| 1. |
|
|
| 2. |
- Glasbey, JC, et al.
(författare)
-
- 2021
-
swepub:Mat__t
|
|
| 3. |
|
|
| 4. |
|
|
| 5. |
|
|
| 6. |
|
|
| 7. |
- Kaput, J, et al.
(författare)
-
The case for strategic international alliances to harness nutritional genomics for public and personal health
- 2005
-
Ingår i: The British journal of nutrition. - : Cambridge University Press (CUP). - 0007-1145 .- 1475-2662. ; 94:5, s. 623-632
-
Tidskriftsartikel (refereegranskat)abstract
- Nutrigenomics is the study of how constituents of the diet interact with genes, and their products, to alter phenotype and, conversely, how genes and their products metabolise these constituents into nutrients, antinutrients, and bioactive compounds. Results from molecular and genetic epidemiological studies indicate that dietary unbalance can alter gene–nutrient interactions in ways that increase the risk of developing chronic disease. The interplay of human genetic variation and environmental factors will make identifying causative genes and nutrients a formidable, but not intractable, challenge. We provide specific recommendations for how to best meet this challenge and discuss the need for new methodologies and the use of comprehensive analyses of nutrient–genotype interactions involving large and diverse populations. The objective of the present paper is to stimulate discourse and collaboration among nutrigenomic researchers and stakeholders, a process that will lead to an increase in global health and wellness by reducing health disparities in developed and developing countries.
|
|
| 8. |
|
|
| 9. |
- Yaghootkar, Hanieh, et al.
(författare)
-
Genetic Studies of Leptin Concentrations Implicate Leptin in the Regulation of Early Adiposity
- 2020
-
Ingår i: Diabetes. - : American Diabetes Association. - 0012-1797 .- 1939-327X. ; 69:12, s. 2806-2818
-
Tidskriftsartikel (refereegranskat)abstract
- Leptin influences food intake by informing the brain about the status of body fat stores. Rare LEP mutations associated with congenital leptin deficiency cause severe early-onset obesity that can be mitigated by administering leptin. However, the role of genetic regulation of leptin in polygenic obesity remains poorly understood. We performed an exome-based analysis in up to 57,232 individuals of diverse ancestries to identify genetic variants that influence adiposity-adjusted leptin concentrations. We identify five novel variants, including four missense variants, in LEP, ZNF800, KLHL31, and ACTL9, and one intergenic variant near KLF14. The missense variant Val94Met (rs17151919) in LEP was common in individuals of African ancestry only, and its association with lower leptin concentrations was specific to this ancestry (P = 2 × 10-16, n = 3,901). Using in vitro analyses, we show that the Met94 allele decreases leptin secretion. We also show that the Met94 allele is associated with higher BMI in young African-ancestry children but not in adults, suggesting that leptin regulates early adiposity.
|
|
| 10. |
- Brinkman, Arie B., et al.
(författare)
-
Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation
- 2019
-
Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1
-
Tidskriftsartikel (refereegranskat)abstract
- Global loss of DNA methylation and CpG island (CGI) hypermethylation are key epigenomic aberrations in cancer. Global loss manifests itself in partially methylated domains (PMDs) which extend up to megabases. However, the distribution of PMDs within and between tumor types, and their effects on key functional genomic elements including CGIs are poorly defined. We comprehensively show that loss of methylation in PMDs occurs in a large fraction of the genome and represents the prime source of DNA methylation variation. PMDs are hypervariable in methylation level, size and distribution, and display elevated mutation rates. They impose intermediate DNA methylation levels incognizant of functional genomic elements including CGIs, underpinning a CGI methylator phenotype (CIMP). Repression effects on tumor suppressor genes are negligible as they are generally excluded from PMDs. The genomic distribution of PMDs reports tissue-of-origin and may represent tissue-specific silent regions which tolerate instability at the epigenetic, transcriptomic and genetic level.
|
|
| 11. |
- Cadenas-Sanchez, Cristina, et al.
(författare)
-
Physical fitness reference standards for preschool children : The PREFIT project.
