CN103233016A - GmD2IN transposon and application thereof - Google Patents
GmD2IN transposon and application thereof Download PDFInfo
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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
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 | ? | |
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 | ? | |
0 |
Gm04 | 1658390 | 1659034 | solo | ? | Glyma04g02380 | 156 |
Gm04 | 6181740 | 6182363 | solo | ? | Glyma04g07921 | 1670 |
Gm04 | 6959135 | 6959744 | solo | ? | |
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 | ? | |
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 | ? | |
0 |
Gm07 | 9919867 | 9920308 | solo | ? | Glyma07g11700 | 3394 |
Gm07 | 20822896 | 20823525 | solo | ? | |
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 | ? | |
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 | ? | |
0 |
Gm15 | 5974924 | 5975535 | solo | ? | Glyma15g08430 | 1266 |
Gm15 | 8877745 | 8878269 | solo | ? | |
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 | ? | |
0 |
Gm10 | 9581858 | 9582403 | truncated | ? | Glyma10g10040 | 7888 |
Gm12 | 15231012 | 15363234 | truncated | ? | |
0 |
Gm13 | 6335300 | 6335941 | truncated | ? | Glyma13g06025 | 2276 |
Gm13 | 7325270 | 7325876 | truncated | ? | Glyma13g07151 | 2443 |
Gm13 | 26983072 | 26986370 | truncated | ? | |
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.
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.
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