Gibbon assembly and gene annotation

Assembly

The Northern white-cheeked gibbon (Nomascus leucogenys) genome of a wild-born female named 'Asia' (international studbook #0098) was sequenced to 5.6x whole genome coverage. The sequencing was provided by The Baylor College of Medicine Human Genome Sequencing Center, and the Genome Center at Washington University using Sanger methods. The sequencing method combined whole genome shotgun plasmid, fosmid and BAC end sequences.

The sequence was assembled at The Broad Institute of Harvard and MIT using the Arachne Assembler and assisted with the Human NCBI36 assembly. This draft sequence assembly submitted to Genbank is referred to as Nleu1.0 (GCA_000146795.1).

Funding for the sequencing of the Nomascus leucogenys genome was provided by the National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH).

The N50 size is the median sequence length, i.e. 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 size of the contigs is 35.1 kb. The total length of all contigs is 2.76 Gb. When the gaps between contigs in scaffolds are included, the total span of the assembly is 2.88 Gb.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000146795.1

Gene annotation

The gene set for gibbon was built using the Ensembl gene annotation pipeline. Species-specific resources for gibbon are very limited and therefore sequences from human were used as supporting evidence for coding transcript models: Gibbon and human proteins were mapped to the genome using Genewise. Gibbon cDNAs, human cDNAs and human Ensembl translations from e!61 were mapped to the genome using Exonerate. In addition to the coding transcript models, non-coding RNAs and pseudogenes were also annotated.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyNleu1.0, INSDC Assembly GCA_000146795.1, Jan 2010
Database version75.1
Base Pairs2,756,591,777
Golden Path Length2,936,035,333
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedOct 2010
Genebuild releasedApr 2011
Genebuild last updated/patchedOct 2012

Gene counts

Coding genes

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

18,575
Short non coding genes

Short 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 short non coding genes: miRNA, miscRNA, rRNA, tRNA, ncRNA, scRNA, snlRNA, snoRNA, snRNA, tRNA, and also the pseudogenic form of these biotypes. The majority of the short non coding genes in Ensembl are annotated automatically by our ncRNA pipeline.

7,172
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.

1,192
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.28,352

Other

Genscan gene predictions45,092
Short Variants1,173,215

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