title: Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation.
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%.
authors.affiliation: Department of Plant Sciences, University of California, Davis, California 95616.
authors.forename: Jill L
authors.initials: JL
authors.lastname: Wegrzyn
authors.forename: John D
authors.initials: JD
authors.lastname: Liechty
authors.forename: Kristian A
authors.initials: KA
authors.lastname: Stevens
authors.forename: Le-Shin
authors.initials: LS
authors.lastname: Wu
authors.forename: Carol A
authors.initials: CA
authors.lastname: Loopstra
authors.forename: Hans A
authors.initials: HA
authors.lastname: Vasquez-Gross
authors.forename: William M
authors.initials: WM
authors.lastname: Dougherty
authors.forename: Brian Y
authors.initials: BY
authors.lastname: Lin
authors.forename: Jacob J
authors.initials: JJ
authors.lastname: Zieve
authors.forename: Pedro J
authors.initials: PJ
authors.lastname: Martínez-García
authors.forename: Carson
authors.initials: C
authors.lastname: Holt
authors.forename: Mark
authors.initials: M
authors.lastname: Yandell
authors.forename: Aleksey V
authors.initials: AV
authors.lastname: Zimin
authors.forename: James A
authors.initials: JA
authors.lastname: Yorke
authors.forename: Marc W
authors.initials: MW
authors.lastname: Crepeau
authors.forename: Daniela
authors.initials: D
authors.lastname: Puiu
authors.forename: Steven L
authors.initials: SL
authors.lastname: Salzberg
authors.forename: Pieter J
authors.initials: PJ
authors.lastname: Dejong
authors.forename: Keithanne
authors.initials: K
authors.lastname: Mockaitis
authors.forename: Doreen
authors.initials: D
authors.lastname: Main
authors.forename: Charles H
authors.initials: CH
authors.lastname: Langley
authors.forename: David B
authors.initials: DB
authors.lastname: Neale
mesh_terms: D018744:DNA, Plant / Q000032:analysis; D019143:Evolution, Molecular; D017343:Genes, Plant; D018745:Genome, Plant; D058977:Molecular Sequence Annotation / Q000379:methods*; D005810:Multigene Family; D010802:Phylogeny; D041603:Pinus taeda / Q000235:genetics*; D016415:Sequence Alignment
chemical_list: D018744:DNA, Plant
keywords: conifer; gene family; introns; repeats; retrotransposons