Erratum: Corrigendum: Genome sequencing in microfabricated high-density picolitre reactors

Margulies, Marcel; Egholm, Michael; Altman, William E.; Attiya, Said; Bader, Joel S.; Bemben, Lisa A.; Berka, Jan; Braverman, Michael; Chen, Yi–Ju; Chen, Zhoutao; Dewell, Scott; Winter, Alex de; Drake, James; Du, Lei; Fierro, Joseph; Forte, Robin; Gomes, Xavier V.; Godwin, Brian; He, Wen; Helgesen, Scott; Ho, Chun Heen; Hutchison, Stephen; Irzyk, Gerard P.; Jando, Szilveszter C.; Alenquer, Maria L. I.; Jarvie, Thomas; Jirage, Kshama B.; Kim, Jong Bum; Knight, James; Lanza, Janna R.; Leamon, John H.; Lee, William L.; Lefkowitz, Steven M.; Lei, Ming; Li, Jing; Lohman, Kenton L.; Liang, Hong; Makhijani, Vinod B.; McDade, Keith E.; McKenna, Michael; Myers, Eugene W.; Nickerson, Elizabeth; Nobile, John R.; Plant, Ramona; Puc, Bernard P.; Reifler, Michael; Ronan, M. T.; Roth, George T.; Sarkis, Gary J.; Simons, Jan Fredrik; Simpson, John; Srinivasan, Maithreyan; Tartaro, Karrie; Tomasz, Alexander; Vogt, Kari A.; Volkmer, Greg A.; Wang, Shally H.; Wang, Yong; Weiner, Michael P.; Willoughby, David A.; Yu, Pengguang; Begley, R. F.; Rothberg, Jonathan M.

doi:10.1038/nature04726

Cited by 33 publications

(9 citation statements)

References 1 publication

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…BAC DNA extractions, sequencing library generation, and sequencing were performed by Cogenics (Grenoble, France). BAC insert were sequenced by pyrosequencing using a Roche GS FLX Life Sciences instrument (Branford, CT, USA) [70,71]. The Newbler software (454 Life Sciences, Branford, CT, USA) was used to perform de novo assembly of the Roche GS FLX.…”

Section: Methodsmentioning

confidence: 99%

Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries

Paiva

Prat²,

Vautrin³

et al. 2011

BMC Genomics

View full text Add to dashboard Cite

BackgroundEucalyptus species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC) libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing.ResultsWe describe the construction and characterization of two deep-coverage BAC libraries EG_Ba and EG_Bb obtained from nuclear DNA fragments of E. grandis (clone BRASUZ1) digested with HindIII and BstYI, respectively. Genome coverages of 17 and 15 haploid genome equivalents were estimated for EG_Ba and EG_Bb, respectively. Both libraries contained large inserts, with average sizes ranging from 135 Kb (Eg_Bb) to 157 Kb (Eg_Ba), very low extra-nuclear genome contamination providing a probability of finding a single copy gene ≥ 99.99%. Libraries were screened for the presence of several genes of interest via hybridizations to high-density BAC filters followed by PCR validation. Five selected BAC clones were sequenced and assembled using the Roche GS FLX technology providing the whole sequence of the E. grandis chloroplast genome, and complete genomic sequences of important lignin biosynthesis genes.ConclusionsThe two E. grandis BAC libraries described in this study represent an important milestone for the advancement of Eucalyptus genomics and forest tree research. These BAC resources have a highly redundant genome coverage (> 15×), contain large average inserts and have a very low percentage of clones with organellar DNA or empty vectors. These publicly available BAC libraries are thus suitable for a broad range of applications in genetic and genomic research in Eucalyptus and possibly in related species of Myrtaceae, including genome sequencing, gene isolation, functional and comparative genomics. Because they have been constructed using the same tree (E. grandis BRASUZ1) whose full genome is being sequenced, they should prove instrumental for assembly and gap filling of the upcoming Eucalyptus reference genome sequence.

show abstract

Section: Methodsmentioning

confidence: 99%

Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries

Paiva

Prat²,

Vautrin³

et al. 2011

BMC Genomics

View full text Add to dashboard Cite

show abstract

“…Applied Biosystems, through the Life Technology subsidiary, introduced the SOLiD platform in 2007. The system employs a unique chemistry for sequencing by ligating oligonucleotide adapters to DNA fragments and immobilizing the ligation products on beads, which are then placed on a water-oil emulsion (116). The beads on which DNA amplification occurs are deposited on glass slides and subjected to sequential hybridization with a universal PCR primer complementary to the adapters.…”