- 2019
-
Ingår i: Journal of Science and Medicine in Sport. - : Elsevier. - 1440-2440 .- 1878-1861. ; 22:4, s. 430-437
-
Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: Reference values are necessary for classifying children, for health screening, and for early prevention as many non-communicable diseases aggravate during growth and development. While physical fitness reference standards are available in children aged 6 and older, such information is lacking in preschool children. Therefore, the purposes of this study were (1) to provide sex-and age-specific physical fitness reference standards for Spanish preschool children; and (2) to study sex differences across this age period and to characterise fitness performance throughout the preschool period.DESIGN: Cross-sectional.METHODS: A total of 3179 preschool children (1678 boys) aged 2.8-6.4 years old from Spain were included in the present study. Physical fitness was measured using the PREFIT battery.RESULTS: Age- and sex-specific percentiles for the physical fitness components are provided. Boys performed better than girls in the cardiorespiratory fitness, muscular strength, and speed-agility tests over the whole preschool period studied and for the different percentiles. In contrast, girls performed slightly better than boys in the balance test. Older children had better performance in all fitness tests than their younger counterparts.CONCLUSIONS: Our study provides age- and sex-specific physical fitness reference standards in preschool children allowing interpretation of fitness assessment. Sexual dimorphism in fitness tests exists already at preschool age, and these differences become larger with age. These findings will help health, sport, and school professionals to identify preschool children with a high/very low fitness level, to examine changes in fitness over time, and to analyse those changes obtained due to intervention effects.
|
|
| 12. |
- Davidsson, P., et al.
(författare)
-
A proteomic study of the apolipoproteins in LDL subclasses in patients with the metabolic syndrome and type 2 diabetes
- 2005
-
Ingår i: J Lipid Res. - 0022-2275. ; 46:9, s. 1999-2006
-
Tidskriftsartikel (refereegranskat)abstract
- The exchangeable apolipoproteins present in small, dense LDL (sdLDL) and large, buoyant LDL subclasses were evaluated with a quantitative proteomic approach in patients with the metabolic syndrome and with type 2 diabetes, both with subclinical atherosclerosis and the B LDL phenotype. The analyses included surface-enhanced laser adsorption/ionization, time-of-flight mass spectrometry, and subsequent identification by mass spectrometry or immunoblotting and were carried out in LDL subclasses isolated by ultracentrifugation in deuterium oxide gradients with near physiological salt concentrations. The sdLDLs of both types of patients were enriched in apolipoprotein C-III (apoC-III) and were depleted of apoC-I, apoA-I, and apoE compared with matched healthy controls with the A phenotype. The LDL complexes formed in serum from patients with diabetes with the arterial proteoglycan (PG) versican were also enriched in apoC-III. In addition, there was a significant correlation between the apoC-III content in sdLDL in patients and the apparent affinity of their LDLs for arterial versican. The unique distribution of exchangeable apolipoproteins in the sdLDLs of the patients studied, especially high apoC-III, coupled with the augmented affinity with arterial PGs, may contribute to the strong association of the dyslipidemia of insulin resistance with increased risk for cardiovascular disease.
|
|
| 13. |
- Nik-Zainal, Serena, et al.
(författare)
-
Landscape of somatic mutations in 560 breast cancer whole-genome sequences
- 2016
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 534:7605, s. 47-54
-
Tidskriftsartikel (refereegranskat)abstract
- We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.
|
|
| 14. |
|
|
| 15. |
|
|
| 16. |
- Axfors, Cathrine, et al.
