Functional requirements driving the gene duplication in 12 Drosophila species

Yan Zhong,Xiaohui Zhang,Yanxiao Jia,Dacheng Tian,Sihai Yang,Yang Gao

doi:10.1186/1471-2164-14-555

Abstract

BackgroundGene duplication supplies the raw materials for novel gene functions and many gene families arisen from duplication experience adaptive evolution. Most studies of young duplicates have focused on mammals, especially humans, whereas reports describing their genome-wide evolutionary patterns across the closely related Drosophila species are rare. The sequenced 12 Drosophila genomes provide the opportunity to address this issue.ResultsIn our study, 3,647 young duplicate gene families were identified across the 12 Drosophila species and three types of expansions, species-specific, lineage-specific and complex expansions, were detected in these gene families. Our data showed that the species-specific young duplicate genes predominated (86.6%) over the other two types. Interestingly, many independent species-specific expansions in the same gene family have been observed in many species, even including 11 or 12 Drosophila species. Our data also showed that the functional bias observed in these young duplicate genes was mainly related to responses to environmental stimuli and biotic stresses.ConclusionsThis study reveals the evolutionary patterns of young duplicates across 12 Drosophila species on a genomic scale. Our results suggest that convergent evolution acts on young duplicate genes after the species differentiation and adaptive evolution may play an important role in duplicate genes for adaption to ecological factors and environmental changes in Drosophila.

Highlights

Gene duplication supplies the raw materials for novel gene functions and many gene families arisen from duplication experience adaptive evolution
In these young duplicate gene families, three types were defined based on their expansion patterns: species-specific expansions, lineagespecific expansions and complex expansions
This uneven distribution of the young duplicate genes was found in the lineage-specific expansions and the complex expansions

Summary

Introduction

Gene duplication supplies the raw materials for novel gene functions and many gene families arisen from duplication experience adaptive evolution. Most studies of young duplicates have focused on mammals, especially humans, whereas reports describing their genome-wide evolutionary patterns across the closely related Drosophila species are rare. At the genome-wide level, the signatures of adaptive natural selection of young gene duplicates are found with high frequency in the human, macaque, mouse and rat genomes [16]. Gene gain and loss is estimated with a Drosophila-wide perspective [25], a systematic investigation of the genetic character and evolutionary pattern of young duplicate genes across the closely related Drosophila species has not been reported

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