Estimating the Time to the Whole-Genome Duplication and the Duration of Concerted Evolution via Gene Conversion in Yeast

We characterized ectopic gene conversions in the genome of ten hemiascomycete yeast species. Of the ten species, three diverged prior to the whole genome duplication (WGD) event present in the yeast lineage and seven diverged after it. We analyzed gene conversions from three separate datasets: paralogs from the three pre-WGD species, paralogs from the seven post-WGD species, and common ohnologs from the seven post-WGD species. Gene conversions have similar lengths and frequency and occur between sequences having similar degrees of divergence, in paralogs from pre- and post-WGD species. However, the sequences of ohnologs are both more divergent and less frequently converted than those of paralogs. This likely reflects the fact that ohnologs are more often found on different chromosomes and are evolving under stronger selective pressures than paralogs. Our results also show that ectopic gene conversions tend to occur more frequently between closely linked genes. They also suggest that the mechanisms responsible for the loss of introns in S. cerevisiae are probably also involved in the gene 3'-end gene conversion bias observed between the paralogs of this species.

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Visual pigment evolution in Characiformes: the dynamic interplay of teleost whole-genome duplication, surviving opsins and spectral tuning

10.1101/695544 ◽

2019 ◽

Cited By ~ 1

Author(s):

Daniel Escobar-Camacho ◽

Karen L. Carleton ◽

Devika W. Narain ◽

Michele E.R. Pierotti

Keyword(s):

Visual System ◽

Gene Conversion ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Opsin Gene ◽

Whole Genome ◽

Gene Repertoire ◽

Spectral Tuning ◽

Diverse Range ◽

System Evolution

AbstractVision represents an excellent model for studying adaptation, given the genotype-to-phenotype-map that has been characterized in a number of taxa. Fish possess a diverse range of visual sensitivities and adaptations to underwater light making them an excellent group to study visual system evolution. In particular, some speciose but understudied lineages can provide a unique opportunity to better understand aspects of visual system evolution such as opsin gene duplication and neofunctionalization. In this study, we characterized the visual system of Neotropical Characiformes, which is the result of several spectral tuning mechanisms acting in concert including gene duplications and losses, gene conversion, opsin amino acid sequence and expression variation, and A1/A2-chromophore shifts. The Characiforms we studied utilize three cone opsin classes (SWS2, RH2, LWS) and a rod opsin (RH1). However, the characiform’s entire opsin gene repertoire is a product of dynamic evolution by opsin gene loss (SWS1, RH2) and duplication (LWS, RH1). The LWS- and RH1-duplicates originated from a teleost specific whole-genome duplication as well as characiform-specific duplication events. Both LWS-opsins exhibit gene conversion and, through substitutions in key tuning sites, one of the LWS-paralogs has acquired spectral sensitivity to green light. These sequence changes suggest reversion and parallel evolution of key tuning sites. In addition, characiforms exhibited species-specific differences in opsin expression. Finally, we found interspecific and intraspecific variation in the use of A1/A2-chromophores correlating with the light environment. These multiple mechanisms may be a result of the highly diverse visual environments where Characiformes have evolved.

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Faculty Opinions recommendation of Reciprocal gene loss following experimental whole-genome duplication causes reproductive isolation in yeast.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.10069956.10824063 ◽

2011 ◽

Author(s):

Santiago F Elena ◽

Stéphanie Bedhomme

Keyword(s):

Reproductive Isolation ◽

Whole Genome Duplication ◽

Gene Loss ◽

Genome Duplication ◽

Whole Genome

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Phylogenetic Analysis of T-Box Genes Demonstrates the Importance of Amphioxus for Understanding Evolution of the Vertebrate Genome

Genetics ◽

10.1093/genetics/156.3.1249 ◽

2000 ◽

Vol 156 (3) ◽

pp. 1249-1257

Author(s):

Ilya Ruvinsky ◽

Lee M Silver ◽

Jeremy J Gibson-Brown

Keyword(s):

Phylogenetic Analysis ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Gene Families ◽

Vertebrate Evolution ◽

Whole Genome ◽

Vertebrate Genome ◽

T Box ◽

Genetic Complexity ◽

History Of

Abstract The duplication of preexisting genes has played a major role in evolution. To understand the evolution of genetic complexity it is important to reconstruct the phylogenetic history of the genome. A widely held view suggests that the vertebrate genome evolved via two successive rounds of whole-genome duplication. To test this model we have isolated seven new T-box genes from the primitive chordate amphioxus. We find that each amphioxus gene generally corresponds to two or three vertebrate counterparts. A phylogenetic analysis of these genes supports the idea that a single whole-genome duplication took place early in vertebrate evolution, but cannot exclude the possibility that a second duplication later took place. The origin of additional paralogs evident in this and other gene families could be the result of subsequent, smaller-scale chromosomal duplications. Our findings highlight the importance of amphioxus as a key organism for understanding evolution of the vertebrate genome.

