MitoHiFi:来自PacBio的线粒体基因组组装的Python管道读取了高保真度的读数
Marcela Uliano-Silva1, João Gabriel R N Ferreira2,3, Ksenia Krasheninnikova4
1Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK. mu2@sanger.ac.uk.
BMC bioinformatics
|July 18, 2023
概括
一个新的工具,MitoHiFi,使用PacBio HiFi测序数据高效地组装线粒体基因组. 这种方法有助于发现新的重复和准确注释不同物种的基因.
科学领域:
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
- 分子生物学分子生物学
背景情况:
- PacBio HiFi 测序提供了长时间和高度准确的读数,彻底改变了基因组组装.
- 细胞线粒体基因组通常与核基因组一起以高覆盖率进行测序.
- 使用HiFi读取的线粒体基因组组装的专用工具以前没有.
研究的目的:
- 开发一个专门的工具,MitoHiFi,用于从PacBio HiFi阅读器组装线粒体基因组.
- 为了使组装的线粒体基因组内蛋白质和RNA基因的准确注释.
- 识别和排除从有机细胞基因组组装中线粒体DNA的核插入.
主要方法:
- MitoHiFi接受原始读取或组装的连接作为输入.
- 该工具以FASTA格式输出线粒体基因组序列,并附带基因注释.
- 它独立地从异质质体组装变体,并识别核线粒体序列.
主要成果:
- 为了主要的基因组项目,MitoHiFi成功地组装了甲基动物和真菌的374个线粒体基因组.
- 对60个组件的分析揭示了线粒体基因组中广泛的,以前未报告的重复.
- 该工具在广泛的种系学范围的种类中表现出能力.
结论:
- MitoHiFi是有效的组装线粒体基因组从PacBio HiFi数据跨不同的种类.
- 该软件以Python和GitHub上的Docker容器免费提供.
- MitoHiFi有助于更全面,更准确的线粒体基因组测序工作.
相关概念视频
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
12.6K
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...
12.6K
Export of Mitochondrial and Chloroplast Genes
3.7K
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...
3.7K
Translocation of Proteins into the Mitochondria
3.2K
Mitochondrial precursors are translocated to the internal subcompartments via independent mechanisms involving distinct protein machineries called translocases.
Sorting of outer membrane proteins:
Mitochondrial outer membrane proteins are of two types: the transmembrane, beta-barrel porins, and the membrane-anchored, alpha-helical proteins. Beta-barrel porin precursors are translocated by the TOM complex and inserted into the outer mitochondrial membrane by the SAM complex. In contrast,...
Sorting of outer membrane proteins:
Mitochondrial outer membrane proteins are of two types: the transmembrane, beta-barrel porins, and the membrane-anchored, alpha-helical proteins. Beta-barrel porin precursors are translocated by the TOM complex and inserted into the outer mitochondrial membrane by the SAM complex. In contrast,...
3.2K
Mitochondrial Protein Sorting
4.4K
Mitochondria are double-membrane organelles of the eukaryotes involved in cellular metabolism, signaling, ATP synthesis, and programmed cell death. Each of these processes requires specific proteins and enzymes that must be correctly sorted to the right mitochondrial subcompartment for the proper functioning of the organelle.
Most of these mitochondrial proteins are encoded by the nucleus and imported to the mitochondria as unfolded or loosely folded precursors. Mitochondrial precursors...
Most of these mitochondrial proteins are encoded by the nucleus and imported to the mitochondria as unfolded or loosely folded precursors. Mitochondrial precursors...
4.4K
The Inner Mitochondrial Membrane
3.4K
The inner mitochondrial membrane is the primary site of ATP synthesis. The inner membrane domain that forms a smooth layer adjacent to the outer membrane is called the inner boundary membrane. This domain contains membrane transporters that drive metabolites in and out of the mitochondria. In contrast, the inner membrane network that invaginates into the matrix space is called the cristae membrane. This domain accounts for principle mitochondrial function as it accommodates the protein...
3.4K
Animal Mitochondrial Genetics
7.7K
Among all the organelles in an animal cell, only mitochondria have their own independent genomes. Animal mitochondrial DNA is a double-stranded, closed-circular molecule with around 20,000 base pairs. Mitochondrial DNA is unique in that one of its two strands, the heavy, or H, -strand is guanine rich, whereas the complementary strand is cytosine rich and called the light, or L, -strand. Compared to nuclear DNA, mitochondrial DNA has a very low percentage of non-coding regions and is marked by...
7.7K


