De novo assembly of the common marmoset transcriptome from NextGen mRNA sequences
Tóm tắt
Nonhuman primates are important for both biomedical studies and understanding human evolution. Although research in these areas has mostly focused on Old World primates, such as the rhesus macaque, the common marmoset (Callithrix jacchus), a New World primate, offers important advantages in comparison to other primates, such as an accelerated lifespan. To conduct Next Generation expression studies or to study primate evolution, a high quality annotation of the marmoset genome is required. The availability of marmoset transcriptome data from five tissues, including both raw sequences and assembled transcripts, will aid in the annotation of the newly released marmoset assembly. RNA was extracted from five tissues: skeletal muscle, bladder and hippocampus from a male common marmoset, and cerebral cortex and cerebellum from a female common marmoset. All five RNA samples were sequenced on the Illumina HiSeq 2000 platform. Sequences were deposited in the NCBI Sequence Read Archive. Transcripts were assembled, annotated and deposited in the NCBI Transcriptome Shotgun Assembly database. We have provided a high quality annotation of 51,163 transcripts with full-length coding sequence. This set represented a total of 10,833 unique genes. In addition to providing empirical support for the existence of these 10,833 genes, we also provide sequence information for 2,422 genes that were not previously identified in the Ensembl annotation of the marmoset genome.
Tài liệu tham khảo
Phillips KA, Bales KL, Capitanio JP, Conley A, Czoty PW, ‘t Hart BA, Hopkins WD, Hu SL, Miller LA, Nader MA, Nathanielsz PW, Rogers J, Shively CA, Voytko ML: Why primate models matter. Am J Primatol. 2014, 76: 801-827. 10.1002/ajp.22281.
Abbott DH, Barnett DK, Colman RJ, Yamamoto ME, Schultz-Darken NJ: Aspects of common marmoset basic biology and life history important for biomedical research. Comp Med. 2003, 53: 339-350.
Tardif SD, Araujo A, Arruda MF, French JA, Sousa MB, Yamamoto ME: Reproduction and aging in marmosets and tamarins. Interdiscip Top Gerontol. 2008, 36: 29-48.
Mansfield K: Marmoset models commonly used in biomedical research. Comp Med. 2003, 53: 383-392.
Ward JM, Vallender EJ: The resurgence and genetic implications of New World primates in biomedical research. Trends Genet. 2012, 28: 586-591. 10.1016/j.tig.2012.09.003.
The Marmoset Genome Sequencing and Analysis Consortium: The common marmoset genome provides insight into primate biology and evolution. Nature Genet. 2014, 46: 850-857. 10.1038/ng.3042.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410. 10.1016/S0022-2836(05)80360-2.
Zerbino DR, Birney E: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008, 18: 821-829. 10.1101/gr.074492.107.
Schulz MH, Zerbino DR, Vingron M, Birney E: Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics. 2012, 28: 1086-1092. 10.1093/bioinformatics/bts094.
Gish W, States DJ: Identification of protein coding regions by database similarity search. Nature Genet. 1993, 3: 266-272. 10.1038/ng0393-266.
Maudhoo MD, Ren D, Gradnigo JS, Gibbs RM, Lubker AC, Moriyama EN, French JA, Norgren RB: Supporting materials for the “De novo assembly of the common marmoset transcriptome from NextGen mRNA sequences”. GigaScience Database. GigaScience Database. 2014,http://dx.doi.org/10.5524/100103,