scholarly journals Gene fractionation and function in the ancient subgenomes of maize

2016 ◽  
Author(s):  
Simon Renny-Byfield ◽  
Eli Rodgers-Melnick ◽  
Jeffrey Ross-Ibarra
Keyword(s):  
Gene Loss ◽  
Genome Duplication ◽  
Phenotypic Diversity ◽  
Single Copy ◽  
Maize Genome ◽  
Gene Deletions ◽  
Genome Wide ◽  
Association Data ◽  
Gene Fractionation ◽  
And Function

AbstractThe maize genome experienced an ancient whole genome duplication approximately 10 million years ago and the duplicate subgenomes have since experienced reciprocal gene loss (fractionation) such that many genes have returned to single-copy status. This process has not affected the subgenomes equally; reduced gene expression in one of the subgenomes mitigates the consequences of mutations and gene deletions and is thought to drive higher rates of fractionation. Here we take advantage of published genome-wide SNP and phenotype association data to show that, in accordance with predictions of this model, paralogs with greater expression contribute more to phenotypic variation compared to their lowly expressed counterparts. Furthermore, paralogous genes in the least-fractionated subgenome account for a greater degree of phenotypic diversity than those resident on the more-fractionated subgenome. We also show that the two subgenomes of maize are distinct in epigenetic characteristics. Intriguingly, analysis of singleton genes reveals that these differences persist even after fractionation is complete.

scholarly journals Molecular Polymorphism and Divergence of Duplicated Genes in Tetraploid African Clawed Frogs (Xenopus)

2015 ◽  
Vol 145 (3-4) ◽  
pp. 243-252 ◽  
Author(s):  
Ben J. Evans ◽  
Taejoon Kwon
Keyword(s):  
Genome Duplication ◽  
Gene Dosage ◽  
Functional Divergence ◽  
Single Copy ◽  
Duplicated Genes ◽  
Genetic Redundancy ◽  
Molecular Polymorphism ◽  
Genome Wide ◽  
Extant Species ◽  
Almost All

Genome duplication creates redundancy in proteins and their interaction networks, and subsequent smaller-scale gene duplication can further amplify genetic redundancy. Mutations then lead to the loss, maintenance or functional divergence of duplicated genes. Genome duplication occurred many times in African clawed frogs (genus Xenopus), and almost all extant species in this group evolved from a polyploid ancestor. To better understand the nature of selective constraints in a polyploid genome, we examined molecular polymorphism and divergence of duplicates and single-copy genes in 2 tetraploid African clawed frog species, Xenopus laevis and X. victorianus. We found that molecular polymorphism in the coding regions of putative duplicated genes was higher than in singletons, but not significantly so. Our findings also suggest that transcriptome evolution in polyploids is influenced by variation in the genome-wide mutation rate, and do not reject the hypothesis that gene dosage balance is also important.

scholarly journals Divergent Expression Patterns and Function of Two cxcr4 Paralogs in Hermaphroditic Epinephelus coioides

2018 ◽  
Vol 19 (10) ◽  
pp. 2943 ◽  
Author(s):  
Wei-Jia Lu ◽  
Li Zhou ◽  
Fan-Xiang Gao ◽  
Zhi-Hui Sun ◽  
Zhi Li ◽  
...  
Keyword(s):  
Gene Loss ◽  
Genome Duplication ◽  
Expression Patterns ◽  
Gene Clusters ◽  
Epinephelus Coioides ◽  
Adult Tissue ◽  
Receptor Recognition ◽  
And Function ◽  
Neurula Stage ◽  
Specific Ligand

