The altered evolutionary trajectories of gene duplicates

Lynch, Michael; Katju, Vaishali

doi:10.1016/j.tig.2004.09.001

Cited by 270 publications

(236 citation statements)

References 45 publications

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“…It should be interesting to investigate how the processing of NK-lysin gene RNA is controlled at the molecular level in the brain. The spatial differences in expression could indicate spatially partitioned subfunctions, but that does not exclude the possibilities of neofunctions or temporally partitioned subfunctions (Torgerson and Singh, 2004;Lynch and Katju, 2004;Postlethwait et al, 2004;He and Zhang, 2005).…”

Section: Discussionmentioning

confidence: 99%

NK-lysin of channel catfish: Gene triplication, sequence variation, and expression analysis

Wang

et al. 2006

Molecular Immunology

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Section: Discussionmentioning

confidence: 99%

NK-lysin of channel catfish: Gene triplication, sequence variation, and expression analysis

Wang

et al. 2006

Molecular Immunology

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“…Short-term effects have not been easy to track. Very different theories on the forces that drive the retention or loss of gene duplicates include buffering for essential genes, enhancement of metabolic fluxes, protein dosage effects and rapid divergence of gene pairs [23][24][25][26][27][28] . Because these models predict different retention outcomes according to gene classes, we analysed the predicted gene categories in Paramecium for their propensity for duplicate retention.…”

Section: Retention and Evolution Of Duplicate Genesmentioning

confidence: 99%

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia

Aury

Jaillon

Duret

et al. 2006

Nature

759

836

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The duplication of entire genomes has long been recognized as having great potential for evolutionary novelties, but the mechanisms underlying their resolution through gene loss are poorly understood. Here we show that in the unicellular eukaryote Paramecium tetraurelia, a ciliate, most of the nearly 40,000 genes arose through at least three successive whole-genome duplications. Phylogenetic analysis indicates that the most recent duplication coincides with an explosion of speciation events that gave rise to the P. aurelia complex of 15 sibling species. We observed that gene loss occurs over a long timescale, not as an initial massive event. Genes from the same metabolic pathway or protein complex have common patterns of gene loss, and highly expressed genes are over-retained after all duplications. The conclusion of this analysis is that many genes are maintained after whole-genome duplication not because of functional innovation but because of gene dosage constraints.Ciliates are unique among unicellular organisms in that they separate germline and somatic functions 1 . Each cell harbours two kinds of nucleus, namely silent diploid micronuclei and highly polyploid macronuclei. The latter are unusual in that they contain an extensively rearranged genome streamlined for expression and divide by a non-mitotic process. Only micronuclei undergo meiosis to perpetuate genetic information; the macronuclei are lost at each sexual generation and develop anew from the micronuclear lineage.In Paramecium the exact number of micronuclear chromosomes (more than 50) and the structures of their centromeres and telomeres remain unknown. During macronuclear development, these chromosomes are amplified to about 800 copies and undergo two types of DNA elimination event. Tens of thousand of short, unique copy elements (internal eliminated sequences) are removed by a precise mechanism that leads to the reconstitution of functional genes 2 .Transposable elements and other repeated sequences are removed by an imprecise mechanism leading either to chromosome fragmentation and de novo telomere addition or to variable internal deletions 3 . These rearrangements occur after a few rounds of endoreplication, leading to some heterogeneity in the sequences abutting the imprecisely eliminated regions 3 . The sizes of the resulting, acentric macronuclear chromosomes range from 50-1,000 kilobases (kb) as measured by pulsed-field gel electrophoresis. Because the sexual process of autogamy results in an entirely homozygous genotype 4 , the macronuclear DNA that was sequenced was genetically homogeneous.The Paramecium genome sequence The Paramecium macronuclear genome sequence was established with the use of a whole-genome shotgun and assembly strategy. Paired-end sequencing of plasmid and bacterial artificial chromosome (BAC) clones provided a coverage of 13 genome equivalents (Supplementary Table S1). We assembled the sequence reads with Arachne 5 in 1,907 contigs connected in 697 scaffolds of size greater than 2 kb, giving a total coverage of 72...

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“…However, as soon as gene duplication occurs, both homologues experience relaxed selection constraints that allow them to enter a period of accelerated evolution (Lynch and Katju, 2004). This could eventually result in novel functionality, whether through different temporal or spatial expression, the acquisition of additional targets or neofunctionalisation.…”

Section: Discussionmentioning

confidence: 99%

Evolution of the tissue factor pathway inhibitor-like Kunitz domain-containing protein family in Rhipicephalus microplus

Louw

Merwe

Neitz

et al. 2013

International Journal for Parasitology

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One of the principle mechanisms utilised by ticks to obtain a blood meal is the subversion of the host's haemostatic response. This is achieved through the secretion of saliva containing antihaemostatic proteins into the feeding lesion. Lineage-specific expansion of predicted secretory protein families have been observed in all previously studied ticks and occurred in response to adaptation to a blood-feeding environment. Of these, the predominant families are common between both hard and soft ticks. One of these families, namely the Kunitz domain-containing protein family, includes proven tissue factor pathway inhibitor-like (TFPI-like) anti-haemostatics such as ixolaris and penthalaris that play a crucial role during tick feeding. Although Kunitz-type proteins have been found in Rhipicephalus microplus, the TFPI-like Kunitz protein family has not yet been studied. We report a comprehensive search for TFPI-like Kunitz domain-containing proteins in R. microplus expressed sequence tag libraries, resulting in the identification of 42 Page 2 of 36 homologues. The homologues were bioinformatically and phylogenetically studied, including the application of an intensive Bayesian Markov Chain Monte Carlo (MCMC) analysis of the individual Kunitz domain nucleotide sequences. We show that the R. microplus TFPI-like Kunitz protein family groups into two main clades that presumably underwent ancient duplication, which indicates that a whole genome duplication event occurred at least 150 million years ago. Evidence for recent and ancient gene and domain duplication events was also found. Furthermore, the divergence times of the various tick lineages estimated in this paper correspond with those presented in previous studies. The elucidation of this large protein family's evolution within R. microplus adds to current knowledge of this economically important tick.

show abstract

The altered evolutionary trajectories of gene duplicates

Cited by 270 publications

References 45 publications

NK-lysin of channel catfish: Gene triplication, sequence variation, and expression analysis

NK-lysin of channel catfish: Gene triplication, sequence variation, and expression analysis

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia

Evolution of the tissue factor pathway inhibitor-like Kunitz domain-containing protein family in Rhipicephalus microplus

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