Codon based co-occurrence network motifs in human mitochondria(三聯體理論推導人線粒體共生網路草圖)

This article is from nature.comscientific reportsarticles article

• Pramod Shinde,
• Camellia Sarkar &
• Sarika Jalan
• Scientific Reportsvolume 8, Article number: 3060 (2018)
• doi:10.1038/s41598-018-21454-2
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• Complex networks
• Evolutionary genetics

Received:18 May 2017

Accepted:05 February 2018

Published online:15 February 2018 （狗年春節這天正式發表）

Abstract

The nucleotide polymorphism（多態性： poly--mophology；發音重點在：morphism） in the human mitochondrial genome (mtDNA: 細胞線粒體的4種鹼基順序排列) tolled by codon position bias plays an indispensable role in human population dispersion and expansion (人類線粒體4種鹼基順序序列中「三聯體鹼基的位置擺動」造成了地球上人群的分布和繁衍) . Herein, genome-wide nucleotide co-occurrence networks were constructed using data comprised of five different geographical regions and around 3000 samples for each region. We developed a powerful network model to describe complex mitochondrial evolutionary patterns among codon and non-codon positions （根據地球5大洲3000多個地區的人體線粒體樣本資料，我們建立了線粒體核苷酸序列共生網路。在此基礎上，我們設計了高效的線粒體化學關係網路草圖，可以用於在分子水平上描述複雜的人線粒體的「從編碼區到非編碼區」的進化路徑）. We found evidence that the evolution of human mitochondria DNA is dominated by adaptive forces, particularly mutation and selection, which was supported by many previous studies （我們發現的證據表明：人類線粒體脫氧核糖核酸的進化由「適應力」所決定，「特別是突變和選擇」所表現的「適應力」。我們的這些結論跟之前的大量研究相一致。）. The diversity observed in the mtDNA was compared with mutations, co-occurring mutations, network motifs considering codon positions as causing agent. This comparison showed that long-range nucleotide co-occurrences have a large effect on genomic diversity. Most notably, codon motifs apparently underpinned the preferences among codon positions for co-evolution which is probably highly biased during the origin of the genetic code. Our analysis also showed that variable nucleotide positions of different human sub-populations implemented the independent mtDNA evolution to its geographical dispensation. Ergo, this study has provided both a network framework and a codon glance to investigate co-occurring genomic variations that are critical in underlying complex mitochondrial evolution (故， 該項研究有2個意義： 一是提出了線粒體分子進化的網路草圖；二是提供 了研究細粒體四種鹼基序列共生且變化現象時對《Crick 4*4*4遺傳密碼字典》的使用方法) .

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