Abstract
BackgroundAnnotating mammalian genomes for noncoding RNAs (ncRNAs) is nontrivial since far from all ncRNAs are known and the computational models are resource demanding. Currently, the human genome holds the best mammalian ncRNA annotation, a result of numerous efforts by several groups. However, a more direct strategy is desired for the increasing number of sequenced mammalian genomes of which some, such as the pig, are relevant as disease models and production animals.ResultsWe present a comprehensive annotation of structured RNAs in the pig genome. Combining sequence and structure similarity search as well as class specific methods, we obtained a conservative set with a total of 3,391 structured RNA loci of which 1,011 and 2,314, respectively, hold strong sequence and structure similarity to structured RNAs in existing databases. The RNA loci cover 139 cis-regulatory element loci, 58 lncRNA loci, 11 conflicts of annotation, and 3,183 ncRNA genes. The ncRNA genes comprise 359 miRNAs, 8 ribozymes, 185 rRNAs, 638 snoRNAs, 1,030 snRNAs, 810 tRNAs and 153 ncRNA genes not belonging to the here fore mentioned classes. When running the pipeline on a local shuffled version of the genome, we obtained no matches at the highest confidence level. Additional analysis of RNA-seq data from a pooled library from 10 different pig tissues added another 165 miRNA loci, yielding an overall annotation of 3,556 structured RNA loci. This annotation represents our best effort at making an automated annotation. To further enhance the reliability, 571 of the 3,556 structured RNAs were manually curated by methods depending on the RNA class while 1,581 were declared as pseudogenes. We further created a multiple alignment of pig against 20 representative vertebrates, from which RNAz predicted 83,859 de novo RNA loci with conserved RNA structures. 528 of the RNAz predictions overlapped with the homology based annotation or novel miRNAs. We further present a substantial synteny analysis which includes 1,004 lineage specific de novo RNA loci and 4 ncRNA loci in the known annotation specific for Laurasiatheria (pig, cow, dolphin, horse, cat, dog, hedgehog).ConclusionsWe have obtained one of the most comprehensive annotations for structured ncRNAs of a mammalian genome, which is likely to play central roles in both health modelling and production. The core annotation is available in Ensembl 70 and the complete annotation is available at http://rth.dk/resources/rnannotator/susscr102/version1.02.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-459) contains supplementary material, which is available to authorized users.
Highlights
Annotating mammalian genomes for noncoding RNAs is nontrivial since far from all ncRNAs are known and the computational models are resource demanding
The modules of the pipeline we present a pipeline for annotation of structured RNAs
We found 1,032 high confident (95% id over 95% of the query length) RNA loci belonging to a total of 507 different RNA families see Additional file 1: Table S3 for the high confident sequence homology search results; the medium and low confident results are included in the table for completeness
Summary
Annotating mammalian genomes for noncoding RNAs (ncRNAs) is nontrivial since far from all ncRNAs are known and the computational models are resource demanding. With the sequencing of the human genome it became evident that protein coding sequences only make up about ∼1.2% of a mammalian genome [1] It has since been a main challenge to analyze the remaining part of the genome. The challenge is to carefully pin point only functional ncRNAs, which can be done through similarity to existing ncRNAs or de novo through a combination of RNA structure prediction and RNA-seq data. The latter may with subsequent effort reveal full length transcripts, yet with unidentified function [2] and functional assignment will require tedious lab work on each instance
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