Impact of gene gains, losses and duplication modes on the origin and diversification of vertebrates

Cañestro, Cristian; Albalat, Ricard; Irimia, Manuel; Garcia‐Fernàndez, Jordi

doi:10.1016/j.semcdb.2012.12.008

Cited by 89 publications

(96 citation statements)

References 184 publications

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“…It is assumed that the 2 thrα genes appeared during the 2 rounds of whole-genome duplication which are supposed to have occurred during vertebrate evolution. However, many paralogs of the current vertebrate gene families were not originated during the 2 whole-genome duplications, but by extensive events of local duplications, which can be caused by unequal recombination, or by events of transposon mobilization or retrotransposition [Cañestro et al, 2013].…”

Section: Discussionmentioning

confidence: 99%

A Preliminary Genetic Map in Solea senegalensis (Pleuronectiformes, Soleidae) Using BAC-FISH and Next-Generation Sequencing

García-Cegarra¹,

Merlo²,

Ponce³

et al. 2013

Cytogenet Genome Res

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This article presents the first physical mapping carried out in the Senegalese sole (Solea senegalensis), an important marine fish species of Southern Europe. Eight probes were designated to pick up genes of interest in aquaculture (candidate genes) from a bacterial artificial chromosome (BAC) library using a method of rapid screening based on a 4-dimension PCR. Seven known and 3 unknown clones were isolated and labeled. The 10 BAC clones were used as probes to map the karyotype of the species by fluorescence in situ hybridization (FISH). Nine out of the 10 clones were localized in only 1 chromosome pair, whereas the remaining one hybridized on 2 chromosome pairs. The 2-color FISH experiments showed colocation of 4 probes in 2 chromosome pairs. In addition, 2-color FISH was carried out both with 5S rDNA and the BAC containing the lysozyme gene published previously. This first genetic map of the Senegalese sole represents a starting point for future studies of the sole genome. In addition, 7 out of the 10 BAC clones were sequenced using next-generation sequencing, and bioinformatic characterization of the sequences was carried out. Hence the anchoring of the sequences to specific chromosomes or chromosome arms is now possible, leading to an initial scaffold of the Senegalese sole genome.

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Section: Discussionmentioning

confidence: 99%

A Preliminary Genetic Map in Solea senegalensis (Pleuronectiformes, Soleidae) Using BAC-FISH and Next-Generation Sequencing

García-Cegarra¹,

Merlo²,

Ponce³

et al. 2013

Cytogenet Genome Res

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“…Even within mammals, which are generally thought not to tolerate polyploidization, a duplicated genome was 4 identified in a rodent (Gallardo et al, 1999;Gallardo et al, 2004). There is now clear evidence that the radiation of vertebrates was preceded by two rounds of WGD, and it has been suggested that these events have contributed to diversification and evolutionary innovations within vertebrates (Canestro et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Whole-genome duplication in teleost fishes and its evolutionary consequences

2014

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Whole-genome duplication (WGD) events have shaped the history of many evolutionary lineages. One such duplication has been implicated in the evolution of teleost fishes, by far the most species-rich vertebrate clade. After initial controversy, there is now solid evidence that such event took place in the common ancestor of all extant teleosts. It is termed teleost-specific (TS) WGD. After WGD, duplicate genes have different fates. The most likely outcome is non-functionalization of one duplicate gene due to the lack of selective constraint on preserving both. Mechanisms that act on preservation of duplicates are subfunctionalization (partitioning of ancestral gene functions on the duplicates), neofunctionalization (assigning a novel function to one of the duplicates) and dosage selection (preserving genes to maintain dosage balance between interconnected components). Since the frequency of these mechanisms is influenced by the genes' properties, there are over-retained classes of genes, such as highly expressed ones and genes involved in neural function. The consequences of the TS-WGD, especially its impact on the massive radiation of teleosts, have been matter of controversial debate. It is evident that gene duplications are crucial for generating complexity and that WGDs provide large amounts of raw material for evolutionary adaptation and innovation. However, it is less clear whether the TS-WGD is directly linked to the evolutionary success of teleosts and their radiation. Recent studies let us conclude that TS-WGD has been important in generating teleost complexity, but that more recent ecological adaptations only marginally related to TS-WGD might have even contributed more to diversification. It is likely, however, that TS-WGD provided teleosts with diversification potential that can become effective much later, such as during phases of environmental change. AbstractWhole genome duplication (WGD) events have shaped the history of many evolutionary lineages. One such duplication has been implicated in the evolution of teleost fishes, the by far most species-rich vertebrate clade. After initial controversy, evidence is now solid that such an event took place in the common ancestor of all extant teleosts, the so-called teleostspecific (TS) WGD. After WGD, duplicate genes have different fates. The most likely outcome is non-functionalization of one duplicate gene due to the lack of selective constraint on preserving both copies of the gene. Mechanisms that act on preservation of duplicates are subfunctionalization (partitioning of ancestral gene functions on the duplicates), neofunctionalization (assigning a novel function to one of the duplicates) and dosageselection (preserving genes to maintain dosage-balance between interconnected components).Since the frequency of these mechanisms is influenced by the gene's properties, there are over-retained classes of genes, such as highly expressed ones and genes involved in neural function. The consequences of the TS-WGD, especially its impact on the massi...