Section: Deciphering Host-pathogen Interactions In the Era Of Ngs Tecmentioning

confidence: 99%

Exploring the Human Microbiome: The Potential Future Role of Next-Generation Sequencing in Disease Diagnosis and Treatment

et al. 2019

View full text Add to dashboard Cite

The interaction between the human microbiome and immune system has an effect on several human metabolic functions and impacts our well-being. Additionally, the interaction between humans and microbes can also play a key role in determining the wellness or disease status of the human body. Dysbiosis is related to a plethora of diseases, including skin, inflammatory, metabolic, and neurological disorders. A better understanding of the host-microbe interaction is essential for determining the diagnosis and appropriate treatment of these ailments. The significance of the microbiome on host health has led to the emergence of new therapeutic approaches focused on the prescribed manipulation of the host microbiome, either by removing harmful taxa or reinstating missing beneficial taxa and the functional roles they perform. Culturing large numbers of microbial taxa in the laboratory is problematic at best, if not impossible. Consequently, this makes it very difficult to comprehensively catalog the individual members comprising a specific microbiome, as well as understanding how microbial communities function and influence host-pathogen interactions. Recent advances in sequencing technologies and computational tools have allowed an increasing number of metagenomic studies to be performed. These studies have provided key insights into the human microbiome and a host of other microbial communities in other environments. In the present review, the role of the microbiome as a therapeutic agent and its significance in human health and disease is discussed. Advances in high-throughput sequencing technologies for surveying host-microbe interactions are also discussed. Additionally, the correlation between the composition of the microbiome and infectious diseases as described in previously reported studies is covered as well. Lastly, recent advances in state-of-the-art bioinformatics software, workflows, and applications for analysing metagenomic data are summarized.

show abstract

“…Briefly, NGS is accomplished by fragmentation of entire genome into small pieces so as to prepare a library. This is then followed by the random in vitro clonal amplification of these DNA fragments and, finally, by the sequencing of the immobilized DNA on a solid substrate using either: (i) pyro-sequencing on beads [68]; (ii) ion-sequencing (first "post-light sequencing" technology) [69]; (iii) ligation on beads (polony sequencing) [70]; or, (iv) synthesis on a glass substrate [71,72]. The principles underlying each of these technologies are shown in Figure 3.…”

Section: Next-generation Sequencing (2005-to Date)mentioning

confidence: 99%

Impact of Nucleic Acid Sequencing on Viroid Biology

Adkar-Purushothama¹,

Perreault²

2020

IJMS

View full text Add to dashboard Cite

The early 1970s marked two breakthroughs in the field of biology: (i) The development of nucleotide sequencing technology; and, (ii) the discovery of the viroids. The first DNA sequences were obtained by two-dimensional chromatography which was later replaced by sequencing using electrophoresis technique. The subsequent development of fluorescence-based sequencing method which made DNA sequencing not only easier, but many orders of magnitude faster. The knowledge of DNA sequences has become an indispensable tool for both basic and applied research. It has shed light biology of viroids, the highly structured, circular, single-stranded non-coding RNA molecules that infect numerous economically important plants. Our understanding of viroid molecular biology and biochemistry has been intimately associated with the evolution of nucleic acid sequencing technologies. With the development of the next-generation sequence method, viroid research exponentially progressed, notably in the areas of the molecular mechanisms of viroids and viroid diseases, viroid pathogenesis, viroid quasi-species, viroid adaptability, and viroid–host interactions, to name a few examples. In this review, the progress in the understanding of viroid biology in conjunction with the improvements in nucleotide sequencing technology is summarized. The future of viroid research with respect to the use of third-generation sequencing technology is also briefly envisaged.

show abstract

Erratum: Corrigendum: Genome sequencing in microfabricated high-density picolitre reactors

Cited by 33 publications

References 1 publication

Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries

Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries

Exploring the Human Microbiome: The Potential Future Role of Next-Generation Sequencing in Disease Diagnosis and Treatment

Impact of Nucleic Acid Sequencing on Viroid Biology

Contact Info

Product

Resources

About