An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice

Abstract

Gene duplication is an important evolutionary mechanism allowing to provide new genetic material and thus opportunities to acquire new gene functions for an organism, with major implications such as speciation events. Various processes are known to allow a gene to be duplicated and different models explain how duplicated genes can be maintained in genomes. Due to their particular importance, the identification of duplicated genes is essential when studying genome evolution but it can still be a challenge due to the various fates duplicated genes can encounter. In this review, we first describe the evolutionary processes allowing the formation of duplicated genes but also describe the various bioinformatic approaches that can be used to identify them in genome sequences. Indeed, these bioinformatic approaches differ according to the underlying duplication mechanism. Hence, understanding the specificity of the duplicated genes of interest is a great asset for tool selection and should be taken into account when exploring a biological question.

Keywords: bioinformatic tools; gene duplication; genome evolution; paralogous genes; synteny.

Figure 1

The different types of duplications. (A) Whole genome duplication which implies complete chromosome duplication. (B) Tandem duplications which produce identical adjacent sequences. (C) Retroduplication, which produces a retrocopy of a gene devoid of introns and with a polyA tail. (D) Transduplication in which a DNA transposon acquires fragments of genes. (E) Segmental duplications which correspond to long stretches of duplicated sequences with high identity.