Research Progress in the Mechanisms and Functions of Gene Loss in Genome Evolution

doi:10.13560/j.cnki.biotech.bull.1985.2024-1239

Abstract

Abstract:

Gene loss is widespread among organisms and is one of crucial mechanisms in the evolution of genomes, contributing significantly to environmental adaptation and speciation. However, how gene loss happens and its implications remain unclear. This review synthesizes research progress in understanding the molecular mechanisms, functional consequences, and bias patterns of gene loss. Gene loss primarily arises from intrinsic mechanisms such as DNA replication errors, transposon activities, and chromosome structural variations, with additional influences from genetic drift, natural selection and other evolutionary forces. While gene loss can enhance the survival and reproductive capacities of organisms by optimizing resource utilization, streamlining metabolic pathways, and improving environmental adaptability, it likely inhibits adaptive flexibility to environmental changes due to the loss of critical functional genes, thereby increasing survival risks. Gene loss demonstrates non-random preferences, which is influenced by gene function, expression level, dosage sensitivity, genomic location, and protein network topology. Gene loss interacts with gene duplication, horizontal gene transfer (HGT) and other mechanisms to maintain a dynamic balance between genome reduction and expansion. In the future, it is essential to investigate the trade-offs and risks associated with gene loss, to clarify the mechanisms of gene loss in regulating adaptive strategies and its impacts on environmental adaptation, particularly in speciation and adaptive evolution, and ultimately to advance its applications in genetic and bioengineering breeding.

Key words: gene loss, genome evolution, adaptive evolution, gene function, loss bias

ZHOU Yi, LIU Yong-bo. Research Progress in the Mechanisms and Functions of Gene Loss in Genome Evolution[J]. Biotechnology Bulletin, 2025, 41(6): 38-48.

Figures/Tables 2

References 114

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物种 Species	基因组大小 Genome size （Gb）	基因 Gene	丢失机制 Loss mechanisms	参考文献 Reference
人类 Homo sapiens	约3.1	L-古洛糖酸内酯氧化酶	基因失活，无法自行合成维生素 C	［56］
裸鼹鼠 Heterocephalus glaber	约2.5	气味感知能力下降，依赖其他感官	地下生活减少嗅觉依赖，气味基因丢失，触觉或听觉增强	［55］
蝾螈 Salamandridae	14-130	增强再生能力	基因丢失降低炎症反应，提高组织再生能力	［51］
冰鱼 Channichthyidae	-	血红蛋白基因	基因缺失和假基因化影响氧气运输	［53］
海豚 Delphinidae	约2.5	嗅觉受体基因	水生环境嗅觉依赖性降低，相关基因假基因化	［57］
墨西哥盲洞鱼 Astyanax mexicanus	约1.4	眼发育基因（如视蛋白基因）	黑暗环境中视觉基因丢失或突变	［16］
鸡 Gallus gallus	约1.0	牙釉质基因（如牙釉蛋白基因）	牙齿退化导致牙釉质基因丢失	［58］
须鲸 Mysticeti	-	牙发育基因	从牙齿到鲸须的进化过渡中，相关基因假基因化	［59］
大熊猫 Ailuropoda melanoleuca	约2.4	Tas1r1基因	鲜味受体基因假基因化，导致鲜味感知丧失	［54］
象鸟 Aepyornithidae	-	与飞行相关基因（如肌肉发育基因）	不飞行导致相关基因丢失和突变	［60］

物种 Species	基因组大小 Genome size （Gb）	基因 Gene	丢失机制 Loss mechanisms	参考文献 Reference
人类 Homo sapiens	约3.1	L-古洛糖酸内酯氧化酶	基因失活，无法自行合成维生素 C	［56］
裸鼹鼠 Heterocephalus glaber	约2.5	气味感知能力下降，依赖其他感官	地下生活减少嗅觉依赖，气味基因丢失，触觉或听觉增强	［55］
蝾螈 Salamandridae	14-130	增强再生能力	基因丢失降低炎症反应，提高组织再生能力	［51］
冰鱼 Channichthyidae	-	血红蛋白基因	基因缺失和假基因化影响氧气运输	［53］
海豚 Delphinidae	约2.5	嗅觉受体基因	水生环境嗅觉依赖性降低，相关基因假基因化	［57］
墨西哥盲洞鱼 Astyanax mexicanus	约1.4	眼发育基因（如视蛋白基因）	黑暗环境中视觉基因丢失或突变	［16］
鸡 Gallus gallus	约1.0	牙釉质基因（如牙釉蛋白基因）	牙齿退化导致牙釉质基因丢失	［58］
须鲸 Mysticeti	-	牙发育基因	从牙齿到鲸须的进化过渡中，相关基因假基因化	［59］
大熊猫 Ailuropoda melanoleuca	约2.4	Tas1r1基因	鲜味受体基因假基因化，导致鲜味感知丧失	［54］
象鸟 Aepyornithidae	-	与飞行相关基因（如肌肉发育基因）	不飞行导致相关基因丢失和突变	［60］

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