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：
9101686
负责人：
TODD A MINNING
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 2018-03-31
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（通过应用程序证明）：克鲁齐锥虫的基因组研究最持久和重要的是缺乏可接受的Ference基因组。，在克鲁兹基因组基因组中包含高重复含量（50％），用于测序和参考基因组组装，以及参考菌株中的遗传镶嵌性。由于参考菌株的杂合性 - 染色体由基因含量大致不同，因此两个染色体序列对齐，甚至在两个染色体中的长度都大大静止。以前正在进行的整个基因组测序研究在这种病因中，远离人类疾病，并努力仔细检查参考基因组difficalt，我们经常提议解决Cruzi T. cruzi参考基因组的修饰。单分子，长读（最多10 kb）的测序，以封闭差距，并扩展ly sanger读取（700 bp）时发生的组件，以组装原始的Cl-brewery参考基因组。克鲁兹分离株进行测序且没有镶嵌基因组来简化组件。覆盖Cruzi分离株的应对。