Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Data from: Old World and New World Phasmatodea: phylogenomics resolve the evolutionary history of stick and leaf insects
Simon, Sabrina ; Letsch, Harald ; Bank, Sarah ; Buckley, Thomas R. ; Donath, Alexander ; Liu, Shanlin ; Machida, Ryuichiro ; Meusemann, Karen ; Misof, Bernhard ; Podsiadlowski, Lars ; Zhou, Xin ; Wipfler, Benjamin ; Bradler, Sven - \ 2019
Wageningen University & Research
Phasmatodea comprises over 3,000 extant species and stands out as one of the last remaining insect orders for which a robust, higher-level phylogenetic hypothesis is lacking. New research suggests that the extant diversity is the result of a surprisingly recent and rapid radiation that has been difficult to resolve with standard Sanger sequence data. In order to resolve the early branching events of stick and leaf insects, we analyzed transcriptomes from 61 species, including 38 Phasmatodea species comprising all major clades and 23 outgroup taxa, including all other Polyneoptera orders. Using a custom-made ortholog set based on reference genomes from four species, we identified on average 2,274 orthologous genes in the sequenced transcriptomes. We generated various sub-alignments and performed maximum-likelihood analyses on several representative datasets to evaluate the effect of missing data and matrix composition on our phylogenetic estimates. Based on our new data, we are able to reliably resolve the deeper nodes between the principal lineages of extant Phasmatodea. Among Euphasmatodea, we provide strong evidence for a basal dichotomy of Aschiphasmatodea and all remaining euphasmatodeans, the Neophasmatodea. Within the latter clade, we recovered a previously unrecognized major New World and Old World lineage, for which we introduce the new names Oriophasmata tax. nov. (“Eastern phasmids”) and Occidophasmata tax. nov. (“Western phasmids”). Occidophasmata comprise Diapheromerinae, Pseudophasmatinae, and Agathemera, whereas all remaining lineages form the Oriophasmata, including Heteropterygidae, Phylliinae, Bacillus, Lonchodidae (Necrosciinae + Lonchodinae), Clitumninae, Cladomorphinae, and Lanceocercata. We furthermore performed a divergence time analysis and reconstructed the historical biogeography for stick and leaf insects. Phasmatodea either originated in Southeast Asia or in the New World. Our results suggest that the extant distribution of Phasmatodea is largely the result of dispersal events in a recently and rapidly diversified insect lineage rather than the result of vicariant processes.
Poor vitamin d status in active pulmonary tuberculosis patients and its correlation with leptin and tnf-α
Wang, Qiuzhen ; Ma, Aiguo ; Gao, Tianlin ; Liu, Yufeng ; Ren, Lisheng ; Han, Lei ; Wei, Boyang ; Liu, Qian ; Dong, Chunjiang ; Mu, Yuze ; Li, Duo ; Kok, Frans J. ; Schouten, Evert G. - \ 2019
Journal of Nutritional Science and Vitaminology 65 (2019)5. - ISSN 0301-4800 - p. 390 - 398.
Co-morbidity - Diabetes - Immune activity - Inflammatory markers - Leptin - Serum 25(OH)D - TNF-α - Tuberculosis

Summary Vitamin D deficiency (VDD) is common in tuberculosis (TB) and may be implicated in the etiology of the disease and in its clinical course. The aim of this study was to investigate the association between leptin, inflammatory markers and VD status in TB patients, stratified for presence or absence of diabetes mellitus (DM). Two hundred ninety-nine TB patients were recruited from October 2015 to August 2016. Also, 91 normal controls were included. The information including socio-demographics, dietary intake and living habits was obtained by face-to-face interview. Serum concentrations of leptin and TNF-α, CRP and IL-6 were compared between TB patients with and without severe VDD (SVDD). Pearson’s correlation was used to analyze the association between TNF-α, leptin and 25-hydroxyvitamin D (25(OH)D). A significantly higher prevalence of VDD and SVDD was observed in TB patients compared with normal controls (93.0% vs 70.3%, 65.9% vs 3.3% respectively). Concentration of leptin was significantly lower, while TNF-α higher in TB patients with SVDD compared to those without (p<0.05). After adjustment for con-founders, leptin was positively associated with 25(OH)D (r=0.210, p=0.002) with similar correlation in TB patients with DM (r=0.240, p=0.020). A negative association between TNF-α and 25(OH)D was observed (r=-0.197, p=0.003), which was significant only in the subgroup without DM (r=-0.304, p=0.001). Our findings indicate that a higher VD status in TB patients may be related to higher immune activity and less serious tissue damage, and that this relation is different according to presence or absence of DM co-morbidity.

