CN103233016A - GmD2IN transposon and application thereof - Google Patents

GmD2IN transposon and application thereof Download PDF

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CN103233016A
CN103233016A CN2013101554950A CN201310155495A CN103233016A CN 103233016 A CN103233016 A CN 103233016A CN 2013101554950 A CN2013101554950 A CN 2013101554950A CN 201310155495 A CN201310155495 A CN 201310155495A CN 103233016 A CN103233016 A CN 103233016A
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intact
transposon
gmd2in
sequence
solo
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田志喜
房超
李丛丛
王正
周正奎
武云帅
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Institute of Genetics and Developmental Biology of CAS
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Institute of Genetics and Developmental Biology of CAS
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Abstract

The invention discloses GmD2IN transposon and an application thereof. The GmD2IN transposon is a double-strand deoxyribonucleic acid (DNA) molecule indicated by a sequence 1 of a sequence table and is a reversed transposon. The GmD2IN transposon has a characteristic similar to an inserted gene and can facilitate the research of a functional genome.

Description

GmD2IN transposon and application thereof
Technical field
The present invention relates to GmD2IN transposon and application thereof.
Background technology
Transposon claims jumping gene again, its essence is one can be in the biological gene group dna fragmentation from a chromosomal site " jumping " to another site.From nineteen fifty McClintock had at first found the DNA transposon in corn after, transposon was found in genome in a large number.Not being both of transposon content causes the big or small one of the main reasons that makes a variation of Plant Genome.
According to the difference of swivel base mechanism, transposon mainly can be divided into two big classes: retrotransponsons and DNA transposon.The swivel base of retrotransponsons need be through the process of DNA-RNA-DNA.DNA at first is transcribed into RNA, and further reverse transcription becomes cDNA, is incorporated into the new site of genome then under the effect of a series of intergrases etc.Generally speaking, its original copy can not lost, so the process that whole swivel base process is exactly " copy-paste ".And the swivel base of DNA transposon is the process from DNA to DNA, and without transcribing and reverse transcription, whole swivel base process is the process of " shearing-paste ", and copy originally can disappear in the swivel base process.According to the difference of structure, retrotransponsons can be divided into different subclass again with the DNA transposon.For example, retrotransponsons can be divided into long terminal repetition retrotransponsons (the long terminal repeat retrotransposon, LTR) and the terminal repetition retrotransponsons of non-length (the non-long terminal repeat retrotransposon, non-LTR).Wherein, LTR is the main ingredient of transposon in the plant.Complete LTR is made up of two tumor-necrosis factor glycoproteins and intermediate code zones in the same way, two ends.Along with continuous swivel base, same LTR family can form a lot of members.Because the difference in amplification period, they have certain differentiation in sequence, but have very high similarity between the same family different members, and the sequence homology between general two transposons namely can be thought greater than 80% and belongs to same family.
Transposon can cause that variation, the variation of gene-splicing pattern, the epigenetics of sudden change, the genetic expression of gene modify, and also can cause losing, repeat etc. of chromosome segment, has played very important effect in genome evolution.Because for receptor biological, transposon is " viroid " invader, and organism has been evolved a series of defense mechanism to resist the unlimited amplification of transposon, so most of transposon is partial to insert noncoding centriolar region.Yet, also have the transposon of minority to have the characteristic of being partial to insert gene.For example, Tos17 of the Tnt1 of colibacillary Tn7, potato and paddy rice etc.The application of these transposons has greatly advanced the research of functional genome.
Soybean is important economic food crop, because its genomic complicacy, the soybean function genome research is made slow progress.Its genome contains a large amount of transposons, but identify at present all be partial to insert inactive centriolar region.Have the evaluation of the transposon of being partial to insert gene by force and use and to carry forward vigorously the genomic process of soybean function, also can the functional study of other biological be played an important role.
Summary of the invention
The purpose of this invention is to provide GmD2IN transposon and application thereof.
Transposon provided by the invention, called after GmD2IN transposon available from soybean varieties Williams82, is the double chain DNA molecule shown in the sequence 1 of sequence table.
The present invention also protects the gene of the same clan (family member of GmD2IN transposon, 174) of described GmD2IN transposon, and is as shown in table 1.
