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[1]李强,陈诚,熊川,等.杏鲍菇转录组数据SSR位点的生物信息学分析[J].应用与环境生物学报,2017,23(03):454-458.[doi:2016.05014]
 LI Qiang,CHEN Cheng,XIONG Chuan,et al.Bioinformatic analysis of simple sequence repeat (SSR) loci in the Pleurotus eryngii transcriptome[J].Chinese Journal of Applied & Environmental Biology,2017,23(03):454-458.[doi:2016.05014]
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杏鲍菇转录组数据SSR位点的生物信息学分析()
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《应用与环境生物学报》[ISSN:1006-687X/CN:51-1482/Q]

卷:
23卷
期数:
2017年03期
页码:
454-458
栏目:
研究论文
出版日期:
2017-06-25

文章信息/Info

Title:
Bioinformatic analysis of simple sequence repeat (SSR) loci in the Pleurotus eryngii transcriptome
作者:
李强陈诚熊川陈祖琴金鑫黄文丽
1四川省农业科学院生物技术核技术研究所 成都 610061 2四川省农业科学院植物保护研究所 成都 610066 3四川大学生命科学学院 成都 610065
Author(s):
LI Qiang CHEN Cheng XIONG Chuan CHEN Zuqin JIN Xin & HUANG Wenli
1Institute of Biological & Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China 2Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China 3School of Life Science, Sichuan University, Chengdu 610065, China
关键词:
杏鲍菇转录组SSR分子标记遗传多样性
Keywords:
Pleurotus eryngii transcriptome SSR molecular markers genetic diversity
分类号:
Q811.4 : Q949.329.810.3
DOI:
2016.05014
摘要:
为了开发杏鲍菇分子标记,利用前期高通量测序技术获得的杏鲍菇转录组数据,采用生物信息学软件Trinity拼接,然后通过MISA软件检索并分析杏鲍菇转录组简单重复序列(Simple sequence repeats,SSR)位点. 共获得45 833条unigene,在其中的3 256条unigene中检测到3 811条符合软件参数的SSR序列,发生频率为8.31%. SSR位点平均长度为15 bp,平均分布频率是1/15.91 kb. 在杏鲍菇转录组的SSRs中,单核苷酸与三核苷酸重复基元为主要重复类型,分别占总SSRs的45.24%和35.53%. SSR基元的重复次数为5-24次,其中5次或10次重复是发生频率最高的,SSR重复基元共有85个类型,其中A/T是最常见的重复基元,比例为38.97%,其次为AG/CT,比例为8.24%. 对3 811个SSR位点设计出3 644对SSR引物,随机选择20对引物进行PCR扩增,其中9对在3个杏鲍菇品种中表现出多态性. 本研究表明杏鲍菇转录组SSR位点多态性丰富,具有较高的应用潜力. (图3 表2 参25)
Abstract:
The aim of this study was to develop simple sequence repeat (SSR) molecular markers of Pleurotus eryngii. The transcriptome of P. eryngii was determined by high-throughput RNA sequencing, and unigenes were assembled using Trinity software. Then, SSR loci were analyzed using MISA software. Overall, 45?833 unigenes were assembled from the transcriptome data, and 3?811 SSRs were detected as distributed among 3?256 unigenes, accounting for 8.31% of all unigenes. The average length of the transcriptomic SSRs was 15 bp. The average distribution distance of SSRs was 15.91 kb. Mononucleotide and trinucleotide repeats were the main SSR types, accounting for 45.24% and 35.53%, respectively. The number of SSR locus repeats was 5–24, and the most common SSR loci contained 5 or 10 repeats. There were 85 kinds of repeat motifs in the P. eryngii transcriptome, with A/T and AG/CT being the most frequent motifs, accounting for 38.97% and 8.24%, respectively, of all the SSR repeat motifs. A total of 3?644 pairs of SSR primers were designed for 3?811 SSR loci and twenty pairs of primers were randomly selected to evaluate their application and the polymorphism across three P. eryngii accessions. All the primer pairs successfully amplified the DNA fragments. Nine of the 20 microsatellite loci showed allelic polymorphism. The results show that the polymorphism of P. eryngii transcriptomic SSR loci is rather high; this finding has important implications for the development of molecular markers of P. eryngii and for the research on genetic diversity of P. eryngii.

