Chloroplast genomics: Expanding resources for an evolutionary conserved miniature molecule with enigmatic applications ☆

摘要

Chloroplast, methylation depreived uniparental organelle genome is the most studied organelle genome from the perspective of evolution and functional omics. Recent advances in organelle genome sequencing both in terms of genome or transcriptome sequencing has opened a wide range of opportunities to understand the transcriptional and translational role of the genes mainly involved in the light harvesting apparatus and the evolution of the inverted repeats across the lineage. However, as compared to the nuclear genome, limited resources are available in case of organelle genome. In this review, we discuss the recent advances in the chloroplast genomics and the resources that have been developed for understanding the evolution, repeat patterns, functional genomics of this miniature molecule with enigmatic applications. prs.rt("abs_end"); 1. Chloroplast genomes: dynamic organization and evolutionary fluctuations Photosynthesis is critical to all aspects of plant life and to combat the environmental fluctuations. Chloroplast, evolutionary conserved and endoymbiotically originated molecule play a major role in photosynthesis by acting as host to three major complex such as photosystem II (PSII), the cytochrome b6f complex (Cytb6f), and photosystem I (PSI) [1] . Evolutionary conservation of these complexes in chloroplast genome thylakoid membrane represents the main sites of the light capture and the oxygen production as well as playing a major role in the light state transitions with plastid division apparatus responsible for the binary fission spatially distributed between the stromal and cytosolic space [2] . Among the spatially distributed genes in circular fashion, chloroplast represents a set of genes, which are vital for controlling the photosynthetic efficiency and to determine the dynamic organization of the thylakoid membrane and cyclic electron flow [3] . Evolutionary conserved organization of chloroplast genomes, which is circular in nature and follows a D-loop replication model is structured in a quadripartite structure, which is partitioned into two repeat regions, which are defined by the differences in the length as large single copy (LSC) regions spanning across a length of 80–90?kb and a short single copy region (SSC), representing a 16–27?kb region. Organization of these LSC and SSC regions is a dynamic process and has been widely reported to undergo expansion and contraction [4] . Although the evolutionary conservation of the chloroplast genic regions has been widely reported as exemplified by their use as molecular barcodes, few instances of rapidly evolving genes such as rbcL, which encodes the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RUBISCO), and plays a major role in carbon assimilation and other genes such as matK (maturase K), ndhB and psbA-J, which are involved in modulating the state transitions has also been seen [5] . In contrast, the repeat organization is very dynamic and although conserved across the angiosperms, dynamic loss of the inverted repeat copies has been widely documented amongst the gymnosperms [6] . Taking all these structural variations with in the size of (150–160?kb), it worth to highlight the role of evolutionary conserved, distinct and model genome to understand the genome fluctuations ( Fig. 1 ). From the view point of regulatory genomics, transcriptional and, transcriptional flux, chloroplast genomes have been widely explored in addition to point mutants and also the identification of the RNA Editing events. Fig. 1.?Genomics and applications of chloroplast genomics. Figure options.