Journal article
Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation
Genetics (Austin), Vol.196(3), pp.891-909
03/2014
Handle:
https://hdl.handle.net/2376/106874
PMCID: PMC3948814
PMID: 24653211
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, 2
n
= 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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Details
- Title
- Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation
- Creators
- Jill L Wegrzyn - Department of Plant Sciences, University of California, Davis, California 95616John D Liechty - Department of Plant Sciences, University of California, Davis, California 95616Kristian A Stevens - Department of Evolution and Ecology, University of California, Davis, California 95616Le-Shin Wu - National Center for Genome Analysis Support, Indiana University, Bloomington, Indiana 47405Carol A Loopstra - Department of Ecosystem Science and Management, Texas A&M University, College Station, Texas 77843Hans A Vasquez-Gross - Department of Plant Sciences, University of California, Davis, California 95616William M Dougherty - Department of Evolution and Ecology, University of California, Davis, California 95616Brian Y Lin - Department of Plant Sciences, University of California, Davis, California 95616Jacob J Zieve - Department of Plant Sciences, University of California, Davis, California 95616Pedro J Martínez-García - Department of Plant Sciences, University of California, Davis, California 95616Carson Holt - Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112Mark Yandell - Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112Aleksey V Zimin - Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742James A Yorke - Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742Marc W Crepeau - Department of Evolution and Ecology, University of California, Davis, California 95616Daniela Puiu - Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University, Baltimore, Maryland 21205Steven L Salzberg - Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University, Baltimore, Maryland 21205Pieter J de Jong - Children’s Hospital Oakland Research Institute, Oakland, California 94609Keithanne Mockaitis - Department of Biology, Indiana University, Bloomington, Indiana 47405Doreen Main - Department of Horticulture, Washington State University, Pullman, Washington 99163Charles H Langley - Department of Evolution and Ecology, University of California, Davis, California 95616David B Neale - Department of Plant Sciences, University of California, Davis, California 95616
- Publication Details
- Genetics (Austin), Vol.196(3), pp.891-909
- Academic Unit
- Horticulture, Department of
- Publisher
- Genetics Society of America
- Identifiers
- 99900546870401842
- Language
- English
- Resource Type
- Journal article