Cropland acidification increases risk of yield losses and food insecurity in China
Zhu, Qichao ; Liu, Xuejun ; Hao, Tianxiang ; Zeng, Mufan ; Shen, Jianbo ; Zhang, Fusuo ; Vries, Wim de - \ 2019
Environmental Pollution (2019). - ISSN 0269-7491
Acidification - Field management - Food security - Model - Yield loss

Distinct cropland acidification has been reported in China due to nitrogen (N) fertilizer overuse. However, the impacts on food production and thereby on food security are largely unknown. Yield losses in the period 1980–2050 were therefore assessed by simulating soil pH changes combined with derived pH-yield relationships for wheat, maize and rice. If the N fertilizer input continues to increase at 1% annually, the predicted average soil pH decline is about one unit and relative yield losses are expected to increase from approximately 4%–24% during 2010–2050. If the N fertilizer increase stops in 2020 (N2020), the expected losses are approximately 16% in 2050, which is comparable to a scenario of 100% crop residue return (100%RR). However, if 30% of the N fertilizer is replaced by manure N (30%MR), the losses reduce to near 5% in 2050. Soil acidification was predicted to reverse and expected losses are only 2.5% in 2050 in a combined scenario of N2020, 100%RR and 30%MR. Our results illustrate the potential food insecurity induced by cropland acidification and address the necessity of mitigation.

WGS of pygmy hog and Babyrousa babyrussa
Liu, Langqing ; Bosse, Mirte ; Megens, Hendrik-Jan ; Frantz, Laurent A.F. ; Lee, Young Lim ; Irving-Pease, Evan K. ; Narayan, Goutam ; Groenen, Martien ; Madsen, Ole - \ 2019
Wageningen University & Research
PRJEB30129 - ERP112560 - Babyrousa babyrussa - Porcula salvania
Dietary Protein Sources Differentially Affect the Growth of Akkermansia muciniphila and Maintenance of the Gut Mucus Barrier in Mice
Zhao, Fan ; Zhou, Guanghong ; Liu, Xinyue ; Song, Shangxin ; Xu, Xinglian ; Hooiveld, Guido ; Müller, Michael ; Liu, Li ; Kristiansen, Karsten ; Li, Chunbao - \ 2019
Molecular Nutrition & Food Research (2019). - ISSN 1613-4125
Akkermansia muciniphila - chicken protein - oxidative phosphorylation - soy protein

Scope: The gut microbiota plays an essential role in linking diet to host health. The specific role of different dietary proteins on the gut microbiota and health is less understood. Here, the impact of proteins derived from chicken and soy on the gut microbiota and host gut barrier in C57BL/6 mice is investigated. Methods and results: Specific-pathogen-free and germ-free mice are assigned to either a chicken- or a soy protein-based diet for 4 weeks. Compared with a chicken-protein-based diet, intake of a soy-protein-based diet reduces the abundance of A. muciniphila and the number of goblet cells, lowers the level of Muc2 mRNA, and decreases the thickness of the mucus layer in the colon of specific-pathogen-free mice. In germ-free mice, colonization with A. muciniphila combined with intake of a chicken-protein-based diet results in a higher expression of the Muc2 mRNA in colon, and surprisingly, an increased potential for oxidative phosphorylation in A. muciniphila compared with colonized mice fed a soy-protein-based diet. Conclusion: These findings suggest possible mutually beneficial interactions between the growth and function of A. muciniphila and host mucus barrier in response to intake of a chicken-protein-based diet contrasting the intake of a soy-protein-based diet.

