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Numerical characterization of DNA sequence based on dinucleotides.

ABSTRACT: Sequence comparison is a primary technique for the analysis of DNA sequences. In order to make quantitative comparisons, one devises mathematical descriptors that capture the essence of the base composition and distribution of the sequence. Alignment methods and graphical techniques (where each sequence is represented by a curve in high-dimension Euclidean space) have been used popularly for a long time. In this contribution we will introduce a new nongraphical and nonalignment approach based on the frequencies of the dinucleotide XY in DNA sequences. The most important feature of this method is that it not only identifies adjacent XY pairs but also nonadjacent XY ones where X and Y are separated by some number of nucleotides. This methodology preserves information in DNA sequence that is ignored by other methods. We test our method on the coding regions of exon-1 of ?-globin for 11 species, and the utility of this new method is demonstrated.

SUBMITTER: Qi X

PROVIDER: S-EPMC3349307 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Numerical characterization of DNA sequence based on dinucleotides.

Qi Xingqin X Fuller Edgar E Wu Qin Q Zhang Cun-Quan CQ

TheScientificWorldJournal 20120424

Sequence comparison is a primary technique for the analysis of DNA sequences. In order to make quantitative comparisons, one devises mathematical descriptors that capture the essence of the base composition and distribution of the sequence. Alignment methods and graphical techniques (where each sequence is represented by a curve in high-dimension Euclidean space) have been used popularly for a long time. In this contribution we will introduce a new nongraphical and nonalignment approach based on ...[more]

PMID: 22619571

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Project description:The bacterial communities associated with microalgae are vital for the growth and health of the host, and engineering algal microbiomes can enhance the fitness of the algae. Characterization of these microbiomes mostly relies on sequencing of DNA, which can be extracted with an array of protocols that potentially impact DNA quantity and quality and thus potentially affect subsequent analyses of microbiome composition. Here, we extracted DNA from Isochrysis galbana, Tetraselmis suecica, and Conticribra weissflogii microbiomes using four different protocols. DNA yield and quality was greatly impacted by the choice of extraction protocol, whereas microbiome composition determined by 16S rRNA gene amplicon sequencing was only impacted to a minor degree, with microalgal host species being the main determinant of microbiome composition. The I. galbana microbiome was dominated by the genus Alteromonas, whereas the microbiome associated with T. suecica was dominated by Marinobacteraceae and Rhodobacteraceae family members. While these two families were also prevalent in the microbiome associated with C. weissflogii, Flavobacteriaceae and Cryomorphaceae were also highly dominant. Phenol-chloroform extraction resulted in higher DNA quality and quantity compared to commercial kits; however, because they have other advantages such as high throughput and low toxicity, commercial kits can be employed to great benefit for the characterization of microalgal microbiomes. IMPORTANCE Microalgae are very important as primary producers in the ocean, but also as forthcoming sustainable producers of biotechnologically interesting compounds. Accordingly, the bacterial microbiomes associated with microalgae are attracting increasing attention due to their effects on the growth and health of microalgae. Since most members of these microbiomes cannot be cultured, knowledge about community composition is best obtained using sequencing-based methods. This study evaluates the impact of DNA extraction methods on DNA quantity and quality along with sequence-based characterization of the bacterial microbiome composition of three microalgae: Isochrysis galbana, Tetraselmis suecica, and Conticribra weissflogii.

Dataset Information

Numerical characterization of DNA sequence based on dinucleotides.

Publications

Numerical characterization of DNA sequence based on dinucleotides.

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