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Related Concept Videos

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In order to produce glucose, plants need to capture sufficient light energy. Many modern plants have evolved leaves specialized for light acquisition. Leaves can be only millimeters in width or tens of meters wide, depending on the environment. Due to competition for sunlight, evolution has driven the evolution of increasingly larger leaves and taller plants, to avoid shading by their neighbors with contaminant elaboration of root architecture and mechanisms to transport water and nutrients.
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Related Experiment Video

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IR-TEx: An Open Source Data Integration Tool for Big Data Transcriptomics Designed for the Malaria Vector Anopheles gambiae
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Elucidating and mining the Tulipa and Lilium transcriptomes.

Natalia M Moreno-Pachon1, Hendrika A C F Leeggangers1, Harm Nijveen1,2

  • 1Physiology of Flower Bulbs, Department of Plant Physiology, Wageningen University, Wageningen, Netherlands.

Plant Molecular Biology
|July 9, 2016
PubMed
Summary
This summary is machine-generated.

Generating high-quality transcriptomes for tulip and lily provides valuable gene content data for these complex genomes. This open-access resource aids future genomics research in bulbous plants.

Keywords:
De novo assemblyGenesLily (Lilium sp)SequencingTranscriptome browserTulip (Tulip sp)

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Area of Science:

  • Genomics
  • Bioinformatics
  • Plant Science

Background:

  • Large, complex genomes in plants like tulips and lilies pose challenges for complete genome sequencing.
  • Transcriptome sequencing offers a viable alternative for studying gene content in such species.

Purpose of the Study:

  • To create high-quality, open-access transcriptomes for tulip and lily.
  • To develop a user-friendly web interface for accessing this genomic data.
  • To demonstrate the utility of the transcriptomes for identifying gene families, such as transcription factors.

Main Methods:

  • RNA sequencing was performed on various tissues from lily and tulip using the Illumina HiSeq 2000 platform.
  • De novo transcriptome assembly was conducted with optimized filtering parameters to manage RNAseq data quality.
  • A web-based Transcriptome browser was developed for public data access.

Main Results:

  • High-quality transcriptome datasets for tulip and lily were successfully generated.
  • The study identified limitations in standard de novo transcriptome assembly methods.
  • A functional Transcriptome browser was established, providing a valuable resource for researchers.
  • The transcriptomes enabled the identification of potential transcription factors, including the TCP family, in both species.

Conclusions:

  • The generated transcriptomes represent a significant advancement for genomics research in tulip, lily, and other bulbous plants.
  • The open-access data and browser facilitate further functional genomics studies and genetic analyses.
  • Optimized assembly strategies are crucial for obtaining reliable transcriptome data from complex genomes.