Chemokine receptor Cxcr4 evolved two paralogs in the teleost lineage. However, cxcr4a and cxcr4b have been characterized only in a few species. In this study, we identified two cxcr4 paralogs from the orange-spotted grouper, Epinephelus coioides. The phylogenetic relationship and gene structure and synteny suggest that the duplicated cxcr4a/b should result from the teleost-specific genome duplication (Ts3R). The teleost cxcr4 gene clusters in two paralogous chromosomes exhibit a complementary gene loss/retention pattern. Ec_cxcr4a and Ec_cxcr4b show differential and biased expression patterns in grouper adult tissue, gonads, and embryos at different stages. During embryogenesis, Ec_cxcr4a/b are abundantly transcribed from the neurula stage and mainly expressed in the neural plate and sensory organs, indicating their roles in neurogenesis. Ec_Cxcr4a and Ec_Cxcr4b possess different chemotactic migratory abilities from the human SDF-1α, Ec_Cxcl12a, and Ec_Cxcl12b. Moreover, we uncovered the N-terminus and TM5 domain as the key elements for specific ligand–receptor recognition of Ec_Cxcr4a-Ec_Cxcl12b and Ec_Cxcr4b-Ec_Cxcl12a. Based on the biased and divergent expression patterns of Eccxcr4a/b, and specific ligand–receptor recognition of Ec_Cxcl12a/b–Ec_Cxcr4b/a, the current study provides a paradigm of sub-functionalization of two teleost paralogs after Ts3R.

scholarly journals The continuing impact of an ancient polyploidy on the genomes of teleosts

2019 ◽  
Author(s):  
Gavin C. Conant
Keyword(s):  
Genome Duplication ◽  
Single Copy ◽  
Duplication Event ◽  
Early Embryo ◽  
Genome Duplication Event ◽  
Form And Function ◽  
Teleost Retina ◽  
And Function ◽  
Occupy Central ◽  
Teleost Genome

AbstractThe ancestor of most teleost fishes underwent a whole-genome duplication event three hundred million years ago. Despite its antiquity, the effects of this event are evident both in the structure of teleost genomes and in how those genes still operate to drive form and function. I describe the inference of a set of shared syntenic regions that survive from the teleost genome duplication (TGD) using eight teleost genomes and the outgroup gar genome (which lacks the TGD). I phylogenetically modeled the resolution of the TGD via shared and independent gene losses, concluding that it was likely an allopolyploidy event due to the biased pattern of these gene losses. Duplicate genes surviving from this duplication in zebrafish are less likely to function in early embryo development than are genes that have returned to single copy. As a result, surviving ohnologs function later in development, and the pattern of which tissues these ohnologs are expressed in and their functions lend support to recent suggestions that the TGD was the source of a morphological innovation in the structure of the teleost retina. Surviving duplicates also appear less likely to be essential than singletons, despite the fact that their single-copy orthologs in mouse are no less essential than other genes. Nonetheless, the surviving duplicates occupy central positions in the zebrafish metabolic network.

scholarly journals Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling

2015 ◽  
Vol 112 (48) ◽  
pp. 14918-14923 ◽  
Author(s):  
Jun Inoue ◽  
Yukuto Sato ◽  
Robert Sinclair ◽  
Katsumi Tsukamoto ◽  
Mutsumi Nishida
Keyword(s):  
Mathematical Modeling ◽  
Teleost Fish ◽  
Whole Genome Duplication ◽  
Gene Loss ◽  
Genome Duplication ◽  
Single Copy ◽  
Marker Genes ◽  
Whole Genome ◽  
Protein Coding ◽  
Evolutionary Innovation

Whole-genome duplication (WGD) is believed to be a significant source of major evolutionary innovation. Redundant genes resulting from WGD are thought to be lost or acquire new functions. However, the rates of gene loss and thus temporal process of genome reshaping after WGD remain unclear. The WGD shared by all teleost fish, one-half of all jawed vertebrates, was more recent than the two ancient WGDs that occurred before the origin of jawed vertebrates, and thus lends itself to analysis of gene loss and genome reshaping. Using a newly developed orthology identification pipeline, we inferred the post–teleost-specific WGD evolutionary histories of 6,892 protein-coding genes from nine phylogenetically representative teleost genomes on a time-calibrated tree. We found that rapid gene loss did occur in the first 60 My, with a loss of more than 70–80% of duplicated genes, and produced similar genomic gene arrangements within teleosts in that relatively short time. Mathematical modeling suggests that rapid gene loss occurred mainly by events involving simultaneous loss of multiple genes. We found that the subsequent 250 My were characterized by slow and steady loss of individual genes. Our pipeline also identified about 1,100 shared single-copy genes that are inferred to have become singletons before the divergence of clupeocephalan teleosts. Therefore, our comparative genome analysis suggests that rapid gene loss just after the WGD reshaped teleost genomes before the major divergence, and provides a useful set of marker genes for future phylogenetic analysis.

