| 1. |
- Abbafati, Cristiana, et al.
(författare)
-
- 2020
-
Tidskriftsartikel (refereegranskat)
|
|
| 2. |
- Lin, Yao-Cheng, et al.
(författare)
-
Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen
- 2018
-
Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : NATL ACAD SCIENCES. - 0027-8424 .- 1091-6490. ; 115:46, s. E10970-E10978
-
Tidskriftsartikel (refereegranskat)abstract
- The Populus genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily Populus trichocarpa (Torr. & Gray), which was the first tree with a whole-genome assembly. To further advance evolutionary and functional genomic analyses in Populus, we produced genome assemblies and population genetics resources of two aspen species, Populus tremula L. and Populus tremuloides Michx. The two aspen species have distributions spanning the Northern Hemisphere, where they are keystone species supporting a wide variety of dependent communities and produce a diverse array of secondary metabolites. Our analyses show that the two aspens share a similar genome structure and a highly conserved gene content with P. trichocarpa but display substantially higher levels of heterozygosity. Based on population resequencing data, we observed widespread positive and negative selection acting on both coding and noncoding regions. Furthermore, patterns of genetic diversity and molecular evolution in aspen are influenced by a number of features, such as expression level, coexpression network connectivity, and regulatory variation. To maximize the community utility of these resources, we have integrated all presented data within the PopGenIE web resource (PopGenIE.org).
|
|
| 3. |
- de La Torre, Amanda R., et al.
(författare)
-
Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants
- 2017
-
Ingår i: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 34:6, s. 1363-1377
-
Tidskriftsartikel (refereegranskat)abstract
- The majority of variation in rates of molecular evolution among seed plants remains both unexplored and unexplained. Although some attention has been given to flowering plants, reports of molecular evolutionary rates for their sister plant clade (gymnosperms) are scarce, and to our knowledge differences in molecular evolution among seed plant clades have never been tested in a phylogenetic framework. Angiosperms and gymnosperms differ in a number of features, of which contrasting reproductive biology, life spans, and population sizes are the most prominent. The highly conserved morphology of gymnosperms evidenced by similarity of extant species to fossil records and the high levels of macrosynteny at the genomic level have led scientists to believe that gymnosperms are slow-evolving plants, although some studies have offered contradictory results. Here, we used 31,968 nucleotide sites obtained from orthologous genes across a wide taxonomic sampling that includes representatives of most conifers, cycads, ginkgo, and many angiosperms with a sequenced genome. Our results suggest that angiosperms and gymnosperms differ considerably in their rates of molecular evolution per unit time, with gymnosperm rates being, on average, seven times lower than angiosperm species. Longer generation times and larger genome sizes are some of the factors explaining the slow rates of molecular evolution found in gymnosperms. In contrast to their slow rates of molecular evolution, gymnosperms possess higher substitution rate ratios than angiosperm taxa. Finally, our study suggests stronger and more efficient purifying and diversifying selection in gymnosperm than in angiosperm species, probably in relation to larger effective population sizes.
|
|
| 4. |
- De La Torre, Amanda R., et al.
(författare)
-
Genome-wide admixture and ecological niche modelling reveal the maintenance of species boundaries despite long history of interspecific gene flow
- 2014
-
Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 23:8, s. 2046-2059
-
Tidskriftsartikel (refereegranskat)abstract
- The maintenance of species boundaries despite interspecific gene flow has been a continuous source of interest in evolutionary biology. Many hybridizing species have porous genomes with regions impermeable to introgression, conferring reproductive barriers between species. We used ecological niche modelling to study the glacial and postglacial recolonization patterns between the widely hybridizing spruce species Picea glauca and P.engelmannii in western North America. Genome-wide estimates of admixture based on a panel of 311 candidate gene single nucleotide polymorphisms (SNP) from 290 genes were used to assess levels of admixture and introgression and to identify loci putatively involved in adaptive differences or reproductive barriers between species. Our palaeoclimatic modelling suggests that these two closely related species have a long history of hybridization and introgression, dating to at least 21000years ago, yet species integrity is maintained by a combination of strong environmental selection and reduced current interspecific gene flow. Twenty loci showed evidence of divergent selection, including six loci that were both F-st outliers and associated with climatic gradients, and fourteen loci that were either outliers or showed associations with climate. These included genes responsible for carbohydrate metabolism, signal transduction and transcription factors.
|
|
| 5. |
- De La Torre, Amanda R, et al.
