Finding the Core-Genes of Chloroplasts

TL;DR

This paper investigates methods to identify core and pan genomes of chloroplasts using 99 genomes, focusing on sequence similarity and gene annotation, to enhance understanding of chloroplast gene conservation and specificity.

Contribution

It introduces a comparative analysis of two methodologies for core genome detection in chloroplasts, addressing a gap in systematic approaches for this specific genome type.

Findings

Sequence similarity-based method identified conserved core genes.

Gene name-based approach revealed gene sets with high biological relevance.

Methodologies provide a foundation for future chloroplast genome studies.

Abstract

Due to the recent evolution of sequencing techniques, the number of available genomes is rising steadily, leading to the possibility to make large scale genomic comparison between sets of close species. An interesting question to answer is: what is the common functionality genes of a collection of species, or conversely, to determine what is specific to a given species when compared to other ones belonging in the same genus, family, etc. Investigating such problem means to find both core and pan genomes of a collection of species, \textit{i.e.}, genes in common to all the species vs. the set of all genes in all species under consideration. However, obtaining trustworthy core and pan genomes is not an easy task, leading to a large amount of computation, and requiring a rigorous methodology. Surprisingly, as far as we know, this methodology in finding core and pan genomes has not really been deeply investigated. This research work tries to fill this gap by focusing only on chloroplastic genomes, whose reasonable sizes allow a deep study. To achieve this goal, a collection of 99 chloroplasts are considered in this article. Two methodologies have been investigated, respectively based on sequence similarities and genes names taken from annotation tools. The obtained results will finally be evaluated in terms of biological relevance.