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
Vvi19g634 . Blo03g01476 . Bda09g00421 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma07g01256 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g635 Blo03g00516 Blo03g01477 Bda07g00397 Bda09g00422 . Bpe08g01100 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe11g00576 . Bma07g01254 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g636 . . Bda07g00398 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0019 Cone9ag0018 . . . Csa07g01069 . . . . . . Bpe11g00577 . . Bma14g00695 . . . . . . . . . . . . . . . . . . . . . . . . . Chy01g01084 .
Vvi19g637 . Blo03g01478 . . . Bpe08g01099 . . . . . Cma09g00997 . . Sed04g3670 Cpe06g00806 . Bhi09g01744 Tan01g3175 Cmetu01g2235 . . Mch11g1253 . . . . . . . . Cone6ag0018 Cone9ag0017 . . Lsi02g01846 Csa07g00944 . . . . . . Bpe11g00578 . Bma07g01253 Bma14g00176 . . . . . . . . . . . . . . . . Cla09g02059 Cam09g2148 Cec09g2213 . . . . . . Chy01g01169 Cme01g00937
Vvi19g638 . . Bda07g00399 . . . . . . . Cma01g01084 . Car01g00960 Car09g00907 . . Cpe02g00814 . . . . . . . . . . . . . . Cone6ag0017 Cone9ag0016 . . . . . . . . . . Bpe11g00579 . . Bma14g00175 . Cmo01g01130 Cmo09g00997 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g639 . . Bda07g00400 . . . . . . . Cma01g01083 Cma09g00998 Car01g00959 Car09g00910 . Cpe06g00807 Cpe02g00815 Bhi09g01746 . . . . Mch11g1254 . . . . . . . . Cone6ag0016 Cone9ag0015 . . Lsi02g01845 Csa07g00943 . . . . . . Bpe11g00580 . . Bma14g00174 . Cmo01g01129 Cmo09g00999 . . . . . . . . . . . . . Cla09g02060 Cam09g2149 Cec09g2214 . . . . . . Chy01g01168 Cme01g00936
Vvi19g640 . . Bda07g00401 Bda09g00433 . Bpe08g01098 . . . . Cma01g01082 Cma09g00999 Car01g00957 Car09g00911 Sed07g2739 Cpe06g00808 Cpe02g00816 Bhi09g01747 Tan01g3179 Cmetu01g2567 . . Mch11g1256 . . . . . . . . . . . . Lsi02g01844 Csa07g00941 . . . . . . Bpe11g00581 . Bma07g01252 Bma14g00173 . Cmo01g01128 Cmo09g01000 . . . . . . . . . . . . . Cla09g02061 Cam09g2150 Cec09g2215 . . . . . . Chy01g01167 Cme01g00935
Vvi19g641 . Blo03g01479 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g642 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g643 . . . Bda09g00434 . Bpe08g01097 . . . . . Cma09g01000 . Car09g00912 Sed07g2740 Cpe06g00809 . Bhi09g01748 Tan01g3180 Cmetu01g1710 . . Mch11g1257 . . . . . . . . . . . . Lsi02g01843 Csa07g00940 . . . . . . . . Bma07g01251 . . . Cmo09g01001 . . . . . . . . . . . . . Cla09g02062 Cam09g2151 Cec09g2216 . . . . . . Chy01g01166 Cme01g00934
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 4949489 4950330 - Bda025486.1 Bda07g00397 397
7 4955551 4956968 - Bda025487.1 Bda07g00398 398
7 4963223 4966256 - Bda025488.2 Bda07g00399 399
7 4971192 4973464 - Bda025489.1 Bda07g00400 400
7 4976303 4979622 + Bda025490.2 Bda07g00401 401
9 5327477 5329125 - Bda031002.1 Bda09g00421 421
9 5373589 5374524 + Bda031003.1 Bda09g00422 422
9 5763990 5766248 + Bda031021.1 Bda09g00433 433
9 5767452 5768749 - Bda031022.1 Bda09g00434 434
9 47470445 47476049 + XM_039040581.1 Bhi09g01744 1744