The present invention also protects the application of described GmD2IN transposon in identifying its family member in the soybean gene group.
The present invention also protects described GmD2IN transposon as the application of transposon.Described transposon specifically can be retrotransponsons.
The present invention also protects the application of described GmD2IN transposon in the soybean function genome research.
The present invention also protects the application of described GmD2IN transposon in functional genome research.
The present invention also protects the application that changes in the expression conditions that is inserted in of described GmD2IN transposon.The insertion of GmD2IN transposon can reduce genetic expression, perhaps changes gene expression pattern.
The present invention also protects described GmD2IN transposon in the application that makes up for the mutant library that carries out the soybean function genome research.
The present invention also protects the double chain DNA molecule shown in the sequence 2 of sequence table.
The present invention also protects the double chain DNA molecule shown in the sequence 3 of sequence table
The dna molecular that the present invention finds is a kind of retrotransponsons, has the characteristic of being partial to insert gene, will help to have advanced the research of functional genome.
Description of drawings
Fig. 1 is the structural representation of GmD2IN transposon.
Fig. 2 is that the GmD2IN transposon is in the distribution situation of soybean gene group.
Fig. 3 is the comparison of GmD2IN transposon and other LTR.
Fig. 4 is GmD2IN transposon and the comparison of other LTR family members in insertion gene preference.
Fig. 5 influences genetic expression behind the GmD2IN swivel base.
Embodiment
Following embodiment is convenient to understand better the present invention, but does not limit the present invention.Experimental technique among the following embodiment if no special instructions, is ordinary method.Used test materials among the following embodiment if no special instructions, is to buy from routine biochemistry reagent shop and obtains.Quantitative test in following examples all arranges repeated experiments three times, results averaged.
The soybean varieties Williams82 that is used for this step derives from the kind money resources bank of USDA, and PI 548573, and the kind money resource of this resources bank is open towards the public, and it is relevant to can be used for scientific research, can Import PI among the http://www.ars-grin.gov/npgs/acc/acc_queries.htmlNumbering is found.
Preference is inserted the acquisition of the retrotransponsons of gene in embodiment 1, the soybean
Find the retrotransponsons of a preference insertion gene from soybean varieties Williams82, with its called after GmD2IN transposon, its nucleotide sequence is shown in the sequence 1 of sequence table.
The structural representation of GmD2IN transposon is seen Fig. 1.
GmD2IN transposon total length 5983bp is made up of 2 long terminal repeat (LTR1 and LTR2) and intermediate sequence.LTR1 (is that the sequence 1 of sequence table is from 5 ' terminal the 1st to 650 Nucleotide shown in the sequence 2 of sequence table; 650bp).LTR2 (is that the sequence 1 of sequence table is from 5 ' terminal the 5333rd to 5983 Nucleotide, 651bp) shown in the sequence 3 of sequence table.Intermediate sequence as the sequence 1 of sequence table from shown in 5 ' terminal the 729th to 4709 Nucleotide, the structural domain (being followed successively by UBN2_2, gag_pre, Rve, RVT_2 and RNase_HI_RT_Ty1) of 5 conservative proteins of coding.
Embodiment 2, GmD2IN transposon are in the complete genomic evaluation of soybean
1, the genome sequence of soybean varieties Williams82 is from phytozome free download (http://www.phytozome.net/soybean).
2, use public freeware---formatdb program (the download address http://blast.ncbi.nlm.nih.gov/Blast.cgi among the Blast? CMD=Web﹠amp; PAGE_TYPE=BlastDocs﹠amp; DOC_TYPE=Download) format soybean gene group sequence.
3, respectively with the sequence 3 of the sequence 2 of the sequence 1 of sequence table, sequence table and sequence table as the bait sequence, be database with the soybean gene group sequence of format, with public free search software---Blast searches for, the output file that obtains searching for.
