ArticlePloS one2009
Evolution of genome size and complexity in Pinus.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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Who cites it
73 citing papers in PubMed.
- Cunninghamia lanceolata genome illuminates the evolutionary dynamics of gymnosperms.Cell reports · 2026Article
- Phylogenomic Inference Suggests Differential Deep Time Phylogenetic Signals from Nuclear and Organellar Genomes in Gymnosperms.Plants (Basel, Switzerland) · 2025Article
- gymnotoa-db: a database and application to optimize functional annotation in gymnosperms.Database : the journal of biological databases and curation · 2025Article
- Investigating adaptation to environmental variability in forest trees through molecular phylogenetic analysis.PloS one · 2025Article
- Exploring Taxonomic and Genetic Relationships in theInternational journal of molecular sciences · 2024Article
- From tradition to innovation: conventional and deep learning frameworks in genome annotation.Briefings in bioinformatics · 2024Review
- LocoGSE, a sequence-based genome size estimator for plants.Frontiers in plant science · 2024Article
- Comprehensive Organ-Specific Profiling of Douglas Fir (Biomolecules · 2023Article
- Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica).BMC plant biology · 2022Article
- Evolution of complex genome architecture in gymnosperms.GigaScience · 2022Article
- Identification and Validation of Reliable Reference Genes for Gene Expression Studies inGenes · 2022Article
- Comparative genome sequence and phylogenetic analysis of chloroplast for evolutionary relationship amongSaudi journal of biological sciences · 2022Article
- Analysis on single nucleotide polymorphisms of the PeTPS-(-)Apin gene in Pinus elliottii.PloS one · 2022Article
- Haploid, diploid, and pooled exome capture recapitulate features of biology and paralogy in two non-model tree species.Molecular ecology resources · 2022Article
- Note on the Reliability of Biological vs. Artificial Neural Networks.Frontiers in physiology · 2021Article
- Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks.Genes · 2020Article
- Siberian larch (Larix sibirica Ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome.BMC genomics · 2020Article
- An efficient system forPlant methods · 2020Article
- A Reference Genome Sequence for the European Silver Fir (G3 (Bethesda, Md.) · 2019Article
- Review
13 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors.
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Abstract
backgroundGenome evolution in the gymnosperm lineage of seed plants has given rise to many of the most complex and largest plant genomes, however the elements involved are poorly understood. METHODOLOGY/PRINCIPAL
findingsGymny is a previously undescribed retrotransposon family in Pinus that is related to Athila elements in Arabidopsis. Gymny elements are dispersed throughout the modern Pinus genome and occupy a physical space at least the size of the Arabidopsis thaliana genome. In contrast to previously described retroelements in Pinus, the Gymny family was amplified or introduced after the divergence of pine and spruce (Picea). If retrotransposon expansions are responsible for genome size differences within the Pinaceae, as they are in angiosperms, then they have yet to be identified. In contrast, molecular divergence of Gymny retrotransposons together with other families of retrotransposons can account for the large genome complexity of pines along with protein-coding genic DNA, as revealed by massively parallel DNA sequence analysis of Cot fractionated genomic DNA. CONCLUSIONS/SIGNIFICANCE: Most of the enormous genome complexity of pines can be explained by divergence of retrotransposons, however the elements responsible for genome size variation are yet to be identified. Genomic resources for Pinus including those reported here should assist in further defining whether and how the roles of retrotransposons differ in the evolution of angiosperm and gymnosperm genomes.
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