Faculty of Life Sciences, Faculty of Engineering and Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel 52900.
Bioinformatics. 2014 Feb 1;30(3):310-6. doi: 10.1093/bioinformatics/btt570. Epub 2013 Oct 1.
To understand the molecular mechanisms of neurons, it is imperative to identify genomic dissimilarities within the heterogeneity of the neural system. This is especially true for neuronal disorders in which spatial considerations are of critical nature. For this purpose, Hirudo medicinalis provides here an ideal system in which we are able to follow gene expression along the central nervous system, to affiliate location with gene behavior.
In all, 221.1 million high-quality short reads were sequenced on the Illumina Hiseq2000 platform at the single ganglion level. Thereafter, a de novo assembly was performed using two state-of-the-art assemblers, Trinity and Trans-ABySS, to reconstruct a comprehensive de novo transcriptome. Classification of Trinity and Trans-ABySS transcripts produced a non-redundant set of 76 845 and 268 355 transcripts (>200 bp), respectively. Remarkably, using Trinity, 82% of the published medicinal leech messenger RNAs was identified. For the innexin family, all of the 21 recently reported genes were identified. Spatial regulation analysis across three ganglia throughout the entire central nervous system revealed distinct patterns of gene expression. These transcriptome data were combined with expression distribution to produce a spatio-transcripto map along the ganglia chain. This study provides a resource for gene discovery and gene regulation in future studies.
为了了解神经元的分子机制，必须确定神经系统异质性中的基因组差异。对于空间考虑至关重要的神经元紊乱尤其如此。为此，医用水蛭提供了一个理想的系统，我们可以在其中沿中枢神经系统跟踪基因表达，将位置与基因行为相关联。
总共在 Illumina Hiseq2000 平台上对单个神经节进行了 2.211 亿个高质量短读测序。此后，使用两种最先进的组装器 Trinity 和 Trans-ABySS 进行从头组装，以重建全面的从头转录组。Trinity 和 Trans-ABySS 转录本的分类分别产生了一组非冗余的 76845 和 268355 个转录本（>200bp）。值得注意的是，使用 Trinity 鉴定了 82%的已发表的医用水蛭信使 RNA。对于连接蛋白家族，所有最近报道的 21 个基因都被鉴定出来。对整个中枢神经系统中三个神经节的空间调节分析显示出不同的基因表达模式。这些转录组数据与表达分布相结合，生成了沿神经节链的空间转录图谱。本研究为未来研究中的基因发现和基因调控提供了资源。
