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Related Concept Videos

RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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SSR marker development in Clerodendrum trichotomum using transcriptome sequencing.

Gongwei Chen1, Yuanzheng Yue1, Yajie Hua1

  • 1College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China.

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|November 21, 2019
PubMed
Summary
This summary is machine-generated.

This study generated extensive transcriptome data and identified numerous simple sequence repeats (SSRs) in Clerodendrum trichotomum. These molecular resources are crucial for germplasm conservation and future genetic studies of this ornamental plant.

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Area of Science:

  • Botany
  • Molecular Biology
  • Genomics

Background:

  • Clerodendrum trichotomum, a Lamiaceae family ornamental plant, has limited molecular research despite its wide distribution and applications.
  • Existing studies focus on growth, stress, and pharmacology, necessitating molecular investigations for conservation and utilization.

Purpose of the Study:

  • To establish comprehensive transcriptome resources for Clerodendrum trichotomum.
  • To identify and characterize simple sequence repeat (SSR) markers for genetic analysis and germplasm conservation.

Main Methods:

  • RNA sequencing was employed to generate the transcriptome data.
  • Unigene annotation, classification, and SSR mining were performed using bioinformatic tools (MIcroSAtellite, Oligo 6.0).
  • Primer pairs were designed and validated for SSR polymorphism.

Main Results:

  • Generated over 127 million high-quality reads, yielding 58,345 non-redundant unigenes, with 63.24% annotated.
  • Identified 6,444 SSRs within 5,530 unigenes.
  • Designed 200 primer pairs, with 30 selected for polymorphism screening, revealing high polymorphism rates (197 out of 200 alleles).

Conclusions:

  • This study provides a substantial dataset of unigenes and SSRs for Clerodendrum trichotomum.
  • The identified SSR markers are valuable for germplasm conservation, genetic diversity assessment, and molecular breeding.
  • These findings lay a foundation for advanced molecular biology research in C. trichotomum.