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Comparative Mapping Between Coho Salmon (Oncorhynchus kisutch) and Three Other Salmonids Suggests a Role for Chromosomal Rearrangements in the Retention of Duplicated Regions Following a Whole Genome Duplication Event

G3 Genes|Genome|Genetics ◽

10.1534/g3.114.012294 ◽

2014 ◽

Vol 4 (9) ◽

pp. 1717-1730 ◽

Cited By ~ 37

Author(s):

M. Kodama ◽

M. S. O. Brieuc ◽

R. H. Devlin ◽

J. J. Hard ◽

K. A. Naish

Keyword(s):

Comparative Mapping ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Coho Salmon ◽

Chromosomal Rearrangements ◽

Oncorhynchus Kisutch ◽

Duplication Event ◽

Whole Genome ◽

Genome Duplication Event ◽

Whole Genome Duplication Event

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Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication

Genome Biology ◽

10.1186/s13059-021-02323-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Gareth B. Gillard ◽

Lars Grønvold ◽

Line L. Røsæg ◽

Matilde Mengkrog Holen ◽

Øystein Monsen ◽

...

Keyword(s):

Genome Evolution ◽

Whole Genome Duplication ◽

Genome Stability ◽

Genome Duplication ◽

Gene Dosage ◽

Whole Genome ◽

Specific Expression ◽

Tissue Specific ◽

Genome Doubling ◽

Expression Evolution

Abstract Background Whole genome duplication (WGD) events have played a major role in eukaryotic genome evolution, but the consequence of these extreme events in adaptive genome evolution is still not well understood. To address this knowledge gap, we used a comparative phylogenetic model and transcriptomic data from seven species to infer selection on gene expression in duplicated genes (ohnologs) following the salmonid WGD 80–100 million years ago. Results We find rare cases of tissue-specific expression evolution but pervasive expression evolution affecting many tissues, reflecting strong selection on maintenance of genome stability following genome doubling. Ohnolog expression levels have evolved mostly asymmetrically, by diverting one ohnolog copy down a path towards lower expression and possible pseudogenization. Loss of expression in one ohnolog is significantly associated with transposable element insertions in promoters and likely driven by selection on gene dosage including selection on stoichiometric balance. We also find symmetric expression shifts, and these are associated with genes under strong evolutionary constraints such as ribosome subunit genes. This possibly reflects selection operating to achieve a gene dose reduction while avoiding accumulation of “toxic mutations”. Mechanistically, ohnolog regulatory divergence is dictated by the number of bound transcription factors in promoters, with transposable elements being one likely source of novel binding sites driving tissue-specific gains in expression. Conclusions Our results imply pervasive adaptive expression evolution following WGD to overcome the immediate challenges posed by genome doubling and to exploit the long-term genetic opportunities for novel phenotype evolution.

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Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis

Nature Communications ◽

10.1038/s41467-020-20508-2 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Amit Rai ◽

Hideki Hirakawa ◽

Ryo Nakabayashi ◽

Shinji Kikuchi ◽

Koki Hayashi ◽

...

Keyword(s):

Genome Assembly ◽

Whole Genome Duplication ◽

Experimental Validation ◽

Genome Duplication ◽

Indole Alkaloids ◽

Whole Genome ◽

Comparative Genome Analysis ◽

Plant Genomes ◽

Genome Triplication ◽

Chromosome Level

AbstractPlant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly of Ophiorrhiza pumila, a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb, Ophiorrhiza genome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as the origin of MIA evolution. The emergence of strictosidine biosynthesis-catalyzing enzymes precede downstream enzymes’ evolution post γ whole-genome triplication, which occurred approximately 110 Mya in O. pumila, and before the whole-genome duplication in Camptotheca acuminata identified here. Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, we propose a working model for MIA evolution, and a pangenome for MIA biosynthesis, which will help in establishing a sustainable supply of camptothecin.

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