摘要
采用新一代高通量测序技术Illumina Hi Seq 2000对铁皮石斛(Dendrobium officinale)转录组进行测序,共获得11 153 295 000 nt数据。对测序获得数据(reads)进行序列拼接组装,共获得121 596个单基因簇,序列平均长度为660 bp,整体序列信息达到了40.16 Mb。再应用生物信息学相关数据库进行比对,结果表明,本测定获得的52 345个Unigene能够在数据库中检索到相关功能注释。通过GO数据库比对,测序获得Unigene功能分类可分为3大类57个分支,其中有大量的Unigene与细胞、催化活性、细胞部分、细胞器等相关功能。通过COG数据库比对,测序获得Unigene功能注释到25类直系同源蛋白分类中如转录、复制,重组和修复、翻译,核糖体结构和生物起源等。以KEGG数据库作为参考,依测序获得Unigene可定位到128个代谢途径分支,如脂类代谢、氨基酸代谢、碳水化合物代谢等。进一步利用软件查找SSR位点发现,从Unigene中共找到9 892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AAG/CTT、CCG/CGG和AGG/CCT。
The transcriptome of Dendrobium officinale 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 reads fragment contains 11 153 295 000 nt in sequence information were generated. A total of 121 596 unigenes contains 40.16 Mb in sequence information were formed by initial sequence splicing, with an average read length of 660 bp. 52 345 unigenes were annotated searches against the bioinformatics databases. All assembled unigenes can be broadly divided into 3 types and 57 branches by gene ontology, including cell, catalytic activity, cell part and organelle, etc. Unigenes were further annotated based on COG category, which could be grouped into 25 functional categories, for example, replication, recombination and repair, transcription, translation, ribosomal structure and biogenesis, etc. KEGG pathway analysis showed that unigenes can be broadly divided into 128 classes according to the function, for example, lipid metabolism, amino acid metabolism, carbohydrate metabolism, etc. There were 9 892 SSR in all unigenes were found. The types of SSR were analyzed that AG/CT was the highest repeat, following by AAG/CTT、CCG/CGG and AGG/CCT.
出处
《分子植物育种》
CAS
CSCD
北大核心
2016年第12期3334-3346,共13页
Molecular Plant Breeding
基金
浙江省自然科学基金项目(LQ14C160001)资助
关键词
铁皮石斛转录组
生物信息学
功能注释
SSR
Dendrobium officinale
Transcriptome
Bioinformatics
Gene annotation
Simple sequence repeat
