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
Vvi19g694 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g695 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g696 . . Bda07g00417 . . . . . . . . . Car01g00943 . Sed04g3639 . . Bhi09g01791 Tan01g3207 Cmetu01g1798 . . Mch11g1292 . . . . . . . . . . . . . . . . . . . . Bpe11g00594 . . . . . . . . . . . . . . . . . . . Cla09g02088 Cam09g2175 Cec09g2241 . . . . . . Chy01g01130 .
Vvi19g697 . . . . . . . . . . Cma01g01067 Cma09g01020 Car01g00941 Car09g00924 . Cpe06g00828 Cpe02g00831 . . . . . . . . . . . . . . . . . . Lsi02g01817 . . . . . . . . . . Bma14g00675 . Cmo01g01109 Cmo09g01023 . . . . . . . . . . . . . . . . . . . . . . . Cme01g00884
Vvi19g698 . Blo03g01485 Bda07g00420 . . . . . . . . . . . Sed07g2757 . . Bhi09g01792 Tan01g3208 Cmetu01g1486 . . Mch11g1294 . . . . . . . . . . . . . . . . . . . . Bpe11g00595 . . . . . . . . . . . . . . . . . . . Cla09g02089 Cam09g2176 Cec09g2242 . . . . . . . .
Vvi19g699 . . . . . . . . . . . Cma09g01021 . Car09g00925 . Cpe06g00829 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g01024 . . . . . . Bhi11g00462 . . . . . . . . . . . . . . . . .
Vvi19g700 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g701 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe14g00779 . . . . . . . . . . . . . . . . . . .
Vvi19g702 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g01816 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme01g00881
Vvi19g703 Blo03g00501 . . . . Bpe08g01087 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g00414 . . . . . . . . Bma07g01241 Bma14g00674 . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 5324550 5329337 - Bda025510.1 Bda07g00417 417
7 5387446 5390155 + Bda025515.1 Bda07g00420 420
9 48635898 48641705 - XM_039041967.1 Bhi09g01791 1791
9 48751654 48755256 + XM_039041596.1 Bhi09g01792 1792
11 11040727 11044878 - XM_039047683.1 Bhi11g00462 462
3 18589105 18591818 - BLOR11682 Blo03g00501 501
3 41650031 41652764 + BLOR12666 Blo03g01485 1485
7 47359473 47362211 - Bma026493.1 Bma07g01241 1241
14 7298181 7300659 - Bma011125.1 Bma14g00674 674
14 7308734 7313305 + Bma011126.1 Bma14g00675 675
8 12975886 12978419 - Bpe023212.1 Bpe08g01087 1087
11 4507806 4512568 - Bpe003959.1 Bpe11g00594 594
11 4523670 4526202 + Bpe003960.1 Bpe11g00595 595
9 36259274 36264544 - CaPI482276_09g021750.1 Cam09g2175 2175
9 36281687 36285073 + CaPI482276_09g021760.1 Cam09g2176 2176
1 9071635 9076480 + Carg23339-RA Car01g00941 941
1 9087609 9092609 + Carg22420-RA Car01g00943 943
9 5690978 5696594 - Carg24750-RA Car09g00924 924
9 5704606 5707094 + Carg24749-RA Car09g00925 925
9 39286829 39292160 - CePI673135_09g022410.1 Cec09g2241 2241
9 39310860 39313921 + CePI673135_09g022420.1 Cec09g2242 2242
1 13034098 13043108 + Chy1G011300.1 Chy01g01130 1130
9 38417727 38424198 - ClCG09G021450.1 Cla09g02088 2088
9 38439993 38446734 + ClCG09G021470.2 Cla09g02089 2089
1 7891075 7896146 + CmaCh01G010670.1 Cma01g01067 1067
9 5230930 5236490 - CmaCh09G010200.1 Cma09g01020 1020
9 5245061 5249312 + CmaCh09G010210.1 Cma09g01021 1021
1 10027715 10031020 - MELO3C024959.2.1 Cme01g00881 881
1 10124125 10129405 + MELO3C024955.2.1 Cme01g00884 884
1 14105741 14111425 + PI0009274.4 Cmetu01g1486 1486
1 14058255 14063737 - PI0013340.1 Cmetu01g1798 1798
1 9208937 9214177 + CmoCh01G011090.1 Cmo01g01109 1109
9 5457883 5463352 - CmoCh09G010230.1 Cmo09g01023 1023
9 5472652 5477279 + CmoCh09G010240.1 Cmo09g01024 1024
2 5313319 5318759 - Cp4.1LG02g00440.1 Cpe02g00831 831
6 5316440 5321919 - Cp4.1LG06g08170.1 Cpe06g00828 828
6 5330452 5334831 + Cp4.1LG06g08240.1 Cpe06g00829 829
14 6141649 6146158 - Cp4.1LG14g07830.1 Cpe14g00779 779
3 3504091 3508146 - CsaV3_3G004140.1 Csa03g00414 414
2 23935314 23939230 - Lsi02G018160.1 Lsi02g01816 1816
2 23954349 23996774 + Lsi02G018170.1 Lsi02g01817 1817
11 9141207 9147183 - MC11g1071 Mch11g1292 1292
11 9159600 9166241 + MC11g1072 Mch11g1294 1294
4 45518429 45524975 + Sed0016663.2 Sed04g3639 3639
7 42608493 42613800 - Sed0002732.3 Sed07g2757 2757
1 86171574 86177583 - Tan0001211.1 Tan01g3207 3207
1 86224031 86227209 + Tan0005358.1 Tan01g3208 3208
19 8932024 8934203 + Vvi19g694 Vvi19g694 694
19 8934683 8940263 + Vvi19g695 Vvi19g695 695
19 8940758 8945632 + Vvi19g696 Vvi19g696 696
19 8945633 8949046 + Vvi19g697 Vvi19g697 697
19 8952167 8955081 + Vvi19g698 Vvi19g698 698
19 8962811 8965954 + Vvi19g699 Vvi19g699 699
19 8994329 8994573 - Vvi19g700 Vvi19g700 700
19 8994626 8997460 + Vvi19g701 Vvi19g701 701
19 9002000 9008545 + Vvi19g702 Vvi19g702 702
19 9008548 9009273 + Vvi19g703 Vvi19g703 703
       

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