粗柄羊肚菌转录组的SSR分布和序列特征分析
Distribution and sequence characteristics of SSR in transcriptome of Morchella crassipes
-
摘要: 基于第二代转录组测序技术，对采集自河南省新郑市的粗柄羊肚菌（Morchella crassipes）M10菌株进行了深度转录组测序，分析了全转录组简单重复序列SSR（simple sequence repeat）分布和序列特征.结果表明：1）总计检测到13 044个SSR位点，分布在8851条Trinity genes中，SSR在转录组序列中的平均密度为2067.77 bp/个，远高于其他真菌，其中2858条Trinity genes中包含超过1个SSR位点，复合型SSR位点1925个.2）单碱基重复基元最多，为8600个，其中A/T重复类型远高于C/G重复类型，与多数大型真菌相同；其次是三碱基重复基元，为2497个，其中ACC/GGT，AGC/CTG和AGG/CCT重复类型占60%以上，且明显以GC的高频概率出现，在SSR分子标记或其他重复序列多态性标记的开发上，可优选富含GC的SSR设计引物.Abstract: The transcriptome of Morchella crassipes M10 collected from Xinzheng of He'nan Province was sequenced by the next generation sequencing technology,and distribution characteristic of simple sequence repeats (SSR) were analyzed.The results showed that:1) A total of 13 044 SSR sites were detected,which was distributed in 8851 Trinity genes,about 2858 Trinity genes had more than one SSR loci and the number of compound formation SSR loci was 1925.The average density of SSR loci was 2067.77 bp/piece in the transcriptome sequence of Morchella crassipes, which was much higher than that of other fungi. 2) The number of single base repeat motif was 8600, the largest one, among which the number of A/T repeat types was higher than C/G repeat types and the same as most macro-fungi;the number of tri-nucleotide (TGC) repeat motif was 2497, among which ACC/GGT,AGC/CTG and AGG/CCT accounted for 60% and obviously appeared with GC high probability. In the development of SSR molecular marker or other repeat polymorphic marker, SSR abundant with GC could be chosen as the best primers.
-
-
[1]
KALIA R K,RAI M K,KALIA S,et al.Microsatellite markers:an overview of the recent progress in plants[J].Euphytica,2011,177(3):309.
-
[2]
POWELL W,MACHRAY G C,PROVAN J.Polymorphism revealed by simple sequence repeats[J].Trends in Plant Science,1996,1(7):215.
-
[3]
李炎林,杨星星,张家银,等.南方红豆杉转录组SSR挖掘及分子标记的研究[J].园艺学报,2014,41(4):735.
-
[4]
王燕龙,姜言生,曲志才,等.SSR分子标记在作物种质资源鉴定中的应用[J].山东农业科学,2012,44(10):11.
-
[5]
QU J,HUANG C,ZHANG J.Genome-wide functional analysis of SSR for an edible mushroom Pleurotus ostreatus[J].Gene,2016,575:524.
-
[6]
QIAN J,XU H,SONG J,et al.Genome-wide analysis of simple sequence repeats in the model medicinal mushroom Ganoderma lucidum[J].Gene,2013,512(2):331.
-
[7]
周雁,范秀芝,陈连福,等.SSR在黑木耳和毛木耳转录组中的分布和序列特征[J].菌物学报,2014,33(2):280.
-
[8]
何海,郭继云,马毅平,等.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.
-
[9]
何培新,刘伟,蔡英丽,等.我国人工栽培和野生黑色羊肚菌的菌种鉴定及系统发育分析[J].郑州轻工业学院学报(自然科学版),2015,30(3/4):26.
-
[10]
DALGLEISH H J,JACOBSON K M.A first assessment of genetic variation among Morchella esculenta (Morel) populations[J].Journal of Heredity,2005,96(4):396.
-
[11]
SINGH S K,KAMAL S,TIWARI M,et al.Arbitrary primer based RAPD-A useful genetic marker for species identification in morels[J].Journal of Plant Biochemistry and Biotechnology,2004,13(1):7.
-
[12]
BUNYARD B A,NICHOLSON M S,ROYSE D J.A systematic assessment of Morchella using RFLP analysis of the 28S ribosomal RNA gene[J].Mycologia,1994,88(6):762.
-
[13]
BUSCOT F,WIPF D,DI BATTISTA C,et al.DNA polymorphism in morels:PCR/RFLP analysis of the ribosomal DNA spacers and microsatellite-primed PCR[J].Mycological Research,1996,100(1):63.
-
[14]
PAGLIACCIA D,DOUHAN G W,DOUHAN L A,et al.Development of molecular markers and preliminary investigation of the population structure and mating system in one lineage of black morel (Morchella elata) in the Pacific Northwestern USA[J].Mycologia,2011,103(5):969.
-
[15]
何培新,刘伟.粗柄羊肚菌分子鉴定及羊肚菌属真菌系统发育分析[J].江苏农业学报,2010,26(2):395.
-
[16]
税丕容,郑晓冰,林俊芳,等.简便高质量的食用菌总RNA提取方法[J].食用菌学报,2008,15(1):32.
-
[17]
李满堂,张仕林,邓鹏,等.洋葱转录组SSR信息分析及其多态性研究[J].园艺学报,2015,42(6):1103.
-
[18]
王东,曹玲亚,高建平.党参转录组中SSR位点信息分析[J].中草药,2014,45(16):2390.
-
[19]
鄢秀芹,鲁敏,安华明.刺梨转录组SSR信息分析及其分子标记开发[J].园艺学报,2015,42(2):341.
-
[20]
LI R,ZHU H,RUAN J,et al.De novo assembly of human genomes with massively parallel short read sequencing[J].Genome Research,2010,20(2):265.
-
[1]
-
点击查看大图
计量
- PDF下载量: 79
- 文章访问数: 2471
- 引证文献数: 0
下载:
