TIPPo:一个用户友好的工具,用于De Novo组装有机细胞基因组,具有高可靠性数据
Wenfei Xian1, Ilja Bezrukov1, Zhigui Bao1
1Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany.
Molecular biology and evolution
|January 13, 2025
概括
一个新的工具TIPPo使用长读测序准确地组装了植物细胞器基因组. 它有效地处理核DNA插入,改善叶绿体和线粒体基因组组装完整性.
科学领域:
- 基因组学就是基因组学.
- 分子生物学分子生物学
- 生物信息学是一种生物信息学.
背景情况:
- 植物细胞含有叶绿体和线粒体基因组,而植物线粒体基因组具有显著的结构复杂性.
- 现有的组装工具与植物线粒体基因组的大尺寸和结构变异以及核DNA插入作斗争.
研究的目的:
- 开发一个用户友好的,无参考工具 (TIPPo) 用于组装植物细胞器基因组使用PacBio长读数据.
- 提高植物叶绿体和线粒体基因组组合的完整性,特别是在存在核DNA插入的情况下.
主要方法:
- TIPPo使用了PacBio的高保真度长读数据.
- 采用深度学习模型进行初始读取分类和k-mer计数以进行改进.
- 无参考组合方法,不需要相关物种基因组或核基因组信息.
主要成果:
- TIPPo完全组装了54个质细胞基因组,性能优于其他工具.
- 在大多数物种中,对线粒体基因组组装的完整性与PMAT相当或更高.
- 确定了核塑DNA (NUPT) 和核线粒体DNA (NUMT) 插入,将它们的长度与核基因组大小相关联.
结论:
- TIPPo是一种强大的工具,用于在植物中进行无参考的有机细胞基因组组合.
- 核DNA插入 (NUPTs/NUMTs) 是随机发生的,并通过甲基化细胞因子突变降解.
- 导向RNA的DNA甲基化 (RdDM) 途径可能会在NUPT和NUMT中调解DNA甲基化.
相关概念视频
Genome Annotation and Assembly
18.8K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
18.8K
Export of Mitochondrial and Chloroplast Genes
3.6K
A eukaryotic cell can have up to three different types of genetic systems: nuclear, mitochondrial, and chloroplast. During evolution, organelles have exported many genes to the nucleus; this transfer is still ongoing in some plant species. Approximately 18% of the Arabidopsis thaliana nuclear genome is thought to be derived from the chloroplast’s cyanobacterial ancestor, and around 75% of the yeast genome derived from the mitochondria’s bacterial ancestor. This export has occurred...
3.6K
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
12.0K
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
12.0K
Genomic DNA in Eukaryotes
46.6K
Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
46.6K
Next-generation Sequencing
87.3K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
87.3K
Sanger Sequencing
752.6K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
752.6K