The fertilization effect of global dimming on crop yields is not attributed to an improved light interception
Shao, Liping ; Li, Gang ; Zhao, Qiannan ; Li, Yabing ; Sun, Yutong ; Wang, Weinan ; Cai, Chuang ; Chen, Weiping ; Liu, Ronghua ; Luo, Weihong ; Yin, Xinyou ; Lee, Xuhui - \ 2019
Global Change Biology (2019). - ISSN 1354-1013
acclimation - diffuse radiation - fertilization effect - global dimming - radiation use efficiency - rice - wheat - yield

Global dimming, a decadal decrease in incident global radiation, is often accompanied with an increase in the diffuse radiation fraction, and, therefore, the impact of global dimming on crop production is hard to predict. A popular approach to quantify this impact is the statistical analysis of historical climate and crop data, or use of dynamic crop simulation modelling approach. Here, we show that statistical analysis of historical data did not provide plausible values for the effect of diffuse radiation versus direct radiation on rice or wheat yield. In contrast, our field experimental study of 3 years demonstrated a fertilization effect of increased diffuse radiation fraction, which partly offset yield losses caused by decreased global radiation, in both crops. The fertilization effect was not attributed to any improved canopy light interception but mainly to the increased radiation use efficiency (RUE). The increased RUE was explained not only by the saturating shape of photosynthetic light response curves but also by plant acclimation to dimming that gradually increased leaf nitrogen concentration. Crop harvest index slightly decreased under dimming, thereby discounting the fertilization effect on crop yields. These results challenge existing modelling paradigms, which assume that the fertilization effect on crop yields is mainly attributed to an improved light interception. Further studies on the physiological mechanism of plant acclimation are required to better quantify the global dimming impact on agroecosystem productivity under future climate change.

Comparison of smoking-related DNA methylation between newborns from prenatal exposure and adults from personal smoking
Sikdar, Sinjini ; Joehanes, Roby ; Joubert, Bonnie R. ; Xu, Cheng Jian ; Vives-Usano, Marta ; Rezwan, Faisal I. ; Felix, Janine F. ; Ward, James M. ; Guan, Weihua ; Richmond, Rebecca C. ; Brody, Jennifer A. ; Küpers, Leanne K. ; Baïz, Nour ; Håberg, Siri E. ; Smith, Jennifer A. ; Reese, Sarah E. ; Aslibekyan, Stella ; Hoyo, Cathrine ; Dhingra, Radhika ; Markunas, Christina A. ; Xu, Tao ; Reynolds, Lindsay M. ; Just, Allan C. ; Mandaviya, Pooja R. ; Ghantous, Akram ; Bennett, Brian D. ; Wang, Tianyuan ; Consortium, The Bios ; Bakulski, Kelly M. ; Melen, Erik ; Zhao, Shanshan ; Jin, Jianping ; Herceg, Zdenko ; Meurs, Joyce Van; Taylor, Jack A. ; Baccarelli, Andrea A. ; Murphy, Susan K. ; Liu, Yongmei ; Munthe-Kaas, Monica Cheng ; Deary, Ian J. ; Nystad, Wenche ; Waldenberger, Melanie ; Annesi-Maesano, Isabella ; Conneely, Karen ; Jaddoe, Vincent W.V. ; Arnett, Donna ; Snieder, Harold ; Kardia, Sharon L.R. ; Relton, Caroline L. ; Ong, Ken K. ; Ewart, Susan ; Moreno-Macias, Hortensia ; Romieu, Isabelle ; Sotoodehnia, Nona ; Fornage, Myriam ; Motsinger-Reif, Alison ; Koppelman, Gerard H. ; Bustamante, Mariona ; Levy, Daniel ; London, Stephanie J. - \ 2019
Epigenomics 11 (2019)13. - ISSN 1750-1911 - p. 1487 - 1500.
cigarette smoking - epigenetics - infant - maternal exposure - methylation

Aim: Cigarette smoking influences DNA methylation genome wide, in newborns from pregnancy exposure and in adults from personal smoking. Whether a unique methylation signature exists for in utero exposure in newborns is unknown. Materials & methods: We separately meta-analyzed newborn blood DNA methylation (assessed using Illumina450k Beadchip), in relation to sustained maternal smoking during pregnancy (9 cohorts, 5648 newborns, 897 exposed) and adult blood methylation and personal smoking (16 cohorts, 15907 participants, 2433 current smokers). Results & conclusion: Comparing meta-analyses, we identified numerous signatures specific to newborns along with many shared between newborns and adults. Unique smoking-associated genes in newborns were enriched in xenobiotic metabolism pathways. Our findings may provide insights into specific health impacts of prenatal exposure on offspring.

