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基因组大小和染色体数量是精确的基因组组装评估的关键指标

Carl E Hjelmen¹

¹Department of Biology, Utah Valley University, 800 W. University Parkway, Orem, UT 84058, USA.

|June 13, 2024

概括

许多基因组组合与估计的物种大小不匹配,更大的基因组显示出更大的尺寸偏差. 一个新的比例N50度量提高了基因组组装完整性评估.

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.

背景情况:

NCBI数据库拥有超过41,000个真核生物基因组组合,在连续性和大小方面有显著的改进.
然而,只有大约三分之一的这些集合有相应的公开可用的基因组大小估计.
这种差异凸显了综合性基因组表征中的差距.

研究的目的:

评估基因组组合与它们估计的物种大小相比.
调查影响大小偏差的因素,包括基因组大小,王国,测序平台和组装指标.
为改进基因组组装评估引入一种新型指标.

主要方法:

总基因组组装大小与公开可用的基因组大小估计的比较.
对基因组大小,王国,测序平台和标准指标 (N50,BUSCO) 的尺寸偏差的分析.
与平均染色体大小相对应的比例N50度量的开发和评估.

主要成果:

显著比例的基因组组合偏离估计的大小超过10%.
尺寸偏差随着基因组大小的增加而增加,这表明非编码和结构DNA的作用.
标准指标部分解释,但不能完全解释尺寸变化;测序平台显示了适度的性能差异.

结论:

基因组组装大小偏差是常见的,与基因组大小相关.
一个新型的比例N50度量表现出与完整基因组组合的更强的关系.
比例N50度量为基因组组装质量评估提供了改进的跨物种比较.

关键词:

评估评估的评估评估的评估.染色体数是什么?染色体数是什么?一个真核生物的真核生物.基因组组装组合的基因组.基因组大小基因组大小基因组学就是基因组学.测序的测序是指测序的测序.

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相关概念视频

Genome Annotation and Assembly

Genome Annotation and Assembly

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.

Genomic DNA in Eukaryotes

Genomic DNA in Eukaryotes

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.

Karyotyping

Karyotyping

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

DNA Packaging

DNA Packaging

Chromosome Structure

Chromosome Structure

A functional eukaryotic chromosome must contain three elements: a centromere, telomeres, and numerous origins of replication.
The centromere is a DNA sequence that links sister chromatids. This is also where kinetochores, protein complexes to which spindle microtubules attach, are constructed after the chromosome is replicated. The kinetochores allow the spindle microtubules to move the chromosomes within the cell during cell division.
Telomeres consist of non-coding repetitive nucleotide...