title: Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana).
abstract: Sugar pine (Pinus lambertiana Douglas) is within the subgenus Strobus with an estimated genome size of 31 Gbp. Transcriptomic resources are of particular interest in conifers due to the challenges presented in their megagenomes for gene identification. In this study, we present the first comprehensive survey of the P. lambertiana transcriptome through deep sequencing of a variety of tissue types to generate more than 2.5 billion short reads. Third generation, long reads generated through PacBio Iso-Seq have been included for the first time in conifers to combat the challenges associated with de novo transcriptome assembly. A technology comparison is provided here to contribute to the otherwise scarce comparisons of second and third generation transcriptome sequencing approaches in plant species. In addition, the transcriptome reference was essential for gene model identification and quality assessment in the parallel project responsible for sequencing and assembly of the entire genome. In this study, the transcriptomic data were also used to address questions surrounding lineage-specific Dicer-like proteins in conifers. These proteins play a role in the control of transposable element proliferation and the related genome expansion in conifers.
authors: Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269.
authors: Daniel
authors: D
authors: Gonzalez-Ibeas
authors: Department of Plant Sciences, University of California, Davis, California 95616.
authors: Pedro J
authors: PJ
authors: Martinez-Garcia
authors: Department of Plant Sciences, University of California, Davis, California 95616.
authors: Randi A
authors: RA
authors: Famula
authors: United States Department of Agriculture Forest Service, Institute of Forest Genetics, Placerville, California 95667.
authors: Annette
authors: A
authors: Delfino-Mix
authors: Department of Evolution and Ecology, University of California, Davis, California 95616.
authors: Kristian A
authors: KA
authors: Stevens
authors: Department of Ecosystem Science and Management, Texas A&M University, College Station, Texas 77843.
authors: Carol A
authors: CA
authors: Loopstra
authors: Department of Evolution and Ecology, University of California, Davis, California 95616.
authors: Charles H
authors: CH
authors: Langley
authors: Department of Plant Sciences, University of California, Davis, California 95616 dbneale@ucdavis.edu jill.wegrzyn@uconn.edu.
authors: David B
authors: DB
authors: Neale
authors: Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269 dbneale@ucdavis.edu jill.wegrzyn@uconn.edu.
authors: Jill L
authors: JL
authors: Wegrzyn
mesh_terms: D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D028223:Pinus / Q000235:genetics*; D043244:Ribonuclease III / Q000235:genetics; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D043244:Ribonuclease III
keywords: DCL; RNA-Seq; conifer; dicer; gymnosperm; transcriptome