4, the GmD2IN transposon is in the complete genomic evaluation of soybean
If a certain section sequence in the genome also comprises three zones similar to sequence 2, sequence 3 and sequence 4, and with the homology of sequence 1 be more than 80%, can be considered to intact (complete) GmD2IN transposon.If in the genome a certain section sequence include only with sequence 2 homologys be more than 80% the zone or with sequence 3 homologys be zone 80% or more, adjacent area can be considered to solo (single) GmD2IN transposon less than the zone similar to sequence 4.If a certain section sequence comprised the zone similar to sequence 2 and sequence 4 in the genome, and compared excalation with sequence 1 but homology is more than 80%, or a certain section sequence comprised the zone similar to sequence 3 and sequence 4 in the genome, and compared excalation with sequence 1 but homology is more than 80%, can be considered to truncated (excalation) GmD2IN.
Identify 174 GmD2IN transposon members in the genome of soybean varieties Williams82 altogether, comprising 98 intact members, 50 solo members, 26 truncated members, specifying information sees Table 1.For example, the similarity of intact member of 3490722-3496704 and sequence 1 is 99% in No. 20 karyomit(e).
In the table 1 soybean gene group GmD2IN transposon member's evaluation with close on gene information
Chr. Start End Class Age(Mys) Closed?gene Distance(bp)
Gm01 5343250 5347114 intact 1.728 Glyma01g05540 0
Gm01 37395882 37399637 intact 2.518 Glyma01g27910 7209
Gm01 37612692 37616497 intact 0.770 Glyma01g28196 509
Gm01 46105002 46107886 intact 2.219 Glyma01g33910 17
Gm01 53011768 53015627 intact 0.296 Glyma01g41542 0
Gm02 14668716 14672808 intact 0.177 Glyma02g16260 263
Gm02 32880805 32884656 intact 0.561 Glyma02g30758 5453
Gm03 5980685 5984506 intact 0.925 Glyma03g05650 0
Gm03 6401207 6407151 intact 0.732 Glyma03g06225 0
Gm03 7553842 7559430 intact 0.368 Glyma03g07181 0
Gm03 9159573 9167972 intact 1.415 Glyma03g08346 12579
Gm03 9284470 9288301 intact 0.489 Glyma03g08412 84710
Gm03 24305236 24323417 intact 3.365 Glyma03g19011 3532
Gm03 28442752 28446625 intact 2.361 Glyma03g22260 15485
Gm03 40628117 40631891 intact 0.298 Glyma03g32900 0
Gm03 41009004 41012853 intact 0.182 Glyma03g33460 0
Gm04 10171106 10174877 intact 2.190 Glyma04g11628 11272
Gm04 27613404 27619348 intact 1.088 Glyma04g24054 0
Gm05 15383784 15387543 intact 2.730 Glyma05g14394 3493
Gm05 23716059 23733386 intact 4.115 Glyma05g19690 6370
Gm06 1977109 1980900 intact 1.911 Glyma06g02860 106
Gm06 2677836 2681630 intact 0.242 Glyma06g03820 21
Gm06 3676038 3679563 intact 0.420 Glyma06g05181 10
Gm06 42349267 42353021 intact 0.615 Glyma06g39570 1927
Gm06 45556725 45560506 intact 3.983 Glyma06g42315 3175
Gm07 4702520 4706417 intact 0.919 Glyma07g05990 149
Gm07 12633883 12637713 intact 4.097 Glyma07g13611 15729
Gm07 21538533 21542369 intact 2.008 Glyma07g21110 9365
Gm07 43902529 43906300 intact 0.177 Glyma07g39420 1370
Gm08 34094643 34098447 intact 0.652 Glyma08g36301 0
Gm08 36590402 36596407 intact 2.802 Glyma08g37780 0
Gm08 36718830 36722504 intact 0.656 Glyma08g37925 8901
Gm09 7205552 7211240 intact 1.724 Glyma09g08150 5180
Gm09 12388187 12392071 intact 0.689 Glyma09g12030 3572
Gm09 30014996 30020990 intact 2.344 Glyma09g24270 2101
Gm09 39693533 39697303 intact 0.310 Glyma09g33180 4169
Gm10 267631 272136 intact 0.302 Glyma10g00510 127
