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RNA-seq03:21

RNA-seq

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 microarray-based...

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Identifying Mutations by High Resolution Melting in a TILLING Population of Rice
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Validation of rice genome sequence by optical mapping.

Shiguo Zhou1, Michael C Bechner, Michael Place

  • 1Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, UW Biotechnology Centre, 425 Henry Mall, Madison, Wisconsin 53706, USA. szhou@wisc.edu

BMC Genomics
|August 19, 2007
PubMed
Summary

We created a whole-genome optical restriction map for rice, revealing a smaller genome size and validating sequence data. This map aids in closing gaps and correcting errors in rice genome assemblies.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Rice is a globally important food crop and a model organism for grass family genomics due to its simple genome.
  • Accurate validation and gap-closing of the rice genome sequence require independent methods.

Purpose of the Study:

  • To construct a whole-genome optical restriction map of rice to aid in sequence finishing and validation.
  • To provide an independent physical scaffold for identifying and correcting errors in existing genome assemblies.

Main Methods:

  • Whole-genome SwaI optical restriction mapping of the rice genome.
  • Alignment of the optical map with in silico restriction maps from IRGSP and TIGR genome sequence data.

Main Results:

  • A physical map comprising 14 contigs covering 12 chromosomes was generated, with a total size of 382.17 Mb (11% smaller than previous estimates).
  • Nine gap-free contigs, including centromeres and telomeres, were identified.
  • Alignment revealed comprehensive coverage of published gaps, identification of new gaps, and characterization of approximately 14 Mb of sequence misassemblies.

Conclusions:

  • Optical mapping data effectively validates genome sequence assemblies, particularly for large, repeat-rich genomes.
  • Future applications may combine high-resolution optical maps with short-read sequencing for enhanced genome analysis.
  • The presented map construction techniques enable comparative genomics for identifying structural variations across rice subspecies.