Duplicated Gene Evolution Following Whole-Genome Duplication in Teleost Fish

Guo, Baocheng; Wagner, Andreas; He, Shunping

doi:10.5772/22039

Cited by 8 publications

(5 citation statements)

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“…Similar to Tibetan wild yak [ 2 ] and ground tit [ 3 ], gene families involved in metabolic processes were remarkably expanded in G. przewalskii , indicating the development of strong capacity to meet high energy demands in long-term low temperature aquatic environment. Environmental challenge tended to trigger gene duplication and neofunctionalization, new members in gene families possibly enhanced energy production efficiency in G. przewalskii by acquiring novel functions, which revealed by many cases [ 48 – 51 ]. In addition, genes showing signature of adaptive evolution in G. przewalskii also were involved into energy metabolism.…”

Section: Discussionmentioning

confidence: 99%

Comprehensive transcriptomic analysis of Tibetan Schizothoracinae fish Gymnocypris przewalskii reveals how it adapts to a high altitude aquatic life

et al. 2017

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BackgroundUnderstanding the genetic basis of adaptation to high altitude life is of paramount importance for preserving and managing genetic diversity in highland animals. This objective has been addressed mainly in terrestrial fauna but rarely in aquatic animals. Tibetan Schizothoracinae fish is the ideal model system in evolutionary biology, carrying key insights into evolutionary genetics of speciation and adaptation at high altitude. Gymnocypris przewalskii is the newly formed Schizothoracinae fish species in the Tibetan Plateau, inhabits chronic cold, extreme saline and alkaline aquatic environment in Lake Qinghai, thus evolving the unique genomic signatures to adapt extremely severe environments.ResultsTo characterize its genomic features, we assembled de novo transcriptome of G. przewalskii from Lake Qinghai. Intriguingly, by comparative genomic analyses of G. przewalskii and 8 other fish species, we identified potential expansions in gene families related to energy metabolism, transport and developmental functions, possibly underlying the adaptation to these environmental stresses. Through comprehensive molecular evolution analyses, we found that sets of genes controlling mitochondrion, ion homoeostasis, acid-base balance and innate immunity show significant signals of positive selection. Compared to previous studies on highland fishes, we failed to identify any positively selected genes related to hypoxia response.ConclusionsOur findings provide comprehensive insights into the genetic basis of teleost fish that underlie their adaptation to extreme high altitude aquatic life on the Tibetan Plateau.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-0925-z) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Comprehensive transcriptomic analysis of Tibetan Schizothoracinae fish Gymnocypris przewalskii reveals how it adapts to a high altitude aquatic life

et al. 2017

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“…Gene gains and losses are important processes contributing to evolutionary innovation and differentiation [ 64 , 65 ], perhaps especially so in teleosts because of the teleost-specific whole genome duplication event [ 66 ]. The comparison between stickleback orthologs revealed that some genes are likely to have been lost in the three-spined stickleback, as they exist both in nine-spined sticklebacks and other model fish genomes.…”

Section: Discussionmentioning

confidence: 99%

Genomic divergence between nine- and three-spined sticklebacks

et al. 2013

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BackgroundComparative genomics approaches help to shed light on evolutionary processes that shape differentiation between lineages. The nine-spined stickleback (Pungitius pungitius) is a closely related species of the ecological ‘supermodel’ three-spined stickleback (Gasterosteus aculeatus). It is an emerging model system for evolutionary biology research but has garnered less attention and lacks extensive genomic resources. To expand on these resources and aid the study of sticklebacks in a phylogenetic framework, we characterized nine-spined stickleback transcriptomes from brain and liver using deep sequencing.ResultsWe obtained nearly eight thousand assembled transcripts, of which 3,091 were assigned as putative one-to-one orthologs to genes found in the three-spined stickleback. These sequences were used for evaluating overall differentiation and substitution rates between nine- and three-spined sticklebacks, and to identify genes that are putatively evolving under positive selection. The synonymous substitution rate was estimated to be 7.1 × 10-9 per site per year between the two species, and a total of 165 genes showed patterns of adaptive evolution in one or both species. A few nine-spined stickleback contigs lacked an obvious ortholog in three-spined sticklebacks but were found to match genes in other fish species, suggesting several gene losses within 13 million years since the divergence of the two stickleback species. We identified 47 SNPs in 25 different genes that differentiate pond and marine ecotypes. We also identified 468 microsatellites that could be further developed as genetic markers in nine-spined sticklebacks.ConclusionWith deep sequencing of nine-spined stickleback cDNA libraries, our study provides a significant increase in the number of gene sequences and microsatellite markers for this species, and identifies a number of genes showing patterns of adaptive evolution between nine- and three-spined sticklebacks. We also report several candidate genes that might be involved in differential adaptation between marine and freshwater nine-spined sticklebacks. This study provides a valuable resource for future studies aiming to identify candidate genes underlying ecological adaptation in this and other stickleback species.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-14-756) contains supplementary material, which is available to authorized users.

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“…However, a third round of WGD, restricted to teleosts, was thought to have occurred after the divergence of teleosts and other vertebrates [39]. This third duplication, named as the fish-specific genome duplication (FSGB), has been supported by various comparative genomics studies [40,41].…”

Section: Discussionmentioning

confidence: 99%

Characterization and Evolution of Dishevelled Genes in Paralichthys olivaceus

Peng

et al. 2019

AJAAR

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The study examined the key gene Dishevelled (Dvl or Dsh) in Wnt (Wingless and INT-1) signaling pathways. The gene (Dvl) was characterized in the flat fish Paralichthys olivaceus for its expression pattern structure and phylogenetics at the Ocean University of China in Qingdao, China in 2018. Three gene paralogues (Dvl1, Dvl2 and Dvl3) of the Dvl family were cloned in P. olivaceus and a N-terminal DAX domain, a central PDZ domain and a C-terminal DEP domain were discovered in all three protein paralogues. Phylogenetic analysis revealed that Dvl genes in P. olivaceus are most closely related to those in marine teleosts Larimichthys crocea and Stegastes partitus, followed by those in Cynoglossus semilaevis. For each Dvl gene, the genes in teleosts fall into a clade independent from the ones in other vertebrates, suggesting that the duplication of Dvl genes occurred prior to the divergence of vertebrates. The temporal expression patterns of the three Dvl genes were characterized during the embryonic development of teleosts. In P. olivaceus, all three Dvl genes remain at low expression levels during the early stages of development until gastrula stage, when the expression of Dvl1 was significantly up-regulated. The research revealed vastly different temporal expression patterns of Dvl genes and suggested that the structure of Dvl proteins is conserved, but the expression patterns of Dvl genes vary significantly among different classes.

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Duplicated Gene Evolution Following Whole-Genome Duplication in Teleost Fish

Cited by 8 publications

References 36 publications

Comprehensive transcriptomic analysis of Tibetan Schizothoracinae fish Gymnocypris przewalskii reveals how it adapts to a high altitude aquatic life

Comprehensive transcriptomic analysis of Tibetan Schizothoracinae fish Gymnocypris przewalskii reveals how it adapts to a high altitude aquatic life

Genomic divergence between nine- and three-spined sticklebacks

Characterization and Evolution of Dishevelled Genes in Paralichthys olivaceus

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