ArticleGenetics2014
Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation.
Article in Genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 98 papers.
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98 citing papers in PubMed, 212 citations in OpenAlex.
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- The genome of the Wollemi pine, a critically endangered "living fossil" unchanged since the Cretaceous, reveals extensive ancient transposon activity.bioRxiv : the preprint server for biology · 2023Article
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- Dynamic genome evolution in a model fern.Nature plants · 2022Article
- Annotation of Siberian Larch (Plants (Basel, Switzerland) · 2022Article
- Coalescent-based species delimitation in North American pinyon pines using low-copy nuclear genes and plastomes.American journal of botany · 2022Article
- Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research.The Plant journal : for cell and molecular biology · 2022Article
- NLR diversity and candidate fusiform rust resistance genes in loblolly pine.G3 (Bethesda, Md.) · 2022Article
- Genome-Wide Prediction of Transcription Start Sites in Conifers.International journal of molecular sciences · 2022Article
- Application of crop wild relatives in modern breeding: An overview of resources, experimental and computational methodologies.Frontiers in plant science · 2022Review
38 more citing papers are in PubMed but not listed here.
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Authors and funding
22 authors at 7 institutions in 1 country.
Funding
Abstract
The largest genus in the conifer family Pinaceae is Pinus, with over 100 species. The size and complexity of their genomes (∼20-40 Gb, 2n = 24) have delayed the arrival of a well-annotated reference sequence. In this study, we present the annotation of the first whole-genome shotgun assembly of loblolly pine (Pinus taeda L.), which comprises 20.1 Gb of sequence. The MAKER-P annotation pipeline combined evidence-based alignments and ab initio predictions to generate 50,172 gene models, of which 15,653 are classified as high confidence. Clustering these gene models with 13 other plant species resulted in 20,646 gene families, of which 1554 are predicted to be unique to conifers. Among the conifer gene families, 159 are composed exclusively of loblolly pine members. The gene models for loblolly pine have the highest median and mean intron lengths of 24 fully sequenced plant genomes. Conifer genomes are full of repetitive DNA, with the most significant contributions from long-terminal-repeat retrotransposons. In depth analysis of the tandem and interspersed repetitive content yielded a combined estimate of 82%.
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