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
Vvi5g219 . . . . . . Bma04g01161 . Cmo08g01262 . . . . . . . . . . . . . . . Cla06g00403 Cam06g0425 Cec06g0432 Cco06g0432 Clacu06g0411 Cmu06g0411 Cre06g1191 . Cone15ag0704 . . . . . . . . . . . . Bma02g00942 . Sed09g0625 . . Cma08g01298 . . . . . Bhi12g01972 Tan06g2803 Cmetu11g0409 . . . Lcy12g0891 . . . . . . . . . . .
Vvi5g220 . . . . . Bpe14g01082 . . . . . . Car06g01342 . . Cpe08g00138 . Bhi01g01110 . . . Hepe05g1357 . Lcy11g1319 . . . . . . . . . . . Lsi05g01401 . . Cme06g00818 . . . . . . Bma02g00943 . . Cmo06g01573 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g221 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g222 . Blo12g00381 Bda03g00826 . Bpe04g00783 . Bma04g00725 . . . . Cma14g01572 . Car14g01385 . . Cpe03g01313 Bhi01g01112 . . . Hepe05g1356 . Lcy11g1316 . . . . . . . Cone14ag0690 . . . Lsi05g01400 . . . . . . . . . . . . . Cmo14g01605 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g223 . Blo12g00380 Bda03g00827 . Bpe04g00784 . Bma04g00726 . . . . . . . . . . . . . . . . . Cla06g00402 Cam06g0424 Cec06g0431 Cco06g0431 Clacu06g0410 Cmu06g0410 Cre06g1190 Cone14ag0689 . . . . Csa06g01542 . . . . . . . . . . . . . . . . . Cpe12g00343 Cpe17g00094 Bhi12g01974 . . . . . Lcy12g0892 . . . . . . . . . . .
Vvi5g224 . . . . . Bpe14g01081 . . . . . . . . Sed02g1120 . . Bhi01g01114 Tan10g1100 Cmetu06g1680 . Hepe05g1355 . . . . . . . . . . . . . Lsi05g01398 . . Cme06g00820 . . . . . . Bma02g00944 . . Cmo06g01574 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g225 . Blo12g00379 Bda03g00828 . Bpe04g00785 . Bma04g00727 . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0688 Cone15ag0701 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g226 . Blo12g00378 Bda03g00829 . Bpe04g00786 . Bma04g00728 . . . . . . . . . . . . . . . . . Cla06g00401 Cam06g0423 Cec06g0430 Cco06g0430 Clacu06g0409 Cmu06g0409 Cre06g1189 . . . . . . . . . . . . . . . . . . . . . . . . . Bhi12g01980 . . . . . . . . . . . . . . . . .
Vvi5g227 . . . . . Bpe14g01080 . . . . . . . . . . . . . . . . . . Cla06g00400 Cam06g0422 Cec06g0429 Cco06g0429 Clacu06g0408 Cmu06g0408 Cre06g1188 Cone14ag0687 Cone15ag0700 . . . . . . . . . . . . Bma02g00945 . Sed08g1182 . . . . . . Cpe12g00344 . Bhi12g01981 Tan06g2807 Cmetu02g1103 . . . Lcy12g0894 . . . . . . . . . . .