Self-assembled egg yolk peptide micellar nanoparticles as a versatile emulsifier for food-grade oil-in-water pickering nanoemulsions
Du, Zhenya ; Li, Qing ; Li, Junguang ; Su, Enyi ; Liu, Xiao ; Wan, Zhili ; Yang, Xiaoquan - \ 2019
Journal of Agricultural and Food Chemistry 67 (2019)42. - ISSN 0021-8561 - p. 11728 - 11740.
Egg yolk peptides - Food-grade pickering nanoemulsions - Nanomicelles - Particulate emulsifiers - Self-assembly

Pickering emulsions stabilized by food-grade particles have garnered increasing interest in recent years due to their promising applications in bio-related fields such as foods, cosmetics, and drug delivery. However, it remains a big challenge to formulate nanoscale Pickering emulsions from these edible particles. Herein, we show that a new Pickering nanoemulsion that is stable, monodisperse and controllable can be produced by employing the spherical micellar nanoparticles (EYPN), self- A ssembled from the food-derived, amphiphilic egg yolk peptides, as an edible particulate emulsifier. As natural peptide-based nanoparticles, the EYPN have small particle size, intermediate wettability, high surface activity, and deformability at the interface, which enable the formation of stable Pickering nanodroplets with a mean DLS diameter below 200 nm and a PDI below 0.2. This nanoparticle system is versatile for different oil phases with various polarities and demonstrates easy control of nanodroplet size through tuning the microfluidization conditions and/or the ratio of EYPN to oil phase. These food-grade Pickering nanoemulsions, obtained when the internal phase is an edible vegetable oil, have superior stability during long-term storage and spray-drying, based on the irreversible and compact adsorption of intact EYPN at the nanodroplet surface. This is the first finding of a natural edible nano-Pickering emulsifier that can be used solely to make stable food Pickering nanoemulsions with the qualities of simplicity, versatility, low cost, and the possibility of controllable and mass production, which make them viable for many sustainable applications.

Earthworms Coordinate Soil Biota to Improve Multiple Ecosystem Functions
Liu, Ting ; Chen, Xiaoyun ; Gong, Xin ; Lubbers, Ingrid M. ; Jiang, Yangyang ; Feng, Wen ; Li, Xianping ; Whalen, Joann K. ; Bonkowski, Michael ; Griffiths, Bryan S. ; Hu, Feng ; Liu, Manqiang - \ 2019
Current Biology 29 (2019)20. - ISSN 0960-9822 - p. 3420 - 3429.
bacterial-dominated channel - earthworm - ecosystem engineer - ecosystem service - soil fauna - soil microbe - sustainable agriculture

Liu et al. study a 13-year-old field experiment to show that earthworms are beneficial to agroecosystems from a multifunctional perspective. This work incorporates the concerns of negative effects of earthworms in recently published syntheses and highlights the potential pathways in which earthworms contribute to sustainable agriculture.

Using poly(β-hydroxybutyrate-β-hydroxyvalerate) as carbon source in biofloc-systems : Nitrogen dynamics and shift of Oreochromis niloticus gut microbiota
Liu, Gang ; Deng, Yale ; Verdegem, Marc ; Ye, Zhangying ; Zhu, Songming - \ 2019
Science of the Total Environment 694 (2019). - ISSN 0048-9697
Biodegradable polymers (BDPs) - Biofloc system - Carbohydrate - Gut microbiota - Nitrogen dynamic

Inorganic‑nitrogen removal is essential for the sustainable operation of aquaculture industry and also influences the health of aquatic animals, which may be accomplished by utilizing biofloc technology. In this paper, we studied the use of three different carbon sources 1) longan seed powder (LP), 2) Poly(β-hydroxybutyrate-β-hydroxyvalerate) (PHBV) and 3) synthesized PHBV and LP (PHBVL) in biofloc systems for 90 days to investigate the nitrogen dynamics and gut microbiota of Nile tilapia (Oreochromis niloticus). The PHBVL and PHBV groups had higher total inorganic‑nitrogen removal efficiencies (70.99 ± 19.45% and 63.54 ± 19.44%) than the LP group (35.02 ± 11.21%), which had an accumulation of nitrate. Meanwhile, the biofloc in PHBVL and PHBV group generally had a higher amino acid composition, particularly for methionine and lysine, but was not reflected in the tilapia muscle. High-throughput sequencing indicated that the different carbohydrates shaped different bacterial community compositions in the fish gut after exposure in the three environments for 90-day. These differences, which resulted in different gut digestive enzyme activities (amylase, lipase and trypsin), and growth performance, which the food conversion ratio in the PHBVL group was lower than LP and PHBV group, the final body weight in PHBVL group was average 4.33% and 3.65% bigger than in LP and PHBV group. Network analysis revealed that the keystone taxa (90.33%) were Proteobacteria, Chloroflexi, Actinobacteria, Planctomycetes, Verrucomicrobia and Bacteroidetes, which relative abundance varied in the fish gut in the three groups. The experiment verified the feasibility and advantage to use biodegradable polymers (BDPs) as carbohydrates for biofloc systems.