Gm10 8879669 8883403 intact 1.148 Glyma10g09626 7325
Gm10 9339298 9343072 intact 1.087 Glyma10g09960 4127
Gm10 14306148 14312827 intact 1.280 Glyma10g12780 1234
Gm10 16952548 16958508 intact 0.604 Glyma10g14701 15580
Gm10 34291164 34297147 intact 2.493 Glyma10g26200 9526
Gm10 35647344 35651082 intact 1.878 Glyma10g27051 6608
Gm11 4876883 4880852 intact 0.551 Glyma11g06911 96
Gm11 6937365 6941171 intact 0.774 Glyma11g09730 1650
Gm11 7985941 7989585 intact 1.782 Glyma11g11230 4537
Gm11 8073010 8076947 intact 0.486 Glyma11g11336 0
Gm11 33866939 33870651 intact 0.903 Glyma11g32315 1266
Gm12 7729257 7732846 intact 1.950 Glyma12g09980 11984
Gm12 8476935 8480709 intact 1.489 Glyma12g10530 0
Gm12 15006699 15010671 intact 0.538 Glyma12g15980 7058
Gm12 34160990 34164880 intact 0.433 Glyma12g30530 2972
Gm12 37421201 37425066 intact 0.177 Glyma12g34250 0
Gm13 6280558 6286530 intact 2.266 Glyma13g05980 1031
Gm13 6604712 6608490 intact 1.397 Glyma13g06340 6756
Gm13 6750768 6756106 intact 2.066 Glyma13g06530 2508
Gm13 12173342 12179319 intact 0.177 Glyma13g10386 15856
Gm13 12372669 12379623 intact 1.670 Glyma13g10503 0
Gm13 12378980 12382798 intact 0.178 Glyma13g10503 2567
Gm13 13804111 13807436 intact 2.808 Glyma13g11311 10477
Gm13 38624202 38627804 intact 1.635 Glyma13g37570 450
Gm14 7255443 7259158 intact 1.496 Glyma14g09211 3433
Gm14 15915125 15919021 intact 0.830 Glyma14g15120 43858
Gm14 18366863 18370433 intact 0.663 Glyma14g16883 3685
Gm14 24840262 24844715 intact 1.544 Glyma14g21360 24426
Gm14 42341187 42344987 intact 1.352 Glyma14g33930 0
Gm14 42360426 42364018 intact 1.185 Glyma14g33940 3858
Gm15 1761835 1765494 intact 2.457 Glyma15g02590 493
Gm15 12163728 12168228 intact 1.795 Glyma15g15830 590
Gm15 36704011 36709410 intact 1.651 Glyma15g33353 1005
Gm15 37112810 37117332 intact 1.917 Glyma15g33520 5264
Gm15 37463377 37467280 intact 0.610 Glyma15g33680 4532
Gm15 43526215 43528929 intact 0.448 Glyma15g37631 5249
Gm16 31256589 31260494 intact 3.600 Glyma16g27250 374
Gm17 698761 702500 intact 0.366 Glyma17g01210 1829
Gm17 22571217 22574974 intact 1.062 Glyma17g22808 60406
Gm17 29674805 29695739 intact 1.580 Glyma17g27610 2156
Gm17 31168683 31189713 intact 0.810 Glyma17g29101 36232
Gm17 32463815 32468169 intact 1.422 Glyma17g29690 4598
Gm17 36175916 36181775 intact 0.599 Glyma17g32584 24741
Gm17 41535675 41539457 intact 0.430 Glyma17g37810 2568
Gm18 1853241 1857025 intact 0.488 Glyma18g02850 2727
Gm18 7841276 7845056 intact 2.237 Glyma18g09070 1099
Gm18 10013224 10016993 intact 0.966 Glyma18g11170 0
Gm18 10207824 10211884 intact 2.266 Glyma18g11480 3978
Gm18 15882922 15886676 intact 1.012 Glyma18g15695 8483
Gm18 31748763 31754706 intact 2.063 Glyma18g27710 5489
Gm18 39967683 39971540 intact 0.658 Glyma18g33890 4906
Gm18 40503676 40509655 intact 0.892 Glyma18g34490 1048
Gm18 53324930 53328798 intact 3.057 Glyma18g43760 5126
Gm19 1052798 1056613 intact 0.969 Glyma19g01430 336
Gm19 2033865 2037778 intact 1.072 Glyma19g02292 805
Gm19 2843326 2847270 intact 0.413 Glyma19g02850 15933
Gm19 8615079 8618849 intact 1.182 Glyma19g07287 632
Gm19 26939953 26943659 intact 2.133 Glyma19g22320 4403
Gm19 40100729 40104571 intact 1.357 Glyma19g32350 299
Gm20 3455438 3459174 intact 1.036 Glyma20g03610 0
Gm20 3490722 3496704 intact 0.177 Glyma20g03640 0
Gm01 52979274 52979892 solo ? Glyma01g41491 0
Gm02 50491489 50492140 solo ? Glyma02g46590 5252
