Method of developing elderberry SSR primer on the basis of transcriptome sequencing

A technology of transcriptome sequencing and elderberry, which is applied in the fields of molecular biology and bioinformatics, can solve the problems of less comprehensive utilization, insufficient resource utilization, and more medicinal uses, and achieve the effect of fast method

Active Publication Date: 2018-12-14
SHANDONG FOREST SCI RES INST
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Problems solved by technology

my country's elderberry resources are very rich, it has strong adaptability, cold resistance, drought resistance, and disease resistance, but most of them sleep in the mountains and forests and have not been utilized. The development and utilization of elderberry plants in my country is still in its infancy. Resources Insufficient utilization, only medicinal use, other comp...

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  • Method of developing elderberry SSR primer on the basis of transcriptome sequencing
  • Method of developing elderberry SSR primer on the basis of transcriptome sequencing
  • Method of developing elderberry SSR primer on the basis of transcriptome sequencing

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Embodiment

[0078] 1 Materials and methods

[0079] 1.1 Transcriptome data sources

[0080] The Western Elderberry transcriptome data comes from the results of Illumina HiSeq 2000 high-throughput sequencing of an adult Western Elderberry fruit carried out by our research group in 2016. During the sequencing, the fruits of three developmental stages (green fruit, mid-ripening, and late-maturing) were used to extract RNA and entrust Beijing Nuohezhiyuan Gene Co., Ltd. to perform RNA-Seq transcriptome sequencing, and assembled 257,975 Unigenes by De Novo method for analysis. background data.

[0081] 1.2 Transcriptome SSR site identification

[0082] The Western elderberry transcriptome data was spliced ​​using Trinity software, and the spliced ​​transcript sequence information was stored in FASTA format. The main splicing parameters were SS_lib_type, min_kmer_cov, and min_glue. The Unigenes library was obtained by splicing, and the SSR site search was performed on the mixed Unigenes libr...

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Abstract

The invention provides a method of developing elderberry SSR primer on the basis of transcriptome sequencing. The method includes: S1) establishing and sequencing elderberry transcriptome library andsplicing and jointing sequencing results to form a complete transcriptome, and with the longest transcript in every gene being Unigene, splicing the Unigenes to form a blend Unigenes library; S2) performing SSR detection to the blend Unigenes library in the step S1); S3) performing SSR primer design and identifying the polymorphism of the SSR primer. In the invention, 64148 pairs of SSR specific primers are designed, wherein through experimenal optimization, a fluorescent SSR-PCR optimum system of golden elder is acquired; among the synthesized 100 pairs of the fluorescence label SSR primers,25 pairs of primers show excellent polymorphism. The method of developing elderberry SSR primer on the basis of transcriptome sequencing is quick and accurate.

Description

technical field [0001] The invention belongs to the technical fields of molecular biology and bioinformatics, and in particular relates to a method for developing elderberry SSR primers based on transcriptome sequencing. Background technique [0002] Simple sequence repeat (SSR) is a kind of simple tandem repeat sequence composed of 1-6 bases, which is widely distributed in eukaryotic and prokaryotic genomes. According to the source of SSR, it can be divided into EST-SSR and genomic SSR. The traditional use of genomic data to develop SSR markers has the disadvantages of high cost, cumbersome test steps, and fewer sites. In recent years, with the reduction of sequencing costs, transcriptome sequencing has become One of the short and fast ideas for studying molecular biology-related content, the transcriptome data of different plants have been developed and utilized one after another, and there are more and more studies on the development of SSR markers in different plants bas...

Claims

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Application Information

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IPC IPC(8): C12Q1/6895C12Q1/686C12N15/11
CPCC12Q1/686C12Q1/6895C12Q2600/13C12Q2600/156C12Q2525/151
Inventor 姚俊修吴德军李善文燕丽萍王因花刘翠兰任飞李庆华
Owner SHANDONG FOREST SCI RES INST
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