共查询到20条相似文献,搜索用时 640 毫秒
1.
Advances in plant genome sequencing 总被引:1,自引:0,他引:1
2.
Meyer M Briggs AW Maricic T Höber B Höffner B Krause J Weihmann A Pääbo S Hofreiter M 《Nucleic acids research》2008,36(1):e5
Current efforts to recover the Neandertal and mammoth genomes by 454 DNA sequencing demonstrate the sensitivity of this technology. However, routine 454 sequencing applications still require microgram quantities of initial material. This is due to a lack of effective methods for quantifying 454 sequencing libraries, necessitating expensive and labour-intensive procedures when sequencing ancient DNA and other poor DNA samples. Here we report a 454 sequencing library quantification method based on quantitative PCR that effectively eliminates these limitations. We estimated both the molecule numbers and the fragment size distributions in sequencing libraries derived from Neandertal DNA extracts, SAGE ditags and bonobo genomic DNA, obtaining optimal sequencing yields without performing any titration runs. Using this method, 454 sequencing can routinely be performed from as little as 50 pg of initial material without titration runs, thereby drastically reducing costs while increasing the scope of sample throughput and protocol development on the 454 platform. The method should also apply to Illumina/Solexa and ABI/SOLiD sequencing, and should therefore help to widen the accessibility of all three platforms. 相似文献
3.
Next-generation DNA sequencing 总被引:17,自引:0,他引:17
4.
Schubert M Ginolhac A Lindgreen S Thompson JF Al-Rasheid KA Willerslev E Krogh A Orlando L 《BMC genomics》2012,13(1):178
ABSTRACT: BACKGROUND: Next-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species. However, the recovery of genetic material from long-dead organisms is still complicated by a number of issues, including post-mortem DNA damage and high levels of environmental contamination. Together with error profiles specific to the type of sequencing platforms used, these specificities could limit our ability to map sequencing reads against modern reference genomes and therefore limit our ability to identify endogenous ancient reads, reducing the efficiency of shotgun sequencing aDNA. RESULTS: In this study, we compare different computational methods for improving the accuracy and sensitivity of aDNA sequence identification, based on shotgun sequencing reads recovered from Pleistocene horse extracts using Illumina GAIIx and Helicos Heliscope platforms. We show that the performance of the Burrows Wheeler Aligner (BWA), that has been developed for mapping of undamaged sequencing reads using platforms with low rates of indel-types of sequencing errors, can be employed at acceptable run-times by modifying default parameters in a platform-specific manner. We also examine if trimming likely damaged positions at read ends can increase the recovery of genuine aDNA fragments and if accurate identification of human contamination can be achieved using a strategy previously suggested based on best hit filtering. We show that combining our different mapping and filtering approaches can increase the number of high-quality endogenous hits recovered by up to 33%. CONCLUSIONS: We have shown that Illumina and Helicos sequences recovered from aDNA extracts could not be aligned to modern reference genomes with the same efficiency unless mapping parameters are optimized for the specific types of errors generated by these platforms and by post-mortem DNA damage. Our findings have important implications for future aDNA research, as we define mapping guidelines that improve our ability to identify genuine aDNA sequences, which in turn could improve the genotyping accuracy of ancient specimens. Our framework provides a significant improvement to the standard procedures used for characterizing ancient genomes, which is challenged by contamination and often low amounts of DNA material. 相似文献
5.
Next generation sequencing based approaches to epigenomics 总被引:1,自引:0,他引:1
Next generation sequencing has brought epigenomic studies to the forefront of current research. The power of massively parallel sequencing coupled to innovative molecular and computational techniques has allowed researchers to profile the epigenome at resolutions that were unimaginable only a few years ago. With early proof of concept studies published, the field is now moving into the next phase where the importance of method standardization and rigorous quality control are becoming paramount. In this review we will describe methodologies that have been developed to profile the epigenome using next generation sequencing platforms. We will discuss these in terms of library preparation, sequence platforms and analysis techniques. 相似文献
6.
Genome sequencing efforts have provided a wealth of new biological information that promises to have a major impact on our understanding of parasites. Microarrays provide one of the major high-throughput platforms by which this information can be exploited in the laboratory. Many excellent reviews and technique articles have recently been published on applying microarrays to organisms for which fully annotated genomes are at hand. However, many parasitologists work on organisms whose genomes have been only partially sequenced and where little, if any, annotation is available. The focus of this review is on how to use and apply microarrays to these situations. 相似文献
7.