Vvi5g228 . . . . . . . . . . . Cma14g01570 . Car14g01384 . Cpe08g00137 Cpe03g01312 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo14g01604 . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 7022918 7086702 - Bda016813.1 Bda03g00826 826
3 7102193 7104300 + Bda016814.2 Bda03g00827 827
3 7104994 7108801 - Bda016815.1 Bda03g00828 828
3 7110983 7117773 - Bda016816.1 Bda03g00829 829
1 21470762 21475986 + XM_039022175.1 Bhi01g01110 1110
1 21507602 21619635 + XM_039028029.1 Bhi01g01112 1112
1 21705735 21708332 + XM_039023034.1 Bhi01g01114 1114
12 62369543 62375684 - XM_039019527.1 Bhi12g01972 1972
12 62438623 62441308 + XM_039050720.1 Bhi12g01974 1974
12 62442312 62453825 - XM_039050719.1 Bhi12g01980 1980
12 62458111 62462631 - XM_039018620.1 Bhi12g01981 1981
12 20196209 20202767 + BLOR04397 Blo12g00378 378
12 20242750 20247391 + BLOR04398 Blo12g00379 379
12 20247929 20250051 - BLOR04399 Blo12g00380 380
12 20312352 20326614 + BLOR04400 Blo12g00381 381
2 49321058 49321663 - Bma015736.1 Bma02g00942 942
2 49325120 49329233 - Bma015737.1 Bma02g00943 943
2 49330677 49331542 + Bma015738.1 Bma02g00944 944
2 49332303 49335032 - Bma015739.2 Bma02g00945 945
4 7491482 7555953 - Bma019231.1 Bma04g00725 725
4 7595405 7598081 + Bma019234.1 Bma04g00726 726
4 7598757 7603474 - Bma019235.1 Bma04g00727 727
4 7605934 7609161 - Bma019236.1 Bma04g00728 728
4 29994211 29995970 - Bma019896.1 Bma04g01161 1161
4 5039459 5109199 - Bpe015445.3 Bpe04g00783 783
4 5114657 5116778 + Bpe015446.1 Bpe04g00784 784
4 5117577 5121335 - Bpe015447.1 Bpe04g00785 785
4 5123703 5126944 - Bpe015448.1 Bpe04g00786 786
14 8095786 8098621 + Bpe014454.1 Bpe14g01080 1080
14 8099205 8100232 - Bpe014455.1 Bpe14g01081 1081
14 8104649 8108677 + Bpe014456.1 Bpe14g01082 1082
6 6354043 6357559 + CaPI482276_06g004220.1 Cam06g0422 422
6 6361715 6367623 + CaPI482276_06g004230.1 Cam06g0423 423
6 6368703 6370919 - CaPI482276_06g004240.1 Cam06g0424 424
6 6378151 6382992 + CaPI482276_06g004250.1 Cam06g0425 425
6 9621799 9628038 + Carg25651-RA Car06g01342 1342
14 11643573 11649020 + Carg19605-RA Car14g01384 1384
14 11650171 11718239 - Carg19606-RA Car14g01385 1385
6 4725868 4733592 + CcPI632755_06g004290.1 Cco06g0429 429
6 4733632 4739510 + CcPI632755_06g004300.1 Cco06g0430 430
6 4740577 4742789 - CcPI632755_06g004310.1 Cco06g0431 431
6 4750148 4755037 + CcPI632755_06g004320.1 Cco06g0432 432
6 4862631 4870304 + CePI673135_06g004290.1 Cec06g0429 429
6 4870344 4876252 + CePI673135_06g004300.1 Cec06g0430 430
6 4877306 4879510 - CePI673135_06g004310.1 Cec06g0431 431
6 4890063 4895006 + CePI673135_06g004320.1 Cec06g0432 432
6 4892341 4895880 + ClG42_06g0040800.10 Clacu06g0408 408
6 4900002 4905903 + ClG42_06g0040900.10 Clacu06g0409 409
6 4906980 4909219 - ClG42_06g0041000.10 Clacu06g0410 410
6 4916388 4920674 + ClG42_06g0041100.10 Clacu06g0411 411
6 4917266 4922059 + ClCG06G004290.2 Cla06g00400 400
6 4928225 4934126 + ClCG06G004300.2 Cla06g00401 401
6 4935667 4938372 - ClCG06G004310.1 Cla06g00402 402
6 4945314 4950158 + ClCG06G004320.1 Cla06g00403 403
8 7867236 7875776 - CmaCh08G012980.1 Cma08g01298 1298
14 11765231 11771724 + CmaCh14G015700.1 Cma14g01570 1570
14 11773027 11841275 - CmaCh14G015720.1 Cma14g01572 1572
