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.     

Fast protein sequencing of monoclonal antibody by real-time digestion on emitter during nanoelectrospray

Growth in the pharmaceutical industry has led to an increasing demand for rapid characterization of therapeutic monoclonal antibodies. The current methods for antibody sequence confirmation (e.g., N-terminal Edman sequencing and traditional peptide mapping methods) are not sufficient; thus, we developed a fast method for sequencing recombinant monoclonal antibodies using a novel digestion-on-emitter technology. Using this method, a monoclonal antibody can be denatured, reduced, digested, and sequenced in less than an hour. High throughput and satisfactory protein sequence coverage were achieved by using a non-specific protease from Aspergillus saitoi, protease XIII, to digest the denatured and reduced monoclonal antibody on an electrospray emitter, while electrospray high voltage was applied to the digestion mixture through the emitter. Tandem mass spectrometry data was acquired over the course of enzyme digestion, generating similar information compared to standard peptide mapping experiments in much less time. We demonstrated that this fast protein sequencing method provided sufficient sequence information for bovine serum albumin and two commercially available monoclonal antibodies, mouse IgG1 MOPC21 and humanized IgG1 NISTmAb. For two monoclonal antibodies, we obtained sequence coverage of 90.5–95.1% for the heavy chains and 98.6–99.1% for the light chains. We found that on-emitter digestion by protease XIII generated peptides of various lengths during the digestion process, which was critical for achieving sufficient sequence coverage. Moreover, we discovered that the enzyme-to-substrate ratio was an important parameter that affects protein sequence coverage. Due to its highly automatable and efficient design, our method offers a major advantage over N-terminal Edman sequencing and traditional peptide mapping methods in the identification of protein sequence, and is capable of meeting an ever-increasing demand for monoclonal antibody sequence confirmation in the biopharmaceutical industry.     

基于地理探测器的宁夏贺兰山植被覆盖度时空分异及驱动因子

监测区域植被覆盖变化并分析其驱动因子,有利于实现生态环境的可持续发展。本研究以1989—2021年Landsat 5/8遥感影像为数据源,利用像元二分模型获取宁夏贺兰山植被覆盖度,基于地理探测器量化了环境和人为等10个因子对其时空分布的影响。结果表明: 1989—2021年间,宁夏贺兰山平均植被覆盖度为35.8%,时间尺度上总体呈增加趋势,平均增幅为0.043·(10 a)^-1,空间尺度上呈现从西南向东北递减的分布特征;研究区58.1%的区域植被覆盖度未来将持续性改善,但仍有30.7%的植被存在退化的潜在风险。降水是影响植被分布的主要环境因子,与单因子相比,环境因子和人为因子的交互作用对植被覆盖度的解释力更强,降水与其他因子的交互作用处于主导作用。     

宁夏东部风沙区沙化草地土壤水分和植被的空间特征

土壤水分作为土壤-植被-大气连续体的关键因子,对沙化草地的演化过程具有重要作用。为探讨宁夏东部风沙区沙化草地土壤水分、物种丰富度指数及植被盖度的空间变异及其相互关系,以哈巴湖自然保护区沙化草地为对象,采用样线法自潜在沙化草地至重度沙化草地进行植被调查和土壤取样,通过经典统计学和地统计学分析,得出以下结果：0—100 m各土层土壤水分含量、植被盖度和物种丰富度指数的分布范围分别为0.82%—28.22%、41.00%—93.00%和0.82—2.80,变异系数范围为0.20—0.48,均属于中等变异。各土层土壤水分和物种丰富度指数表现为中等的空间自相关性,植被盖度则表现为强烈的空间自相关性。Kriging插值结果表明,0—100 cm各土层土壤水分和植被盖度的空间插值图呈条带状和斑块状的梯度变化,物种丰富度呈斑块分布,自潜在沙化草地至重度沙化草地,表现为逐渐降低的趋势。相关分析表明,植被盖度与0—40 cm各土层土壤水分呈显著正相关,与40—100 cm各土层土壤水分呈极显著正相关。宁夏东部风沙区沙化草地土壤水分含量总体较低,由于结构因素和随机因素的共同作用,随草地沙化程度的加重,表现为...     