(författare)
-
Association between convalescent plasma treatment and mortality in COVID-19 : a collaborative systematic review and meta-analysis of randomized clinical trials
- 2021
-
Ingår i: BMC Infectious Diseases. - : BioMed Central (BMC). - 1471-2334. ; 21:1
-
Forskningsöversikt (refereegranskat)abstract
- Background: Convalescent plasma has been widely used to treat COVID-19 and is under investigation in numerous randomized clinical trials, but results are publicly available only for a small number of trials. The objective of this study was to assess the benefits of convalescent plasma treatment compared to placebo or no treatment and all-cause mortality in patients with COVID-19, using data from all available randomized clinical trials, including unpublished and ongoing trials (Open Science Framework, ). Methods: In this collaborative systematic review and meta-analysis, clinical trial registries (ClinicalTrials.gov, WHO International Clinical Trials Registry Platform), the Cochrane COVID-19 register, the LOVE database, and PubMed were searched until April 8, 2021. Investigators of trials registered by March 1, 2021, without published results were contacted via email. Eligible were ongoing, discontinued and completed randomized clinical trials that compared convalescent plasma with placebo or no treatment in COVID-19 patients, regardless of setting or treatment schedule. Aggregated mortality data were extracted from publications or provided by investigators of unpublished trials and combined using the Hartung-Knapp-Sidik-Jonkman random effects model. We investigated the contribution of unpublished trials to the overall evidence. Results: A total of 16,477 patients were included in 33 trials (20 unpublished with 3190 patients, 13 published with 13,287 patients). 32 trials enrolled only hospitalized patients (including 3 with only intensive care unit patients). Risk of bias was low for 29/33 trials. Of 8495 patients who received convalescent plasma, 1997 died (23%), and of 7982 control patients, 1952 died (24%). The combined risk ratio for all-cause mortality was 0.97 (95% confidence interval: 0.92; 1.02) with between-study heterogeneity not beyond chance (I-2 = 0%). The RECOVERY trial had 69.8% and the unpublished evidence 25.3% of the weight in the meta-analysis. Conclusions: Convalescent plasma treatment of patients with COVID-19 did not reduce all-cause mortality. These results provide strong evidence that convalescent plasma treatment for patients with COVID-19 should not be used outside of randomized trials. Evidence synthesis from collaborations among trial investigators can inform both evidence generation and evidence application in patient care.
|
|
| 17. |
- Brunk, Elizabeth, et al.
(författare)
-
Recon3D enables a three-dimensional view of gene variation in human metabolism
- 2018
-
Ingår i: Nature Biotechnology. - : Springer Science and Business Media LLC. - 1087-0156 .- 1546-1696. ; 36:3, s. 272-281
-
Tidskriftsartikel (refereegranskat)abstract
- Genome-scale network reconstructions have helped uncover the molecular basis of metabolism. Here we present Recon3D, a computational resource that includes three-dimensional (3D) metabolite and protein structure data and enables integrated analyses of metabolic functions in humans. We use Recon3D to functionally characterize mutations associated with disease, and identify metabolic response signatures that are caused by exposure to certain drugs. Recon3D represents the most comprehensive human metabolic network model to date, accounting for 3,288 open reading frames (representing 17% of functionally annotated human genes), 13,543 metabolic reactions involving 4,140 unique metabolites, and 12,890 protein structures. These data provide a unique resource for investigating molecular mechanisms of human metabolism. Recon3D is available at http://vmh.life.
|
|
| 18. |
- Burraco, Pablo, et al.
(författare)
-
Climate change and ageing in ectotherms
- 2020
-
Ingår i: Global Change Biology. - : WILEY. - 1354-1013 .- 1365-2486. ; 26:10, s. 5371-5381
-
Tidskriftsartikel (refereegranskat)abstract
- Human activity is changing climatic conditions at an unprecedented rate. The impact of these changes may be especially acute on ectotherms since they have limited capacities to use metabolic heat to maintain their body temperature. An increase in temperature is likely to increase the growth rate of ectothermic animals, and may also induce thermal stress via increased exposure to heat waves. Fast growth and thermal stress are metabolically demanding, and both factors can increase oxidative damage to essential biomolecules, accelerating the rate of ageing. Here, we explore the potential impact of global warming on ectotherm ageing through its effects on reactive oxygen species production, oxidative damage, and telomere shortening, at the individual and intergenerational levels. Most evidence derives primarily from vertebrates, although the concepts are broadly applicable to invertebrates. We also discuss candidate mechanisms that could buffer ectotherms from the potentially negative consequences of climate change on ageing. Finally, we suggest some potential applications of the study of ageing mechanisms for the implementation of conservation actions. We find a clear need for more ecological, biogeographical, and evolutionary studies on the impact of global climate change on patterns of ageing rates in wild populations of ectotherms facing warming conditions. Understanding the impact of warming on animal life histories, and on ageing in particular, needs to be incorporated into the design of measures to preserve biodiversity to improve their effectiveness.
|
|
| 19. |
- Carreira, B. M., et al.
