Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L.

The RADseq technology allows researchers to efficiently develop thousands of polymorphic loci across multiple individuals with little or no prior information on the genome. However, many questions remain about the biases inherent to this technology. Notably, sequence misalignments arising from paralogy may affect the development of single nucleotide polymorphism (SNP) markers and the estimation of genetic diversity. We evaluated the impact of putative paralog loci on genetic diversity estimation during the development of SNPs from a RADseq dataset for the nonmodel tree species Robinia pseudoacacia L. We sequenced nine genotypes and analyzed the frequency of putative paralogous RAD loci as a function of both the depth of coverage and the mismatch threshold allowed between loci. Putative paralogy was detected in a very variable number of loci, from 1% to more than 20%, with the depth of coverage having a major influence on the result. Putative paralogy artificially increased the observed degree of polymorphism and resulting estimates of diversity. The choice of the depth of coverage also affected diversity estimation and SNP validation: A low threshold decreased the chances of detecting minor alleles while a high threshold increased allelic dropout. SNP validation was better for the low threshold (4×) than for the high threshold (18×) we tested. Using the strategy developed here, we were able to validate more than 80% of the SNPs tested by means of individual genotyping, resulting in a readily usable set of 330 SNPs, suitable for use in population genetics applications.     

A scale‐down mimic for mapping the process performance of centrifugation,depth and sterile filtration

In the production of biopharmaceuticals disk‐stack centrifugation is widely used as a harvest step for the removal of cells and cellular debris. Depth filters followed by sterile filters are often then employed to remove residual solids remaining in the centrate. Process development of centrifugation is usually conducted at pilot‐scale so as to mimic the commercial scale equipment but this method requires large quantities of cell culture and significant levels of effort for successful characterization. A scale‐down approach based upon the use of a shear device and a bench‐top centrifuge has been extended in this work towards a preparative methodology that successfully predicts the performance of the continuous centrifuge and polishing filters. The use of this methodology allows the effects of cell culture conditions and large‐scale centrifugal process parameters on subsequent filtration performance to be assessed at an early stage of process development where material availability is limited. Biotechnol. Bioeng. 2016;113: 1934–1941. © 2016 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.     

Effect of Inoculum Density on Verticillium Wilt Incidence in Commercial Olive Orchards

Verticillium wilt, caused by Verticillium dahliae Kleb., is presently the most destructive disease of olive, particularly in Andalucía (southern Spain). ‘Picual’ and ‘Arbequina’ are the dominant cultivars being planted in Spain. Both cultivars are highly susceptible to the defoliating pathotype of V. dahliae when artificially inoculated by root‐dipping or stem injection. Conversely, ‘Arbequina’ is considered more resistant than ‘Picual’ based on field observations and farmer's experience. In this study, the differential reaction between of cultivars was confirmed by surveys of naturally infested orchards with different inoculum densities of the pathogen. The average percentage of affected olive trees of ‘Picual’ was 60.2%, while only 13.1% of trees of ‘Arbequina’ showed disease symptoms. Overall, the pathogen caused extensive wilting of branches and defoliation on the trees of ‘Picual’, whereas ‘Arbequina’‐infected trees showed chlorotic symptoms and slight defoliation. The relationship between inoculum density and disease incidence fit a logarithmic function for both cultivars. The percentage of affected trees of ‘Arbequina’ per year increased linearly (y = 0.3559x, R² = 0.5652, and P = 0.0195) with the inoculum density in the soil, whereas this relationship was not observed for the ‘Picual’. Planting density had no effect on disease incidence for any of the two cultivars.     

区域种植业气候适宜度及其对种植活动的响应——以四川省盐亭县为例

在分析盐亭县近63年来(1950—2012)种植业生产发展的基础上,选取该县农村社会经济条件相对稳定的近32年(1981—2012)为研究时段。运用农业生态气候适宜度方法,依据水稻、红薯、玉米、小麦和油菜等5种主要作物生育期的光、热、水等气候条件,分别估算各种作物的资源适宜指数、效能适宜指数和利用指数,构建小尺度区域种植业气候适宜度模型和种植活动对区域种植业气候适宜度的影响度模型,进行小尺度区域种植业气候适宜度以及种植活动对种植业气候适宜度的影响度估算,并对种植业生产对气候变化的适应进行探讨。研究结果表明,(1)近32年来盐亭县大春作物的平均资源适宜指数、效能适宜指数和利用指数(分别为0.578、0.281和48.37%)均大于小春作物(分别为0.304、0.128和42.24%),大春作物的气候适宜度高于小春作物,且作物间的气候适宜度差异较大。(2)受季风气候波动的影响,该县作物气候适宜度有明显的年际波动;该县近32年来气候变化对大春作物气候适宜度有轻微不利影响,而对小春作物气候适宜度趋于有利。(3)盐亭县近32年来种植业平均的资源适宜指数为0.466、效能适宜指数为0.212、利用指数为45.49%;受5种作物资源适宜指数、效能适宜指数,以及作物播种面积与产量年际波动的综合影响,该县种植业气候适宜度亦有明显的年际波动;气候变化对该县种植业气候适宜度总体上有不利影响。(4)近32年来该县种植活动对种植业气候适宜度的影响度平均值为0.00092,其年际波动较大。通过作物种植组合结构的调整,在20世纪90年代中期前对种植业气候适宜度的提高有微弱的正向影响,对气候变化有一定程度的适应;而后期则有负向作用。     

