De novo assembly of the common marmoset transcriptome from NextGen mRNA sequences.
De novo assembly of the common marmoset transcriptome from NextGen mRNA sequences.
复制标题
DOI：
10.1186/2047-217x-3-14
复制
发表时间：
2014
期刊：
影响因子：
9.2
通讯作者：
Norgren RB Jr
中科院分区：
文献类型：
--
作者：
Maudhoo MD;Ren D;Gradnigo JS;Gibbs RM;Lubker AC;Moriyama EN;French JA;Norgren RB Jr
非人类灵长类动物对生物医学研究和理解人类进化都很重要。虽然这些领域的研究主要集中在旧大陆灵长类动物，如恒河猴，但普通狨猴（Callithrix jacchus），一种新世界灵长类动物，与其他灵长类动物相比，具有重要的优势，例如寿命缩短。为了进行下一代表达研究或研究灵长类动物的进化，需要对狨猴基因组进行高质量的注释。来自五个组织的狨猴转录组数据，包括原始序列和组装的转录本，将有助于对新发布的狨猴组合进行注释。从雄性普通狨猴的骨骼肌、膀胱和海马以及雌性普通狨猴的大脑皮层和小脑等5个组织中提取RNA。所有5个RNA样本在Illumina HiSeq 2000平台上测序。序列存储在NCBI序列读取档案中。转录本被组装、注释并存入NCBI转录组Shotgun汇编数据库。我们提供了51,163个转录本的高质量注释，并提供了完整的编码序列。这一组共有10833个独特的基因。除了为这10833个基因的存在提供经验支持外，我们还提供了2422个基因的序列信息，这些基因以前没有在狨猴基因组的Ensembl注释中被识别出来。
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.