Rabbit assembly and gene annotation

Assembly

OryCun2 (GCA_000003625.1) is an assembly of rabbit (Oryctolagus cuniculus). It was sequenced to a 7X. The genome sequencing and assembly are provided by the Broad Institute within the mammalian genome project.

Of the 2.74 Gb genome, approximately 82% has been anchored to chromosomes, which include autosomes 1-21 and sex chromosome X. The remaining unanchored contigs have been concatenated into virtual chromosomes "Un".The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for supercontigs is 35348.54kb and is 64.65kb for contigs. The total number of bases in supercontigs is 2.66 Gb and in contigs is 2.60 Gb.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000003625.1

Gene annotation

The gene set for rabbit was built using the Ensembl genebuild pipeline. Gene models are based on genewise alignments of glire proteins as well as genetically distant proteins from other species, including most mammal proteins from Uniprot. To improve the accuracy of models generated from distant species, the Genewise alignments were made to stretches of genomic sequence rather than to 'miniseqs'. Additionnaly, human and mouse one-to-one orthologues were aligned using exonerate, combined with rabbit-specific proteins. The protein based gene models were then extended using rabbit cDNA and EST alignments. The resulting gene models were then assessed by generating sets of potential orthologs to genes from other vertebrate species. Potentially missing predictions and partial gene predictions were identified by examining the orthologs, which were then used to build new gene models.

Mammalian Genome Project

Oryctolagus cuniculus is one of 24 mammals that will be sequenced as part of the Mammalian Genome Project, funded by the National Institutes of Health (NIH). The species were chosen to maximise the branch length of the evolutionary tree while representing the diversity of mammalian species. Low-coverage 2X assemblies will be produced for these mammals and used in alignments for cross-species comparison. The aim is to increase our understanding of functional elements, especially in the human genome.

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 vertebrate 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
blood11980
brain16017
heart14476
kidney14813
liver13907
lung15473
merged22042
ovary15958
skeletal muscle13593
skin15398
testis19135

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyOryCun2.0, INSDC Assembly GCA_000003625.1, Nov 2009
Database version76.2
Base Pairs2,604,023,284
Golden Path Length2,737,490,501
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedNov 2009
Genebuild releasedMar 2010
Genebuild last updated/patchedJun 2013

Gene counts

Coding genes

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

19,293
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.

3,375
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.

1,001
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.24,964

Other

Genscan gene predictions55,138