Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds

Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds

links: doi:10.1038/nature12309
Genome Sequence and assembly

The assembly of E. guineensis (AVROS, pisifera fruit form) genome P5-build was constructed from sequences from a total of 148 linker libraries and 81 fragment libraries (Roche/454). Reads were generated from genomic DNA fragment libraries (53.5 million reads), BAC pool DNA fragment libraries (3.6 million reads), and from a series of genomic (89.1 million reads) and BAC (8.6 million reads) paired-end linker libraries. In total, 46.8 billion bases of raw sequence were generated, representing approximately 26-fold raw sequence coverage of the 1.8-Gb oil palm genome. Sequence data were assembled using the Newbler algorithm28 (Supplementary Table 4). The seventh assembly and genome build of E. oleifera (O7-build) was constructed from a total of 127 linker libraries and 68 fragment libraries. In total, 130 million E. oleifera reads, representing approximately 25-fold raw sequence coverage, were generated (Supplementary Table 2).

High information content restriction fragment fingerprints were generated for 124,286 BAC clones from the E. guineensis genome with an average size of 150 kb. BAC fingerprints were used to construct a physical map of the reference genome (Supplementary Figs 2 and 3). In addition, BAC ends from this library were sequenced using Sanger sequencing to generate 235,613 paired reads with an average read length of approximately 600 bp. BAC end reads were used to create the shotgun assembly, as well as to locate individual BACs within the assembled genome.

Before assembly, all Roche/454 sequence runs were screened for quality based on average read length, linker library efficiency and library redundancy using a custom pipeline based on the SSAHA program29. For linker positive reads, library insert sizes were estimated by aligning both ends to a draft assembly of oil palm, and measuring the intervening sequence in cases in which both ends matched a single draft scaffold. In order to minimize the negative impact of chimaeras in the linker libraries, we removed all identical reads that were due to library redundancy, not independent observations. In addition to the Roche/454 data, a set of 235,613 BAC end reads from the Origen_1 BAC library were included in the P5 assembly, with an average BAC size of 150 kb. These data were assembled using the Newbler algorithm28 on a Dell PowerEdge R910 server with 512 Gb of RAM, and 32 cores running Ubuntu Linux 10.04. The P5 assembly took 15 days and 5 h to complete.

因组大小确定为1.8Gb(拼接大小为1.535 Gb), 共有34,802 基因,测序方案为454 GS FLX Titanium + Sanger 。按照1.8Gb算,接近26X覆盖度,这样的测序方案也很烧钱的。

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