在八种Sapindaceae物种中对核基因组进行比较分析
Yuxuan Song1, Meng Shen1, Fuliang Cao1
1Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
International journal of molecular sciences
|January 11, 2025
概括
在Sapindaceae物种中Codon使用偏差揭示了A/T丰富性和自然选择对突变的影响. 这种分析有助于理解家族内部的进化关系.
科学领域:
- 基因组学就是基因组学.
- 分子进化分子进化
- 生物信息学是一种生物信息学.
背景情况:
- 代码使用偏差 (CUB) 描述了基因组内代码频率的变化,对于理解基因组结构,功能和进化至关重要.
- 关于CUB模式和影响八种生态重要Sapindaceae物种核基因组的因素的知识有限.
研究的目的:
- 调查八种Sapindaceae物种的核基因组中的codon使用模式及其决定因素.
- 通过CUB分析,探索Sapindaceae物种之间的进化关系.
主要方法:
- 分析核酸组成和密码体使用模式.
- 关于相对同义码子使用 (RSCU) 的对应性分析.
- 分析ENC-GC3图谱,PR2-Bias和中立图谱.
- 聚类热图分析,包括桑比属和其他物种.
主要成果:
- 在八种Sapindaceae物种中观察到A/T丰富度和在第三个码头位置偏好A/T.
- 发现自然选择对CUB的影响比突变压力更大.
- 确定了两种不同的群体 (单和双),表明CUB在阐明家族层面的进化关系方面的有效性.
结论:
- 在Sapindaceae中,Codon的使用是由自然选择和其他因素塑造的,自然选择占主导地位.
- CUB分析是推断家族层面进化关系的一个有价值的工具.
- 这项研究突出了研究Sapindaceae物种的独特的密码使用特征和进化特征.
相关概念视频
Evolutionary Relationships through Genome Comparisons
5.7K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.7K
Gene Evolution - Fast or Slow?
7.0K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
7.0K
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
Cis-regulatory Sequences
9.7K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
9.7K
Comparing Copy Number Variations and SNPs
17.1K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
17.1K
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