Gm02 50524410 50525051 solo ? Glyma02g46610 1200
Gm02 50603968 50604609 solo ? Glyma02g46740 750
Gm03 41123041 41123526 solo ? Glyma03g33590 5422
Gm03 41876659 41877299 solo ? Glyma03g34451 0
Gm04 1658390 1659034 solo ? Glyma04g02380 156
Gm04 6181740 6182363 solo ? Glyma04g07921 1670
Gm04 6959135 6959744 solo ? Glyma04g08847 0
Gm04 10424528 10425190 solo ? Glyma04g11780 33596
Gm04 10779467 10780130 solo ? Glyma04g11960 32254
Gm04 12009559 12010192 solo ? Glyma04g?12729 15450
Gm05 1405498 1406144 solo ? Glyma05g01956 347
Gm06 1532078 1532669 solo ? Glyma06g02310 0
Gm06 4575835 4576473 solo ? Glyma06g06400 298
Gm06 14234215 14234856 solo ? Glyma06g17875 382
Gm06 18268647 18269299 solo ? Glyma06g21710 4454
Gm06 40867779 40868386 solo ? Glyma06g38076 12864
Gm06 40969539 40970190 solo ? Glyma06g38140 3224
Gm06 45651917 45652530 solo ? Glyma06g42375 1795
Gm07 66096 66730 solo ? Glyma07g00240 0
Gm07 9919867 9920308 solo ? Glyma07g11700 3394
Gm07 20822896 20823525 solo ? Glyma07g20451 0
Gm07 38269214 38269964 solo ? Glyma07g33330 802
Gm09 29922606 29923186 solo ? Glyma09g24190 3495
Gm10 9584864 9585512 solo ? Glyma10g10040 10894
Gm10 17140974 17141630 solo ? Glyma10g14750 68884
Gm10 37288269 37288918 solo ? Glyma10g28410 1936
Gm12 7378362 7379005 solo ? Glyma12g09615 5464
Gm12 15365710 15366353 solo ? Glyma12g16217 17753
Gm12 18687520 18688149 solo ? Glyma12g18094 0
Gm12 25527794 25528442 solo ? Glyma12g23200 22926
Gm12 34299706 34300341 solo ? Glyma12g30670 7008
Gm13 4584677 4585296 solo ? Glyma13g04230 3267
Gm13 13807648 13808297 solo ? Glyma13g11311 9616
Gm14 8436003 8436684 solo ? Glyma14g10270 1696
Gm14 24847814 24848255 solo ? Glyma14g21360 20886
Gm14 24961497 24962131 solo ? Glyma14g21440 11591
Gm14 49212375 49212582 solo ? Glyma14g40245 0
Gm15 5974924 5975535 solo ? Glyma15g08430 1266
Gm15 8877745 8878269 solo ? Glyma15g11980 0
Gm15 20768181 20768824 solo ? Glyma15g22121 10481
Gm16 19091216 19092696 solo ? Glyma16g17580 7566
Gm16 19099108 19099779 solo ? Glyma16g17580 483
Gm16 29048279 29048892 solo ? Glyma16g25110 1804
Gm20 1353534 1354151 solo ? Glyma20g01785 267
Gm20 1378849 1379462 solo ? Glyma20g01800 3845
Gm20 11675681 11676340 solo ? Glyma20g08323 7303
Gm20 24263678 24264327 solo ? Glyma20g17221 1911
Gm20 30897903 30898548 solo ? Glyma20g21575 11811
Gm01 35586049 35586705 truncated ? Glyma01g26766 1013
Gm02 50488203 50488845 truncated ? Glyma02g46580 2385
Gm03 7211812 7212435 truncated ? Glyma03g06950 5562
Gm04 983 1616 truncated ? Glyma04g00200 5634
Gm07 9922810 9923392 truncated ? Glyma07g11700 310
Gm07 37526686 37527330 truncated ? Glyma07g32620 3791
Gm09 18499738 18500379 truncated ? Glyma09g15650 3315
Gm09 35776497 35777143 truncated ? Glyma09g28814 0
Gm10 9581858 9582403 truncated ? Glyma10g10040 7888
Gm12 15231012 15363234 truncated ? Glyma12g16120 0
Gm13 6335300 6335941 truncated ? Glyma13g06025 2276
Gm13 7325270 7325876 truncated ? Glyma13g07151 2443
Gm13 26983072 26986370 truncated ? Glyma13g23610 0
Gm14 3813498 3814111 truncated ? Glyma14g05375 1072
Gm14 6378096 6378742 truncated ? Glyma14g08340 4226
Gm14 8439144 8439760 truncated ? Glyma14g10270 4837
Gm14 24958350 24959001 truncated ? Glyma14g21440 8444
Gm15 1361022 1361667 truncated ? Glyma15g02040 5936
Gm15 5486648 5487248 truncated ? Glyma15g07800 517
Gm16 28733077 28733719 truncated ? Glyma16g24751 1263
Gm18 9933566 9934212 truncated ? Glyma18g11080 1645
