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采用高通量测序-分子鉴定分级技术于2019年对长山群岛全海域真核微藻粒级结构进行了研究。结果发现,春季以中（47%）、小粒级（41%）为主,夏季以小（39%）、大粒级（38%）为主,秋季以大粒级（60%）为主,春、夏、秋季小、中、大粒级微藻比例为42：47：11、39：23：38、22：18：60。小粒级微藻优势种为细小微胞藻（Micromonas pusilla）、融合微胞藻（Micromonas commoda）和金牛微球藻（Ostreococcus tauri）,中粒级微藻优势种为剧毒卡尔藻（Karlodinium veneficum）、大粒级微藻优势种为柔弱几内亚藻（Guinardia delicatula）、平野亚历山大藻（Alexandrium hiranoi）、多纹膝沟藻（Gonyaulax polygramma）,综合整个真核微藻群落,春季由中粒径的剧毒卡尔藻占据优势（23.9%）,夏季由大粒径的平野亚历山大藻占据优势（29.4%）,秋季由大粒径的多纹膝沟藻占据优势（66.8%）,有毒甲藻在该海域中占有绝对优势,贝毒累积风险较高,小粒径微藻中金牛微球藻和抑食金球藻曾在渤海引发褐潮,潜在威胁该海域贝类养殖业。虾夷扇贝对小粒级和大粒级微藻的选择性较低,对中粒级微藻的选择性较高,尤其对水体中优势种剧毒卡尔藻一直表现出主动选择。光学需氧量、无机氮、溶解氧、石油类及部分重金属Cd、As、Hg影响着整个长山群岛海域真核微藻粒级结构时空演变。 相似文献
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研究藻华水体中浮游植物群落对除藻剂的响应,可为在实际应用中选择合适的除藻剂提供理论依据。近年来,高通量测序技术已逐步用于表征藻类群落结构,然而它无法区分群落中的“死亡”和“存活”个体。本研究利用经叠氮溴化丙锭(PMA)前处理和未经PMA前处理的高通量测序技术,探究Ca(ClO)2、CuSO4和一种市售生物除藻剂对某一存在藻华的景观水体中藻类群落组成、多样性和标志物种的影响。结果显示,3种除藻剂均能有效降低水样的藻密度;初始水样中绿藻门的单针藻属(Monoraphidium)相对丰度最大(74.34%),是造成藻华的优势藻;与非PMA处理组相比,经PMA处理后的测序结果更能体现不同除藻剂处理后活藻群落组成和多样性差异：在除藻剂作用下,绿藻门相对丰度下降至1.50%-24.61%,蓝藻门优势种Leptolyngbya boryana相对丰度上升至27.85%-41.52%;50 mg/L生物除藻剂能显著提升群落的Chao1指数、observed species指数、Pielou’s evenness指数和Shannon指数,增加了群落的多样性、均... 相似文献
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蛋白核（pyrenoid）作为真核藻类重要的、相对独立的固碳结构,在CO2高效浓缩和固定过程中发挥中重要作用,可为开发高效生物固碳技术提供理论支持。染色法是快速观察蛋白核的最佳方法之一,有助于深入研究蛋白核的结构和功能,但目前对染色法仍缺乏系统研究。本文以较易染色的莱茵衣藻（Chlamydomonas reinhardtii）和较难染色的斜生栅藻（Scenedesmus obliquus）为材料,探讨了碘染和溴酚蓝（BPB）染色观察蛋白核的方法。结果表明,碘染法最适用于蛋白核外周淀粉观察,最适染色液浓度和时间分别是0．1％～0．2％（w／v）和5min。热激预处理和溴酚蓝染色相结合的蛋白核染色效果更好,优化条件为：70℃水浴热激40s,0．05％（w／v）BPB染色15min。本方法为研究微藻蛋白核提供了一种快速有效的直接观察方法。 相似文献
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微生物对外界环境变化较为敏感,常被作为指示生物用于监测和反映水质情况。为满足延庆世园会和冬奥会举办对妫水河水质的调控要求,探讨妫水河底泥微生物群落结构特征及环境因子对其分布的影响。基于妫水河12个不同断面的水样和底泥样品,进行了水质、底泥理化性质分析,并对底泥的微生物群落结构特征进行了研究。结果表明,妫水河中、下游水体水质COD、NH~+_4-N、TN超标,其中上覆水TN含量与底泥TN含量呈极显著正相关(P=0.914);MiSeq高通量测序发现,妫水河底泥微生物共检出70门228纲1168属,变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)、酸杆菌门(Acidobacteria)、放线菌门(Actinobacteria)、绿弯菌门(Chloroflexi)、厚壁菌门(Firmicutes)、蓝细菌门(Cyanobacteria)、绿菌门(Chlorobi)、疣微菌门(Verrucomicrobia)和硝化螺旋菌门(Nitrospirae)是妫水河底泥微生物群落结构中的主要菌门,在各个样品中相对丰度之和均占84%以上,其中变形菌门为第一优势门,占比达到45.3%—69.1%,而不同断面样品的优势菌属有所不同。妫水河底泥微生物群落丰度总体较高,多样性也相对较高,其中世园段D7点Ace丰富度指数和Shannon多样性指数均较其他点位低,分别为2673和6.56。RDA(redundancy analysis)分析表明,底泥氨氮和温度是影响其微生物群落结构的主要因子(F=2.92,P=0.038;F=2.81,P=0.014),妫水河底泥的优势反硝化菌属为脱氮单孢菌属和硫杆状菌属,其丰度与NH~+_4-N、水温呈正相关,同时与DO呈负相关。研究结果对妫水河水生态环境保护和水质管理提供数据支撑及理论指导意义。 相似文献
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为探究海州湾浅海域的细菌群落结构多样性及其影响因素,选取海州湾6个点位的表层水和底层水样品,基于高通量测序技术,对海州湾浅海域细菌群落结构多样性及其分布特征与环境因子的关系进行了分析。实验结果表明,底层水样的细菌群落丰度和多样性优于表层水样,二者细菌群落间的进化方向具有一定的差异,但二者的细菌群落间差异不显著;海州湾水域共发现2 491个操作分类单元(operational taxonomic unit,OTU),分别属于32个门、74个纲、116个目、200个科和364个属;在门水平上,海州湾水域的主要优势菌群为变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)和蓝细菌门(Cyanobacteria)等;铵盐(ammonium, NH4-N)和叶绿素(chlorophyll, Chl)是影响海州湾细菌群落结构的主要环境因子。本研究证实海州湾浅海域细菌群落结构多样性分布与环境因子有一定的关联性,为海州湾浅海域生态系统的可持续发展提供了理论依据。 相似文献
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染色体外环状DNA (extrachromosomal circular DNA, eccDNA)是一种真核生物染色体外的闭合环状DNA结构,长度和染色体起源具有较高异质性。ecc DNA这一名称目前主要指大小在数百kb以内的小分子染色体外环状DNA,包括micro DNA、小多分散环状DNA (small polydispersed circular DNA, spcDNA)以及其他未分类的小分子eccDNA等。高通量测序技术(high-throughput sequencing, HTS)是一种可以同时对百万条DNA分子进行序列测定的技术,又名新一代测序技术(next generation sequencing, NGS),具有高通量、高灵敏度、高准确度等优势。近年来高通量测序结合生物信息学分析技术不仅在揭示eccDNA染色体起源、分子结构、发生机制和潜在功能以及循环系统中的eccDNA分子特征研究等方面发挥了重要作用,而且推动了eccDNA在甲基化等表观遗传学方面的研究。生物信息学软件的发展和eccDNA分析算法的开发也对其研究提供了重要帮助。血浆以及尿液等液体活检常用体液样本中... 相似文献
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细胞DNA的完整性受到不同因素的影响,可分为内源性及外源性因素,这些因素均可引起不同程度的DNA损伤.其中,DNA双链断裂是最严重的一种DNA损伤,若未能进行及时的修复,则会引起一系列的损伤反应.严重的DNA双链断裂甚至可以造成细胞凋亡、肿瘤的发生等严重后果.因此,快速并准确地检测细胞DNA双链断裂程度能帮助评估DNA... 相似文献
