Large Scale Sequencing and Analysis of AT Rich Eukaryote Genomes

Glöckner, Gernot

doi:10.2174/1389202003351472

Cited by 13 publications

(9 citation statements)

References 77 publications

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“…To avoid contamination with bacterial DNA, which would be preferentially cloned (Glöckner 2000), PP PN500 was grown in axenic medium, and DF SH3, which cannot grow axenically, was harvested from bacterial growth plates well after the plates had cleared, and starved for another 6 h, while shaking in phosphate buffer. Plasmid (pUC)-based sequencing libraries were constructed as previously described (Glöckner et al 2002).…”

Section: Sequencing and Assemblymentioning

confidence: 99%

Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication

Heidel¹,

Lawal²,

Felder³

et al. 2011

Genome Res.

150

161

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Dictyostelium discoideum (DD), an extensively studied model organism for cell and developmental biology, belongs to the most derived group 4 of social amoebas, a clade of altruistic multicellular organisms. To understand genome evolution over long time periods and the genetic basis of social evolution, we sequenced the genomes of Dictyostelium fasciculatum (DF ) and Polysphondylium pallidum (PP), which represent the early diverging groups 1 and 2, respectively. In contrast to DD, PP and DF have conventional telomere organization and strongly reduced numbers of transposable elements. The number of proteincoding genes is similar between species, but only half of them comprise an identifiable set of orthologous genes. In general, genes involved in primary metabolism, cytoskeletal functions and signal transduction are conserved, while genes involved in secondary metabolism, export, and signal perception underwent large differential gene family expansions. This most likely signifies involvement of the conserved set in core cell and developmental mechanisms, and of the diverged set in niche-and species-specific adaptations for defense and food, mate, and kin selection. Phylogenetic dating using a concatenated data set and extensive loss of synteny indicate that DF, PP, and DD split from their last common ancestor at least 0.6 billion years ago.[Supplemental material is available for this article.]The central and most fascinating problem in biology is how natural selection has acted on random changes in the genomes of individuals to generate the immense range and complexity of extinct and extant living forms. However, understanding the relationship between genotypic and phenotypic change on a genomewide scale is complicated by the large number of loci involved and the range of phenotypic change. Comparative genomics is the tool of choice to define common gene sets and the first occurrence of genetic changes that may have caused phenotypic innovation. Genetic manipulation of altered genes can then reveal whether the genomic change was causal to the phenotypic alteration.The social amoeba Dictyostelium discoideum (DD) is a widely used model system for studying a range of problems in cell and developmental biology and more recently the evolution of social behavior and multicellularity.

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Section: Sequencing and Assemblymentioning

confidence: 99%

Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication

Heidel¹,

Lawal²,

Felder³

et al. 2011

Genome Res.

150

161

View full text Add to dashboard Cite

show abstract

“…A rigorous performance test demands the examination of amplicons with varied GC content and with substantial genetic divergence to reveal error biases dependent on sequence context [ 16 ]. For example, long homopolymer runs are a challenge for Sanger sequencing [ 17 , 18 ], while Illumina platforms are subject to GC bias [ 16 ]. Specimens employed to create DNA barcode reference libraries provide an ideal test system as Sanger reference sequences are available for a 648 bp region of the mitochondrial cytochrome c oxidase I (COI) gene from more than 500,000 species [ 19 ].…”

Section: Introductionmentioning

confidence: 99%

A Sequel to Sanger: amplicon sequencing that scales

et al. 2018

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BackgroundAlthough high-throughput sequencers (HTS) have largely displaced their Sanger counterparts, the short read lengths and high error rates of most platforms constrain their utility for amplicon sequencing. The present study tests the capacity of single molecule, real-time (SMRT) sequencing implemented on the SEQUEL platform to overcome these limitations, employing 658 bp amplicons of the mitochondrial cytochrome c oxidase I gene as a model system.ResultsBy examining templates from more than 5000 species and 20,000 specimens, the performance of SMRT sequencing was tested with amplicons showing wide variation in GC composition and varied sequence attributes. SMRT and Sanger sequences were very similar, but SMRT sequencing provided more complete coverage, especially for amplicons with homopolymer tracts. Because it can characterize amplicon pools from 10,000 DNA extracts in a single run, the SEQUEL can reduce greatly reduce sequencing costs in comparison to first (Sanger) and second generation platforms (Illumina, Ion).ConclusionsSMRT analysis generates high-fidelity sequences from amplicons with varying GC content and is resilient to homopolymer tracts. Analytical costs are low, substantially less than those for first or second generation sequencers. When implemented on the SEQUEL platform, SMRT analysis enables massive amplicon characterization because each instrument can recover sequences from more than 5 million DNA extracts a year.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4611-3) contains supplementary material, which is available to authorized users.

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“…In yeast it has been found (3) that poly(dA-dT) stretches are regularly present in nucleosome-free regions where they probably play a structural role. In the case of lower organisms, some genomes have a very high AT content (4). The social ameba Dictyostelium discoideum, for example, has 78% AT content.…”

Section: Introductionmentioning

confidence: 99%

Overview of the Structure of All-AT Oligonucleotides: Organization in Helices and Packing Interactions

Campos

Valls

Urpí

et al. 2006

Biophysical Journal

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We present the crystalline organization of 33 all-AT deoxyoligonucleotide duplexes, studied by x-ray diffraction. Most of them have very similar structures, with Watson-Crick basepairs and a standard average twist close to 36 degrees. The molecules are organized as parallel columns of stacked duplexes in a helical arrangement. Such organization of duplexes is very regular and repetitive: all sequences show the same pattern. It is mainly determined by the stacking of the terminal basepairs, so that the twist in the virtual TA base step between neighbor duplexes is always negative, approximately -22 degrees. The distance between the axes of parallel columns is practically identical in all cases, approximately 26 A. Interestingly, it coincides with that found in DNA viruses and fibers in their hexagonal phase. It appears to be a characteristic distance for ordered parallel DNA molecules. This feature is due to the absence of short range intermolecular forces, which are usually due to the presence of CG basepairs at the end of the oligonucleotide sequence. The duplexes apparently interact only through their diffuse ionic atmospheres. The results obtained can thus be considered as intermediate between liquid crystals, fibers, and standard crystal structures. They provide new information on medium range DNA-DNA interactions.

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Large Scale Sequencing and Analysis of AT Rich Eukaryote Genomes

Cited by 13 publications

References 77 publications

Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication

Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication

A Sequel to Sanger: amplicon sequencing that scales

Overview of the Structure of All-AT Oligonucleotides: Organization in Helices and Packing Interactions

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