生物工程学报  2016, Vol. 32 Issue (9): 1264-1272
http://dx.doi.org/10.13345/j.cjb.150554
中国科学院微生物研究所、中国微生物学会主办
0

文章信息

张宁, 阮亚男, 王姗姗, 刘洋, 赵宸, 王晶晶, 王凯玺, 王艳丽, 王红艳
Zhang Ning, Ruan Yanan, Wang Shanshan, Liu Yang, Zhao Chen, Wang Jingjing, Wang Kaixi, Wang Yanli, Wang Hongyan
MITE类转座子mPing在水稻不同亚种间的差异分析
Comparison of MITE transposons mPing in different rice subspecies
生物工程学报, 2016, 32(9): 1264-1272
Chin J Biotech, 2016, 32(9): 1264-1272
10.13345/j.cjb.150554

文章历史

Received: December 25, 2015
Accepted: April 12, 2016
MITE类转座子mPing在水稻不同亚种间的差异分析
张宁1, 阮亚男1, 王姗姗1,2, 刘洋1, 赵宸1, 王晶晶1, 王凯玺3, 王艳丽1, 王红艳1     
1 辽宁大学 生命科学院 植物表观遗传与进化实验室,辽宁 沈阳 110036
2 西藏自治区农牧科学院农业研究所 品种资源研究室,西藏 拉萨 850000
3 辽宁省水土保持研究所,辽宁 朝阳 122000
摘要: mPing是水稻中第一个被鉴定出的有活性的MITE类转座子,为了探索mPing在水稻粳稻品种日本晴和籼稻品种93-11基因组中的分布差异,本研究首先运用Southern杂交的方法初步检测mPing在两个亚种中拷贝数的差异,然后通过同源性探寻方法发现,mPing在水稻亚种日本晴和93-11基因组中拷贝数分别为52和14,并且日本晴基因组中的mPing均为mPing-1,93-11中mPing-1的拷贝数为3,mPing-2的拷贝数为11。通过分析mPing上下游5 kb侧翼序列发现mPing在日本晴和93-11中分别与23和3个已知基因相关联。本研究为阐明以mPing的分布多样性为主要原因的粳稻和籼稻之间的遗传差异提供初步理论基础。
关键词: 粳稻     籼稻     转座子     mPing     水稻    
Comparison of MITE transposons mPing in different rice subspecies
Ning Zhang1, Yanan Ruan1, Shanshan Wang1,2, Yang Liu1, Chen Zhao1, Jingjing Wang1, Kaixi Wang3, Yanli Wang1, Hongyan Wang1     
1 Laboratory of Plant Epigenetics and Evolution, School of Life Science, Liaoning University, Shenyang 110036, Liaoning, China ;
2 Germplasm Resources Laboratory, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850000, Tibet, China ;
3 Liaoning Institute of Soil and Water Conservation, Chaoyang 122000, Liaoning, China
Abstract: The mPing family is the first active MITE TE family identified in rice genome. In order to compare the compositions and distributions of mPing family in the genomes of two rice subspecies japonica (cv. Nipponbare) and indica (cv. 93-11), we initially estimated the copy numbers of mPing family in those two subspecies using Southern blot and then confirmed the results by searching homologous copies in each reference genome using Blastn program, which turned out to have 52 and 14 mPing copies in corresponding reference genome, respectively. All mPing members in Nipponbare genome belong to mPing-1, while there are 3 mPing-1 and 11 mPing-2 copies in 93-11 genome. By further investigating the 5-kb flanking sequences of those mPing copies, it was found that 23 and 3 protein-coding genes in Nipponbare and 93-11 genome are residing adjacent to those mPing copies respectively. These results establish the preliminary theoretical foundation for further dissecting the genetic differences of japonica and indica rice in terms of the diversities and distributions of their component mPing.
Key words: Japonica     Indica     transposon     mPing     rice    

