Ferret assembly and gene annotation

Assembly

The ferret (Mustela putorius furo) genome was produced by the Broad Institute. Illumina technology was used to produced this high quality draft. The whole genome shotgun data was assembled with Allpaths-LG. It is composed of 117441 contigs with an N50 value of 44.8kb and 7741 scaffolds with an N50 value of 9.3Mb.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000215625.1

Gene annotation

The gene set was built using a mixed approach. First the Ensembl pipeline was used to generate 264,684 models from orthologous vertebrate proteins from UniprotKB with a protein existence level of 1 or 2. Then, due to the lack of species specific sequences and the availability of RNA-Seq for ferret, we used 1.1G paired-end reads sequenced by the Broad Institute. The RNA-Seq data contains tissues from a male ferret, from a female ferret, from an influenza infected ferret and from different developmental stage. We pooled the tissues to avoid creating too many fragmented models. Using the RNA-Seq pipeline, we created 22,299 models from the pooled set. When a pooled model was missing but we had a consensus with the tissues models, the consensus model was added to the pooled set, which brought the number of RNA-Seq models up to 24,837. By combining the orthologous set, the RNA-Seq set and our ncRNA pipeline we built the final gene set: 19910 protein coding gene models, 270 pseudogenes, 17 retrotransposed and 3,614 non coding RNA.

RNASeq data set

In addition to the main set, we have predicted gene models for each tissue type using the RNA-Seq pipeline. We did a BLASTp of these models against UniProt proteins of protein existence level 1 and 2 in order to confirm the open reading frame (ORF). The best BLAST hit is displayed as a transcript supporting evidence.

The tissue-specific sets of transcript models built using our RNAseq pipeline are as follows:

TissueNumber of gene models
21 days post fertilization embryo:
Brain13252
Development mix13659
28 days post fertilization embryo:
Brain14086
Development mix14717
36 days post fertilization embryo:
Brain13822
Development mix14007
Adult ferret:
Brain14230
Lung and trachea13960
Lymph12370
Pancreas8058
Influenza infected ferret:
Spleen14391
Lung and trachea11911
Female ferret:
Lymph13876
Pancreas11696
Skeletal muscle14423
Skin12359
Spleen13576
Male ferret:
Brain13876
Heart11696
Kidney14423
Liver12359
Lung13576
Testis20738
Lung and trachea19824

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyMusPutFur1.0, INSDC Assembly GCA_000215625.1, Jun 2011
Database version76.1
Base Pairs2,277,906,570
Golden Path Length2,410,758,013
Genebuild byEnsembl
Genebuild methodMixed strategy build
Genebuild startedApr 2012
Genebuild releasedAug 2012
Genebuild last updated/patchedAug 2012

Gene counts

Coding genes

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

19,910
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.

3,614
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.

287
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.23,963

Other

Genscan gene predictions48,640