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Whittle, Carrie A.
Publications (4 of 4) Show all publications
Whittle, C. A., Sun, Y. & Johannesson, H. (2012). Genome-Wide Selection on Codon Usage at the Population Level in the Fungal Model Organism Neurospora crassa. Molecular biology and evolution, 29(8), 1975-1986
Open this publication in new window or tab >>Genome-Wide Selection on Codon Usage at the Population Level in the Fungal Model Organism Neurospora crassa
2012 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 29, no 8, p. 1975-1986Article in journal (Refereed) Published
Abstract [en]

Many organisms exhibit biased codon usage in their genome, including the fungal model organism Neurospora crassa. The preferential use of subset of synonymous codons (optimal codons) at the macroevolutionary level is believed to result from a history of selection to promote translational efficiency. At present, few data are available about selection on optimal codons at the microevolutionary scale, that is, at the population level. Herein, we conducted a large-scale assessment of codon mutations at biallelic sites, spanning more than 5,100 genes, in 2 distinct populations of N. crassa: the Caribbean and Louisiana populations. Based on analysis of the frequency spectra of synonymous codon mutations at biallelic sites, we found that derived (nonancestral) optimal codon mutations segregate at a higher frequency than derived nonoptimal codon mutations in each population; this is consistent with natural selection favoring optimal codons. We also report that optimal codon variants were less frequent in longer genes and that the fixation of optimal codons was reduced in rapidly evolving long genes/proteins, trends suggestive of genetic hitchhiking (Hill-Robertson) altering codon usage variation. Notably, nonsynonymous codon mutations segregated at a lower frequency than synonymous nonoptimal codon mutations (which impair translational efficiency) in each N. crassa population, suggesting that changes in protein composition are more detrimental to fitness than mutations altering translation. Overall, the present data demonstrate that selection, and partly genetic interference, shapes codon variation across the genome in N. crassa populations.

Keywords
Neurospora crassa, microevolution, codon, selection, genetic hitchhiking
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-181129 (URN)10.1093/molbev/mss065 (DOI)000307171300009 ()
Available from: 2012-09-18 Created: 2012-09-17 Last updated: 2017-12-07Bibliographically approved
Sun, Y., Corcoran, P., Menkis, A., Whittle, C. A., Andersson, S. G. E. & Johannesson, H. (2012). Large-Scale Introgression Shapes the Evolution of the Mating-Type Chromosomes of the Filamentous Ascomycete Neurospora tetrasperma. PLOS Genetics, 8(7), e1002820
Open this publication in new window or tab >>Large-Scale Introgression Shapes the Evolution of the Mating-Type Chromosomes of the Filamentous Ascomycete Neurospora tetrasperma
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2012 (English)In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 8, no 7, p. e1002820-Article in journal (Refereed) Published
Abstract [en]

The significance of introgression as an evolutionary force shaping natural populations is well established, especially in animal and plant systems. However, the abundance and size of introgression tracts, and to what degree interspecific gene flow is the result of adaptive processes, are largely unknown. In this study, we present medium coverage genomic data from species of the filamentous ascomycete Neurospora, and we use comparative genomics to investigate the introgression landscape at the genomic level in this model genus. We revealed one large introgression tract in each of the three investigated phylogenetic lineages of Neurospora tetrasperma (sizes of 5.6 Mbp, 5.2 Mbp, and 4.1 Mbp, respectively). The tract is located on the chromosome containing the locus conferring sexual identity, the mating-type (mat) chromosome. The region of introgression is confined to the region of suppressed recombination and is found on one of the two mat chromosomes (mat a). We used Bayesian concordance analyses to exclude incomplete lineage sorting as the cause for the observed pattern, and multilocus genealogies from additional species of Neurospora show that the introgression likely originates from two closely related, freely recombining, heterothallic species (N. hispaniola and N. crassa/N. perkinsii). Finally, we investigated patterns of molecular evolution of the mat chromosome in Neurospora, and we show that introgression is correlated with reduced level of molecular degeneration, consistent with a shorter time of recombination suppression. The chromosome specific (mat) and allele specific (mat a) introgression reported herein comprise the largest introgression tracts reported to date from natural populations. Furthermore, our data contradicts theoretical predictions that introgression should be less likely on sex-determining chromosomes. Taken together, the data presented herein advance our general understanding of introgression as a force shaping eukaryotic genomes.

National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-181143 (URN)10.1371/journal.pgen.1002820 (DOI)000306840400034 ()
Available from: 2012-09-18 Created: 2012-09-17 Last updated: 2017-12-07Bibliographically approved
Whittle, C. A. & Johannesson, H. (2012). Neurospora as a model to empirically test central hypotheses in eukaryotic genome evolution. Bioessays, 34(11), 934-937
Open this publication in new window or tab >>Neurospora as a model to empirically test central hypotheses in eukaryotic genome evolution
2012 (English)In: Bioessays, ISSN 0265-9247, E-ISSN 1521-1878, Vol. 34, no 11, p. 934-937Article in journal (Refereed) Published
Abstract [en]

The fungus Neurospora comprises a novel model for testing hypotheses involving the role of sex and reproduction in eukaryotic genome evolution. Its variation in reproductive mode, lack of sex-specific genotypes, availability of phylogenetic species, and young sex-regulating chromosomes make research in this genus complementary to animal and plant models.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-185478 (URN)10.1002/bies.201200110 (DOI)000309910400008 ()
Available from: 2012-11-27 Created: 2012-11-26 Last updated: 2017-12-07Bibliographically approved
Whittle, C. A., Sun, Y. & Johannesson, H. (2011). Evolution of Synonymous Codon Usage in Neurospora tetrasperma and Neurospora discreta. Genome Biology and Evolution, 3, 332-343
Open this publication in new window or tab >>Evolution of Synonymous Codon Usage in Neurospora tetrasperma and Neurospora discreta
2011 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 3, p. 332-343Article in journal (Refereed) Published
Abstract [en]

Neurospora comprises a primary model system for the study of fungal genetics and biology. In spite of this, little is known about genome evolution in Neurospora. For example, the evolution of synonymous codon usage is largely unknown in this genus. In the present investigation, we conducted a comprehensive analysis of synonymous codon usage and its relationship to gene expression and gene length (GL) in Neurospora tetrasperma and Neurospora discreta. For our analysis, we examined codon usage among 2,079 genes per organism and assessed gene expression using large-scale expressed sequenced tag (EST) data sets (279,323 and 453,559 ESTs for N. tetrasperma and N. discreta, respectively). Data on relative synonymous codon usage revealed 24 codons (and two putative codons) that are more frequently used in genes with high than with low expression and thus were defined as optimal codons. Although codon-usage bias was highly correlated with gene expression, it was independent of selectively neutral base composition (introns); thus demonstrating that translational selection drives synonymous codon usage in these genomes. We also report that GL (coding sequences [CDS]) was inversely associated with optimal codon usage at each gene expression level, with highly expressed short genes having the greatest frequency of optimal codons. Optimal codon frequency was moderately higher in N. tetrasperma than in N. discreta, which might be due to variation in selective pressures and/or mating systems.

Keywords
Neurospora tetrasperma, Neurospora discreta, optimal codons, gene expression, bias, gene length
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-161301 (URN)10.1093/gbe/evr018 (DOI)000295693200001 ()
Available from: 2011-11-11 Created: 2011-11-10 Last updated: 2017-12-08Bibliographically approved
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