Gm19 3027697 3028320 truncated ? Glyma19g02920 14198
Gm19 5926946 5927582 truncated ? Glyma19g05450 1536
Gm20 1371058 1371688 truncated ? Glyma20g01800 11619
Gm20 5272050 5272758 truncated ? Glyma20g04870 9510
Gm20 11672544 11673191 truncated ? Glyma20g08323 10452
The specificity analysis of embodiment 3, GmD2IN transposon
One, the GmD2IN transposon is in the chromosomal distribution of soybean
The GmD2IN transposon member that embodiment 2 is identified is illustrated on the coloured differently body of soybean gene group, sees Fig. 2, and from outside to inside, outermost layer is 20 karyomit(e) essential informations, and the grey cover part represents the centriole near zone; The second layer is the content distribution curve of tumor-necrosis factor glycoproteins; The 3rd layer of distribution situation that represents gene; The 4th layer of different GmD2IN member of representative are in genomic distribution, and peripheral lines represent intact (structural integrity), and inferior peripheral lines represent solo (having only single LTR), and inner ring lines represent truncated.
Further analysis finds that GmD2IN transposon member is slightly higher than centriole near zone upper density on chromosome arm, and concrete comparative result sees that (B:GmD2IN compares in the distribution of centriole near zone and chromosome arm Fig. 3; C: other LTR family members of soybean gene group compare in the distribution of centriole near zone and chromosome arm; Peri: centriole near zone, arm: chromosome arm).In order to study the difference of this family and other families, other LTR family members in the soybean gene group are analyzed in the distribution of centriole near zone and chromosome arm, and distribution density will be well below the centriole near zone on chromosome arm to found that other LTR family members.As seen, GmD2IN transposon family is different from the soybean other most of LTR families on genome distributes, and be uniformly distributed on the karyomit(e) substantially, and the frequency on chromosome arm is slightly high.
Two, the GmD2IN transposon inserts the preference of gene
With each member of GmD2IN transposon of evaluation and the corresponding analysis of note gene location of soybean gene group, find out the distance (specifying information sees Table 1) of the nearest gene of each GmD2IN transposon.Then discovery is added up in the frequency distribution of distance, have the member of 17% GmD2IN transposon to insert in the gene of note, other about 13% member inserts in the scope of distance gene 500bp that (Fig. 4 is that GmD2IN transposon and other LTR family members are in the comparison of inserting the gene preference; The frequency distribution of gene distance recently in A:GmD2IN and the genome; B: the frequency distribution of gene distance recently in other LTR family members of soybean gene group and the genome).In order to study the difference of this family and other families, distance to other LTR family members in the soybean gene group and soybean gene group note gene is analyzed, find most of other LTR family members all with the distance of gene more than 10kb, have only few part to insert gene inside.As seen GmD2IN family is different from the soybean other most of LTR families aspect the preference of swivel base, has very high insertion gene preference.