6 5533866 5539107 + MELO3C006736.2.1 Cme06g00818 818
6 5621869 5624351 + MELO3C006742.2.1 Cme06g00820 820
2 8267303 8276889 - PI0028396.1 Cmetu02g1103 1103
6 5718532 5720181 + PI0024597.1 Cmetu06g1680 1680
11 3494129 3497146 + PI0012389.1 Cmetu11g0409 409
6 11080973 11085368 + CmoCh06G015730.1 Cmo06g01573 1573
6 11086042 11087753 + CmoCh06G015740.1 Cmo06g01574 1574
8 7944398 7953347 - CmoCh08G012620.1 Cmo08g01262 1262
14 12689868 12696115 + CmoCh14G016040.1 Cmo14g01604 1604
14 12697108 12768820 - CmoCh14G016050.1 Cmo14g01605 1605
6 4687540 4691079 + CmPI595203_06g004080.1 Cmu06g0408 408
6 4691104 4701087 + CmPI595203_06g004090.1 Cmu06g0409 409
6 4702170 4704409 - CmPI595203_06g004100.1 Cmu06g0410 410
6 4711647 4715951 + CmPI595203_06g004110.1 Cmu06g0411 411
14 3561401 3565748 + Conep14aG0070200.1 Cone14ag0687 687
14 3566315 3571111 + Conep14aG0070300.1 Cone14ag0688 688
14 3576641 3578871 - Conep14aG0070400.1 Cone14ag0689 689
14 3584074 3634451 + Conep14aG0070500.1 Cone14ag0690 690
15 3806209 3810331 + Conep15aG0071400.1 Cone15ag0700 700
15 3815406 3819429 + Conep15aG0071500.1 Cone15ag0701 701
15 3824156 3826654 + Conep15aG0071800.1 Cone15ag0704 704
3 10621417 10627229 + Cp4.1LG03g12010.1 Cpe03g01312 1312
3 10627892 10696001 - Cp4.1LG03g11990.1 Cpe03g01313 1313
8 882415 888857 + Cp4.1LG08g05560.1 Cpe08g00137 137
8 889073 897067 - Cp4.1LG08g05320.1 Cpe08g00138 138
12 2295190 2299042 + Cp4.1LG12g03440.1 Cpe12g00343 343
12 2300766 2305218 - Cp4.1LG12g03450.1 Cpe12g00344 344
17 572064 574296 + Cp4.1LG17g00910.1 Cpe17g00094 94
6 5743956 5750885 + CrPI670011_06g011880.1 Cre06g1188 1188
6 5751015 5756921 + CrPI670011_06g011890.1 Cre06g1189 1189
6 5758004 5760215 - CrPI670011_06g011900.1 Cre06g1190 1190
6 5767442 5775511 + CrPI670011_06g011910.1 Cre06g1191 1191
6 12913955 12917814 + CsaV3_6G017400.1 Csa06g01542 1542
5 61989613 61992836 - Hsped.05g13550.1 Hepe05g1355 1355
5 61998558 62117370 - Hsped.05g13560.1 Hepe05g1356 1356
5 62119512 62124676 - Hsped.05g13570.1 Hepe05g1357 1357
11 36715229 36728718 - Maker00031713 Lcy11g1316 1316
11 36773860 36778379 - Maker00031568 Lcy11g1319 1319
12 12724307 12726944 - Maker00024963 Lcy12g0891 891
12 12744375 12746334 + Maker00024887 Lcy12g0892 892
12 12758873 12765960 - Maker00024913 Lcy12g0894 894
5 21820603 21823249 - Lsi05G013980.1 Lsi05g01398 1398
5 21853844 21925390 - Lsi05G014000.1 Lsi05g01400 1400
5 21928532 21933010 - Lsi05G014010.1 Lsi05g01401 1401
2 48404877 48408639 - Sed0013937.2 Sed02g1120 1120
8 24493026 24511360 - Sed0027025.1 Sed08g1182 1182
9 7796229 7809640 - Sed0009437.1 Sed09g0625 625
6 80128457 80135262 - Tan0017236.1 Tan06g2803 2803
6 80152770 80155835 - Tan0002661.1 Tan06g2807 2807
10 10630032 10635693 + Tan0014064.1 Tan10g1100 1100
5 2201429 2203055 - Vvi5g219 Vvi5g219 219
5 2207621 2213580 - Vvi5g220 Vvi5g220 220
5 2215300 2216352 - Vvi5g221 Vvi5g221 221
5 2216357 2322673 - Vvi5g222 Vvi5g222 222
5 2340664 2343191 + Vvi5g223 Vvi5g223 223
5 2344271 2348279 + Vvi5g224 Vvi5g224 224
5 2350352 2356081 - Vvi5g225 Vvi5g225 225
5 2361511 2376608 - Vvi5g226 Vvi5g226 226
5 2377859 2383123 - Vvi5g227 Vvi5g227 227
5 2387833 2390890 - Vvi5g228 Vvi5g228 228
       

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