Inferring Orthologs: Open Questions and Perspectives:

Genomics Insights

FredjTekaia¹ 

关键词: evolutionary processes;    genome annotation quality;    taxon sampling;    synteny;    phylogeny;    HGT;    multidomains;    genome trees;   

DOI  :  10.4137/GEI.S37925

学科分类：生物科学（综合）

来源: Sage Journals

【 摘 要 】

With the increasing number of sequenced genomes and their comparisons, the detection of orthologs is crucial for reliable functional annotation and evolutionary analyses of genes and species. Yet, the dynamic remodeling of genome content through gain, loss, transfer of genes, and segmental and whole-genome duplication hinders reliable orthology detection. Moreover, the lack of direct functional evidence and the questionable quality of some available genome sequences and annotations present additional difficulties to assess orthology. This article reviews the existing computational methods and their potential accuracy in the high-throughput era of genome sequencing and anticipates open questions in terms of methodology, reliability, and computation. Appropriate taxon sampling together with combination of methods based on similarity, phylogeny, synteny, and evolutionary knowledge that may help detecting speciation events appears to be the most accurate strategy. This review also raises perspectives on the potential determination of orthology throughout the whole species phylogeny.

【 授权许可】

CC BY