Recently duplicated sesterpene (C25) gene clusters in Arabidopsis thaliana modulate root microbiota.
Chen, Qingwen ; Jiang, Ting ; Liu, Yong-Xiu ; Haili, Liu ; Zhao, T. ; Liu, Zhixi ; Gan, Xiangchao ; Hallab, Asis ; Wang, Xuemei ; He, Juan ; Ma, Yihua ; Zhang, Fengxia ; Jin, Tao ; Schranz, M.E. ; Wang, Yong ; Yang, Bai - \ 2019
Science in China Series C-Life Sciences 62 (2019)7. - ISSN 1006-9305 - p. 947 - 958.
Consumer confidence in the safety of milk and infant milk formula in China
Li, Saiwei ; Sijtsema, Siet J. ; Kornelis, Marcel ; Liu, Yumei ; Li, Shengli - \ 2019
Journal of Dairy Science 102 (2019)10. - ISSN 0022-0302 - p. 8807 - 8818.
ABA-mediated regulation of leaf and root hydraulic conductance in tomato grown at elevated CO2 is associated with altered gene expression of aquaporins
Fang, Liang ; Abdelhakim, Lamis Osama Anwar ; Hegelund, Josefine Nymark ; Li, Shenglan ; Liu, Jie ; Peng, Xiaoying ; Li, Xiangnan ; Wei, Zhenhua ; Liu, Fulai - \ 2019
Horticulture Research 6 (2019)1. - ISSN 2052-7276

Elevated CO2 concentration in the air (e[CO2]) decreases stomatal density (SD) and stomatal conductance (gs) where abscisic acid (ABA) may play a role, yet the underlying mechanism remains largely elusive. We investigated the effects of e[CO2] (800 ppm) on leaf gas exchange and water relations of two tomato (Solanum lycopersicum) genotypes, Ailsa Craig (WT) and its ABA-deficient mutant (flacca). Compared to plants grown at ambient CO2 (400 ppm), e[CO2] stimulated photosynthetic rate in both genotypes, while depressed the gs only in WT. SD showed a similar response to e[CO2] as gs, although the change was not significant. e[CO2] increased leaf and xylem ABA concentrations and xylem sap pH, where the increases were larger in WT than in flacca. Although leaf water potential was unaffected by CO2 growth environment, e[CO2] lowered osmotic potential, hence tended to increase turgor pressure particularly for WT. e[CO2] reduced hydraulic conductance of leaf and root in WT but not in flacca, which was associated with downregulation of gene expression of aquaporins. It is concluded that ABA-mediated regulation of gs, SD, and gene expression of aquaporins coordinates the whole-plant hydraulics of tomato grown at different CO2 environments.