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DNA microarray and next-generation DNA sequencing technologies are important tools for high-throughput genome research, in revealing both the structural and functional characteristics of genomes. In the past decade the DNA microarray technologies have been widely applied in the studies of functional genomics, systems biology and pharmacogenomics. The next-generation DNA sequencing method was first introduced by the 454 Company in 2003, immediately followed by the establishment of the Solexa and Solid techniques by other biotech companies. Though it has not been long since the first emergence of this technology, with the fast and impressive improvement, the application of this technology has extended to almost all fields of genomics research, as a rival challenging the existing DNA microarray technology. This paper briefly reviews the working principles of these two technologies as well as their application and perspectives in genome research. Supported by the National High-Tech Research Program of China (Grant No.2006AA020704) and Shanghai Science and Technology Commission (Grant No. 05DZ22201) 相似文献
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Clio Der Sarkissian Morten E. Allentoft María C. ávila-Arcos Ross Barnett Paula F. Campos Enrico Cappellini Luca Ermini Ruth Fernández Rute da Fonseca Aurélien Ginolhac Anders J. Hansen Hákon Jónsson Thorfinn Korneliussen Ashot Margaryan Michael D. Martin J. Víctor Moreno-Mayar Maanasa Raghavan Morten Rasmussen Marcela Sandoval Velasco Hannes Schroeder Mikkel Schubert Andaine Seguin-Orlando Nathan Wales M. Thomas P. Gilbert Eske Willerslev Ludovic Orlando 《Philosophical transactions of the Royal Society of London. Series B, Biological sciences》2015,370(1660)
The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field''s focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past. 相似文献
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Shin-ichiro Takebayashi Shin Ogata Masato Ogata Katsuzumi Okumura 《Bioscience, biotechnology, and biochemistry》2013,77(12):2098-2100
ABSTRACTHere, we show that semiconductor-based sequencing technology can be used to map mammalian replication domains, chromosomal units with similar DNA replication timing. Replicating DNA purified from mammalian cells was successfully sequenced by the Ion Torrent platform. The resultant replication domain map of mouse embryonic stem cells is comparable to those obtained by the conventional microarray-based method. 相似文献
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Katherine D. Balasingham Ryan P. Walter Nicholas E. Mandrak Daniel D. Heath 《Molecular ecology》2018,27(1):112-127
The extraction and characterization of DNA from aquatic environmental samples offers an alternative, noninvasive approach for the detection of rare species. Environmental DNA, coupled with PCR and next‐generation sequencing (“metabarcoding”), has proven to be very sensitive for the detection of rare aquatic species. Our study used a custom‐designed group‐specific primer set and next‐generation sequencing for the detection of three species at risk (Eastern Sand Darter, Ammocrypta pellucida; Northern Madtom, Noturus stigmosus; and Silver Shiner, Notropis photogenis), one invasive species (Round Goby, Neogobius melanostomus) and an additional 78 native species from two large Great Lakes tributary rivers in southern Ontario, Canada: the Grand River and the Sydenham River. Of 82 fish species detected in both rivers using capture‐based and eDNA methods, our eDNA method detected 86.2% and 72.0% of the fish species in the Grand River and the Sydenham River, respectively, which included our four target species. Our analyses also