光动力疗法辅助治疗轻中度牙周炎的疗效观察

目的:探讨光动力疗法(PDT)辅助治疗轻中度牙周炎患者的临床疗效。方法:选取我院2016年1月-2017年8月收治的轻中度牙周炎患者46例为研究对象,共选取患牙276颗,随机分为观察组与对照组,每组138颗患牙,对照组予以龈下刮治术和根面平整术(SRP)治疗,观察组在对照组的基础上联合PDT治疗,比较治疗前、治疗后1个月、2个月、3个月观察两组患者的牙周袋探诊深度(PD)、探诊出血(BOP)阳性率、出血指数(BI)。结果:治疗后1个月、2个月、3个月,两组PD均随着时间的推移逐渐变浅(P0.05),且观察组治疗后各时间点均浅于对照组(P0.05);两组BOP阳性率均较治疗前降低,且观察组治疗后各时间均低于对照组(P0.05);两组BI随着时间的推移呈逐渐下降趋势(P0.05),且观察组治疗后各时间点BI均低于对照组(P0.05)。结论:PDT辅助治疗轻中度牙周炎患者的临床疗效较好,其能减小PD,降低BI和BOP阳性率。     

Strong Interplay between Sodium and Oxygen in Kesterite Absorbers: Complex Formation,Incorporation, and Tailoring Depth Distributions

Sodium and oxygen are prevalent impurities in kesterite solar cells. Both elements are known to strongly impact performance of the kesterite devices and can be connected to efficiency improvements seen after heat treatments. The sodium distribution in the kesterite absorber is commonly reported, whereas the oxygen distribution has received less attention. Here, a direct relationship between sodium and oxygen in kesterite absorbers is established using secondary ion mass spectrometry and explained by defect analyses within the density functional theory. The calculations reveal a binding energy of 0.76 eV between the substitutional defects Na_Cu and O_S in the nearest neighbor configuration, indicating an abundance of Na? O complexes in kesterite absorbers at relevant temperatures. Oxygen incorporation is studied by introducing isotopic ¹⁸O at different stages of the Cu₂ZnSnS₄/Mo/soda‐lime glass baseline processing. It is observed that oxygen from the Mo back contact and contaminations during the sulfurization are primary contributors to the oxygen distribution. Indeed, unintentional oxygen incorporation leads to immobilization of sodium. This results in a strong correlation between sodium and oxygen, in excellent agreement with the theoretical calculations. Consequently, oxygen availability should be monitored to optimize postdeposition heat treatments to control impurities in kesterite absorbers and ultimately, the solar cell efficiency.     

Phylogenomics using low‐depth whole genome sequencing: A case study with the olive tribe

Species trees have traditionally been inferred from a few selected markers, and genome‐wide investigations remain largely restricted to model organisms or small groups of species for which sampling of fresh material is available, leaving out most of the existing and historical species diversity. The genomes of an increasing number of species, including specimens extracted from natural history collections, are being sequenced at low depth. While these data sets are widely used to analyse organelle genomes, the nuclear fraction is generally ignored. Here we evaluate different reference‐based methods to infer phylogenies of large taxonomic groups from such data sets. Using the example of the Oleeae tribe, a worldwide‐distributed group, we build phylogenies based on single nucleotide polymorphisms (SNPs) obtained using two reference genomes (the olive and ash trees). The inferred phylogenies are overall congruent, yet present differences that might reflect the effect of distance to the reference on the amount of missing data. To limit this issue, genome complexity was reduced by using pairs of orthologous coding sequences as the reference, thus allowing us to combine SNPs obtained using two distinct references. Concatenated and coalescence trees based on these combined SNPs suggest events of incomplete lineage sorting and/or hybridization during the diversification of this large phylogenetic group. Our results show that genome‐wide phylogenetic trees can be inferred from low‐depth sequence data sets for eukaryote groups with complex genomes, and histories of reticulate evolution. This opens new avenues for large‐scale phylogenomics and biogeographical analyses covering both the extant and the historical diversity stored in museum collections.     

An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity

Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low‐coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high‐density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low‐density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.     

Genome‐based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles

Ribosomal DNA (rDNA) copy number variation (CNV) has major physiological implications for all organisms, but how it varies for fungi, an ecologically ubiquitous and important group of microorganisms, has yet to be systemically investigated. Here, we examine rDNA CNV using an in silico read depth approach for 91 fungal taxa with sequenced genomes and assess copy number conservation across phylogenetic scales and ecological lifestyles. rDNA copy number varied considerably across fungi, ranging from an estimated 14 to 1,442 copies (mean = 113, median = 82), and copy number similarity was inversely correlated with phylogenetic distance. No correlations were found between rDNA CNV and fungal trophic mode, ecological guild or genome size. Taken together, these results show that like other microorganisms, fungi exhibit substantial variation in rDNA copy number, which is linked to their phylogeny in a scale‐dependent manner.