Gardner Paul P, Fasold Mario, Burge Sarah W, Ninova Maria, Hertel Jana, Kehr Stephanie, Steeves Tammy E, Griffiths-Jones Sam, Stadler Peter F
School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany; ecSeq Bioinformatics, Brandvorwerkstr.43, D-04275 Leipzig, Germany.
PLoS One. 2015 Mar 30;10(3):e0121797. doi: 10.1371/journal.pone.0121797. eCollection 2015.
Here we present the results of a large-scale bioinformatics annotation of non-coding RNA loci in 48 avian genomes. Our approach uses probabilistic models of hand-curated families from the Rfam database to infer conserved RNA families within each avian genome. We supplement these annotations with predictions from the tRNA annotation tool, tRNAscan-SE and microRNAs from miRBase. We identify 34 lncRNA-associated loci that are conserved between birds and mammals and validate 12 of these in chicken. We report several intriguing cases where a reported mammalian lncRNA, but not its function, is conserved. We also demonstrate extensive conservation of classical ncRNAs (e.g., tRNAs) and more recently discovered ncRNAs (e.g., snoRNAs and miRNAs) in birds. Furthermore, we describe numerous "losses" of several RNA families, and attribute these to either genuine loss, divergence or missing data. In particular, we show that many of these losses are due to the challenges associated with assembling avian microchromosomes. These combined results illustrate the utility of applying homology-based methods for annotating novel vertebrate genomes.
在此，我们展示了对48种鸟类基因组中非编码RNA基因座进行大规模生物信息学注释的结果。我们的方法使用来自Rfam数据库的人工整理家族的概率模型，来推断每个鸟类基因组中的保守RNA家族。我们用tRNA注释工具tRNAscan-SE的预测结果以及来自miRBase的微小RNA对这些注释进行补充。我们鉴定出34个在鸟类和哺乳动物之间保守的长链非编码RNA相关基因座，并在鸡中验证了其中12个。我们报道了几个有趣的案例，即已报道的哺乳动物长链非编码RNA（但不是其功能）是保守的。我们还证明了经典非编码RNA（如tRNA）以及最近发现的非编码RNA（如核仁小RNA和微小RNA）在鸟类中具有广泛的保守性。此外，我们描述了几个RNA家族的众多“缺失”情况，并将这些归因于真正的缺失、分歧或数据缺失。特别是，我们表明其中许多缺失是由于与鸟类微小染色体组装相关的挑战所致。这些综合结果说明了应用基于同源性的方法注释新的脊椎动物基因组的实用性。