(författare)
-
Warm vegetarians? : Heat waves and diet shifts in tadpoles
- 2016
-
Ingår i: Ecology. - : Wiley. - 0012-9658 .- 1939-9170. ; 97:11, s. 2964-2974
-
Tidskriftsartikel (refereegranskat)abstract
- Temperature can play an important role in determining the feeding preferences of ectotherms. In light of the warmer temperatures arising with the current climatic changes, omnivorous ectotherms may perform diet shifts toward higher herbivory to optimize energetic intake. Such diet shifts may also occur during heat waves, which are projected to become more frequent, intense, and longer lasting in the future. Here, we investigated how heat waves of different duration affect feeding preferences in omnivorous anuran tadpoles and how these choices affect larval life history. In laboratory experiments, we fed tadpoles of three species on animal, plant, or mixed diet and exposed them to short heat waves (similar to the heat waves these species experience currently) or long heat waves (predicted to increase under climate change). We estimated the dietary choices of tadpoles fed on the mixed diet using stable isotopes and recorded tadpole survival and growth, larval period, and mass at metamorphosis. Tadpole feeding preferences were associated with their thermal background, with herbivory increasing with breeding temperature in nature. Patterns in survival, growth, and development generally support decreased efficiency of carnivorous diets and increased efficiency or higher relative quality of herbivorous diets at higher temperatures. All three species increased herbivory in at least one of the heat wave treatments, but the responses varied among species. Diet shifts toward higher herbivory were maladaptive in one species, but beneficial in the other two. Higher herbivory in omnivorous ectotherms under warmer temperatures may impact species differently and further contribute to changes in the structure and function of freshwater environments.
|
|
| 20. |
- Comina Bellido, German
(författare)
-
Autonomous Lab-on-a-chip: solutions and fast prototyping tools
- 2021
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis, solutions for the development of autonomous Lab-on-a-chip (LOC), and 3D printing for fast prototyping of LOC devices are investigated. Lab-on-a-chip devices integrate analytical systems and conditioning processes in a compact package. Small sample volume, disposability, ability to perform complex analysis and performance comparable to classical instrumentation are characteristics that make LOCs excellent candidates for biomedical applications, environmental monitoring and food analysis. Classical LOC configurations usually require additional elements such as pumps, valves, fluidics interface connectors, and even pneumatic control to operate. Also, in most cases, a computer-capable device, or standalone control system, is needed in connection with the measurements. Autonomous LOCs avoid the use of additional components, as they are designed to integrate all necessary parts in one design. Cell phones are the most wide spread computer capable devices, and the advantage to exploit them as analytical instruments is obvious. They have been used in connection with microfluidic LOC measurements, typically using accessory dongles. To connect to the LOCs, in some cases, even permanent modifications of the phones were required. In this thesis, direct coupling to cell phone readout, without accessories beyond the LOC, has been investigated. Autonomous LOC development demands extensive time and resources for prototype optimization. Classical LOC fabrication methods, which are based on lithographic microfabrication, require special equipment and facilities. Additionally, the fabrication of 3D structures require multiple fabrication steps with numerous intermediate alignment. In this thesis, commercial-grade, low-cost 3D printers have been investigated as fast LOC prototyping platforms. The printers (Miicraft® DLP-3D printer and Formlabs Inc. Form+1) are based on Stereo Lithography (SLA). In this additive fabrication technique, a 3D computer model of the LOC is designed. Later, the 3D model is sliced in 2D patterns along the height of the design, and each of the 2D patterns is projected through the printer transparent tank bottom, which contains a liquid photocurable resin. Each exposure cures a thin layer of the resin, and the procedure is repeated adding layer after layer