identified significant positive and negative species co‐occurrence patterns between our target species and other identified species. Our results demonstrate that eDNA metabarcoding that targets the fish community as well as individual species of interest provides a better understanding of factors affecting the target species spatial distribution in an ecosystem than possible with only target species data. Additionally, eDNA is easily implemented as an initial survey tool, or alongside capture‐based methods, for improved mapping of species distribution patterns. 相似文献
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ZHOU XiaoGuang REN LuFeng LI YunTao ZHANG Meng YU YuDe & YU Jun Key Laboratory of Genome Sciences Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing China 《中国科学：生命科学英文版》2010,(1)
As one of the most powerful tools in biomedical research,DNA sequencing not only has been improving its productivity at an exponential growth rate but has also been evolving into a new layout of technological territories toward engineering and physical disciplines over the past three decades.In this technical review,we look into technical characteristics of the next-generation sequencers and provide insights into their future development and applications.We envisage that some of the emerging platforms are c... 相似文献
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Sean W. J. Prosser Jeremy R. deWaard Scott E. Miller Paul D. N. Hebert 《Molecular ecology resources》2016,16(2):487-497
Type specimens have high scientific importance because they provide the only certain connection between the application of a Linnean name and a physical specimen. Many other individuals may have been identified as a particular species, but their linkage to the taxon concept is inferential. Because type specimens are often more than a century old and have experienced conditions unfavourable for DNA preservation, success in sequence recovery has been uncertain. This study addresses this challenge by employing next‐generation sequencing (NGS) to recover sequences for the barcode region of the cytochrome c oxidase 1 gene from small amounts of template DNA. DNA quality was first screened in more than 1800 century‐old type specimens of Lepidoptera by attempting to recover 164‐bp and 94‐bp reads via Sanger sequencing. This analysis permitted the assignment of each specimen to one of three DNA quality categories – high (164‐bp sequence), medium (94‐bp sequence) or low (no sequence). Ten specimens from each category were subsequently analysed via a PCR‐based NGS protocol requiring very little template DNA. It recovered sequence information from all specimens with average read lengths ranging from 458 bp to 610 bp for the three DNA categories. By sequencing ten specimens in each NGS run, costs were similar to Sanger analysis. Future increases in the number of specimens processed in each run promise substantial reductions in cost, making it possible to anticipate a future where barcode sequences are available from most type specimens. 相似文献
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Tom Oosting Elena Hilario Maren Wellenreuther Peter A. Ritchie 《Ecology and evolution》2020,10(16):8643-8651