Three, the GmD2IN transposon inserts the influence to genetic expression
In order to identify the GmD2IN transposon to being inserted into the influence of expression conditions, by the characteristic of soybean duplicate genes, there is not the expression of the duplicate genes of insertion to be analyzed being inserted into gene with its correspondence.The insertion of finding the GmD2IN transposon can reduce genetic expression, perhaps changes gene expression pattern.
Soybean material Willams82 gathers different tissues at 23 different growing stages and (is respectively germination period cotyledon S1, germination period young root S2, germination period children stem S3, germination period primary leaf S4, tri-leaf period new leave S5, first couple of true leaf S6, tri-leaf period cotyledon S7, tri-leaf period stem S8, become new leave S9 of florescence, become florescence Lao Ye 10, bud S11, leaf bud S12, newborn flower S13, contain flower S14/S15, the flower phase S16 that declines, one all pod S17, two all pod S18, three all pod S19,6 all pod S20,8 all pod S21,10 all pod S22, old and feeble blade S23) extracts total RNA, and reverse transcription is cDNA, with test kit (Illumina company, TruSeq DNA Sample Preparation kits, Catalog#:FC-121-2001) build the storehouse, adopt High-seq 2000 sequenators to carry out the both-end order-checking then.At first utilize BWA software to carry out sequence location (http://bio-bwa.sourceforge.net/bwa.shtml) from the raw data that High-seq 2000 sequenators obtain, with Cufflinks software the file after locating is analyzed then, obtained each expression of gene value.
To having carried out the RNAseq analysis in 23 soyabean tissue's materials, can reduce genetic expression by gene expression analysis being found the GmD2IN transposon inserts altogether, perhaps change gene expression pattern.The results are shown in Figure 5.Among Fig. 5, X-coordinate represents the growth course of plant from left to right.Fig. 5 A:GmD2IN transposon inserts Glyma01g05540, and the expression amount that the expression of Glyma01g05540 contrasts its corresponding duplicate genes Glyma02g11860 reduces.Fig. 5 B:GmD2IN inserts Glyma18g11170, and the expression amount that the expression of Glyma18g11170 contrasts its corresponding duplicate genes Glyma08g42750 reduces.The C:GmD2IN transposon inserts Glyma12g10530, and the expression amount that the expression of Glyma12g10530 contrasts its corresponding duplicate genes Glyma06g46220 reduces.The D:GmD2IN transposon inserts Glyma0lg41540, and the expression pattern that the expression of Glyma01g41540 contrasts its corresponding duplicate genes Glyma11g03890 changes.
Figure IDA00003126041200011
Figure IDA00003126041200021
Figure IDA00003126041200031
Figure IDA00003126041200041
Figure IDA00003126041200051

Claims (10)

1. the double chain DNA molecule shown in the sequence 1 of sequence table.
2. the gene of the same clan of the described double chain DNA molecule of claim 1 is as shown in table 1.
3. the application of the described double chain DNA molecule of claim 1 in identifying its family member in the soybean gene group.
4. the described double chain DNA molecule of claim 1 is as the application of transposon.Described transposon specifically can be retrotransponsons.
5. the application of the described double chain DNA molecule of claim 1 in the soybean function genome research.
6. the application of the described double chain DNA molecule of claim 1 in functional genome research.
7.GmD2IN transposon be inserted in the application that changes in the expression conditions.
8. the described double chain DNA molecule of claim 1 is in the application that makes up for the mutant library that carries out the soybean function genome research.
9. the double chain DNA molecule shown in the sequence 2 of sequence table.
10. the double chain DNA molecule shown in the sequence 3 of sequence table.
CN2013101554950A 2013-04-28 2013-04-28 GmD2IN transposon and application thereof Pending CN103233016A (en)

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* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN111088278A (en) * 2019-12-31 2020-05-01 中山大学 Retrotransposon Ra-RARE-1 with autonomous transposition activity and application thereof
CN111088278B (en) * 2019-12-31 2023-06-27 中山大学 Retrotransposon Ra-RARE-1 with autonomous transposition activity and application thereof

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Application publication date: 20130807