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Organization and variability of the maize genome
Joachim Messing1, Hugo K Dooner
1Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, USA.
Current Opinion in Plant Biology
|February 7, 2006
Summary
The maize genome, one of the largest sequenced plant genomes, is being analyzed using over 2 million cDNA sequences. This approach helps understand gene content due to repetitive DNA and aids genome sequencing efforts.
Area of Science:
- Genomics
- Plant Biology
- Bioinformatics
Background:
- The maize genome is exceptionally large due to whole-genome duplication and retrotransposition, resulting in significant repetitive DNA.
- Repetitive DNA is under-represented in complementary DNA (cDNA) collections, complicating gene content analysis.
- Maize is the third most studied organism, with over 2 million cDNA sequences available.
Purpose of the Study:
- To assess the gene content of the maize genome.
- To facilitate the large-scale genome sequencing effort of maize.
- To investigate the variability of repetitive DNA in maize inbred lines.
Main Methods:
- Analysis of the maize transcriptome through over 2 million cDNA sequences.
- Construction of a physical map anchored to the genetic map.
- Vertical sampling of specific genomic regions.
Main Results:
- The maize transcriptome analysis provides an expedient assessment of gene content.
- A physical map anchored to the genetic map is available to aid sequencing.
- Repetitive DNA is highly polymorphic among maize inbred lines.
Conclusions:
- Transcriptome analysis is crucial for understanding gene content in complex genomes like maize.
- The physical map is a valuable resource for ongoing maize genome sequencing.
- Further studies are needed to evaluate the extent and importance of repetitive DNA variability.