@article{771c9d5c5a104b788730bc5ebd9c5ec3,
title = "An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing",
abstract = "The 22-gigabase genome of loblolly pine (Pinus taeda) is one of the largest ever sequenced. The draft assembly published in 2014 was built entirely from short Illumina reads, with lengths ranging from 100 to 250 base pairs (bp). The assembly was quite fragmented, containing over 11 million contigs whose weighted average (N50) size was 8206 bp. To improve this result, we generated approximately 12-fold coverage in long reads using the Single Molecule Real Time sequencing technology developed at Pacific Biosciences. We assembled the long and short reads together using the MaSuRCA mega-reads assembly algorithm, which produced a substantially better assembly, P. taeda version 2.0. The new assembly has an N50 contig size of 25 361, more than three times as large as achieved in the original assembly, and an N50 scaffold size of 107 821, 61% larger than the previous assembly.",
keywords = "Conifers, Genome assembly, Genomics, Next-gen sequencing, Pine genomes",
author = "Zimin, {Aleksey V.} and Stevens, {Kristian A.} and Crepeau, {Marc W.} and Daniela Puiu and Wegrzyn, {Jill L.} and Yorke, {James A.} and Langley, {Charles H.} and Neale, {David B.} and Salzberg, {Steven L.}",
note = "Funding Information: This work was supported in part by the U.S. Department of Agriculture{\textquoteright}s National Institute of Food and Agriculture under grant 2011-67009-30030, and by the National Institutes of Health under grant R01-HG006677 and R01-GM083873. The authors gratefully acknowledge the assistance of the DNA Technologies Core at the Genome Center of the University of California at Davis, the IGM Genomics Center at the University of California at San Diego, the JHMI Deep Sequencing and Microarray Core Facility at Johns Hopkins University, and the Washington State University Molecular Biology and Genomics Core, all of whom provided sequencing services for this project. Publisher Copyright: {\textcopyright} The Author 2017. Published by Oxford University Press.",
year = "2017",
month = jan,
day = "1",
doi = "10.1093/gigascience/giw016",
language = "English (US)",
volume = "6",
journal = "GigaScience",
issn = "2047-217X",
publisher = "BioMed Central",
number = "1",
}