参考文献/References:

1 Mau JL, Lin YP, Chen PT, Wu YH, Peng JT. Flavor compounds in king oyster mushrooms Pleurotus eryngii [J]. J Agric Food Chem, 1998, 46 (11): 4587-4591
2 Guillén F, Mu?oz C, Gómez-Toribio V, Martínez AT, Martínez MJ. Oxygen activation during oxidation of methoxyhydroquinones by laccase from Pleurotus eryngii [J]. Appl Environ Microbiol, 2000, 66 (1): 170-175
3 Kim SW, Kim HG, Lee BE, Hwang HH, Baek DH, Ko SY. Effects of mushroom, Pleurotus eryngii, extracts on bone metabolism [J]. Clin Nutr, 2006, 25 (1): 166-170
4 Carbonero ER, Gracher AHP, Smiderle FR, Rosado FR, Sassaki GL, Gorin PA, Iacomini M. A β-glucan from the fruit bodies of edible mushrooms Pleurotus eryngii and Pleurotus ostreatoroseus [J]. Carbohyd Polym, 2006, 66 (2): 252-257
5 Mori K, Kobayashi C, Tomita T, Inatomi S, Ikeda M. Antiatherosclerotic effect of the edible mushrooms Pleurotus eryngii (Eringi), Grifola frondosa (Maitake), and Hypsizygus marmoreus (Bunashimeji) in apolipoprotein E-deficient mice [J]. Nutr Res, 2008, 28 (5): 335-342
6 Deng W, Cao X, Wang Y, Yu Q, Zhang Z, Qu R, Yu J. Pleurotus eryngii polysaccharide promotes pluripotent reprogramming via facilitating epigenetic modification [J]. J Agric Food Chem, 2016, 64 (6): 1264-1273
7 Ro HS, Kim SS, San Ryu J, Jeon CO, Lee TS, Lee HS. Comparative studies on the diversity of the edible mushroom Pleurotus eryngii: ITS sequence analysis, RAPD fingerprinting, and physiological characteristics [J]. Mycol Res, 2007, 111 (6): 710-715
8 Zervakis GI, Venturella G, Papadopoulou K. Genetic polymorphism and taxonomic infrastructure of the Pleurotus eryngii species-complex as determined by RAPD analysis, isozyme profiles and ecomorphological characters [J]. Microbiology, 2001, 147 (11): 3183-3194
9 许峰, 刘宇, 尹永刚, 王守现, 张英春, 赵爽, 耿小丽. 北京地区杏鲍菇菌株遗传多样性的RAPD分析[J]. 中国食用菌, 2012, 31 (6): 35-37 [Xu F, Liu Y, Yin YG, Wang SX, Zhang YC, Zhao S, Gen XL. RAPD analysis of Pleurotus eryngii strains in Beijing region [J]. Edible Fungi China, 2012, 31 (6): 35-37]
10 宿红艳, 王磊, 刘林德, 迟晓燕, 许珊珊, 蔡德华. RF-RAPD分子标记在杏鲍菇菌株鉴定上的应用[J]. 食品科学, 2008, 29 (3): 264-267 [Su HY, Wang L, Liu LD, Chi XY, Xu SS, Cai DH. Application of RF-RAPD in identification of Pleurotus eryngii strains [J]. Chin Food Sci, 2008, 29 (3): 264-267]
11 冯伟林, 蔡为明, 金群力, 范丽军. ISSR分子标记分析杏鲍菇菌株遗传差异研究[J]. 中国食用菌, 2009, 28 (1): 47-49 [Feng WL, Cai WM, Jin QL, Fan LJ. Analysis of genetic variation of Pleurotus eryngii strains by ISSR marker [J]. Edible Fungi China, 2009, 28 (1): 47-49]
12 Aldrich PR, Hamrick J, chavarriaga P, Kochert G. Microsatellite analysis of demographic genetic structure in fragmented populations of the tropical tree Symphonia globulifera [J]. Molec Ecol, 1998, 7 (8): 933-944
