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.
journal_name
Geneticsjournal_title
Geneticsauthors
Zimin A,Stevens KA,Crepeau MW,Holtz-Morris A,Koriabine M,Marçais G,Puiu D,Roberts M,Wegrzyn JL,de Jong PJ,Neale DB,Salzberg SL,Yorke JA,Langley CHdoi
10.1534/genetics.113.159715subject
Has Abstractpub_date
2014-03-01 00:00:00pages
875-90issue
3eissn
0016-6731issn
1943-2631pii
196/3/875journal_volume
196pub_type
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