Genomic Signature in Evolutionary Biology: A Review

Abstract

Organisms are unique physical entities in which information is stored and continuously processed. The digital nature of DNA sequences enables the construction of a dynamic information reservoir. However, the distinction between the hardware and software components in the information flow is crucial to identify the mechanisms generating specific genomic signatures. In this work, we perform a bibliometric analysis to identify the different purposes of looking for particular patterns in DNA sequences associated with a given phenotype. This study has enabled us to make a conceptual breakdown of the genomic signature and differentiate the leading applications. On the one hand, it refers to gene expression profiling associated with a biological function, which may be shared across taxa. This signature is the focus of study in precision medicine. On the other hand, it also refers to characteristic patterns in species-specific DNA sequences. This interpretation plays a key role in comparative genomics, identifying evolutionary relationships. Looking at the relevant studies in our bibliographic database, we highlight the main factors causing heterogeneities in genome composition and how they can be quantified. All these findings lead us to reformulate some questions relevant to evolutionary biology.

Keywords: alignment-free methods; chaos game representation; evolutionary biology; genome sequence; genomic signature.

Figure 1

Co-word network characterizing the structure of keyword co-occurrences. The five clusters obtained from VosViewer are represented by colors and named as C1, C2, C3, C4, and C5.

Figure 2

Bibliographic coupling of articles where ‘genomic signature’ appears as a Keyword. A total of 12 clusters is obtained from VosViewer, which are represented with colors and named as C1, …, C12.

Figure 3

Iterative application of the contraction mappings of the system represented in Table 3 starting from an initial square box.

Figure 4

Visual representation of the Chaos Game Representation. (a) Sub-quadrants associated to the sequences of size $k=1$ and (b) $k=2$. (c) CGR of a random sequence. (d) Fractal-like structure of empty regions corresponding to the absence of the word “CG”.

Figure 5

The $2^8\times 2^8$ FCGR images of genomic DNA sequences from H. sapiens, E. coli, S. cerevisiae, A. thailana, P. falciparum, and P. furiosus. The color map corresponds to word abundancies, i.e., the number of times each word of size $k=8$ appears in DNA sequences.