转座子(Transpososable elements或transposons)是指基因组中可移动或复制自身DNA并整合到新位点的DNA片段[1]。转座子在基因组中常常具有很多拷贝,是真核生物基因组重要的组成部分[2]。人类基因组中转座子约占整个基因组的45%,植物中约为50%−90%[3]。由于转座子激活可造成基因的失活或缺失、基因组重排、甚至是着丝粒区序列的进化和分化[4-7],因此对于研究基因组结构、侧翼基因表达调控以及物种进化等都起到重要作用[3]

根据转座方式可将转座子分为两类:Class Ⅰ称为反转录转座子(Retrotransposon),是利用RNA介导的转座[8]。根据其是否包含有长末端重复序列(LTR),分为LTR类反转座子(LTR retrotransposon)和非LTR类反转座子(Non-LTR retrotransposon),由于其利用复制/插入方式实现转座,因此可改变基因组的大小[3]。Class Ⅱ称为转座子(Transposons),是利用DNA介导转座。根据其转座的自主性,可分为自主性转座子(Autonomous element)、非自主性转座子(Non-autonomous element)及微型反向重复转座子(Miniature inverted-repeat transposable element, MITE),由于其利用切除/修复方式实现转座,因此基因组大小一般不会发生改变[9-10]

MITE类转座子是一类在植物中分布广泛的非自主性转座子,自身不具编码转座酶的基因,序列只有100−500 bp[11],常常位于基因组的常染色质区[12-13]。水稻中第一个被鉴定的有活性的MITE类转座子是mPing (GenBank Accession No. BK000588),序列长430 bp[14],mPing的结构中包括15 bp的TIRs (Terminal inverted repeats),但不带有ORF (Open reading frame),它的转座依靠自主类转座子PingPong的ORF2编码的转座酶进行转座[15-17]。mPing在水稻中的突变体有两种类型:mPing-1和mPing-2,其中mPing-1序列长430 bp,mPing-2序列长419 bp[18]

水稻作为世界一半人口的食物来源,对人类的生存与发展有着重要的意义,在其9 000多年的驯化历史中[18-19],有20多个稻属物种,其主要分化为籼稻Indica和粳稻Japonica两种生态型[20]。籼稻和粳稻有着形态、生理、遗传等方面的差异。比如籼稻植株一般高于粳稻植株,抗倒伏能力较强,发芽较快,分蘖数较强,但籼稻比粳稻有更高的净光合速率[21];蔡星星等[20]利用籼稻93-11和粳稻日本晴基因组序列的差异片段进行研究,结果显示这两种生态型全基因序列具有很大的差异性。mPing的拷贝数差异就是其中的一个原因,为了更加完整地探寻mPing在水稻亚种分化以及基因组形成中的可能作用,本研究主要运用Southern杂交分析并结合生物信息学的方法,利用日本晴和93-11全基因组信息,对mPing在水稻两个亚种基因组中的结构特点、分布特征、以及mPing的插入对侧翼基因的影响进行研究,探寻mPing在水稻亚种形成过程中的可能作用。本研究为阐明粳稻和籼稻之间的遗传差异、探索粳稻和籼稻的进化历史提供初步理论基础。

1 材料与方法 1.1 材料来源

本研究采用的实验材料为粳稻品种日本晴(Oryza sativa Japonica. cv. Nipponbare)和籼稻品种93-11 (Oryza sativa Indica. cv. 93-11)。

1.2 Southern杂交

利用Hind Ⅲ (购自New England Biolabs公司)分别对日本晴和93-11的DNA样品进行酶切,选取这个酶的目的在于mPing中不存在Hind Ⅲ的酶切位点,因此我们可以估测mPing在这两个水稻亚种中的拷贝数。根据Shan等[5]提供的方法进行Southern杂交分析,以mPing-1 (AB087615)全长设计探针引物(由上海生工生物技术有限公司合成),具体序列为mPing-1 (positions 6-430):forward,5’-GTCACAATGGG GGTTTCACT-3’,reverse,5’-GGCCAGTCACA ATGGCTAGT-3’。