scholarly journals Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris

2014 ◽  
Author(s):  
Gavin Douglas ◽  
Gesseca Gos ◽  
Kim Steige ◽  
Adriana Salcedo ◽  
Karl Holm ◽  
...  
Keyword(s):  
Positive Selection ◽  
Whole Genome Duplication ◽  
Gene Loss ◽  
Genome Duplication ◽  
Strong Support ◽  
Plant Evolution ◽  
Flowering Plant ◽  
Whole Genome ◽  
Widespread Species ◽  
Genome Wide

Whole genome duplication events have occurred repeatedly during flowering plant evolution, and there is growing evidence for predictable patterns of gene retention and loss following polyploidization. Despite these important insights, the rate and processes governing the earliest stages of diploidization remain poorly understood, and the relative importance of genetic drift, positive selection and relaxed purifying selection in the process of gene degeneration and loss is unclear. Here, we conduct whole genome resequencing in Capsella bursa-pastoris, a recently formed tetraploid with one of the most widespread species distributions of any angiosperm. Whole genome data provide strong support for recent hybrid origins of the tetraploid species within the last 100-300,000 years from two diploid progenitors in the Capsella genus. Major-effect inactivating mutations are frequent, but many were inherited from the parental species and show no evidence of being fixed by positive selection. Despite a lack of large-scale gene loss, we observe a decrease in the efficacy of natural selection genome-wide, due to the combined effects of demography, selfing and genome redundancy from whole genome duplication. Our results suggest that the earliest stages of diploidization are associated with quantitative genome-wide decreases in the strength and efficacy of selection rather than rapid gene loss, and that non-functionalization can receive a 'head start' through a legacy of deleterious variants and differential expression originating in parental diploid populations.

GENE LOSS UNDER NEIGHBORHOOD SELECTION FOLLOWING WHOLE GENOME DUPLICATION AND THE RECONSTRUCTION OF THE ANCESTRAL POPULUS GENOME

2009 ◽  
Vol 07 (03) ◽  
pp. 499-520 ◽  
Author(s):  
CHUNFANG ZHENG ◽  
P. KERR WALL ◽  
JAMES LEEBENS-MACK ◽  
CLAUDE DE PAMPHILIS ◽  
VICTOR A. ALBERT ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Gene Loss ◽  
Genome Duplication ◽  
Chromosome Doubling ◽  
Populus Trichocarpa ◽  
Single Copy ◽  
Whole Genome ◽  
Gene Sets ◽  
Large Numbers ◽  
Neighborhood Selection

We develop criteria to detect neighborhood selection effects on gene loss following whole genome duplication, and apply them to the recently sequenced poplar (Populus trichocarpa) genome. We improve on guided genome halving algorithms so that several thousand gene sets, each containing two paralogs in the descendant T of the doubling event and their single ortholog from an undoubled reference genome R, can be analyzed to reconstruct the ancestor A of T at the time of doubling. At the same time, large numbers of defective gene sets, either missing one paralog from T or missing their ortholog in R, may be incorporated into the analysis in a consistent way. We apply this genomic rearrangement distance-based approach to the poplar and grapevine (Vitis vinifera) genomes, as T and R respectively. We conclude that, after chromosome doubling, the "choice" of which paralogous gene pairs will lose copies is random, but that the retention of strings of single-copy genes on one chromosome versus the other is decidedly non-random.

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