13 Morgante M, Olivieri A. PCR-amplifi ed microsatellites as markers in plant genetics [J]. Plant J, 1993, 3 (1): 175-182
14 Pinto LR, Oliveira KM, Marconi T, Garcia AAF, Ulian EC, De Souza AP. Characterization of novel sugarcane expressed sequence tag microsatellites and their comparison with genomic SSRs [J]. Plant Breeding, 2006, 125 (4): 378-384
15 Kalia RK, Rai MK, Kalia S. Microsatellite markers: an overview of the recent progress in plants [J]. Euphytica, 2011, 177 (3): 309-334
16 孙蛟龙, 方扬, 靳艳玲, 马欣荣, 陶向, 赵海. 浮萍转录组数据SSR位点的生物信息学分析[J]. 应用与环境生物学报, 2015,21 (3): 401-405 [Sun JL, Fang Y, Jin YL, Ma XR, Tao X, Zhao H. Bioinformatic analysis on SSR information in duckweed transcriptome [J]. Chin J Appl Environ Biol, 2015,21 (3): 401-405]
17 Emnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential [J]. Genome Res, 2001, 11 (8): 1441-1452
18 Dreisigacker S, Zhang P, Warburton ML. SSR and pedigree analyses of genetic diversity among CIMMYT wheat lines targeted to different megaenvironments [J]. Crop Sci, 2004, 44 (2): 381-388
19 Zhou Y, Chen L, Fan X, Bian Y. De novo assembly of Auricularia polytricha transcriptome using Illumina sequencing for gene discovery and SSR marker identification [J]. PLoS ONE, 2014, 9 (3): e91740
20 何海, 郭继云, 马毅平, 周梦春, 王沫, 舒少华. 茯苓转录组SSR序列特征及其基因功能分析[J]. 中草药, 2015, 46 (23): 3558-3563 [He H, Guo JY, Ma YP, Zhou MC, Wang M, Shu SH. Characterization and gene function analysis of SSR sequences in Poria cocos transcriptome [J]. Chin Trad Herb Drugs, 2015, 46 (23): 3558-3563]
21 袁卫东, 陆娜, 陈青, 宋吉玲, 王伟科. 灰树花子实体转录组测序和分析[J]. 复旦学报(自然科学版), 2015, 54 (5): 673-678 [Yuan WD, Lu N, Chen Q, Song JL, Wang WK. Analysis on transcriptome sequenced of Maitake [J]. J Fudan Univ (Nat Sci), 2015, 54 (5): 673-678]
22 杨华, 陈琪, 韦朝领, 史成颖, 方从兵, 宛晓春. 茶树转录组中SSR位点的信息分析[J]. 安徽农业大学学报, 2012, 38 (6): 882-886 [Yang H, Chen Q, Wei CL, Shi CY, Fang CB, Wan XC. Analysis on SSR information in Camellia sinensis transcriptom e[J]. J Anhui Agric Univ, 2012, 38 (6): 882-886]
23 Chen C, Zhou P, Choi YA, Huang S, Gmitter Jr FG. Mining and characterizing microsatellites from citrus ESTs [J]. Theor Appl Genet, 2006, 112 (7): 1248-1257
24 Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R. Computational and experimental characterization of physically clustered simple sequence repeats in plants [J]. Genetics, 2000, 156 (2): 847-854
25 孟蒙, 唐维, 刘嘉, 黄胜雄, 余进德, 刘方方, 林琳, 张霞, 刘永胜. 基于中华猕猴桃“红阳”转录组序列开发EST-SSR分子标记[J]. 应用与环境生物学报, 2014, 20 (4): 564-570 [Meng M, Tang W, Liu J, Huang SX, Yu JD, Liu FF, Lin L, Zhang X, Liu YS. Development of EST-SSR markers in Actinidia chinesis cv ‘Hongyang’ based on transcriptomic sequences [J]. Chin J Appl Environ Biol, 2014, 20 (4): 564-570]

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更新日期/Last Update: 2017-06-25