e-journal

Decoding the oak genome: public release of sequence data,assembly, annotation and publication strategies

---

The 1.5 Gbp/2C genome of pedunculate oak (Quercus robur) has been sequenced. A strategy was established for dealing
with the challenges imposed by the sequencing of such a large, complex and highly heterozygous genome by a
whole-genome shotgun (WGS) approach, without the use of costly and time-consuming methods, such as fosmid or
BAC clone-based hierarchical sequencing methods. The sequencing strategy combined short and long reads. Over 49
million reads provided by Roche 454 GS-FLX technology were assembled into contigs and combined with shorter
Illumina sequence reads from paired-end and mate-pair libraries of different insert sizes, to build scaffolds. Errors were corrected and gaps filled with Illumina paired-end reads and contaminants detected, resulting in a total of 17 910 scaffolds (>2 kb) corresponding to 1.34 Gb. Fifty per cent of the assembly was accounted for by 1468 scaffolds
(N50 of 260 kb). Initial comparison with the phylogenetically related Prunus persica gene model indicated that genes
for 84.6% of the proteins present in peach (mean protein coverage of 90.5%) were present in our assembly. The second
and third steps in this project are genome annotation and the assignment of scaffolds to the oak genetic linkage
map. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement, the
oak genome data have been released into public sequence repositories in advance of publication. In this presubmission
paper, the oak genome consortium describes its principal lines of work and future directions for analyses of the
nature, function and evolution of the oak genome.

Keywords: genome sequence, genomic resources, Quercus robur Received 17 February 2015; revision received 27 April 2015; accepted 30 April 2015

---

Ketersediaan

Tidak ada salinan data

Informasi Detail

Judul Seri

Molecular Ecology Resources

No. Panggil

-

Penerbit

: John Wiley & Sons, Ltd.., 2016

Deskripsi Fisik

Molecular Ecology Resources (2016) 16, 254–265

Bahasa

English

ISBN/ISSN

doi: 10.1111/1755-09

Klasifikasi

-

Tipe Isi

-

Tipe Media

-

Tipe Pembawa

-

Edisi

-

Subjek

BIOLOGI

Info Detail Spesifik

-

Pernyataan Tanggungjawab

Wati/Agus

Versi lain/terkait

Lampiran Berkas

Komentar

---

Anda harus masuk sebelum memberikan komentar