ArticleGenome biology and evolution2011
Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians.
Article in Genome biology and evolution, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers.
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100 citing papers in PubMed.
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- Benchmarking long-read variant calling in diploid and polyploid genomes: insights from human and plants.BMC genomics · 2026Article
- LTR retrotransposons shape genome architecture, function, and evolution in diverse plant species.Frontiers in plant science · 2026Article
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- Previously unmeasured genetic diversity explains part of Lewontin's paradox in abioRxiv : the preprint server for biology · 2024Article
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- Characteristics of Amorphophallus konjac as indicated by its genome.Scientific reports · 2023Article
- Discovering the Repeatome of Five Species Belonging to the Asteraceae Family: A Computational Study.Plants (Basel, Switzerland) · 2023Article
- Chromosome-Level Assembly of Flowering Cherry (Genes · 2023Article
- Genome sequencing reveals evidence of adaptive variation in the genus Zea.Nature genetics · 2022Article
- A chromosome-level genome assembly of chia provides insights into high omega-3 content and coat color variation of its seeds.Plant communications · 2022Article
- Genome-Wide Identification of Long Noncoding RNA and Their Potential Interactors inInternational journal of molecular sciences · 2022Article
- The Singular Evolution ofFrontiers in plant science · 2022Article
- Chromosome and Genome Diversity in the GenusPlants (Basel, Switzerland) · 2021Review
- The genomic ecosystem of transposable elements in maize.PLoS genetics · 2021Article
- A high-quality chromosome-scale assembly of the centipedegrass [Eremochloa ophiuroides (Munro) Hack.] genome provides insights into chromosomal structural evolution and prostrate growth habit.Horticulture research · 2021Article
40 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
The genome of maize (Zea mays ssp. mays) consists mostly of transposable elements (TEs) and varies in size among lines. This variation extends to other species in the genus Zea: although maize and Zea luxurians diverged only ∼140,000 years ago, their genomes differ in size by ∼50%. We used paired-end Illumina sequencing to evaluate the potential contribution of TEs to the genome size difference between these two species. We aligned the reads both to a filtered gene set and to an exemplar database of unique repeats representing 1,514 TE families; ∼85% of reads mapped against TE repeats in both species. The relative contribution of TE families to the B73 genome was highly correlated with previous estimates, suggesting that reliable estimates of TE content can be obtained from short high-throughput sequencing reads, even at low coverage. Because we used paired-end reads, we could assess whether a TE was near a gene by determining if one paired read mapped to a TE and the second read mapped to a gene. Using this method, Class 2 DNA elements were found significantly more often in genic regions than Class 1 RNA elements, but Class 1 elements were found more often near other TEs. Overall, we found that both Class 1 and 2 TE families account for ∼70% of the genome size difference between B73 and luxurians. Interestingly, the relative abundance of TE families was conserved between species (r = 0.97), suggesting genome-wide control of TE content rather than family-specific effects.
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