图 1 mPing在日本晴和93-11中的Southern杂交分析 Figure 1 Analysis of mPing in Nipponbare and 93-11 in the Southern blotting hybridization patterns. 1–3 means repeating three times.
1.3 生物信息学及比较基因组学

mPing-1 (AB087615)的基因序列在NCBI网站(http://archive-dtd.ncbi.nlm.nih.gov/)中下载,根据mPing-1的序列,可得到mPing-2的序列[18]。根据GRAMENE (http://www.gramene.org/)网站,做Blast分析获得mPing在日本晴和93-11中的拷贝信息,根据RICE-MAP (http://www.ricemap.org/)数据库网站,可得到该mPing拷贝所在染色体的上下游5 kb的碱基序列信息,再根据KOME数据库(http://cdna01.dna.affrc.go.jp/cDNA/),E值设为0,即只有100%同源序列才被挑选出来,以此方法进行同源性探寻可得到侧翼序列的外显子信息及表达蛋白的功能信息。

2 结果与分析 2.1 日本晴和93-11的Southern杂交分析

通过Hind Ⅲ酶切的Southern杂交分析可保守估测mPing在日本晴和93-11中的拷贝数。由结果可知(图 1),mPing在日本晴中和93-11中均存在,且mPing在两亚种中的数量是不同的,在日本晴中的拷贝数明显多于93-11,说明mPing在水稻亚种的分布有明显的差异,暗示其在物种分化中可能存在某些作用。

2.2 mPing不同拷贝在籼稻品种93-11和粳稻品种日本晴基因组中的定位情况

为了进一步确定mPing在两个亚种中的差别信息,通过同源性探寻方法,对mPing进行定位分析。结果表明,mPing在水稻亚种中分布数量和位置均不相同(表 1表 2),mPing在93-11中的拷贝数是14 (图 2),在日本晴中的拷贝数是52 (图 3)。其中93-11中mPing-1的拷贝数是3,mPing-2的拷贝数是11,日本晴中的mPing均为mPing-1,mPing在日本晴中的拷贝数是93-11的3.7倍。此外,日本晴每条染色体均有mPing的分布,拷贝数最多的是10号染色体,最少的是1号染色体,93-11中7、8、10号染色体没有mPing的拷贝,1号染色体上的拷贝数最多,为3个拷贝。mPing在日本晴和93-11基因组中结构特点和分布特征的多样性,进一步说明它们是导致水稻不同亚种间基因组差异的原因。

