CcPI632755_06g005180.1 Cco06g0518 518
5 5984900 5986208 - CePI673135_05g007260.1 Cec05g0726 726
5 5995607 6000745 + CePI673135_05g007280.1 Cec05g0728 728
6 5754210 5761385 - CePI673135_06g005150.1 Cec06g0515 515
6 4808479 4809804 - Chy6G112340.1 Chy06g00706 706
6 4818579 4823894 + Chy6G112360.1 Chy06g00708 708
11 21734139 21738262 + Chy11G200880.1 Chy11g01508 1508
5 5989685 5990993 - ClG42_05g0070800.10 Clacu05g0708 708
5 6000425 6005548 + ClG42_05g0071200.10 Clacu05g0712 712
6 5763156 5765969 - ClG42_06g0049800.10 Clacu06g0498 498
5 6087624 6088932 - ClCG05G006120.2 Cla05g00654 654
5 6103639 6109641 + ClCG05G006140.2 Cla05g00656 656
6 5809880 5831662 - ClCG06G005110.2 Cla06g00479 479
6 9539084 9544866 + CmaCh06G015020.1 Cma06g01502 1502
14 12139725 12141822 + CmaCh14G016180.1 Cma14g01618 1618
6 4852930 4860707 - MELO3C006666.2.1 Cme06g00735 735
6 4862976 4869491 + MELO3C006668.2.1 Cme06g00736 736
11 27991522 27996232 + MELO3C021329.2.1 Cme11g02010 2010
6 5053879 5060178 + PI0001563.1 Cmetu06g1851 1851
6 5043674 5045586 - PI0026551.1 Cmetu06g2058 2058
11 4205285 4209998 - PI0016155.1 Cmetu11g2440 2440
6 10739978 10742164 - CmoCh06G014970.1 Cmo06g01497 1497
6 10748290 10754345 + CmoCh06G015000.1 Cmo06g01500 1500
14 13078944 13081525 + CmoCh14G016550.1 Cmo14g01655 1655
17 1899106 1902601 + CmoCh17G003130.1 Cmo17g00313 313
5 5832896 5834204 - CmPI595203_05g006750.1 Cmu05g0675 675
5 5843614 5848775 + CmPI595203_05g006770.1 Cmu05g0677 677
6 5565019 5567673 - CmPI595203_06g005000.1 Cmu06g0500 500
4 676309 681139 - Conep04aG0015400.1 Cone4ag0148 148
14 4328683 4330354 + Conep14aG0078000.1 Cone14ag0763 763
3 10999632 11001711 + Cp4.1LG03g11470.1 Cpe03g01359 1359
8 1243240 1249588 - Cp4.1LG08g04920.1 Cpe08g00182 182
8 1256011 1257861 + Cp4.1LG08g05030.1 Cpe08g00184 184
12 1839629 1843485 + Cp4.1LG12g02720.1 Cpe12g00276 276
5 6633020 6634328 - CrPI670011_05g007480.1 Cre05g0748 748
5 6643667 6648805 + CrPI670011_05g007510.1 Cre05g0751 751
6 6625946 6633143 - CrPI670011_06g012710.1 Cre06g1271 1271
3 10919544 10922278 - CsaV3_3G014660.1 Csa03g01466 1466
3 10929567 10936156 + CsaV3_3G014700.1 Csa03g01470 1470
3 1262472 1266089 - Hsped.03g01030.1 Hepe03g0103 103
5 63732126 63739630 - Hsped.05g14440.1 Hepe05g1444 1444
5 63745149 63750039 + Hsped.05g14450.1 Hepe05g1445 1445
5 63752287 63754603 + Hsped.05g14460.1 Hepe05g1446 1446
11 8969660 8974003 + Lag0031476.1 Lac11g0838 838
11 37905710 37907543 + Maker00032057 Lcy11g1412 1412
12 9277784 9282363 + Maker00025120 Lcy12g0730 730
5 23203780 23205835 - Lsi05G015410.1 Lsi05g01541 1541
5 23214540 23220497 + Lsi05G015440.1 Lsi05g01544 1544
9 22294199 22307169 + Lsi09G014290.1 Lsi09g01429 1429
2 48826397 48828734 + Sed0000385.1 Sed02g1179 1179
4 32567339 32571555 - Sed0007886.1 Sed04g1796 1796
12 5181129 5191694 + Sed0007600.1 Sed12g0842 842
6 79233742 79237696 + Tan0008088.2 Tan06g2675 2675
10 8927277 8929011 - Tan0022236.1 Tan10g1009 1009
10 8932194 8938282 - Tan0011657.2 Tan10g1011 1011
10 8944903 8951803 + Tan0021363.1 Tan10g1013 1013
5 2987200 2989765 - Vvi5g299 Vvi5g299 299
5 2991070 2993240 - Vvi5g300 Vvi5g300 300
5 2993280 2998576 - Vvi5g301 Vvi5g301 301
5 3001168 3003605 + Vvi5g302 Vvi5g302 302
5 3005062 3006659 + Vvi5g303 Vvi5g303 303
5 3006671 3013146 - Vvi5g304 Vvi5g304 304
5 3014204 3018323 + Vvi5g305 Vvi5g305 305
5 3023193 3024895 + Vvi5g306 Vvi5g306 306
5 3031097 3046782 - Vvi5g307 Vvi5g307 307
5 3050542 3051394 - Vvi5g308 Vvi5g308 308
       

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