What is a transcriptome?

A transcriptome is the RNA expressed in a cell, tissue or organ. Which genes are being transcribed depend on the environmental conditions and the stage of development of the organism. Chamaecristahas one genome, but many transcriptomes. We isolated total RNA, but then selected for mRNA before sequencing our Chamaecristatranscriptomes.

  • What types of RNA would you find in total RNA?
  • How might you separate mRNA from total RNA?

  • Which transcriptomes are you exploring?

    You have access to whole transcriptome sequences from shoots, roots, and nodules of the Minnesota ecotype of Chamaecrista fasciulata plants at different developmental stages. Because differences have been observed among Minnesota, Kansas, and Oklahoma ecotypes, you also have whole transcriptome sequences for shoots KS, and OK ecotypes. The Minnesota data alone can be used to analyze levels of gene expression. You can look for genetic variation among ecotypes by comparing the transcriptomes of MN, KS, and OK. Here's a summary of the sequencing results (PowerPoint 2007 (.pptx) 457kB Jan19 09). One of the first things you may notice is the vast amount of data available to you. The interface strategies are designed to reduce the how overwhelming data sets like this can seem when you are just getting started.

    The Chamaecrista genomics project is funded by two NSF grants. Here are the links to the abstracts if you'd like to know more about the projects:

    Grant from the Division of Environmental Biology
    Grant for the Division of Undergraduate Education

    RNA was isolated from shoots, roots, and nodules of Chamaecrista fasciculata, a native prairie plant, at many different developmental stages. Details about the stages can be found in the "Gene expression" strategy section. These plants were a Minnesota ecotype (MN). RNA was also isolated from shoots of Kansas (KS) and Oklahoma (OK) ecotypes, but not separated based on develomental age. You can find out more about the ecotypes in the "Variation among ecotypes" strategy section and also in the "Chamaecrista biology" strategy section.

    Messenger RNA was purified from total RNA and then sequenced using Solexa or 454 Titanium sequencers. Solexa was purchased by Illumina which is why you may see both names in the literature. Our Solexa reads are 46 bp long and were single-end, not paired-end sequenced (click on the Solexa link if you're curious about the sequencing method). Solexa sequencing was done at the National Center for Genome Research (NCGR). The 454 Titanium came to market in October 2008 and our sequencing was done at the University of Illinois in November of 2008. Our reads averaged 370 bp. Both Solexa and 454 Titanium sequencers are next-generation sequencers where sequence information is obtained during synthesis, not after as is the case with the Sanger method. The research team that is working on the Chamaecrista transcriptome includes: Susan Singer and Sonja Maki at Carleton, Jeff Doyle and Dan Ilut at Cornell, Steven Cannon at Iowa State, and Greg May, Andrew Farmer, and Joann Mudge at NCGR.
    Review Sanger sequencing from introductory biology and compare what happens in Sanger sequencing with Solexa and 454 sequencing

    Pick a strategy and get started.