表 1 mPing在日本晴基因组中的定位信息 Table 1 Location information of mPing in Nipponbare genome
Copy Ori Chr Start End %ID Length Type
1 + 1 17 513 834 17 514 263 100.00 430 mPing-1
2 + 1 23 332 547 23 332 976 100.00 430 mPing-1
3 + 1 24 779 771 24 780 200 100.00 430 mPing-1
4 + 1 25 261 112 25 261 541 100.00 430 mPing-1
5 + 1 29 931 517 29 931 946 100.00 430 mPing-1
6 + 2    214 437    214 866 100.00 430 mPing-1
7 + 2    617 949    618 378 100.00 430 mPing-1
8 + 2 13 161 938 13 162 367 100.00 430 mPing-1
9 + 2 18 534 787 18 535 216  99.77 430 mPing-1
10 + 2 22 549 115 22 549 544 100.00 430 mPing-1
11 + 2 28 008 341 28 008 770  99.77 430 mPing-1
12 + 2 29 244 327 29 244 756 100.00 430 mPing-1
13 + 3  5 504 299  5 504 728 100.00 430 mPing-1
14 + 3  6 513 589  6 514 018 100.00 430 mPing-1
15 + 3  9 240 074  9 240 503 100.00 430 mPing-1
16 + 3  9 427 120  9 427 549 100.00 430 mPing-1
17 + 3  9 568 670  9 569 099 100.00 430 mPing-1
18 + 3 12 735 756 12 736 185  99.77 430 mPing-1
19 + 3 17 575 717 17 576 146 100.00 430 mPing-1
20 + 3 21 360 120 21 360 549 100.00 430 mPing-1
21 + 3 21 026 572 21 027 001 100.00 430 mPing-1
22 + 3 34 592 545 34 592 974  99.77 430 mPing-1
23 + 4 19 021 060 19 021 489  99.77 430 mPing-1
24 + 4 33 021 868 33 022 297 100.00 430 mPing-1
25 + 4 34 302 847 34 303 276 100.00 430 mPing-1
26 + 4 34 688 306 34 688 735 100.00 430 mPing-1
27 + 4 35 421 806 35 422 235  99.77 430 mPing-1
28 + 5 18 747 498 18 747 927 100.00 430 mPing-1
29 + 5 19 328 618 19 329 047 100.00 430 mPing-1
30 + 5 22 235 594 22 236 023 100.00 430 mPing-1
31 + 6 13 737 618 13 738 047 100.00 430 mPing-1
32 + 6 18 136 422 18 136 851 100.00 430 mPing-1
33 + 6 23 521 641 23 521 893  99.60 253 mPing-1
33 + 6 23 526 804 23 526 981 100.00 178 mPing-1
34 + 6 30 099 538 30 099 967  99.77 430 mPing-1
35 + 7  4 560 975  4 561 404 100.00 430 mPing-1
36 + 8  1 019 672  1 020 101 100.00 430 mPing-1
37 + 8  4 712 970  4 713 399 100.00 430 mPing-1
38 + 8 16 683 588 16 684 017 100.00 430 mPing-1
39 + 8 20 442 416 20 442 845 100.00 430 mPing-1
40 + 8 20 674 237 20 674 666 100.00 430 mPing-1