until the 3D printout is completed. With this technique it was possible to obtain real 3D LOC structures with unlimited number of 3D features in one step, within the hour, and at low-cost for prototyping, which constitutes a superb tool for fast and affordable sophistication of LOC architecture. The process was extended in this thesis to another area of complex and costly development: the manufacture of optical components. It was shown that optical components with arbitrary geometry could be obtained within the hour and typically for less than 1€/prototype. The first use of the technique was to produce templates for classical LOCs of polydimethylsiloxane (PDMS) on glass. The procedure was the first, to our knowledge, implemented with consumer grade printers, and included a demonstration of template fabrication for the development of a multilayer PDMS-LOC for colorimetric detection of glucose. The technique then evolved to the complete replacement of the PDMS stage, by conceiving the LOC architecture as a single monolithic printout. This concept was coined Unibody LOC (ULOC) and was used in this thesis for the development of all the autonomous Lab on a Chip solutions. Numerous solutions towards autonomous LOCs were developed such as: multidimensional adaptors that connect for example 1.6mm diameter tubing directly to 50μm wide microfluidic channels, several on plane and multilayer mixers, hybrid ULOC with paper channels, finger-pumps, check-valves, optical couplers and 3D printed optics. Time-dependent optical response bio-chemical reactions were identified as key to implement the link between autonomous LOC with cell phones without other accessories, and relying on ambient light as illumination. Such approach improves the analytical resolution of a colorimetric measurement using essentially the same camera. Finally, all those solutions were integrated to develop a chemical sensing interface for universal cell phone readout, and a 3D printed device for quantitative enzymatic detection using cell phones.
|
|
| 21. |
- Cuenca-Garcia, Magdalena, et al.
(författare)
-
More Physically Active and Leaner Adolescents Have Higher Energy Intake
- 2014
-
Ingår i: The Journal of Pediatrics. - : Elsevier BV. - 0022-3476 .- 1097-6833. ; 164:1, s. 159-166
-
Tidskriftsartikel (refereegranskat)abstract
- Objective To test whether youths who engage in vigorous physical activity are more likely to have lean bodies while ingesting relatively large amounts of energy. For this purpose, we studied the associations of both physical activity and adiposity with energy intake in adolescents.Study design The study subjects were adolescents who participated in 1 of 2 cross-sectional studies, the Healthy Lifestyle in Europe by Nutrition in Adolescence (HELENA) study (n = 1450; mean age, 14.6 years) or the European Youth Heart Study (EYHS; n = 321; mean age, 15.6 years). Physical activity was measured by accelerometry, and energy intake was measured by 24-hour recall. In the HELENA study, body composition was assessed by 2 or more of the following methods: skinfold thickness, bioelectrical impedance analysis, plus dual-energy X-ray absorptiometry or air-displacement plethysmography in a subsample. In the EYHS, body composition was assessed by skinfold thickness.Results Fat mass was inversely associated with energy intake in both studies and using 4 different measurement methods (P <=.006). Overall, fat-free mass was positively associated with energy intake in both studies, yet the results were not consistent across measurement methods in the HELENA study. Vigorous physical activity in the HELENA study (P<.05) and moderate physical activity in the EYHS (P<.01) were positively associated with energy intake. Overall, results remained unchanged after adjustment for potential confounding factors, after mutual adjustment among the main exposures (physical activity and fat mass), and after the elimination of obese subjects, who might tend to under-report energy intake, from the analyses.Conclusion Our data are consistent with the hypothesis that more physically active and leaner adolescents have higher energy intake than less active adolescents with larger amounts of fat mass.
|
|
| 22. |
- Elsik, Christine G., et al.
(författare)
-
The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
-
Tidskriftsartikel (refereegranskat)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
|
|
| 23. |
- Faure, B., et al.