Old World and New World Phasmatodea: Phylogenomics Resolve the Evolutionary History of Stick and Leaf Insects
Simon, Sabrina ; Letsch, Harald ; Bank, Sarah ; Buckley, Thomas R. ; Donath, Alexander ; Liu, Shanlin ; Machida, Ryuichiro ; Meusemann, Karen ; Misof, Bernhard ; Podsiadlowski, Lars ; Zhou, Xin ; Wipfler, Benjamin ; Bradler, Sven - \ 2019
Frontiers in Ecology and Evolution 7 (2019). - ISSN 2296-701X
Phasmatodea comprises over 3,000 extant species and stands out as one of the last remaining insect orders for which a robust, higher-level phylogenetic hypothesis is lacking. New research suggests that the extant diversity is the result of a surprisingly recent and rapid radiation that has been difficult to resolve with standard Sanger sequence data. In order to resolve the early branching events of stick and leaf insects, we analyzed transcriptomes from 61 species, including 38 Phasmatodea species comprising all major clades and 23 outgroup taxa, including all other Polyneoptera orders. Using a custom-made ortholog set based on reference genomes from four species, we identified on average 2,274 orthologous genes in the sequenced transcriptomes. We generated various sub-alignments and performed maximum-likelihood analyses on several representative datasets to evaluate the effect of missing data and matrix composition on our phylogenetic estimates. Based on our new data, we are able to reliably resolve the deeper nodes between the principal lineages of extant Phasmatodea. Among Euphasmatodea, we provide strong evidence for a basal dichotomy of Aschiphasmatodea and all remaining euphasmatodeans, the Neophasmatodea. Within the latter clade, we recovered a previously unrecognized major New World and Old World lineage, for which we introduce the new names Oriophasmata tax. nov. (“Eastern phasmids”) and Occidophasmata tax. nov. (“Western phasmids”). Occidophasmata comprise Diapheromerinae, Pseudophasmatinae, and Agathemera, whereas all remaining lineages form the Oriophasmata, including Heteropterygidae, Phylliinae, Bacillus, Lonchodidae (Necrosciinae + Lonchodinae), Clitumninae, Cladomorphinae, and Lanceocercata. We furthermore performed a divergence time analysis and reconstructed the historical biogeography for stick and leaf insects. Phasmatodea either originated in Southeast Asia or in the New World. Our results suggest that the extant distribution of Phasmatodea is largely the result of dispersal events in a recently and rapidly diversified insect lineage rather than the result of vicariant processes.
A forecasting model for aflatoxins contamination in maize: case study in Serbia
Liu, N. ; Liu, C. ; Bagi, F. ; Sulyok, Michael ; Dudas, Tatjana ; Savic, Zagorka ; Stankov, Aleksandra ; Loc, Marta ; Fels, H.J. van der - \ 2019
Maize is one of the major crops produced in Serbia. The produced maize is mainly used as ingredient for compound feed for animals, but also for human consumption
and starch production. The presence
of aflatoxins, produced by Aspergillus
flavus, in maize grain is an increasing
problem since this secondary
metabolite is very toxic to human
and animal health.
De novo transcriptome analysis of Viola × wittrockiana exposed to high temperature stress
Du, Xiaohua ; Zhu, Xiaopei ; Yang, Yaping ; Wang, Yanli ; Arens, Paul ; Liu, Huichao - \ 2019
PLoS ONE 14 (2019)9. - ISSN 1932-6203

Around the world, pansies are one of the most popular garden flowers, but they are generally sensitive to high temperatures, and this limits the practicality of planting them during the warmest days of the year. However, a few pansy germplasms with improved heat tolerance have been discovered or bred, but the mechanisms of their heat resistance are not understood. In this study, we investigated the transcript profiles of a heat-tolerant pansy inbred line, DFM16, in response to high temperatures using RNAseq. Approximately 55.48 Gb of nucleotide data were obtained and assembled into 167,576 unigenes with an average length of 959 bp, of which, 5,708 genes were found to be differentially expressed after heat treatments. Real-time qPCR was performed to validate the expression profiles of the selected genes. Nine metabolic pathways were found to be significantly enriched, in the analysis of the differentially expressed genes. Several potentially interesting genes that encoded putative transcription regulators or key components involving heat shock protein (HSP), heat shock transcription factors (HSF), and antioxidants biosynthesis, were identified. These genes were highlighted to indicate their significance in response to heat stress and will be used as candidate genes to improve pansy heat-tolerance in the future.

Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)
Xing, Yu ; Liu, Yang ; Zhang, Qing ; Nie, Xinghua ; Sun, Yamin ; Zhang, Zhiyong ; Li, Huchen ; Fang, Kefeng ; Wang, Guangpeng ; Huang, Hongwen ; Bisseling, Ton ; Cao, Qingqin ; Qin, Ling - \ 2019
GigaScience 8 (2019)9. - ISSN 2047-217X
Castanea mollissima - annotation - evolution - genome assembly

BACKGROUND: The Chinese chestnut (Castanea mollissima) is widely cultivated in China for nut production. This plant also plays an important ecological role in afforestation and ecosystem services. To facilitate and expand the use of C. mollissima for breeding and its genetic improvement, we report here the whole-genome sequence of C. mollissima. FINDINGS: We produced a high-quality assembly of the C. mollissima genome using Pacific Biosciences single-molecule sequencing. The final draft genome is ∼785.53 Mb long, with a contig N50 size of 944 kb, and we further annotated 36,479 protein-coding genes in the genome. Phylogenetic analysis showed that C. mollissima diverged from Quercus robur, a member of the Fagaceae family, ∼13.62 million years ago. CONCLUSIONS: The high-quality whole-genome assembly of C. mollissima will be a valuable resource for further genetic improvement and breeding for disease resistance and nut quality.