41 + 8 28 186 241 28 186 670 100.00 430 mPing-1
42 + 9    694 483    694 912  99.77 430 mPing-1
43 + 9 16 698 141 16 698 570  99.77 430 mPing-1
44 + 10  4 320 421  4 320 850 100.00 430 mPing-1
45 + 10 21 716 391 21 716 819  99.77 430 mPing-1
46 + 11    393 598    394 027 100.00 430 mPing-1
47 + 11 23 200 105 23 200 534 100.00 430 mPing-1
48 + 12    839 604    840 033 100.00 430 mPing-1
49 + 12  1 045 463  1 045 892 100.00 430 mPing-1
50 + 12  2 734 541  2 734 970  99.77 430 mPing-1
51 + 12  3 285 787  3 286 216 100.00 430 mPing-1
52 + 12  9 951 106  9 951 535 100.00 430 mPing-1
表 2 mPing在93-11基因组中的定位信息 Table 2 Location information of mPing in 93-11 genome
Copy Ori Chr Start End %ID Length Type
1 + 1 28 368 367 28 368 786 100.00 420 mPing-2
2 + 1 12 119 746 12 119 983 100.00 238 mPing-2
2 + 1 12 119 565 12 119 742 100.00 178 mPing-2
3 + 1 13 010 583 13 010 823  99.59 241 mPing-2
3 + 1 13 010 835 13 011 012 100.00 178 mPing-2
4 + 2 30 104 358 30 104 595 100.00 238 mPing-2
4 + 2 30 104 177 30 104 354 100.00 178 mPing-2
5 + 3 31 477 707  3 477 884  99.44 178 mPing-2
5 + 3 31 477 888 31 478 125 100.00 238 mPing-2
6 + 4 31 613 909 31 614 146 100.00 238 mPing-2
6 + 4 31 614 150 31 614 327  99.44 178 mPing-2
7 + 4 34 250 349 34 250 586 100.00 238 mPing-2
7 + 4 34 250 590 34 250 767  99.44 178 mPing-2
8 + 5 23 911 981 23 912 158 100.00 178 mPing-2
8 + 5 23 912 162 23 912 399  99.58 238 mPing-2
9 + 5  3 467 412  3 467 589 100.00 178 mPing-2
9 + 5  3 467 593  3 467 830 100.00 238 mPing-2
10 + 6  5 018 844  5 019 273 100.00 430 mPing-1
11 + 9  7 850 636  7 850 813  99.44 178 mPing-2
11 + 9  7 850 817  7 851 054 100.00 238 mPing-2
12 + 11 14 458 178 14 458 355 100.00 178 mPing-2
12 + 11 14 458 359 14 458 596 100.00 238 mPing-2
13 + 11 17 209 369 17 209 686  95.61 319 mPing-1
13 + 11 17 209 678 17 209 814  93.43 137 mPing-1
14 + 12 17 627 576 17 628 005 100.00 430 mPing-1
图 2 mPing在93-11基因组染色体上的定位 Figure 2 Chromosomal location of mPing in 93-11 genome.
图 3 mPing在日本晴基因组染色体上的定位 Figure 3 Chromosomal location of mPing in Nipponbare genome.
2.3 日本晴与93-11的mPing插入位点侧翼序列分析

