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                             analysis and application in Nicotiana

 

Some statics for the informations of the 5267 germplasm and six Nicotiana sequences.


The informations of 5267 Nicotiana germplasms

 

Table 1 The species of these germplasm

 

Species Number
Nicotiana tabacum L. 4887
Nicotiana rustica L. 345
Nicotiana alata Link 3
Others 32

 

Table 2 The type of these germplasm

 

Germplasm Type Number
Aromatic tobacco 95
Burley tobacco 200
Cigar tobacco 55
Flue-cured tobacco 2203
Nicotiana gossei 35
Rustica tobacco 344
Sun-curing tobacco 2335
Total 5267

 

Figure 1 The type of these germplasm

 

 

Table 3 The origin of these germplasm

 

Origin Number
China 4472
America 400
Zimbabwe 24
Poland 21
Yugoslavia 17
Japan 31
Bulgaria 14
Canada 13
Australia 10
Others 265

 

Figure 2 The origin of these germplasm

 

 

Table 4 The disease resistance of these germplasm

 

Type Black Shank Granville Wilt Root knot Nematode Brown Spot TMV CMV PVY Total
High Resistance 13 1 4 5 14 8 18 63
High Susceptibility 32 2 18 55 41 242 2 392
Immune - - - - 91 - - 91
Moderate Resistance 458 251 505 262 381 381 183      2,421
Moderate Susceptibility 401 389 551 339 749 538 445      3,412
Resistance 621 89 223 102 196 166 75      1,472
Susceptibility 1160 1497 734 412 367 465 427      5,062
Tolerant - - - - - 2 - 2
Total       2,685            2,229                2,035      1,175     1,839      1,802    1,150    12,915

 

Figure 3 The disease resistance of these germplasm

 

 

 


SSR Statics

 

Table 5 The SSR numbers of six Nicotiana species

 

Species SSR Numbers  Total 
genome gene cds exon intron
Nicotiana benthamiana        492,540        61,568         2,428         2,412        59,134           618,082
Nicotiana otophora        358,420  -   -   -   -            358,420
Nicotiana sylvestris        420,177        63,159         2,333         2,323        60,821           548,813
Nicotiana tabacum BX        594,364        47,536         3,602  -   -            645,502
Nicotiana tabacum K326        620,818        45,437         3,644  -   -            669,899
Nicotiana tabacum TN90        637,331        44,660         3,842  -   -            685,833
Nicotiana tomentosiformis        306,151        63,893         2,636         2,613        61,277           436,570
Total     3,429,801      326,253       18,485         7,348      181,232        3,963,119

 

Figure 6 The SSR distribution of the six Nicotiana species

 

 

Table 6 The number of different SSR types

 

Species Monomer Dimer Trimer Tetramer Pentamer Hexamer Total
Nicotiana benthamiana         232,598      165,757     86,895         4,615          996             1,679      492,540
Nicotiana otophora         141,993      131,663     78,429         4,171        1,031             1,133      358,420
Nicotiana sylvestris         240,835      120,195     53,127         4,067        1,058               895      420,177
Nicotiana tabacum BX         336,050      154,345     94,110         6,745        1,613             1,501      594,364
Nicotiana tabacum K326         345,113      169,533     96,027         6,860        1,655             1,630      620,818
Nicotiana tabacum TN90         356,006      174,965     96,249         6,897        1,626             1,588      637,331
Nicotiana tomentosiformis         148,362      106,823     46,312         3,045          677               932      306,151
Total      1,800,957    1,023,281   551,149       36,400        8,656             9,358   3,429,801

 

Figure 7 The proportion of different SSR types

 

 

Table 7 The primer numbers of six Nicotiana species

 

Species Primer Numbers  Total 
gene cds exon intron utr
Nicotiana benthamiana     51,044     2,056   3,859     57,130     3,833        117,922
Nicotiana sylvestris     48,316     1,951   1,795     40,171  -           92,233
Nicotiana tabacum BX     40,389     2,996  -   -   -           43,385
Nicotiana tabacum K326     38,412     3,025  -   -   -           41,437
Nicotiana tabacum TN90     37,997     3,199  -   -   -           41,196
Nicotiana tomentosiformis     51,541     2,268   2,058     42,650  -           98,517
Total   267,699   15,495   7,712   139,951     3,833        434,690

 

Figure 8 The primer numbers of six Nicotiana species

 

 


SNP Statics

 

Table 8 The SNP number of the Nicotiana species

 

Reference Query SNP Number
Nicotiana benthamiana Nicotiana otophora                   785,204
Nicotiana sylvestris                1,872,257
Nicotiana tabacum BX                2,391,165
Nicotiana tabacum K326                2,403,132
Nicotiana tabacum TN90                2,442,813
Nicotiana tomentosiformis                   726,445
Total              10,621,016

