Back to Search Start Over

Sequencing and assembly of the 22-gb loblolly pine genome.

Authors :
Zimin, Aleksey
Zimin, Aleksey
Stevens, Kristian A
Crepeau, Marc W
Holtz-Morris, Ann
Koriabine, Maxim
Marçais, Guillaume
Puiu, Daniela
Roberts, Michael
Wegrzyn, Jill L
de Jong, Pieter J
Neale, David B
Salzberg, Steven L
Yorke, James A
Langley, Charles H
Zimin, Aleksey
Zimin, Aleksey
Stevens, Kristian A
Crepeau, Marc W
Holtz-Morris, Ann
Koriabine, Maxim
Marçais, Guillaume
Puiu, Daniela
Roberts, Michael
Wegrzyn, Jill L
de Jong, Pieter J
Neale, David B
Salzberg, Steven L
Yorke, James A
Langley, Charles H
Source :
Genetics; vol 196, iss 3, 875-890; 0016-6731
Publication Year :
2014

Abstract

Conifers are the predominant gymnosperm. The size and complexity of their genomes has presented formidable technical challenges for whole-genome shotgun sequencing and assembly. We employed novel strategies that allowed us to determine the loblolly pine (Pinus taeda) reference genome sequence, the largest genome assembled to date. Most of the sequence data were derived from whole-genome shotgun sequencing of a single megagametophyte, the haploid tissue of a single pine seed. Although that constrained the quantity of available DNA, the resulting haploid sequence data were well-suited for assembly. The haploid sequence was augmented with multiple linking long-fragment mate pair libraries from the parental diploid DNA. For the longest fragments, we used novel fosmid DiTag libraries. Sequences from the linking libraries that did not match the megagametophyte were identified and removed. Assembly of the sequence data were aided by condensing the enormous number of paired-end reads into a much smaller set of longer "super-reads," rendering subsequent assembly with an overlap-based assembly algorithm computationally feasible. To further improve the contiguity and biological utility of the genome sequence, additional scaffolding methods utilizing independent genome and transcriptome assemblies were implemented. The combination of these strategies resulted in a draft genome sequence of 20.15 billion bases, with an N50 scaffold size of 66.9 kbp.

Details

Database :
OAIster
Journal :
Genetics; vol 196, iss 3, 875-890; 0016-6731
Notes :
application/pdf, Genetics vol 196, iss 3, 875-890 0016-6731
Publication Type :
Electronic Resource
Accession number :
edsoai.on1377969982
Document Type :
Electronic Resource