(författare)
-
2D to 3D crossover of the magnetic properties in ordered arrays of iron oxide nanocrystals
- 2013
-
Ingår i: Nanoscale. - : Royal Society of Chemistry (RSC). - 2040-3364 .- 2040-3372. ; 5:3, s. 953-960
-
Tidskriftsartikel (refereegranskat)abstract
- The magnetic 2D to 3D crossover behavior of well-ordered arrays of monodomain γ-Fe2O3 spherical nanoparticles with different thicknesses has been investigated by magnetometry and Monte Carlo (MC) simulations. Using the structural information of the arrays obtained from grazing incidence small-angle X-ray scattering and scanning electron microscopy together with the experimentally determined values for the saturation magnetization and magnetic anisotropy of the nanoparticles, we show that MC simulations can reproduce the thickness-dependent magnetic behavior. The magnetic dipolar particle interactions induce a ferromagnetic coupling that increases in strength with decreasing thickness of the array. The 2D to 3D transition in the magnetic properties is mainly driven by a change in the orientation of the magnetic vortex states with increasing thickness, becoming more isotropic as the thickness of the array increases. Magnetic anisotropy prevents long-range ferromagnetic order from being established at low temperature and the nanoparticle magnetic moments instead freeze along directions defined by the distribution of easy magnetization directions.
|
|
| 24. |
- G. Trainer, Melissa, et al.
(författare)
-
Seasonal Variations in Atmospheric Composition as Measured in Gale Crater, Mars
- 2019
-
Ingår i: Journal of Geophysical Research - Planets. - : John Wiley & Sons. - 2169-9097 .- 2169-9100. ; 124:11, s. 3000-3024
-
Tidskriftsartikel (refereegranskat)abstract
- The Sample Analysis at Mars (SAM) instrument onboard the Mars Science Laboratory Curiosity rover measures the chemical composition of major atmospheric species (CO2, N2, 40Ar, O2, and CO) through a dedicated atmospheric inlet. We report here measurements of volume mixing ratios in Gale Crater using the SAM quadrupole mass spectrometer, obtained over a period of nearly 5 years (3 Mars years) from landing. The observation period spans the northern summer of MY 31 and solar longitude (LS) of 175° through spring of MY 34, LS = 12°. This work expands upon prior reports of the mixing ratios measured by SAM QMS in the first 105 sols of the mission. The SAM QMS atmospheric measurements were taken periodically, with a cumulative coverage of four or five experiments per season on Mars. Major observations include the seasonal cycle of CO2, N2, and Ar, which lags approximately 20–40° of LS behind the pressure cycle driven by CO2 condensation and sublimation from the winter poles. This seasonal cycle indicates that transport occurs on faster timescales than mixing. The mixing ratio of O2 shows significant seasonal and interannual variability, suggesting an unknown atmospheric or surface process at work. The O2 measurements are compared to several parameters, including dust optical depth and trace CH4 measurements by Curiosity. We derive annual mean volume mixing ratios for the atmosphere in Gale Crater: CO2 = 0.951 (±0.003), N2 = 0.0259 (±0.0006), 40Ar = 0.0194 (±0.0004), O2 = 1.61 (±0.09) x 10‐3, and CO = 5.8 (±0.8) x 10‐4.
|
|
| 25. |
- Hendriks, Kasper P., et al.
(författare)
-
Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset
- 2023
-
Ingår i: Current Biology. - : Elsevier. - 0960-9822 .- 1879-0445. ; 33:19, s. 4052-4068
-
Tidskriftsartikel (refereegranskat)abstract
- The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Bras-sicaceae Tree of Life or BrassiToL) based on nuclear (1,081 genes, 319 of the 349 genera; 57 of the 58 tribes) and plastome (60 genes, 265 genera; all tribes) data. We found cytonuclear discordance between the two, which is likely a result of rampant hybridization among closely and more distantly related lineages. To eval-uate the impact of such hybridization on the nuclear phylogeny reconstruction, we performed five different gene sampling routines, which increasingly removed putatively paralog genes. Our cleaned subset of 297 genes revealed high support for the tribes, whereas support for the main lineages (supertribes) was moder-ate. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene origin of the family. Finally, our results strongly support a recently published new family classification, dividing the family into two subfamilies (one with five supertribes), together representing 58 tribes. This includes five recently described or re-established tribes, including Arabidopsideae, a monogeneric tribe accommodating Arabidopsis without any close relatives. With a worldwide community of thousands of researchers working on Brassicaceae and its diverse members, our new genus-level family phylogeny will be an indispensable tool for studies on biodiversity and plant biology.
|
|
