Articles
Genome-wide survey of repetitive element content in dioecious garden asparagus
Article number
1301_6
Pages
37 – 42
Language
English
Abstract
Eukaryotic genomes are often dominated by the integration and proliferation of repetitive elements.
Plant genome sizes are particularly labile due to the expansion and elimination of repetitive DNA. The repetitive content of a large plant genome can be analyzed directly from a genome assembly and annotation, but the assembly of large, transposon-rich plant genomes is often difficult and time consuming.
Instead, a random sampling of shotgun genomic DNA can be used to estimate the repetitive content and construct consensus assemblies for high-copy repeats.
We utilize this method with high-throughput 454 pyrosequencing long reads to analyze 0.31X coverage of the garden asparagus (Asparagus officinalis) genome.
We find that A. officinalis is more than 70% repetitive, dominated largely by Class I Gypsy and Copia LTR retroelements, while Class II DNA elements represent less than 1.5% of the genome.
We hypothesize that the high copy number of these Class I retroelements contributed to the recent genome size increase in Asparagus.
Plant genome sizes are particularly labile due to the expansion and elimination of repetitive DNA. The repetitive content of a large plant genome can be analyzed directly from a genome assembly and annotation, but the assembly of large, transposon-rich plant genomes is often difficult and time consuming.
Instead, a random sampling of shotgun genomic DNA can be used to estimate the repetitive content and construct consensus assemblies for high-copy repeats.
We utilize this method with high-throughput 454 pyrosequencing long reads to analyze 0.31X coverage of the garden asparagus (Asparagus officinalis) genome.
We find that A. officinalis is more than 70% repetitive, dominated largely by Class I Gypsy and Copia LTR retroelements, while Class II DNA elements represent less than 1.5% of the genome.
We hypothesize that the high copy number of these Class I retroelements contributed to the recent genome size increase in Asparagus.
Publication
Authors
A. Harkess, J. Leebens-Mack
Keywords
Asparagus officinalis, transposons, genome size
Groups involved
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