转座子的转座会影响其侧翼基因的表达,在基因的结构和进化过程中具有重要的作用[8]。因此对mPing所有拷贝的侧翼序列上下游5 kb进行功能基因的同源性探寻。研究发现,mPing插入到了日本晴基因组中的某些基因的上游、下游以及内部,93-11基因组中的某些基因的上游和下游。日本晴中有23个mPing侧翼序列与已知功能基因有100%的同源性,这些已知基因中有与拟南芥相关的转座酶蛋白基因、与抗性相关的蛋白基因等(表 3)。同时,mPing插入到了1号染色体中的AK073838,11号染色体中的AK109523,12号染色体中的AK243131基因的内部。93-11中有3个mPing侧翼序列与已知的功能基因有100%的同源性,且mPing均插入到了基因的上游区域(表 4)。

表 3 日本晴中mPing的侧翼序列分析 Table 3 Sequence analysis of mPing flanking regions in Nipponbare
Chromsome GenBank Accession No. Flanking sequence Putative protein function predicted by blast X
1-1 AK073838 Up Hordeum vulgare BRI1 mRNA for putative brassinosteroid-insensitive protein 1, complete cds.
1-2 AK100804 Up Arabidopsis thaliana clone 94974 mRNA, complete sequence.
AK073838 Down Hordeum vulgare BRI1 mRNA for putative brassinosteroid-insensitive protein 1, complete cds.
1-4 AK071288 Up Arabidopsis thaliana mutator-like transposase-like protein (MQK4.25) mRNA, complete cds.
AK069334 Down Arabidopsis thaliana putative protein (At5g19590) mRNA, complete cds.
1-5 AK122047 Up Triticum aestivum clone wlp1c.pk006.j5:fis, full insert mRNA sequence.
3-1 AK061148 Up Zea mays (clone wusl1032) mRNA sequence.
AK111899 Down Zea mays ZmRR8 mRNA for response regulator 8, complete cds.
4-2 AK121689 Up Daucus carota pskr mRNA for phytosulfokine receptor, complete cds.
AK071468 Down Arabidopsis thaliana AT5g42940/MBD2_14 mRNA, complete cds.
4-4 AK068257 Up Arabidopsis thaliana At1g71010 mRNA, complete cds.
5-1 AK288267 Up AY518220 Oryza sativa (Indica cultivar-group) NBS-LRR-like protein A (NL-A), NBS-LRR-like protein B (NL-B), NBS-LRR-like protein C (NL-C), and NBS-LRR-like protein D (NL-D) genes, complete cds.
6-1 AK242258 Up AY459336 Oryza sativa (Japonica cultivar-group) clone CL034244.2 R2R3-MYB gene region.
6-5 AK068363 Up Arabidopsis thaliana unknown protein (At3g15310) mRNA, complete cds.
7-1 AK063035 Up Triticum aestivum clone wr1.pk182.b10:fis, full insert mRNA sequence.
8-1 AK120080 Up Arabidopsis thaliana At1g71010 mRNA, complete cds.
8-3 AK100130 Up Arabidopsis thaliana putative DNA-binding protein (At1g50410) mRNA, complete cds.
8-4 AK288678 Up AF259976 Oryza sativa subsp. indica polyprotein mRNA, complete cds.
AK288293 Down AB110444 Oryza sativa (Japonica cultivar-group) rf-1gene for fertility restorer, hypothetical proteins, complete cds.
8-5 AK105950 Up Lycopersicon esculentum putative anthocyanin permease mRNA, complete cds.
11-1 AK109523 Up Arabidopsis thaliana laccase (lac1) mRNA, complete cds.
AK109523 Down Arabidopsis thaliana laccase (lac1) mRNA, complete cds.
11-2 AK070903 Up Arabidopsis thaliana unknown protein (At1g14330/F14L17_7) mRNA, complete cds.
12-1 AK120100 Up Prunus dulcis SLFd mRNA for S locus F-box protein d, complete cds.
12-2 AK243131 Up AB180961 Oryza sativa (Japonica cultivar-group) OsSCR mRNA for SCARECROW, complete cds.
AK243131 Down AB180961 Oryza sativa (Japonica cultivar-group) OsSCR mRNA for SCARECROW, complete cds.
表 4 93-11中mPing的侧翼序列分析 Table 4 Sequence analysis of mPing flanking regions in 93-11
Chromsome GenBank Accession No. Flanking sequence Putative protein function predicted by blast X
1-1 AK100804 Up Arabidopsis thaliana clone 94974 mRNA, complete sequence.
5-1 AK102420 Up Arabidopsis thaliana MFP2 mRNA, complete cds.
5-2 AK120742 Up Physcomitrella patens mRNA for PPR986-12, complete cds.
3 讨论

转座子的移动会影响宿主基因组的结构、功能和进化[2-5, 22-26]。在本研究中,我们以MITE类转座子mPing为研究对象,探讨了以其多样性为主要原因的水稻亚种间的基因组差异。结果表明,在日本晴和93-11基因组中,mPing的分布和类型均有较大差异。日本晴基因组中只存在mPing-1一种类型,共有52个拷贝;93-11基因组中有mPing 14个,包括3个mPing-1和11个mPing-2。这与Hu等的研究结果,粳稻品种中mPing-1所占比例高于mPing-2,而籼稻品种mPing-2所占比例高于mPing-1一致[18]。mPing在水稻亚种基因组中分布比例和位置的差异,暗示mPing在水稻驯化历史中有着不可忽视的作用;同时,mPing有望作为一种分子标签来快速鉴别水稻亚种。另一方面,mPing往往会插入到基因中或者基因附近[14],为了研究mPing与侧翼基因的关系,本研究对mPing所在位置的上下游延伸5 kb序列进行功能基因的同源性探寻,发现日本晴中有24个序列与已知基因序列100%同源,93-11中有3个序列与已知基因100%同源,并且日本晴中有3个基因内部插入了mPing,这3个基因与抗性基因、漆酶基因和细胞分裂基因有关,暗示着mPing在调控这3类基因表达的过程中存在一定的潜在影响。同时,日本晴和93-11中除了1个已知基因相同,剩余基因不相同,说明这些原因可能是导致日本晴和93-11基因组差异性的原因。然而mPing的插入机制、它在宿主基因组中对侧翼基因表达的影响、及其在水稻进化历史中的作用,有待进一步探索和研究。

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