Veral rhesus tissues into transcripts which allowed us to identify a

Veral rhesus tissues into transcripts which Marimastat allowed us to identify a total of 11,712 complete proteins representing 9,524 distinct genes. Using a combination of our assembled rhesus macaque transcripts and human transcripts, we annotated 18,757 transcripts and 16,050 genes with complete coding sequences in the MacaM assembly. Further, we demonstrate that the new annotations provide greatly improved accuracy as compared to the current annotations of rheMac2. Finally, we show that the MacaM genome provides an accurate resource for alignment of reads produced by RNA sequence expression studies. Conclusions: The MacaM assembly and annotation files provide a substantially more complete and accurate representation of the rhesus macaque genome than rheMac2 or CR_1.0 and will serve as an important resource for investigators conducting next-generation sequencing studies with nonhuman primates. Reviewers: This article was reviewed by Dr. Lutz Walter, Dr. Soojin Yi and Dr. Kateryna Makova. Keywords: Macaca mulatta, Rhesus macaque, Genome, Assembly, Annotation, Transcriptome, Next-generation sequencing* Correspondence: rnorgren@unmc.edu 2 Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA Full list of author information is available at the end of the article?2014 Zimin et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.Zimin et al. Biology Direct 2014, 9:20 http://www.biologydirect.com/content/9/1/Page 2 ofBackground Rhesus macaques (Macaca mulatta) already play an important role in biomedical research because their anatomy and physiology are similar to humans. However, the full potential of these animals as models for preclinical research can only be realized with a relatively complete and PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/9282946 accurate rhesus macaque reference genome. To take advantage of the powerful and inexpensive next-generation sequencing (NGS) technology, a high quality assembly (chromosome file) and annotation (GTF or GFF files) are necessary to serve as a reference. Short NGS reads are aligned against chromosomes; the annotation file is used to determine to which genes these reads map. For example, in mRNA-seq analysis, mRNA reads are aligned against the reference chromosomes. The GTF file is used to determine which exons of which genes are expressed. If the genome used as a reference is incomplete or incorrect, then mRNA-seq analysis will be impaired. The publication of the draft Indian-origin rhesus macaque assembly rheMac2 [1] was an important landmark in nonhuman primate (NHP) genomics. However, rheMac2 contains many gaps [1] and some sequencing errors [2,3]. Further, some scaffolds were PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/18218841 misassembled [3,4] while others were assigned to the wrong positions on chromosomes [3-5]. There have been a number of attempts to annotate rheMac2 including efforts by NCBI, Ensembl and others [6,7]. However, it is not possible to confidently and correctly annotate a gene in an assembly with missing, wrong or misassembled sequence. It is important to note that even a single error in the ass.