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:
  • 金额:
    $ 7.5万
  • 依托单位:
  • 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.


项目成果

期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)

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Rick L Tarleton其他文献

The importance of persistence and dormancy in emTrypanosoma cruzi/em infection and Chagas disease
克氏锥虫感染和恰加斯病中持续性和休眠的重要性
  • DOI:
    10.1016/j.mib.2025.102615
  • 发表时间:
    2025-08-01
  • 期刊:
  • 影响因子:
    7.500
  • 作者:
    Molly E Bunkofske;Fernando J Sanchez-Valdez;Rick L Tarleton
  • 通讯作者:
    Rick L Tarleton

Rick L Tarleton的其他文献

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{{ truncateString('Rick L Tarleton', 18)}}的其他基金

The activation of benzoxaborole prodrug AN15368, a clinical candidate for Chagas disease
苯并氧杂硼罗前药 AN15368 的激活,恰加斯病的临床候选药物
  • 批准号:
    10667721
  • 财政年份:
    2023
  • 资助金额:
    $ 7.5万
  • 项目类别:
Optimizing blood PCR as test of cure in Chagas disease
优化血液 PCR 作为恰加斯病的治愈测试
  • 批准号:
    10451977
  • 财政年份:
    2022
  • 资助金额:
    $ 7.5万
  • 项目类别:
Optimizing blood PCR as test of cure in Chagas disease
优化血液 PCR 作为恰加斯病的治愈测试
  • 批准号:
    10590740
  • 财政年份:
    2022
  • 资助金额:
    $ 7.5万
  • 项目类别:
Trypanosoma cruzi dormancy and its implications for therapeutic treatment
克氏锥虫休眠及其对治疗的影响
  • 批准号:
    10573204
  • 财政年份:
    2020
  • 资助金额:
    $ 7.5万
  • 项目类别:
Trypanosoma cruzi dormancy and its implications for therapeutic treatment
克氏锥虫休眠及其对治疗的影响
  • 批准号:
    10368984
  • 财政年份:
    2020
  • 资助金额:
    $ 7.5万
  • 项目类别:
Purchase of an imaging flow cytometer 2016
2016年购买成像流式细胞仪
  • 批准号:
    9273704
  • 财政年份:
    2017
  • 资助金额:
    $ 7.5万
  • 项目类别:
Mechanisms of persistence in Trypanosoma cruzi infection
克氏锥虫感染的持续机制
  • 批准号:
    9754759
  • 财政年份:
    2016
  • 资助金额:
    $ 7.5万
  • 项目类别:
Multiplex treatment outcomes test for Chagas disease
恰加斯病多重治疗结果测试
  • 批准号:
    9305839
  • 财政年份:
    2016
  • 资助金额:
    $ 7.5万
  • 项目类别:
Mechanisms of persistence in Trypanosoma cruzi infection
克氏锥虫感染的持续机制
  • 批准号:
    9237877
  • 财政年份:
    2016
  • 资助金额:
    $ 7.5万
  • 项目类别:
Mechanisms of persistence in Trypanosoma cruzi infection
克氏锥虫感染的持续机制
  • 批准号:
    9979735
  • 财政年份:
    2016
  • 资助金额:
    $ 7.5万
  • 项目类别:

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