9 47476902 47480112 - XM_039042417.1 Bhi09g01746 1746
9 47502529 47506690 + XM_039042105.1 Bhi09g01747 1747
9 47507305 47512052 - XM_039042103.1 Bhi09g01748 1748
3 19379784 19380983 - BLOR11697 Blo03g00516 516
3 41530251 41536942 + BLOR12657 Blo03g01476 1476
3 41544939 41545937 - BLOR12658 Blo03g01477 1477
3 41564299 41565395 + BLOR12659 Blo03g01478 1478
3 41571753 41573033 - BLOR12660 Blo03g01479 1479
7 47484975 47486259 + Bma026505.1 Bma07g01251 1251
7 47488058 47490278 - Bma026506.1 Bma07g01252 1252
7 47499335 47501216 - Bma026508.2 Bma07g01253 1253
7 47505325 47506347 + Bma026509.1 Bma07g01254 1254
7 47701647 47702926 + Bma026513.1 Bma07g01256 1256
14 2300898 2302939 - Bma010583.1 Bma14g00173 173
14 2305981 2308226 + Bma010584.1 Bma14g00174 174
14 2310756 2313649 + Bma010585.1 Bma14g00175 175
14 2314174 2315619 - Bma010586.1 Bma14g00176 176
14 7563936 7565360 + Bma011147.1 Bma14g00695 695
8 13030904 13032166 + Bpe026164 Bpe08g01097 1097
8 13032798 13035002 - Bpe023222.4 Bpe08g01098 1098
8 13037297 13039018 - Bpe023223.1 Bpe08g01099 1099
8 13041603 13042625 + Bpe023224.1 Bpe08g01100 1100
11 4410377 4411393 - Bpe003942.1 Bpe11g00576 576
11 4413291 4414708 - Bpe003943.1 Bpe11g00577 577
11 4417256 4418712 + Bpe024764 Bpe11g00578 578
11 4419244 4422248 - Bpe003944.2 Bpe11g00579 579
11 4424887 4427163 - Bpe003945.1 Bpe11g00580 580
11 4427968 4430732 + Bpe003946.1 Bpe11g00581 581
9 36027755 36032110 + CaPI482276_09g021480.1 Cam09g2148 2148
9 36033231 36035579 - CaPI482276_09g021490.1 Cam09g2149 2149
9 36037277 36040361 + CaPI482276_09g021500.1 Cam09g2150 2150
9 36041425 36045313 - CaPI482276_09g021510.1 Cam09g2151 2151
1 9175065 9176437 - Carg22406-RA Car01g00957 957
1 9179395 9182177 + Carg22404-RA Car01g00959 959
1 9183146 9187509 - Carg22403-RA Car01g00960 960
9 5594523 5598771 + Carg12861-RA Car09g00907 907
9 5606480 5607231 - Carg12865-RA Car09g00910 910
9 5608735 5612466 + Carg12866-RA Car09g00911 911
9 5613211 5615864 - Carg12867-RA Car09g00912 912
9 39055389 39059622 + CePI673135_09g022130.1 Cec09g2213 2213
9 39060740 39063108 - CePI673135_09g022140.1 Cec09g2214 2214
9 39064779 39067856 + CePI673135_09g022150.1 Cec09g2215 2215
9 39068940 39072800 - CePI673135_09g022160.1 Cec09g2216 2216
1 12245479 12247400 + Chy1G010840.1 Chy01g01084 1084
1 13563646 13566678 + Chy1G011660.1 Chy01g01166 1166
1 13567693 13571424 - Chy1G011670.1 Chy01g01167 1167
1 13586770 13595006 + Chy1G011680.1 Chy01g01168 1168
1 13596924 13600625 - Chy1G011690.1 Chy01g01169 1169
9 38176455 38181252 + ClCG09G021160.1 Cla09g02059 2059
9 38181977 38185010 - ClCG09G021170.2 Cla09g02060 2060
9 38186172 38189623 + ClCG09G021180.2 Cla09g02061 2061
9 38190499 38194287 - ClCG09G021190.1 Cla09g02062 2062
1 7972613 7976969 - CmaCh01G010820.1 Cma01g01082 1082
1 7979453 7986187 + CmaCh01G010830.1 Cma01g01083 1083
1 7982906 7988248 - CmaCh01G010840.1 Cma01g01084 1084
9 5088741 5091114 + CmaCh09G009970.1 Cma09g00997 997
9 5090093 5094725 - CmaCh09G009980.1 Cma09g00998 998
9 5095454 5099930 + CmaCh09G009990.1 Cma09g00999 999