广西桉树人工林叶面积指数的估测及其校正

叶面积指数(Leaf area index, LAI)是森林生态系统重要的结构参数,通过遥感技术可反演区域LAI,但其可靠性需要地面准确的实测数据进行验证。选取广西国有高峰林场不同林龄的桉树(Eucalyptus robusta)人工林为对象,以异速生长法(Allometry)为对照,综合利用植物冠层分析仪法(LAI-2200)、跟踪辐射和冠层结构分析仪法(TRAC)、半球摄影法(DHP)以及地基激光雷达法(TLS)等间接法估测样地的LAI,并考虑木质成分以及聚集效应影响,进行相应的校正处理,为地面快速、准确测量桉树人工林LAI提供参考。结果表明：桉树人工林的比叶面积为125.37±13.38 cm~2/g,通过Allometry获得的LAI变化范围在1.65—3.84,平均为2.73,不同林龄间的差异均显著(P<0.05),随着林龄的增加呈现先增加后减少的趋势。在未校正情况下,LAI-2200、TRAC、DHP、TLS估算的LAI存在显著差异(P<0.05)。与对照相比,LAI-2200在幼龄林和过熟林中估算误差最小,TRAC在成熟林中估算误差最小。相对于完全去除法,利用...     

近20年来京津冀地区土壤风蚀扬尘颗粒物排放变化

京津冀地区是我国大气污染严重区域,土壤扬尘颗粒物排放变化研究对于改善京津冀地区空气质量具有重要意义。收集2000-2019年京津冀地区气候、土壤、植被覆盖数据,分析近20年来京津冀地区土壤扬尘颗粒物排放变化,揭示其变化的影响因素。结果显示2000-2019年京津冀地区土壤扬尘源总悬浮颗粒物（TSP）排放系数均值为1.79 t km^-2 a^-1,其中PM10占8.99%,PM2.5占0.25%。近20年土壤扬尘源TSP排放系数具有下降趋势,PM10和PM2.5排放系数变化过程与TSP一致。上述变化主要受气候因子变化影响,其次受植被覆盖度影响。分析发现近20年来京津冀地区土壤扬尘源TSP排放系数变化主要受年降水量影响。沧州市、天津市和石家庄市土壤扬尘源TSP、PM10和PM2.5排放系数均值较高,张家口市、保定市和沧州市土壤扬尘源TSP排放量占京津冀地区总量的19.18%、12.98%和11.63%。耕地土壤扬尘排放量最大占京津冀地区总量的59.83%,是抑制土壤扬尘源颗粒物排放的重点关注对象,其次为草地占15.66%。2019年邢台市土壤扬尘源PM10排放占观测值比例最高为12.66%,石家庄市和天津市占比也较高分别为11.09%和10.30%,沧州市和邯郸市占比分别为8.63%和8.02%。上述地区环境管理部门均应关注土壤扬尘源颗粒物排放对空气质量的影响。     

植被覆盖度对夏季降温效应的影响——以内蒙古为例

随着全球变暖的加剧,区域热环境问题日益凸显,植被的降温作用逐渐得到广泛关注。目前已有的研究多从样地尺度分析不同类型植被的降温效应。而区域尺度的研究多从定性的角度揭示地表温度与植被覆盖的关系,对评估植被的实际降温效应具有一定的局限性。以内蒙古为研究区,以MODIS地表温度数据为基础,采用近邻分析法,将森林、灌丛和草地的MODIS地表温度与相邻5km范围内的低覆盖地表作为对照,分析植被的降温效应以及植被覆盖度对降温效应的影响。从2015年7月地表温度平均值的结果来看,降温度数在蒙东、蒙中和蒙甘区均呈现森林>灌丛>草地。森林的降温范围在0.67-1.03℃,灌丛为0.60-0.95℃,草地为0.47-0.86℃。植被降温度数与植被覆盖度的回归拟合为对数分布,均呈显著正相关（P<0.01）。且在不同的植被覆盖度范围内植被降温效应具有显著差异,植被覆盖度水平较低时（<40%）,植被覆盖度的增加能更显著地降低地表温度。从整体来看,植被覆盖度每增加10%,森林降温0.12-0.39℃;灌丛降温0.1-0.2℃;草地降温0.049-0.075℃。综上,内蒙古作为全球气候变化最为敏感的区域之一,研究植被的夏季降温效应能够为内蒙古的气候调节服务评估提供重要的理论支撑及案例参考。     

