First draft genome sequence of the Japanese eel, Anguilla japonica

The Japanese eel is a much appreciated research object and very important for Asian aquaculture; however, its genomic resources are still limited. We have used a streamlined bioinformatics pipeline for the de novo assembly of the genome sequence of the Japanese eel from raw Illumina sequence reads....

Full description

Saved in:
Bibliographic Details
Published in:Gene 2012-12, Vol.511 (2), p.195-201
Main Authors: Henkel, Christiaan V., Dirks, Ron P., de Wijze, Daniëlle L., Minegishi, Yuki, Aoyama, Jun, Jansen, Hans J., Turner, Ben, Knudsen, Bjarne, Bundgaard, Martin, Hvam, Kenneth Lyneborg, Boetzer, Marten, Pirovano, Walter, Weltzien, Finn-Arne, Dufour, Sylvie, Tsukamoto, Katsumi, Spaink, Herman P., van den Thillart, Guido E.E.J.M.
Format: Article
Language:English
Subjects:
Anguilla
Anguilla - genetics
Anguilla japonica
Animals
aquaculture
Assembly pipeline
bioinformatics
Computational Biology
De novo genome
Eel
fish
Genome
genome assembly
homeotic genes
Hox genes
Illumina sequencing
Marine
nucleotide sequences
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:The Japanese eel is a much appreciated research object and very important for Asian aquaculture; however, its genomic resources are still limited. We have used a streamlined bioinformatics pipeline for the de novo assembly of the genome sequence of the Japanese eel from raw Illumina sequence reads. The total assembled genome has a size of 1.15Gbp, which is divided over 323,776 scaffolds with an N50 of 52,849bp, a minimum scaffold size of 200bp and a maximum scaffold size of 1.14Mbp. Direct comparison of a representative set of scaffolds revealed that all the Hox genes and their intergenic distances are almost perfectly conserved between the European and the Japanese eel. The first draft genome sequence of an organism strongly catalyzes research progress in multiple fields. Therefore, the Japanese eel genome sequence will provide a rich resource of data for all scientists working on this important fish species. ► The de novo assembled genome sequence of the Japanese eel is presented. ► The total assembled genome size is 1.15Gbp and divided over 323,776 scaffolds. ► The scaffold N50 is 52,849bp, with scaffold sizes ranging from 200bp to 1.14Mbp. ► Hox genes are almost perfectly conserved between European and Japanese eel.
ISSN:0378-1119
1879-0038
DOI:10.1016/j.gene.2012.09.064