9 5100852 5103550 - CmaCh09G010000.1 Cma09g01000 1000
1 10831566 10834799 + MELO3C024920.2.1 Cme01g00934 934
1 10834984 10845050 - MELO3C024919.2.1 Cme01g00935 935
1 10847898 10850962 + MELO3C024918.2.1 Cme01g00936 936
1 10852824 10856505 - MELO3C024917.2.1 Cme01g00937 937
1 13136562 13140424 - PI0006176.1 Cmetu01g1710 1710
1 13111252 13114935 + PI0003337.1 Cmetu01g2235 2235
1 13126268 13130081 + PI0027071.1 Cmetu01g2567 2567
1 9301487 9304945 - CmoCh01G011280.1 Cmo01g01128 1128
1 9305283 9309445 + CmoCh01G011290.1 Cmo01g01129 1129
1 9309608 9314315 - CmoCh01G011300.1 Cmo01g01130 1130
9 5302278 5306527 + CmoCh09G009970.1 Cmo09g00997 997
9 5313329 5315303 - CmoCh09G009990.1 Cmo09g00999 999
9 5316518 5321053 + CmoCh09G010000.1 Cmo09g01000 1000
9 5321822 5324758 - CmoCh09G010010.1 Cmo09g01001 1001
6 103886 104559 + Conep06aG0001600.1 Cone6ag0016 16
6 111705 115762 + Conep06aG0001700.1 Cone6ag0017 17
6 116009 117725 - Conep06aG0001800.1 Cone6ag0018 18
6 118873 120746 + Conep06aG0001900.1 Cone6ag0019 19
9 87602 89901 + Conep09aG0001500.1 Cone9ag0015 15
9 91229 93947 + Conep09aG0001600.1 Cone9ag0016 16
9 94586 96292 - Conep09aG0001700.1 Cone9ag0017 17
9 97423 99331 + Conep09aG0001800.1 Cone9ag0018 18
2 5212763 5217963 + Cp4.1LG02g00630.1 Cpe02g00814 814
2 5218449 5221613 - Cp4.1LG02g00580.1 Cpe02g00815 815
2 5222923 5226510 + Cp4.1LG02g00670.1 Cpe02g00816 816
6 5162260 5164999 + Cp4.1LG06g08580.1 Cpe06g00806 806
6 5163262 5168439 - Cp4.1LG06g08470.1 Cpe06g00807 807
6 5169592 5174532 + Cp4.1LG06g08520.1 Cpe06g00808 808
6 5174903 5178066 - Cp4.1LG06g08450.1 Cpe06g00809 809
7 8188845 8195851 + CsaV3_7G018310.1 Csa07g00940 940
7 8189434 8197814 - CsaV3_7G018320.1 Csa07g00941 941
7 8218043 8229425 + CsaV3_7G018340.1 Csa07g00943 943
7 8228368 8231995 - CsaV3_7G018350.1 Csa07g00944 944
7 10249886 10262402 - CsaV3_7G021580.1 Csa07g01069 1069
2 24208141 24212408 + Lsi02G018430.1 Lsi02g01843 1843
2 24211475 24217449 - Lsi02G018440.1 Lsi02g01844 1844
2 24220380 24223139 + Lsi02G018450.1 Lsi02g01845 1845
2 24224202 24228436 - Lsi02G018460.1 Lsi02g01846 1846
11 8910276 8913830 + MC11g1036 Mch11g1253 1253
11 8912823 8918181 - MC11g1037 Mch11g1254 1254
11 8922913 8927311 + MC11g1038 Mch11g1256 1256
11 8928308 8931455 - MC11g1039 Mch11g1257 1257
4 45704661 45708671 - Sed0008909.1 Sed04g3670 3670
7 42513415 42518957 + Sed0026445.1 Sed07g2739 2739
7 42519442 42522941 - Sed0006368.1 Sed07g2740 2740
1 85355794 85358778 + Tan0007145.1 Tan01g3175 3175
1 85398226 85409813 + Tan0021806.1 Tan01g3179 3179
1 85413856 85419153 - Tan0007107.1 Tan01g3180 3180
19 8052647 8091236 - Vvi19g634 Vvi19g634 634
19 8107459 8115536 - Vvi19g635 Vvi19g635 635
19 8116654 8120740 - Vvi19g636 Vvi19g636 636
19 8126478 8128014 + Vvi19g637 Vvi19g637 637
19 8128769 8134567 - Vvi19g638 Vvi19g638 638
19 8137616 8146878 - Vvi19g639 Vvi19g639 639
19 8197975 8202530 + Vvi19g640 Vvi19g640 640
19 8202623 8204603 - Vvi19g641 Vvi19g641 641
19 8205247 8211487 + Vvi19g642 Vvi19g642 642
19 8223430 8225593 - Vvi19g643 Vvi19g643 643
       

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