 

Figure 9 The SNP number of the Nicotiana species

 

 

Table 9 The deferent SNP type number of the Nicotiana species

 

Species A->T A->C A->G T->A T->C T->G
Nicotiana otophora     50,881      41,006   123,297      50,757     123,495    123,495
Nicotiana sylvestris    113,461    104,059   311,489    113,048     311,662    311,662
Nicotiana tabacum BX    147,149    130,127   391,290    147,257     390,785    390,785
Nicotiana tabacum K326    147,710    130,592   393,846    147,495     394,445    394,445
Nicotiana tabacum TN90    149,891    133,384   401,483    150,476     400,109    400,109
Nicotiana tomentosiformis     47,490      37,609   114,426      47,699     114,344    114,344

 

Species C->A C->T C->G G->A G->T G->C
Nicotiana otophora     35,241    110,757     25,609    111,243      35,287     25,715
Nicotiana sylvestris     77,169    255,115     55,436    255,071      77,307     55,430
Nicotiana tabacum BX    100,424    327,469     72,533    327,312     100,374     72,785
Nicotiana tabacum K326    100,042    329,091     72,694    328,065     100,964     73,088
Nicotiana tabacum TN90    102,125    333,869     73,703    333,330     102,066     73,769
Nicotiana tomentosiformis     32,642    102,757     24,014    103,188      32,779     24,100

 

Figure 10 The deferent SNP type number of the Nicotiana species

 

 


 

RT-PCR Statics

 

Table 10 The PCR number of the Nicotiana species

 

Species PCR Number
Nicotiana benthamiana                          29,644
Nicotiana sylvestris                          21,434
Nicotiana tabacum BX                          11,454
Nicotiana tabacum K326                          10,992
Nicotiana tabacum TN90                          10,163
Nicotiana tomentosiformis                          19,172

 

Figure 11 The PCR number of the Nicotiana species

 

 

 

KEGG Annotation

 

Table 11 The KEGG annotation of the Nicotiana species

 

Species KEGG Pathway Number KO Number
Nicotiana benthamiana 368 255
Nicotiana sylvestris 372 283
Nicotiana tabacum BX 372 411
Nicotiana tabacum K326 377 416
Nicotiana tabacum TN90 374 438
Nicotiana tomentosiformis 374 312

 

 

Pfam Annotation

 

Table 12 The deferent type number of six Nicotiana species

 

Species Coiled-coil Disordered Domain Family Motif Repeat
Nicotiana benthamiana 11 15 29363 26261 391 6105
Nicotiana sylvestris 8 7 28438 26616 479 8198
Nicotiana tabacum BX 23 26 46020 42658 699 13193
Nicotiana tabacum K326 22 24 46071 42509 672 13617
Nicotiana tabacum TN90 23 21 47536 43900 669 14596
Nicotiana tomentosiformis 7 10 30164 27919 495 9787

 

Table 13 The top ten of domains of Nicotiana species

 

Nicotiana benthamiana Nicotiana sylvestris Nicotiana tomentosiformis
Domain Number Domain Number Domain Number
PPR_2 1531 PPR_2 3214 PPR_2 4120
PPR 1450 PPR 2921 PPR 3229
Pkinase 1394 WD40 1171 WD40 1384
WD40 1035 Pkinase 1127 Pkinase 1287
RRM_1 701 RRM_1 784 RRM_1 875
LRR_8 693 LRR_8 755 PPR_1 766
Pkinase_Tyr 614 Pkinase_Tyr 592 LRR_8 704
Myb_DNA-binding 609 NB-ARC 560 Myb_DNA-binding 619
p450 480 Myb_DNA-binding 538 Pkinase_Tyr 594
LRRNT_2 374 PPR_1 497 NB-ARC 505

 

Nicotiana tabacum BX Nicotiana tabacum K326 Nicotiana tabacum TN90
Domain Number Domain Number Domain Number
PPR_2 4778 PPR_2 4813 PPR_2 5483
PPR 4184 PPR 3985 PPR 4464
WD40 2151 WD40 2336 WD40 2436
Pkinase 1999 Pkinase 2065 Pkinase 2127
RRM_1 1268 RRM_1 1303 RRM_1 1359
LRR_8 1129 Pkinase_Tyr 1099 Pkinase_Tyr 1159
Pkinase_Tyr 1120 LRR_8 1067 LRR_8 1100
NB-ARC 1014 NB-ARC 965 PPR_1 1048
PPR_1 815 PPR_1 913 NB-ARC 1031
Myb_DNA-binding 794 Myb_DNA-binding 824 Myb_DNA-binding 826

 

Figure 12 The top fifty-seven of domains of all Nicotiana species

 

 

 
 

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