库布齐沙漠南缘风沙-植被相互作用及其景观效应

干旱区尤其沙漠边缘地区的风沙与植被相互作用对塑造地表景观具有重要意义。选择库布齐沙漠南缘的油蒿灌丛地为研究区,开展了植被调查、风沙流观测和表层沉积物粒度采样测试,分析了顺风向植被盖度、风沙流结构与沉积物特征的沿程变化,探讨了风沙-植被相互作用及其对地表景观格局的影响。结果表明,风沙流与植被相互作用方式的改变使植物生长状况与地表蚀积模式发生变化,进而导致顺风向景观表现出明显的空间异质性。自上风向裸地过渡到均匀分布的新生油蒿和油蒿灌丛再至斑块状分布的灌丛沙堆,植被盖度与覆沙厚度先增大后减小,空气动力学粗糙度沿程不断增加且在过渡时其增幅最大,输沙率与沉积物粒度呈先减小后增大趋势,并在植被盖度与覆沙厚度最大处出现最小值。在沙漠边缘剥蚀高原上,起初适量风沙堆积促进油蒿定植与生长,均匀分布的油蒿灌丛进一步促进沙物质堆积,但当堆积厚度超过油蒿耐沙埋深度时发生退化,灌丛出现斑块状分布且风沙流在丘间地处侵蚀。据此,可理解为剥蚀高原风沙区景观异质性是风沙与植被相互协同与抑制作用的结果。     

Historical demography of freshwater mussels (Bivalvia: Unionidae): genetic evidence for population expansion and contraction during the late Pleistocene and Holocene

Genetic variation was examined in two endangered mussel species, Epioblasma brevidens and Epioblasma capsaeformis, and in a non‐listed species, Lampsilis fasciola, in the Clinch River, Tennessee, USA, by screening mitochondrial DNA (mtDNA) sequences and nuclear DNA microsatellites. Patterns of mtDNA polymorphism exhibited different trends in long‐term population sizes for each species during the late Pleistocene and Holocene (～20 000 ya to present); namely, E. brevidens has declined over time, E. capsaeformis has remained demographically stable, and L. fasciola has expanded. However, analyses using microsatellites did not exhibit similar trends, perhaps because homoplasy had eliminated long‐term population signatures for the loci examined. For both marker types, long‐term effective population size (N_e) was low in E. brevidens, intermediate in E. capsaeformis, and high in L. fasciola. Moderately diverged mtDNA lineages, perhaps indicative of secondary contact, were observed in E. brevidens and E. capsaeformis. Perhaps the most surprising result of this study was the high level of genetic variation observed at both mtDNA and microsatellite DNA markers for L. fasciola, variation seemingly contrary to the relatively small demes that currently reside in the Clinch River. However, the data are consistent with known demographic and life‐history traits of these three mussel species and their fish hosts, namely that they each use hosts with different dispersal capabilities, ranging from low, moderate, and high, respectively. The low divergence of mtDNA sequence variation reported in this and other recent mussel studies indicates that considerable extant population genetic variation probably originated during the late Pleistocene and Holocene. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 376–397.     

Proteome analysis of the plant-pathogenic bacterium Xanthomonas oryzae pv. oryzae

The plant-pathogenic bacterium Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of bacterial blight, which is one of the most serious diseases of rice. Xoo has been studied for over one century, and much has been learned about it, but proteomic investigation has been neglected. In this study, proteome reference maps of Xoo were constructed by two-dimensional gel electrophoresis, and 628 spots in the gels representing 469 different protein species were identified with MALDI-TOF/TOF MS. The identified spots were assigned to 15 functional categories according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and the annotations from the National Center for Biotechnology Information (NCBI) database. The data set has been deposited in the World-2DPAGE database (Database ID: 0044). In addition, comparative proteomic analysis revealed that proteins related to the TonB-dependent transportation system and energy metabolism are involved in the phenazine-1-carboxylic acid resistance in Xoo. In conclusion, we have established a proteome database for Xoo and have used this database in a comparative proteomic analysis that identified proteins potentially contributing to phenazine-1-carboxylic acid resistance in Xoo.