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“…The role of both gene duplication and whole-genome duplication is now widely accepted as a key driver of evolution as it is the most frequent mechanism responsible for the generation of genes with new functions (Ohno et al, 1968;Cañestro et al, 2013). It is through the accumulation of mutations and repeated rounds of duplication of existing genes that new functions are acquired (Zhang, 2003).…”

Section: Gene Duplicationmentioning

confidence: 99%

“…Gene duplication is known to have four possible outcomes (Zhang, 2003;Cañestro et al, 2013). One possible outcome is dosage repetition, where limited sequence evolution is seen, and gene function is conserved (Zhang, 2003;Cañestro et al, 2013).…”

Section: Gene Duplicationmentioning

confidence: 99%

“…One possible outcome is dosage repetition, where limited sequence evolution is seen, and gene function is conserved (Zhang, 2003;Cañestro et al, 2013). Another outcome following a duplication event may be pseudogenisation of one duplicated copy through the accumulation of mutations creating a non-functional gene (pseudogene) (Force et al, 1999;Zhang, 2003;Bischof et al, 2006).…”

Section: Gene Duplicationmentioning

confidence: 99%

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Characterisation of Duplicated Haemoglobin Genes in Bivalves

Klein¹

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Haemoglobins (Hbs) are found in virtually all phyla and are some of the most investigated proteins in biomedical sciences. These proteins exhibit an extraordinary diversity of form and function in invertebrate lineages. This provides a unique opportunity to explore the origin and evolution of Hbs yet little is known about their distribution, function and evolution in invertebrate lineages. To explore further the functions and evolution of those Hbs, recent transcriptome data for the Arcid bivalve Anadara trapezia is investigated here. This species shows the presence of duplicated Hb encoding genes suggesting that gene duplication may have been more extensive than previously thought in bivalves. This study tests the hypothesis that these duplicated genes show patterns of tissue specific expression and evidence of neofunctionalisation. This is shown here for at least three Hb encoding genes present in A. trapezia with strong tissue specific expression in haemolymph compared to other tissues. Furthermore, the expression of these genes remains unaffected by prolonged air exposure suggesting that neofunctionalisation may confer an evolutionary advantage to this bivalve. As well as the unique Hbs found in the bivalve order Arcoida, Hbs are also found in three other bivalve orders: Carditoida, Solemyoida and Veneroida. These four orders that possess Hbs provide compelling evidence for the independent evolution of these proteins in multiple bivalve lineages.To expand data on the distribution of Hbs in bivalves, a transcriptome sequence for Ctenoides ales in the order Limoida was generated in this project. Interrogation of the transcriptome shows the presence of at least three globin-like encoding genes including two Hb-like encoding genes providing preliminary evidence for another independent origin of Hb in a bivalve lineage. Overall, this study provides novel insights into the function, evolution and distribution of Hbs in bivalves by investigating two distantly related species. Results of this study are consistent with current theories that Hb diversity in bivalves is a result of repeated rounds of gene duplication providing the raw material for evolution. Investigation of hypoxic resistance also reinforces that greater expression of Hbs in haemolymph confers a physiological advantage suggesting that Hb would evolve more often in some lineages during adaptation to unfavourable environment conditions, particularlyAbstract ii hypoxia and prolonged air exposure.The finding of Hb-like encoding genes in another bivalve lineage also supports the evolution of this gene family through independent evolution and gene duplication, and gives insight into the distribution of globin genes in bivalves which is still poorly understood. The investigation of Hb genes in these bivalves also contributes to further understand the role of Hbs and provides potential novel insights for resistance in hypoxic environments, disease control and resistance to pollution in aquaculture.Abstract iii

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Impact of gene gains, losses and duplication modes on the origin and diversification of vertebrates

Cited by 89 publications

References 184 publications

A Preliminary Genetic Map in <b><i>Solea senegalensis</i></b> (Pleuronectiformes, Soleidae) Using BAC-FISH and Next-Generation Sequencing

A Preliminary Genetic Map in <b><i>Solea senegalensis</i></b> (Pleuronectiformes, Soleidae) Using BAC-FISH and Next-Generation Sequencing

Whole-genome duplication in teleost fishes and its evolutionary consequences

Characterisation of Duplicated Haemoglobin Genes in Bivalves

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