(författare)
-
Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in Picea gene families
- 2015
-
Ingår i: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 7:4, s. 1002-1015
-
Tidskriftsartikel (refereegranskat)abstract
- The recent sequencing of several gymnosperm genomes has greatly facilitated studying the evolution of their genes and gene families. In this study, we examine the evidence for expression-mediated selection in the first two fully sequenced representatives of the gymnosperm plant clade (Picea abies and Picea glauca). We use genome-wide estimates of gene expression (> 50,000 expressed genes) to study the relationship between gene expression, codon bias, rates of sequence divergence, protein length, and gene duplication. We found that gene expression is correlated with rates of sequence divergence and codon bias, suggesting that natural selection is acting on Picea protein-coding genes for translational efficiency. Gene expression, rates of sequence divergence, and codon bias are correlated with the size of gene families, with large multicopy gene families having, on average, a lower expression level and breadth, lower codon bias, and higher rates of sequence divergence than single-copy gene families. Tissue-specific patterns of gene expression were more common in large gene families with large gene expression divergence than in single-copy families. Recent family expansions combined with large gene expression variation in paralogs and increased rates of sequence evolution suggest that some Picea gene families are rapidly evolving to cope with biotic and abiotic stress. Our study highlights the importance of gene expression and natural selection in shaping the evolution of protein-coding genes in Picea species, and sets the ground for further studies investigating the evolution of individual gene families in gymnosperms.
|
|
| 6. |
- Li, Zhen, et al.
(författare)
-
Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants
- 2017
-
Ingår i: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 9:5, s. 1130-1147
-
Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic relationships among seed plant taxa, especially within the gymnosperms, remain contested. In contrast to angio-sperms, for which several genomic, transcriptomic and phylogenetic resources are available, there are few, if any, molecular markers that allow broad comparisons among gymnosperm species. With few gymnosperm genomes available, recently obtained transcriptomes in gymnosperms are a great addition to identifying single-copy gene families as molecular markers for phylogenomic analysis in seed plants. Taking advantage of an increasing number of available genomes and transcriptomes, we identified single-copy genes in a broad collection of seed plants and used these to infer phylogenetic relationships between major seed plant taxa. This study aims at extending the current phylogenetic toolkit for seed plants, assessing its ability for resolving seed plant phylogeny, and discussing potential factors affecting phylogenetic reconstruction. In total, we identified 3,072 single-copy genes in 31 gymnosperms and 2,156 single-copy genes in 34 angiosperms. All studied seed plants shared 1,469 single-copy genes, which are generally involved in functions like DNA metabolism, cell cycle, and photosynthesis. A selected set of 106 single-copy genes provided good resolution for the seed plant phylogeny except for gnetophytes. Although some of our analyses support a sister relationship between gnetophytes and other gymnosperms, phylogenetic trees from concatenated alignments without 3rd codon positions and amino acid alignments under the CAT + GTR model, support gnetophytes as a sister group to Pinaceae. Our phylogenomic analyses demonstrate that, in general, single-copy genes can uncover both recent and deep divergences of seed plant phylogeny.
|
|
| 7. |
- Wozniak, Magdalena B., et al.
(författare)
-
Alcohol consumption and the risk of renal cancers in the European prospective investigation into cancer and nutrition (EPIC)
- 2015
-
Ingår i: International Journal of Cancer. - : Wiley. - 0020-7136 .- 1097-0215. ; 137:8, s. 1953-1966
-
Tidskriftsartikel (refereegranskat)abstract
- Epidemiologic studies have reported that moderate alcohol consumption is inversely associated with the risk of renal cancer. However, there is no information available on the associations in renal cancer subsites. From 1992 through to 2010, 477,325 men and women in the European Prospective Investigation into Cancer and Nutrition cohort were followed for incident renal cancers (n=931). Baseline and lifetime alcohol consumption was assessed by country-specific, validated dietary questionnaires. Information on past alcohol consumption was collected by lifestyle questionnaires. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated from Cox proportional hazard models. In multivariate analysis, total alcohol consumption at baseline was inversely associated with renal cancer; the HR and 95% CI for the increasing categories of total alcohol consumption at recruitment versus the light drinkers category were 0.78 (0.62-0.99), 0.82 (0.64-1.04), 0.70 (0.55-0.90), 0.91 (0.63-1.30), respectively, (p(trend)=0.001). A similar relationship was observed for average lifetime alcohol consumption and for all renal cancer subsites combined or for renal parenchyma subsite. The trend was not observed in hypertensive individuals and not significant in smokers. In conclusion, moderate alcohol consumption was associated with a decreased risk of renal cancer. What's new? Previous studies have indicated that environmental or lifestyle factors may be involved in the etiology of renal cancer, and that moderate alcohol consumption may reduce the risk of this type of cancer. In this very large European study (nearly 500,000 subjects), the authors found that, indeed, total alcohol consumption was inversely associated with renal cancer overall (for all subsites combined), and also with cancers of the renal parenchyma.
|
|
| 8. |
- De La Torre, Amanda R., et al.
