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Position: Home > Articles > Sequencing and Analysis of the Transcriptome of Asplenium nidus Acta Horticulturae Sinica 2014,41 (11) 2329-2341

鸟巢蕨转录组高通量测序及分析

作  者：
贾新平;孙晓波;邓衍明;梁丽建;叶晓青
单  位：
江苏省农业科学院农业生物技术研究所;江苏省农业生物学重点实验室
关键词：
鸟巢蕨;转录组;生物信息学;功能注释;SSR
摘  要：
采用新一代高通量测序技术Illumina Hi Seq 2000对鸟巢蕨转录组(Asplenium nidus)进行测序,共获得29 254 595个序列读取片段(reads),包含了5 908 586 517个碱基序列(bp)信息。对reads进行序列组装,共获得42 907个单基因簇(Unigene),平均长度936 bp,序列信息达到了40.16 Mb。数据库中的序列同源性比较表明,24 993个Unigene与其他物种的已知基因具有不同程度的同源性。鸟巢蕨转录组中的Unigene根据GO功能大致可分为细胞组分、分子功能和生物学过程3大类51个分支,其中有大量的Unigene与代谢进程、结合活性、催化活性和细胞进程相关。将Unigene与COG数据库进行比对,根据其功能大致可分为24类。KEGG数据库作为参考,依据代谢途径可将Unigene定位到116个代谢途径分支。SSR位点查找发现,从42 907个Unigene中共找到6 067个SSR位点。SSR不同重复基序类型中,出现频率最高的为AG/CT,其次是AC/GT、A/T和AGG/CCT。针对这些序列,设计了20对引物进行了扩增效率和多态性检测,其中7对引物在不同蕨类材料中表现出多态性。
译  名：
Sequencing and Analysis of the Transcriptome of Asplenium nidus
作  者：
JIA Xin-ping;SUN Xiao-bo;DENG Yan-ming;LIANG Li-jian;YE Xiao-qing;Provincial Key Laboratory of Agro Biology,Institute of Agro-biotechnology,Jiangsu Academy of Agricultural Sciences;
关键词：
Asplenium nidus;;transcriptome;;bioinformatics;;gene annotation;;simple sequence repeat
摘  要：
The transcriptome of Asplenium nidus was sequenced by Illumina Hi Seq 2000 platform that is a new generation of high-throughput sequencing technology to study the expression profiling and predict the functional genes. The target sample sequencing,a total of 29 254 595 reads fragment contains 5 908 586 517 bp in sequence information were generated. A total of 42 907 unigenes contains 40.16 Mb in sequence information were formed by initial sequence splicing,with an average read length of 936 bp. 24 993 unigenes were annotated using BLASTX searches against the Nr and Swiss Prot databases. In this study,all assembled unigenes can be broadly divided into biological processes,cellular components and molecular function categories of 51 branches by gene ontology,including metabolic process,binding,catalytic activity and cellular process. Unigenes were further annotated based on COG category,which could be grouped into 24 functional categories. KEGG pathway analysis showed that unigenes can be broadly divided into 116 classes according to the function. There were 6 067 SSR in 42 907 unigenes were found. The types of SSR were analyzed that AG/CT was the highest repeat,following by AC/GT,A/T and AGG/CCT. Based on flank sequence of detected SSR,20 primer pairs were designed and tested for the amplification efficiency and polymorphism. The results showed that 7 primer pairs showed polymorphism among different fern varieties.

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