scholarly journals Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage

PLoS Biology ◽  
2015 ◽  
Vol 13 (8) ◽  
pp. e1002220 ◽  
Author(s):  
Marina Marcet-Houben ◽  
Toni Gabaldón
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Baker’S Yeast ◽  
Whole Genome ◽  
Baker's Yeast ◽  
Interspecies Hybridization

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

Genetics ◽  
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.

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

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.

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

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.

scholarly journals Resurrected Protein Interaction Networks Reveal the Innovation Potential of Ancient Whole-Genome Duplication

2018 ◽  
Vol 30 (11) ◽  
pp. 2741-2760 ◽  
Author(s):  
Zhicheng Zhang ◽  
Heleen Coenen ◽  
Philip Ruelens ◽  
Rashmi R. Hazarika ◽  
Tareq Al Hindi ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Whole Genome ◽  
Innovation Potential

Whole-Genome Duplication and Yeast’s Fruitful Way of Life

2019 ◽  
Vol 35 (1) ◽  
pp. 42-54 ◽  
Author(s):  
Ximena Escalera-Fanjul ◽  
Héctor Quezada ◽  
Lina Riego-Ruiz ◽  
Alicia González
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Whole Genome ◽  
Way Of Life

scholarly journals Yeast “Make-Accumulate-Consume” Life Strategy Evolved as a Multi-Step Process That Predates the Whole Genome Duplication

PLoS ONE ◽  
2013 ◽  
Vol 8 (7) ◽  
pp. e68734 ◽  
Author(s):  
Arne Hagman ◽  
Torbjörn Säll ◽  
Concetta Compagno ◽  
Jure Piskur
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Life Strategy ◽  
Whole Genome ◽  
Step Process

scholarly journals Mechanism for Restoration of Fertility in Hybrid Zygosaccharomyces rouxii Generated by Interspecies Hybridization

2017 ◽  
Vol 83 (21) ◽  
Author(s):  
Jun Watanabe ◽  
Kenji Uehara ◽  
Yoshinobu Mogi ◽  
Yuichiro Tsukioka
Keyword(s):  
Mating Type ◽  
Whole Genome Duplication ◽  
Gene Loss ◽  
Genome Duplication ◽  
Draft Genome ◽  
Content Type ◽  
Zygosaccharomyces Rouxii ◽  
Interspecies Hybridization ◽  
Random Gene Loss ◽  
Interspecies Hybrid

ABSTRACT The mechanism of whole-genome duplication (WGD) in yeast has been intensively studied because it has a large impact on yeast evolution. WGD has shaped the genomic architecture of modern Saccharomyces cerevisiae; however, the mechanism for restoring fertility after interspecies hybridization, which would be involved in the process of WGD, has not been thoroughly elucidated. In this study, we obtained a draft genome sequence of the salt-tolerant yeast Zygosaccharomyces rouxii NBRC110957 and revealed that it is a hybrid lineage of Z. rouxii (allodiploid) with two subgenomes equivalent to NBRC1876. Because this allodiploid yeast can mate with other allodiploid strains and form spores, it can be a good model of restoring fertility after interspecies hybridization. We observed that NBRC110957 and NBRC1876 contain six mating-type-like (MTL) loci. There are no large deletions or deleterious mutations in MTL loci, except for several-base-pair deletions in the X region in certain MTL loci. We also assigned only one mating-type (MAT) locus that exclusively determines mating types from six MTL loci. These results suggest that it is possible to recover mating competence regardless of whether cells lose one MAT locus through random gene loss by mitotically dividing after interspecies hybridization. Moreover, we propose that perturbation of gene expression and substantial breakdown of MAT heterozygosity caused by chromosomal rearrangement at MTL loci play roles in restoring the mating competence of allodiploids. This scenario can provide a mechanism for restoring fertility after interspecies hybridization that is compatible with random gene loss models and suggests genomic plasticity during WGD in yeast. IMPORTANCE A whole-genome duplication occurred in an ancestor of the baker's yeast Saccharomyces cerevisiae. The origins of this complex and multifaceted process, which requires intra- or interspecies hybridization followed by dysfunction of one mating-type (MAT) locus to regain mating competence, has not been thoroughly elucidated. In this study, we provide a mechanism for regaining fertility in an interspecies hybrid, Zygosaccharomyces rouxii. The draft genome sequence analysis and mating test showed that the Z. rouxii strain used in this study is an intact interspecies hybrid, suggesting that it is possible to recover fertility regardless of whether cells lose one MAT locus.

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