(författare)
-
Adaptation and exogenous selection in a Picea glauca x Picea engelmannii hybrid zone : implications for forest management under climate change
- 2014
-
Ingår i: New Phytologist. - Hoboken : Wiley-Blackwell. - 0028-646X .- 1469-8137. ; 201:2, s. 687-699
-
Tidskriftsartikel (refereegranskat)abstract
- The nature of selection responsible for the maintenance of the economically and ecologically important Picea glaucaxPicea engelmannii hybrid zone was investigated. Genomic, phenotypic and climatic data were used to test assumptions of hybrid zone maintenance and to model future scenarios under climate change. Genome-wide estimates of admixture based on a panel of 86 candidate gene single nucleotide polymorphisms were combined with long-term quantitative data on growth and survival (over 20yr), as well as one-time assessments of bud burst and bud set phenology, and cold hardiness traits. A total of 15498 individuals were phenotyped for growth and survival. Our results suggest that the P.glaucaxP.engelmannii hybrid zone is maintained by local adaptation to growing season length and snowpack (exogenous selection). Hybrids appeared to be fitter than pure species in intermediate environments, which fits expectations of the bounded hybrid superiority model of hybrid zone maintenance. Adaptive introgression from parental species has probably contributed to increased hybrid fitness in intermediate habitats. While P.engelmannii ancestry is higher than P.glauca ancestry in hybrid populations, on average, selective breeding in managed hybrid populations is shifting genomic composition towards P.glauca, potentially pre-adapting managed populations to warmer climates.
|
|
| 9. |
- de La Torre, Amanda R, et al.
(författare)
-
Insights into conifer giga-genomes
- 2014
-
Ingår i: Plant Physiology. - : American Society of Plant Biologists. - 0032-0889 .- 1532-2548. ; 166:4, s. 1724-1732
-
Tidskriftsartikel (refereegranskat)abstract
- Insights from sequenced genomes of major land plant lineages have advanced research in almost every aspect of plant biology. Until recently, however, assembled genome sequences of gymnosperms have been missing from this picture. Conifers of the pine family (Pinaceae) are a group of gymnosperms that dominate large parts of the world's forests. Despite their ecological and economic importance, conifers seemed long out of reach for complete genome sequencing, due in part to their enormous genome size (20-30 Gb) and the highly repetitive nature of their genomes. Technological advances in genome sequencing and assembly enabled the recent publication of three conifer genomes: white spruce (Picea glauca), Norway spruce (Picea abies), and loblolly pine (Pinus taeda). These genome sequences revealed distinctive features compared with other plant genomes and may represent a window into the past of seed plant genomes. This Update highlights recent advances, remaining challenges, and opportunities in light of the publication of the first conifer and gymnosperm genomes.
|
|
| 10. |
- Hamilton, Jill A., et al.
(författare)
-
Fine-scale environmental variation contributes to introgression in a three-species spruce hybrid complex
- 2015
-
Ingår i: Tree Genetics & Genomes. - : Springer Science and Business Media LLC. - 1614-2942 .- 1614-2950. ; 11:1
-
Tidskriftsartikel (refereegranskat)abstract
- Hybridization is common for many forest trees, where weak barriers to reproduction obscure species boundaries. We characterized the genomic structure of Picea populations comprising three species spanning two well-known contact zones, the Picea sitchensisxPicea glauca and the P. engelmanniixP. glauca hybrid zones, using a set of 71 candidate-gene single nucleotide polymorphisms. The genetic structure of populations suggests a complex genomic architecture shaped by interspecific gene flow and strong environmental selection, with increased genetic diversity in hybrids. The presence of admixture among all three species suggests that three-way hybrids with mixed ancestry occur where species ranges overlap in transitional environments. Significant clinal variation and associations with climatic variables (including continentality, temperature, and precipitation) differ between hybrid zones, indicating that individual species and their hybrids are adapted to distinct environmental niches. Allele-environmental association analysis revealed that most of the candidate genes with evidence of selection were unique to either the Sitkaxwhite or the Engelmannxwhite hybrid zones, with few shared between these zones. Management of these widespread and diverse gene pools will be best served through development of climate-based seed transfer, with recommended seed sources informed by a combination of genetic and climatic information for future climates.
|
|