Meldrum C Doyle MA Tothill RW 《The Clinical biochemist. Reviews / Australian Association of Clinical Biochemists》2011,32(4):177-195
Next-generation sequencing (NGS) is arguably one of the most significant technological advances in the biological sciences of the last 30 years. The second generation sequencing platforms have advanced rapidly to the point that several genomes can now be sequenced simultaneously in a single instrument run in under two weeks. Targeted DNA enrichment methods allow even higher genome throughput at a reduced cost per sample. Medical research has embraced the technology and the cancer field is at the forefront of these efforts given the genetic aspects of the disease. World-wide efforts to catalogue mutations in multiple cancer types are underway and this is likely to lead to new discoveries that will be translated to new diagnostic, prognostic and therapeutic targets. NGS is now maturing to the point where it is being considered by many laboratories for routine diagnostic use. The sensitivity, speed and reduced cost per sample make it a highly attractive platform compared to other sequencing modalities. Moreover, as we identify more genetic determinants of cancer there is a greater need to adopt multi-gene assays that can quickly and reliably sequence complete genes from individual patient samples. Whilst widespread and routine use of whole genome sequencing is likely to be a few years away, there are immediate opportunities to implement NGS for clinical use. Here we review the technology, methods and applications that can be immediately considered and some of the challenges that lie ahead. 相似文献
8.
9.
The recent technological advances in next generation sequencing have brought the field closer to the goal of reconstructing all genomes within a community by presenting high throughput sequencing at much lower costs. While these next-generation sequencing technologies have allowed a massive increase in available raw sequence data, there are a number of new informatics challenges and difficulties that must be addressed to improve the current state, and fulfill the promise of, metagenomics. 相似文献
10.
Cristina Gamba Kristian Hanghøj Charleen Gaunitz Ahmed H. Alfarhan Saleh A. Alquraishi Khaled A. S. Al‐Rasheid DANIEL G. Bradley Ludovic Orlando 《Molecular ecology resources》2016,16(2):459-469
The DNA molecules that can be extracted from archaeological and palaeontological remains are often degraded and massively contaminated with environmental microbial material. This reduces the efficacy of shotgun approaches for sequencing ancient genomes, despite the decreasing sequencing costs of high‐throughput sequencing (HTS). Improving the recovery of endogenous molecules from the DNA extraction and purification steps could, thus, help advance the characterization of ancient genomes. Here, we apply the three most commonly used DNA extraction methods to five ancient bone samples spanning a ~30 thousand year temporal range and originating from a diversity of environments, from South America to Alaska. We show that methods based on the purification of DNA fragments using silica columns are more advantageous than in solution methods and increase not only the total amount of DNA molecules retrieved but also the relative importance of endogenous DNA fragments and their molecular diversity. Therefore, these methods provide a cost‐effective solution for downstream applications, including DNA sequencing on HTS platforms. 相似文献
11.
Jaroslav Doležel Jan Vrána Petr Cápal Marie Kubaláková Veronika Burešová Hana Šimková 《Biotechnology advances》2014
Next generation sequencing (NGS) is revolutionizing genomics and is providing novel insights into genome organization, evolution and function. The number of plant genomes targeted for sequencing is rising. For the moment, however, the acquisition of full genome sequences in large genome species remains difficult, largely because the short reads produced by NGS platforms are inadequate to cope with repeat-rich DNA, which forms a large part of these genomes. The problem of sequence redundancy is compounded in polyploids, which dominate the plant kingdom. An approach to overcoming some of these difficulties is to reduce the full nuclear genome to its individual chromosomes using flow-sorting. The DNA acquired in this way has proven to be suitable for many applications, including PCR-based physical mapping, in situ hybridization, forming DNA arrays, the development of DNA markers, the construction of BAC libraries and positional cloning. Coupling chromosome sorting with NGS offers opportunities for the study of genome organization at the single chromosomal level, for comparative analyses between related species and for the validation of whole genome assemblies. Apart from the primary aim of reducing the complexity of the template, taking a chromosome-based approach enables independent teams to work in parallel, each tasked with the analysis of a different chromosome(s). Given that the number of plant species tractable for chromosome sorting is increasing, the likelihood is that chromosome genomics – the marriage of cytology and genomics – will make a significant contribution to the field of plant genetics. 相似文献
12.
Next-generation sequencing of vertebrate experimental organisms 总被引:1,自引:0,他引:1
13.
Dr. P. Krawitz Dipl.-Phys. 《Medizinische Genetik》2010,22(2):248-253
Recent advances in sequencing technology have reduced the costs and time required to decode a single genome to the extent that complete sequencing of personal genomes becomes affordable for both private individuals and the health care system. The broad availability of individual genomes will drive medicine further towards an information-based science and the importance of IT solutions in medicine will increase. 相似文献
14.
