Duck assembly and gene annotation

Assembly

This release features the first draft assembly of the mallard duck (Anas platyrhynchos) genome, BGI_duck_1.0, submitted by the State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing in April 2013. The assembly comprises 78487 toplevel sequences, all of which are unplaced scaffolds (from 227448 contigs). The N50 of the contigs is 26 kb and the N50 of the scaffolds is 1.2 Mb. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000355885.1

Gene annotation

Annotation was performed using the EnsEMBL annotation pipeline, with the gene set being supplemented by the projection of orthologous genes and the inclusion of genes based on alignments with lower coverage than usual. The gene set contains 15,634 protein coding genes, 249 pseudogenes and 567 ncRNAs.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyBGI_duck_1.0, INSDC Assembly GCA_000355885.1, Apr 2013
Database version76.1
Base Pairs1,069,956,150
Golden Path Length1,105,035,747
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedSep 2009
Genebuild releasedFeb 2010
Genebuild last updated/patchedFeb 2010

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

15,634
Small non coding genes

Small non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as small non coding genes: miRNA, miscRNA, rRNA, tRNA, scRNA, snlRNA, snoRNA, snRNA, tRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline.

567
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

249
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.17,169

Other

Genscan gene predictions42,822