基于马铃薯腐烂茎线虫基因组的SSR信息分析
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摘要
为了研究马铃薯腐烂茎线虫在我国的遗传关系,获得稳定的马铃薯腐烂茎线虫分子标记,使用MISA软件对马铃薯腐烂茎线虫全基因组1 761个scaffolds进行搜索,共获得9 745个SSR位点,平均11.40 kb出现一个SSR。在重复基元中,单核苷酸基元出现频率最高(83.06%),其次为二核苷酸重复基元(10.62%);除单核苷酸重复基元外出现次数最多的重复基元是AT/AT(5.36%)。马铃薯腐烂茎线虫基因组SSR位点长度小于12 bp分布最为广泛,占总SSR的59.67%,长度大于30 bp的最少,共有114个,仅占1.17%。研究表明,利用马铃薯腐烂茎线虫基因组数据可作为开发SSR标记的有效来源,为进一步开发马铃薯腐烂茎线虫SSR标记奠定了基础。
In order to study the genetic relation of Ditylenchus destructor Thorne in China, and to obtain their stable molecular marker, the software MISA was used to search and analyze a total of 1 761 scaffolds of whole genome sequences of 9 745 SSR of D. destructor Thorne. This was equivalent to 1 SSR per 11.40 kb genome sequence. In the SSRs, the mononucleotide repeat motifs were the most abundant(83.06%), followed by dinucleotide repeat motifs(10.62%). In additon to mononucleotide repeats, AT/AT was the most frequent repeat unit(5.36%). The SSR which had a length less than 12 bp accounted for 59.67% of total SSR, while the number of SSR over 30 bp was 114, only accounting for 1.17% at the lowest proportion. The results indicated that the genomic data of D.destructor Thorne could be used as an effective source for the development of SSR markers, which could serve as a foundation for the further development of SSR markers.
In order to study the genetic relation of Ditylenchus destructor Thorne in China, and to obtain their stable molecular marker, the software MISA was used to search and analyze a total of 1 761 scaffolds of whole genome sequences of 9 745 SSR of D. destructor Thorne. This was equivalent to 1 SSR per 11.40 kb genome sequence. In the SSRs, the mononucleotide repeat motifs were the most abundant(83.06%), followed by dinucleotide repeat motifs(10.62%). In additon to mononucleotide repeats, AT/AT was the most frequent repeat unit(5.36%). The SSR which had a length less than 12 bp accounted for 59.67% of total SSR, while the number of SSR over 30 bp was 114, only accounting for 1.17% at the lowest proportion. The results indicated that the genomic data of D.destructor Thorne could be used as an effective source for the development of SSR markers, which could serve as a foundation for the further development of SSR markers.
引文
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[6] Muys C,Thienpont C N,Dauchot N,et al.Integration of AFLPs,SSRs and SNPs markers into a new genetic map of industrial chicory(Cichorium intybus L.var.sativum)[J].Plant Breeding,2014,133(1):130-137
[7] Eoche-Bosy D,Gauthier J,Juhel A S,et al.Experimentally evolved populations of the potato cyst nematode Globodera pallida allow the targeting of genomic footprints of selection due to host adaptation[J].Plant Pathology,2017,66(6):1022-1030
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[9] Takeuchi T,Yamaguchi M,Tanaka R,et al.Development and validation of SSR markers for the plant-parasitic nematode Subanguina moxaeusing genome assembly of illumina pair-end reads[J].Nematology,2015,17(5):515-522
[10] Wang G,Li E F,Mao Z C,et al.Development of polymorphic microsatellites for Meloidogyne incognita,through screening predicted microsatellite loci based on genome sequence[J].Genetika,2015,51(1):128-132
[11] 季镭,王金成,杨秀丽,等.3种茎线虫rDNA区的PCR-RFLP分析[J].南京农业大学学报,2006,29(3):39-43
[12] 黄文坤,何旭峰,丁中,等.马铃薯腐烂茎线虫的遗传变异及其与生态因子的相关性[J].农业生物技术学报,2012,20(1):62-69
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[14] 许峻荣,吴小芹,刘云,等.基于松材线虫全基因组序列的SSR标记开发[J].南京林业大学学报,2014,38(2):36-42
[15] Wang H M,Zhao H H,Zhao C Z,et al.EST-SSR markers from Heterodera glycines Ichinohe[J].Genetika,2014,50(10):1259-1262
[16] Wang X,Ma J,Liu H,et al.Development and characterization of EST-derived SSR markers in the cereal cyst nematode Heterodera avenae[J].European Journal of Plant Pathology,2018,150(1):105-113
[17] Metzgar D,Bytof J,Wills C.Selection against frameshift mutations limits microsatellite expansion in coding DNA[J].Genome Research,2000,10(1):72-80
[18] Temnykh S,DeClerck G,Lukashova A,et al.Computational and experimental analysis of microsatellites in rice(Oryza sativa L.):frequency,length variation,transposon associations,and genetic marker potential[J].Genome research,2001,11(8):1441-1452