DNA methylation plays a key role in epigenetic regulation of eukaryotic genomes. Hence the genome-wide distribution of 5-methylcytosine, or the methylome, has been attracting intense attention. In recent years, whole-genome bisulfite sequencing (WGBS) has enabled methylome analysis at single-base resolution. However, WGBS typically requires microgram quantities of DNA as well as global PCR amplification, thereby precluding its application to samples of limited amounts. This is presumably because bisulfite treatment of adaptor-tagged templates, which is inherent to current WGBS methods, leads to substantial DNA fragmentation. To circumvent the bisulfite-induced loss of intact sequencing templates, we conceived an alternative method termed Post-Bisulfite Adaptor Tagging (PBAT) wherein bisulfite treatment precedes adaptor tagging by two rounds of random primer extension. The PBAT method can generate a substantial number of unamplified reads from as little as subnanogram quantities of DNA. It requires only 100 ng of DNA for amplification-free WGBS of mammalian genomes. Thus, the PBAT method will enable various novel applications that would not otherwise be possible, thereby contributing to the rapidly growing field of epigenomics. 相似文献
15.
在分子生物学、细胞生物学、微生物学、遗传学等学科的推动下, 生物多样性研究从仅关注宏观表型的博物学, 迅速演化为涵盖生态系统、物种和遗传多样性等多个维度的综合性生命科学。组学技术, 尤其是DNA测序技术的更新和发展, 使获取DNA序列所需的成本大幅下降, 促进了近年来其在生物多样性研究中取得的一系列令人瞩目成就。本文将从物种水平的遗传多样性和群落水平的物种多样性两个层面总结和介绍与DNA相关的组学技术在生物多样性研究中的一些创新和应用。其中, 物种水平主要是总结单一个体的基因组和单物种多个体在时空多个维度上的群体遗传研究; 而群落水平的物种多样性层面主要总结现有的分子鉴定技术(metabarcoding, eDNA, iDNA等), 以及上述新技术在群落多样性评估、旗舰保护物种监测以及物种间相互作用关系等研究中的应用。 相似文献
16.
RADSeq: next-generation population genetics 总被引:2,自引:0,他引:2
Next-generation sequencing technologies are making a substantial impact on many areas of biology, including the analysis of genetic diversity in populations. However, genome-scale population genetic studies have been accessible only to well-funded model systems. Restriction-site associated DNA sequencing, a method that samples at reduced complexity across target genomes, promises to deliver high resolution population genomic data-thousands of sequenced markers across many individuals-for any organism at reasonable costs. It has found application in wild populations and non-traditional study species, and promises to become an important technology for ecological population genomics. 相似文献
17.
复杂基因组测序技术研究进展 总被引:1,自引:0,他引:1
复杂基因组指的是无法使用常规测序和组装手段直接解析的一类基因组,通常指包含高比例重复序列、高杂合度、极端GC含量、存在难消除异源DNA污染的基因组。为了解决复杂基因组的测序和组装问题,需要分别从基因组测序实验方法、测序技术平台、组装算法与策略3个方面进行深入研究。本文详细介绍了复杂基因组测序组装相关的现有技术与方法,并结合复杂基因组经典实例介绍了复杂基因组测序的技术解决途径和发展历程,可为制订合适的复杂基因组测序策略提供参考。 相似文献
18.
The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human
and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers
based on the Sanger method. With the ongoing developments of high throughput sequencing machines and advancement of modern
bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost
of $1,000 each is seemed to be realistically feasible in the near future. In the relatively short time frame since 2005, the
HT-NGS technologies are revolutionizing the human and animal genome researches by analysis of chromatin immunoprecipitation
coupled to DNA microarray (ChIP-chip) or sequencing (ChIP-seq), RNA sequencing (RNA-seq), whole genome genotyping, genome
wide structural variation, de novo assembling and re-assembling of genome, mutation detection and carrier screening, detection
of inherited disorders and complex human diseases, DNA library preparation, paired ends and genomic captures, sequencing of
mitochondrial genome and personal genomics. In this review, we addressed the important features of HT-NGS like, first generation
DNA sequencers, birth of HT-NGS, second generation HT-NGS platforms, third generation HT-NGS platforms: including single molecule
Heliscope™, SMRT™ and RNAP sequencers, Nanopore, Archon Genomics X PRIZE foundation, comparison of second and third HT-NGS
platforms, applications, advances and future perspectives of sequencing technologies on human and animal genome research. 相似文献
19.
The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation 总被引:1,自引:0,他引:1
Konstantinos Mavromatis Miriam L. Land Thomas S. Brettin Daniel J. Quest Alex Copeland Alicia Clum Lynne Goodwin Tanja Woyke Alla Lapidus Hans Peter Klenk Robert W. Cottingham Nikos C. Kyrpides 《PloS one》2012,7(12)