Water for maize for pigs for pork: An analysis of inter-provincial trade in China
Zhuo, La ; Liu, Yilin ; Yang, Hong ; Hoekstra, Arjen Y. ; Liu, Wenfeng ; Cao, Xinchun ; Wang, Mengru ; Wu, Pute - \ 2019
Water Research 166 (2019). - ISSN 0043-1354
Maize - Pork - Supply chain - Virtual water trade - Water footprint

Trade in commodities implies trade in virtual water (VW), which refers to the water that was used to produce the traded goods. Various studies have quantified international or inter-provincial virtual water (VW) flows related to the trade in crops and animal products. Until date, however, no effort has been undertaken to understand how the water embodied in traded feed crops (trade stage TS1) will be transferred further because of trade in animal products (trade stage TS2). This is the first study showing this mechanism, in a case study in China for maize (the major pig feed) and pork (the dominant meat), considering the period 2000–2013. We estimate the annual green and blue water footprints in maize production and then quantify the inter-provincial VW flows related to trade in maize (TS1) and trade in maize embodied in pork (TS2). Results show that in TS1, maize-related VW flowed from the water-scarce North to the water-rich South, with an increase of 40% over the study period (from 43 to 61 billion m3 y−1). In TS2, about 10% of the water embodied in maize exports from North to South China returns in the form of pork, with an increase in the absolute amount of 25% (from 4.8 to 6.1 billion m3 y−1). Considering blue VW flows specifically, we find that North-to-South blue VW flows decreased by 5% in TS1, while South-to-North blue VW flows increased by 23% in TS2.

Enrichment of nucleic acids
Bau, Haim ; Song, Jinzhao ; Liu, Changchun ; Mauk, Michael ; Oost, J. van der; Hegge, J.W. - \ 2019
Octrooinummer: WO2019178346, verleend: 2019-09-19.
Provided are methods directed to enriching nucleic acids in a biological sample. These methods, in some embodiments can discriminately enrich the abundance of low-copy nucleic acids relative to higher-copy nucleic acids. In some embodiments, the methods provided can enrich a low-copy number mutant allele associated with a disease state, thus allowing early detection and optimized treatment. In other embodiments, the methods can be used for detection of particular molecules, such as antigens, in a sample.
Dynamic virulence-related regions of the plant pathogenic fungus Verticillium dahliae display enhanced sequence conservation
Depotter, Jasper R.L. ; Shi-Kunne, Xiaoqian ; Missonnier, Hélène ; Liu, Tingli ; Faino, Luigi ; Berg, Grardy C.M. van den; Wood, Thomas A. ; Zhang, Baolong ; Jacques, Alban ; Seidl, Michael F. ; Thomma, Bart P.H.J. - \ 2019
Molecular Ecology 28 (2019)15. - ISSN 0962-1083 - p. 3482 - 3495.
comparative genomics - effector - genome evolution - mutagenesis - two-speed genome - Verticillium wilt

Plant pathogens continuously evolve to evade host immune responses. During host colonization, many fungal pathogens secrete effectors to perturb such responses, but these in turn may become recognized by host immune receptors. To facilitate the evolution of effector repertoires, such as the elimination of recognized effectors, effector genes often reside in genomic regions that display increased plasticity, a phenomenon that is captured in the two-speed genome hypothesis. The genome of the vascular wilt fungus Verticillium dahliae displays regions with extensive presence/absence polymorphisms, so-called lineage-specific regions, that are enriched in in planta-induced putative effector genes. As expected, comparative genomics reveals differential degrees of sequence divergence between lineage-specific regions and the core genome. Unanticipated, lineage-specific regions display markedly higher sequence conservation in coding as well as noncoding regions than the core genome. We provide evidence that disqualifies horizontal transfer to explain the observed sequence conservation and conclude that sequence divergence occurs at a slower pace in lineage-specific regions of the V. dahliae genome. We hypothesize that differences in chromatin organisation may explain lower nucleotide substitution rates in the plastic, lineage-specific regions of V. dahliae.

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