Both mechanism and age of duplications contribute to biased gene retention patterns in plants

Background: All extant seed plants are successful paleopolyploids, whose genomes carry duplicate genes that have survived repeated episodes of diploidization. However, the survival of gene duplicates is biased with respect to gene function and mechanism of duplication. Transcription factors, in particular, are reported to be preferentially retained following whole-genome duplications (WGDs), but disproportionately lost when duplicated by tandem events. An explanation for this pattern is provided by the Gene Balance Hypothesis (GBH), which posits that duplicates of highly connected genes are retained following WGDs to maintain optimal stoichiometry among gene products; but such connected gene duplicates are disfavored following tandem duplications. Results We used genomic data from 25 taxonomically diverse plant species to investigate the roles of duplication mechanism, gene function, and age of duplication in the retention of duplicate genes. Enrichment analyses were conducted to identify Gene Ontology (GO) functional categories that were overrepresented in either WGD or tandem duplications, or across ranges of divergence times. Tandem paralogs were much younger, on average, than WGD paralogs and the most frequently overrepresented GO categories were not shared between tandem and WGD paralogs. Transcription factors were overrepresented among ancient paralogs regardless of mechanism of origin or presence of a WGD. Also, in many cases, there was no bias toward transcription factor retention following recent WGDs. Conclusions Both the fixation and the retention of duplicated genes in plant genomes are context-dependent events. The strong bias toward ancient transcription factor duplicates can be reconciled with the GBH if selection for optimal stoichiometry among gene products is strongest following the earliest polyploidization events and becomes increasingly relaxed as gene families expand.Science, Faculty ofNon UBCBotany, Department ofReviewedFacult

Contemporary patterns of genetic diversity of cedrela fissilis offer insight into the shaping of seasonal forests in eastern South America

We investigated how genetic diversity is distributed across the range of Cedrela fissilis, a tree species associated with seasonal neotropical forests, to gain insights into competing biogeographic scenarios that explain how disjunct distributions of these forests were shaped. A total of 250 samples were sampled from 18 sites across the species' range in Brazil and eastern Bolivia and genotyped with 10 microsatellite loci. An array of complementary methods—F statistics, analyses of molecular variance (AMOVA), and clustering analyses—assessed genetic diversity, population differentiation, and structure. Most of the genetic diversity (82.5%) was partitioned within populations, but about 12% was due to differences among groups of populations on either side of the Cerrado or located within the Cerrado; mean expected heterozygosity and mean observed heterozygosity were 0.821 and 0.704, respectively. The 250 samples were sorted into two Bayesian groups: one group for each side of the Cerrado. The populations showed varying levels of admixture, with the greatest admixture evident in populations located toward central Brazil. In C. fissilis, genetic diversity is structured according to geography: the Atlantic range and the Chiquitano range each harbor a genealogical lineage. Interfertility and varying levels of admixture between lineages provide strong evidence that the lineages evolved under geographic, but not genetic, isolation. Admixture is of recent origin, owing to population expansion. Cedrela fissilis shares this dual pattern of distribution of genetic diversity with other phylogenetically unrelated taxa that are typically associated with seasonal forests

Both mechanism and age of duplications contribute to biased gene retention patterns in plants

BACKGROUND: All extant seed plants are successful paleopolyploids, whose genomes carry duplicate genes that have survived repeated episodes of diploidization. However, the survival of gene duplicates is biased with respect to gene function and mechanism of duplication. Transcription factors, in particular, are reported to be preferentially retained following whole-genome duplications (WGDs), but disproportionately lost when duplicated by tandem events. An explanation for this pattern is provided by the Gene Balance Hypothesis (GBH), which posits that duplicates of highly connected genes are retained following WGDs to maintain optimal stoichiometry among gene products; but such connected gene duplicates are disfavored following tandem duplications. RESULTS: We used genomic data from 25 taxonomically diverse plant species to investigate the roles of duplication mechanism, gene function, and age of duplication in the retention of duplicate genes. Enrichment analyses were conducted to identify Gene Ontology (GO) functional categories that were overrepresented in either WGD or tandem duplications, or across ranges of divergence times. Tandem paralogs were much younger, on average, than WGD paralogs and the most frequently overrepresented GO categories were not shared between tandem and WGD paralogs. Transcription factors were overrepresented among ancient paralogs regardless of mechanism of origin or presence of a WGD. Also, in many cases, there was no bias toward transcription factor retention following recent WGDs. CONCLUSIONS: Both the fixation and the retention of duplicated genes in plant genomes are context-dependent events. The strong bias toward ancient transcription factor duplicates can be reconciled with the GBH if selection for optimal stoichiometry among gene products is strongest following the earliest polyploidization events and becomes increasingly relaxed as gene families expand. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3423-6) contains supplementary material, which is available to authorized users

Immunotherapy in Breast Cancer: the Emerging Role of PD-1 and PD-L1

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Alirocumab and cardiovascular outcomes after acute coronary syndrome

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Alirocumab and Cardiovascular Outcomes after Acute Coronary Syndrome

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