化学计量基因组学研究进展

摘要

Stoichiogenomics is a newly arisen research field,which concerns the element usage biases of biological macromolecules at genome,transcriptome,proteome,metabonome levels.Different biological macromolecules have different element compositions and contents.When the supply of some elements was constrained,natural selection might bias the usage of the monomers (amino acid or nucleotide) to reduce constrained element costs in the synthesis of biological macromolecules.This field is flourishing with the intensive applications of high throughput sequencing and assembly technologies,more and more available metagenomic and metatranscriptomic data,and the applications of new analysis strategies.As a newly emerged cross discipline field,stoichiogenomics integrates stoichiometry,ecology,evolutionary biology,genomics and bioinformatics to provide a whole new perspective for investigating the interactions of the macromolecular evolution and ecosystem,and data mining in the post genomic era.In this review,we summarize the latest research progress of stoichiogenomics from the aspect of the element usage biases in proteins and nucleic acids.Furthermore,new research directions are discussed to provide some valuable references for the research and application of stoichiogenomics.%化学计量基因组学是一个新兴的研究领域,研究基因组、转录组、蛋白质组及代谢组等组学数据中生物大分子的元素使用偏好.不同生物大分子的元素组成与数量不同,当元素供应受到限制,自然选择偏好性利用某些单体(氨基酸或核苷酸)来合成生物大分子(DNA、RNA和蛋白质等),从而减少元素成本.随着高通量测序技术和组装技术的大量应用,越来越多的宏基因组、宏转录组数据被公开报道,以及新的分析手段的应用,使得该领域蓬勃发展.作为一门新兴的交叉学科,化学计量基因组学整合了化学计量学、生态学、进化生物学、基因组学和生物信息学,为研究分子进化和生态系统的互作以及后基因组时代数据的挖掘提供了一个全新的视角.本文从蛋白质和核酸的元素使用偏好性方面综述了化学计量基因组学的最新研究成果,并探讨了新的研究方向,以期为该领域的研究和应用提供有益参考.