美国大灵芝（Ganoderma oregonense）转录组SSR位点的生物信息学分析

doi:10.13304/j.nykjdb.2017.0509

中国农业科技导报 ›› 2018, Vol. 20 ›› Issue (7): 48-55.DOI: 10.13304/j.nykjdb.2017.0509

美国大灵芝（Ganoderma oregonense）转录组SSR位点的生物信息学分析

陈诚1,刘晓飞2,李强3,王剑1,伏荣桃1,张鸿1,卢代华1*

1.四川省农业科学院植物保护研究所, 成都 610066; 2.四川省食品药品检验检测院, 成都 611731; 3.四川省农业科学院生物技术核技术研究所, 成都 610061

收稿日期:2017-08-09 出版日期:2018-07-15 发布日期:2017-11-03
作者简介:陈诚，研究实习员，硕士，研究方向为作物病害防控。E-mail：chenfungi@126.com。
基金资助:
农业部公益性行业专项（201503127）；四川省财政创新提升工程项目（2016GYSH-014）；四川省科技支撑计划项目（2014NZ0086）；成都市产业升级牵引工程项目（2015-NY02-00063-NC）资助。

Bioinformatic Analysis of Simple Sequence Repeat (SSR) Loci in Ganoderma oregonense Transcriptome

CHEN Cheng1, LIU Xiaofei2, LI Qiang3, WANG Jian1, FU Rongtao1, ZHANG Hong1, LU Daihua1*

1.Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu 610066; 2.Sichuan Institute for Food and Drug Control, Chengdu 611731; 3.Biotechnology and Nuclear Technology Research Insitute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China

Received:2017-08-09 Online:2018-07-15 Published:2017-11-03
Contact: *通信作者：卢代华，研究员，博士，研究方向为水稻病害防控。E-mail：453831354@qq.com

摘要/Abstract

摘要： 为了解美国大灵芝（Ganoderma oregonense）转录组中的简单重复序列（simple sequence repeat，SSR）位点信息，并为开发灵芝分子标记辅助育种技术奠定基础，将高通量转录组测序获得的美国大灵芝转录组数据通过Trinity软件拼接组装，再利用MISA软件分析其SSR位点信息。随后采用Primer 3根据SSR位点设计特异性鉴别引物，并以灵芝DNA为模板，对其有效性进行验证。共获得65 064条单基因簇（unigene），在其中2 981条unigene中检测到3 380个符合软件参数的SSR位点，发生频率为5.19%，平均分布距离为12.60 kb。美国大灵芝转录组SSR位点总长度为52 168 bp，平均长度为15 bp。单核苷酸、三核苷酸是美国大灵芝转录组SSR的主要重复类型，分别占总SSR的35.33%和38.67%。SSR基元重复次数范围为5~73次，其中5次重复的发生次数最高。SSR重复基元共有98个类型，其中C/G是最常见的重复基元，比例为17.72%，其次是A/T，比例为17.60%。针对3 380个SSR位点设计出2 324对SSR引物，随机选择15对引物对3种灵芝栽培品种进行PCR扩增，10对引物可稳定扩增出条带，其中8对在3个灵芝栽培品种中表现出多态性。说明美国大灵芝转录组SSR位点多态性丰富，对灵芝的功能基因挖掘、分子标记辅助育种开发以及遗传多样性分析等具有重要意义。

关键词: 灵芝, 转录组, SSR, 多态性

Abstract: In order to investigate the simple sequence repeat (SSR) loci information in Ganoderma oregonense transcriptome, and lay a foundation for molecular marker-assisted breeding of Ganoderma, this paper assembled transcriptome data of G. oregonense obtained by high-throughput transcriptome sequencing using Trinity software; and then analyzed SSR information by MISA software. The SSR loci specific primers were designed by primer 3, and their effectiveness was verified taking G. Oregonense DNA as template. A total of 65 064 unigenes were obtained, among which 3 380 SSRs were found distributing in 2 981 unigenes with 5.19% frequency of occurrence. The average distribution distance was 12.60 kb. The total length of G. Oregonense transcriptome SSR loci was 52 168 bp, and the average length was 15 bp. Mononucleotide and trinucleotide repeats were the main SSR types, accounting for 35.33% and 38.67%, respectively. The number range of SSR loci repeats was 5~73, and 5 repeats among them had the highest number of occurrence. There were 98 types of repeat motifs in the G. oregonense transcriptome, among which C/G was the commonest repeat element, accounting for 17.72%, followed by A/T with 17.60% proportion. 2 324 pairs of SSR primers were designed for 3 380 SSR loci using primer-design software, and 15 primer pairs were selected at random to be amplified by PCR on 3 cultivated Ganoderma varieties. 10 pairs of primers were successfully amplified, and 8 of them showed allelic polymorphism among these 3 cultivated varieties, indicating that the transcriptomic SSR loci polymorphism of G.oregonense was abundant. These results were of important significance in excavating functional gene, developing molecular marker-assisted breeding, and analyzing genetic diversity of Ganoderma.

Key words: Ganoderma oregonense, transcriptome, SSR, polymorphism

陈诚1,刘晓飞2,李强3,王剑1,伏荣桃1,张鸿1,卢代华1*. 美国大灵芝（Ganoderma oregonense）转录组SSR位点的生物信息学分析[J]. 中国农业科技导报, 2018, 20(7): 48-55.

CHEN Cheng1, LIU Xiaofei2, LI Qiang3, WANG Jian1, FU Rongtao1, ZHANG Hong1, LU Daihua1*. Bioinformatic Analysis of Simple Sequence Repeat (SSR) Loci in Ganoderma oregonense Transcriptome[J]. Journal of Agricultural Science and Technology, 2018, 20(7): 48-55.

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美国大灵芝（Ganoderma oregonense）转录组SSR位点的生物信息学分析

Bioinformatic Analysis of Simple Sequence Repeat (SSR) Loci in Ganoderma oregonense Transcriptome

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