Guinea Pig assembly and gene annotation

Assembly

This is the first release of the high-coverage 6.79X assembly of the Guinea Pig (Cavia porcellus). The genome sequencing and assembly is provided by the Broad Institute.

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 contigs is 80.58 kb and the N50 of the supercontigs is 27.41 Mb. The total length of all contigs is 2.66 Gb. When the gaps between contigs in scaffolds are included, the total span of the assembly is 2.72 Gb.

Gene annotation

Due to the lack of Guineapig protein and cDNA resources, the majority of the gene models are based on Genewise alignments of proteins from mammals. Alignments made from Guineapig proteins had UTR added using Guineapig cDNAs. The gene models were assessed by generating sets of potential orthologs to genes from other mammalian species. Potentially missing predictions and partial gene predictions were identified by examining the orthologs, and exonerate used to build new gene models for these based on the human ortholog peptide sequence.

Mammalian Genome Project

Cavia porcellus is one of 24 mammals that will be sequenced as part of the Mammalian Genome Project, funded by the National Institutes of Health (NIH). A group of 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. A subset of these species are being sequenced in further depth. The aim is to increase our understanding of functional elements, especially in the human genome.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblycavPor3, Mar 2008
Database version76.3
Base Pairs2,663,369,733
Golden Path Length2,723,219,641
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedMar 2008
Genebuild releasedSep 2008
Genebuild last updated/patchedMay 2010

Gene counts

Coding genes

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

18,673
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.

5,963
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.

392
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.26,129

Other

Genscan gene predictions53,615