Generation of reference genomes for Trypanosoma cruzi using PacBio sequencing

使用 PacBio 测序生成克氏锥虫参考基因组

基本信息

批准号：
9251753
负责人：
Rick L Tarleton
金额：
$ 7.5万
依托单位：
UNIVERSITY OF GEORGIA
依托单位国家：
美国
项目类别：
财政年份：
2016
资助国家：
美国
起止时间：
2016-04-01 至 2019-03-31
项目状态：
已结题

项目摘要

DESCRIPTION (provided by applicant): The most persistent and significant hindrance to genomic studies of Trypanosoma cruzi is the lack of an acceptable reference genome. There are a number of factors that have impeded progress in generating a high quality, fully assembled T. cruzi reference sequence, including high repeat content (50%) in the T. cruzi genome, extreme genome-wide heterozygosity in the reference strain (CL-Brener) that was chosen for sequencing and reference genome assembly, and genetic mosaicism in the reference strain. Thus, the current reference genome for T. cruzi has hundreds of gaps and regions of assembly collapse, has never been fully assembled and is, in fact, presented as two genomes due to the heterozygosity of the reference strain -each chromosome is presented as two versions differing substantially in terms of gene content, sequence identity where the two chromosome sequences align, and even lengths of the two chromosomes in a pair. These issues have greatly muted the efficacy and power of previous and ongoing whole genome sequencing studies in this causative agent of human disease, and have made virtually any endeavor involving the need for scrutinizing the reference genome difficult and frequently unproductive. We propose to tackle the issues with the current T. cruzi reference genome using three modifications of the approach originally used to generate it. First, we propose to use single-molecule, long-read (up to 10 kb) sequencing to close gaps and expand regions of assembly collapse that occurred when primarily Sanger reads (700 bp) were used to assemble the original CL-Brener reference genome. Second, we will select T. cruzi isolates for sequencing that are homozygous and do not have mosaic genomes to simplify the assemblies. Third, because all T. cruzi lines are derived from two ancestral, divergent, homozygous, non-mosaic lineages, we will generate reference sequences to each "parental" lineage in order to cover the scope of genetic content in all T. cruzi isolates.

描述（由适用提供）：克鲁齐锥虫基因组研究最持久和最大的障碍是缺乏可接受的参考基因组。在产生高质量，完全组装的克鲁兹参考序列方面，有许多因素阻碍了进展，包括在T. cruzi基因组中的高重复含量（50％），极端基因组全基因组全基合子的参考菌株（CL-BRENER）（CL-BRENER）被选中用于测序和参考基因组组装和遗传摩西抗性的参考菌株（CL-BRENER）。 That, the current reference genome for T. cruzi has hundreds of gaps and regions of assembly collapse, has never been fully assembled and is, in fact, presented as two genomes due to the heterozygosity of the reference strain -each chromosome is presented as two versions differentially in terms of gene content, sequence identity where the two chromosome sequences align, and even lengths of the two chromosomes in a pair.这些问题极大地突变了这种严重的人类疾病药物的先前和正在进行的整个基因组测序研究的效率和力量，并且实际上做出了任何努力，涉及需要仔细研究参考基因组困难且经常没有生产力。我们建议使用最初用于生成它的方法的三种修改来解决当前克鲁兹参考基因组的问题。首先，我们建议使用单分子，长阅读（最多10 kb）测序来封闭间隙，并扩展当使用初级sanger读数（700 bp）时发生的组装崩溃区域来组装原始的Cl-Brener参考基因组。其次，我们将选择克鲁兹分离株进行纯合且没有镶嵌基因组来简化组件的测序。第三，由于所有t. cruzi线均来自两个祖先，不同的，纯合的非摩西族谱系，因此我们将对每个“父母”谱系生成参考序列，以覆盖所有T. Cruzi分离株中遗传含量的范围。