The more demanding requirements of DNA preservation for genomic research can be difficult to meet when field conditions limit the methodological approaches that can be used or cause samples to be stored in suboptimal conditions. Such limitations may increase rates of DNA degradation, potentially rendering samples unusable for applications such as genome‐wide sequencing. Nonetheless, little is known about the impact of suboptimal sampling conditions. We evaluated the performance of two widely used preservation solutions (1. DESS: 20% DMSO, 0.25 M EDTA, NaCl saturated solution, and 2. Ethanol >99.5%) under a range of storage conditions over a three‐month period (sampling at 1 day, 1 week, 2 weeks, 1 month, and 3 months) to provide practical guidelines for DNA preservation. DNA degradation was quantified as the reduction in average DNA fragment size over time (DNA fragmentation) because the size distribution of DNA segments plays a key role in generating genomic datasets. Tissues were collected from a marine teleost species, the Australasian snapper, Chrysophrys auratus. We found that the storage solution has a strong effect on DNA preservation. In DESS, DNA was only moderately degraded after three months of storage while DNA stored in ethanol showed high levels of DNA degradation already within 24 hr, making samples unsuitable for next‐generation sequencing. Here, we conclude that DESS was the most promising solution when storing samples for genomic applications. We recognize that the best preservation protocol is highly dependent on the organism, tissue type, and study design. We highly recommend performing similar experiments before beginning a study. This study highlights the importance of testing sample preservation protocols and provides both practical and economical advice to improve DNA preservation when sampling for genome‐wide applications. 相似文献
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Stoeckeria algicida为甲藻纲胸甲球藻科,有侵噬鱼类细胞杀鱼的能力,可导致鱼类成群死亡,同时也会杀死其他海洋微藻。由于该藻个体微小、形态学鉴定困难,研究较为迟缓,我国海域几乎没有该藻的研究报道。近几年,高通量测序技术的发展极大地推动了微型/微微型浮游植物的鉴定研究,为了解我国辽东湾海域是否存在Stoeckeria algicida及其分布情况,以18S rD NA V4区作为目标基因,结合高通量测序技术,专门设计了微型/微微型浮游植物鉴定引物对V4(F/R),随后对辽东湾2014年四季海水中微型和微微型浮游植物多样性进行了检测。结果发现,Stoeckeria algicida除了春季未检出外,其他季节均有检出,温度是影响该藻繁殖的主要因素。虽然Stoeckeria algicida在整个环境样品中优势度不太明显,但其夏季密度较高(最高达2.753×10~3个/L),高值区主要分布在辽东湾东西两岸,致灾风险较高,应引起有关方面足够重视。Stoeckeria algicida在我国海域首次报道,其危害后果严峻,必须加强监测监管。 相似文献
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Wendy Wang Wei X. Tan Denis Bertrand Amanda H. Q. Ng Esther J. H. Boey Jayce J. Y. Koh Niranjan Nagarajan Rudolf Meier 《Molecular ecology resources》2018,18(5):1035-1049
DNA barcodes are useful for species discovery and species identification, but obtaining barcodes currently requires a well‐equipped molecular laboratory and is time‐consuming, and/or expensive. We here address these issues by developing a barcoding pipeline for Oxford Nanopore MinION? and demonstrating that one flow cell can generate barcodes for ~500 specimens despite the high basecall error rates of MinION? reads. The pipeline overcomes these errors by first summarizing all reads for the same tagged amplicon as a consensus barcode. Consensus barcodes are overall mismatch‐free but retain indel errors that are concentrated in homopolymeric regions. They are addressed with an optional error correction pipeline that is based on conserved amino acid motifs from publicly available barcodes. The effectiveness of this pipeline is documented by analysing reads from three MinION? runs that represent three different stages of MinION? development. They generated data for (i) 511 specimens of a mixed Diptera sample, (ii) 575 specimens of ants and (iii) 50 specimens of Chironomidae. The run based on the latest chemistry yielded MinION? barcodes for 490 of the 511 specimens which were assessed against reference Sanger barcodes (N = 471). Overall, the MinION? barcodes have an accuracy of 99.3%–100% with the number of ambiguous bases after correction ranging from <0.01% to 1.5% depending on which correction pipeline is used. We demonstrate that it requires ~2 hr of sequencing to gather all information needed for obtaining reliable barcodes for most specimens (>90%). We estimate that up to 1,000 barcodes can be generated in one flow cell and that the cost per barcode can be 相似文献