Dataset Information

An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts.

ABSTRACT: The domestic dog, Canis familiaris, is a well-established model system for mapping trait and disease loci. While the original draft sequence was of good quality, gaps were abundant particularly in promoter regions of the genome, negatively impacting the annotation and study of candidate genes. Here, we present an improved genome build, canFam3.1, which includes 85 MB of novel sequence and now covers 99.8% of the euchromatic portion of the genome. We also present multiple RNA-Sequencing data sets from 10 different canine tissues to catalog ?175,000 expressed loci. While about 90% of the coding genes previously annotated by EnsEMBL have measurable expression in at least one sample, the number of transcript isoforms detected by our data expands the EnsEMBL annotations by a factor of four. Syntenic comparison with the human genome revealed an additional ?3,000 loci that are characterized as protein coding in human and were also expressed in the dog, suggesting that those were previously not annotated in the EnsEMBL canine gene set. In addition to ?20,700 high-confidence protein coding loci, we found ?4,600 antisense transcripts overlapping exons of protein coding genes, ?7,200 intergenic multi-exon transcripts without coding potential, likely candidates for long intergenic non-coding RNAs (lincRNAs) and ?11,000 transcripts were reported by two different library construction methods but did not fit any of the above categories. Of the lincRNAs, about 6,000 have no annotated orthologs in human or mouse. Functional analysis of two novel transcripts with shRNA in a mouse kidney cell line altered cell morphology and motility. All in all, we provide a much-improved annotation of the canine genome and suggest regulatory functions for several of the novel non-coding transcripts.

SUBMITTER: Hoeppner MP

PROVIDER: S-EPMC3953330 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts.

Hoeppner Marc P MP Lundquist Andrew A Pirun Mono M Meadows Jennifer R S JR Zamani Neda N Johnson Jeremy J Sundström Görel G Cook April A FitzGerald Michael G MG Swofford Ross R Mauceli Evan E Moghadam Behrooz Torabi BT Greka Anna A Alföldi Jessica J Abouelleil Amr A Aftuck Lynne L Bessette Daniel D Berlin Aaron A Brown Adam A Gearin Gary G Lui Annie A Macdonald J Pendexter JP Priest Margaret M Shea Terrance T Turner-Maier Jason J Zimmer Andrew A Lander Eric S ES di Palma Federica F Lindblad-Toh Kerstin K Grabherr Manfred G MG

PloS one 20140313 3

The domestic dog, Canis familiaris, is a well-established model system for mapping trait and disease loci. While the original draft sequence was of good quality, gaps were abundant particularly in promoter regions of the genome, negatively impacting the annotation and study of candidate genes. Here, we present an improved genome build, canFam3.1, which includes 85 MB of novel sequence and now covers 99.8% of the euchromatic portion of the genome. We also present multiple RNA-Sequencing data sets ...[more]

PMID: 24625832

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Project description:The mammalian inner ear consists of the cochlea and the vestibular labyrinth (utricle, saccule, and semicircular canals), which participate in both hearing and balance. Proper development and life-long function of these structures involves a highly complex coordinated system of spatial and temporal gene expression. The characterization of the inner ear transcriptome is likely important for the functional study of auditory and vestibular components, yet, primarily due to tissue unavailability, detailed expression catalogues of the human inner ear remain largely incomplete. We report here, for the first time, comprehensive transcriptome characterization of the adult human cochlea, ampulla, saccule and utricle of the vestibule obtained from patients without hearing abnormalities. Using RNA-Seq, we measured the expression of >50,000 predicted genes corresponding to approximately 200,000 transcripts, in the adult inner ear and compared it to 32 other human tissues. First, we identified genes preferentially expressed in the inner ear, and unique either to the vestibule or cochlea. Next, we examined expression levels of specific groups of potentially interesting RNAs, such as genes implicated in hearing loss, long non-coding RNAs, pseudogenes and transcripts subject to nonsense mediated decay (NMD). We uncover the spatial specificity of expression of these RNAs in the hearing/balance system, and reveal evidence of tissue specific NMD. Lastly, we investigated the non-syndromic deafness loci to which no gene has been mapped, and narrow the list of potential candidates for each locus. These data represent the first high-resolution transcriptome catalogue of the adult human inner ear. A comprehensive identification of coding and non-coding RNAs in the inner ear will enable pathways of auditory and vestibular function to be further defined in the study of hearing and balance. Expression data are freely accessible at https://www.tgen.org/home/research/research-divisions/neurogenomics/supplementary-data/inner-ear-transcriptome.aspx.

Dataset Information

An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts.

Publications

An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts.

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