TY - JOUR
T1 - Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation
AU - Wegrzyn, Jill L.
AU - Liechty, John D.
AU - Stevens, Kristian A.
AU - Wu, Le Shin
AU - Loopstra, Carol A.
AU - Vasquez-Gross, Hans A.
AU - Dougherty, William M.
AU - Lin, Brian Y.
AU - Zieve, Jacob J.
AU - Martínez-García, Pedro J.
AU - Holt, Carson
AU - Yandell, Mark
AU - Zimin, Aleksey V.
AU - Yorke, James A.
AU - Crepeau, Marc W.
AU - Puiu, Daniela
AU - Salzberg, Steven L.
AU - de Jong, Pieter J.
AU - Mockaitis, Keithanne
AU - Main, Doreen
AU - Langley, Charles H.
AU - Neale, David B.
PY - 2014/3
Y1 - 2014/3
N2 - 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%.
AB - 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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U2 - 10.1534/genetics.113.159996
DO - 10.1534/genetics.113.159996
M3 - Article
C2 - 24653211
AN - SCOPUS:84899126607
SN - 0016-6731
VL - 196
SP - 891
EP - 909
JO - Genetics
JF - Genetics
IS - 3
ER -