About this Research Topic

Background

The plastid genome has been the most important source of data for the reconstruction of plant phylogeny and taxonomic studies. With the rapid advancement of sequencing technology and bioinformatics, it has become laboratory routine work for obtaining plastid genomes (plastome), and population studies can be performed using chloroplast genome data. However, plastid genomes with specific characters such as pseudogenes, gene losses, gene duplications, gene rearrangements, widespread intra-individual polymorphisms, large-scale horizontal gene transfer, etc. have not been systematically studied. For example, plastomes of several saprophytic plants were confirmed to have lost many photosynthesis genes. The IR region of some plants decreased to several hundred base pairs, disappears completely, increased by dozens of kb, or repeat in the same direction. Most of these chloroplast structural variations are related to import plant evolution or special environmental adaptation, but their mechanisms are still unclear and effective analytical tools are lacking.

Despite the increasing popularity of plastid genomes, obtaining chloroplast genomes and applying them to phylogeny and taxonomic identification studies has become routine works in laboratories. However, the assembly, annotation, and deep analysis of chloroplast genome with complex structures still face great challenges. Plants with these complex chloroplast genomes often live in extreme environments or have unusual lifestyles, which are reflected in the structural variation of the chloroplast genomes. In addition, limited by technical methods or research funding, there is still a lack of extensive research and comparison of population plastid genomes for these plants with high pharmaceutical, economic and ecological values. Here, we hope to receive many reliable plastid genomic studies with complex structures or plastid genomes for population studies, as well as bioinformatics tools for in-depth analysis of these plastid genome data.

In this Research Topic, we would like to collect studies dedicated to plastid genomes studies especially those that focus on:

- Characterization and deep analysis of plastid genomes with specific characters such as pseudogenes, gene losses, gene duplications, gene rearrangements, widespread intra-individual polymorphisms, large-scale horizontal gene transfer, etc.；

- Comparative studies of large-scale chloroplast genomes, such as plastid genome obtained from multiple individuals of a species, multiple species of a genus, multiple species of biodiversity hotspots, etc.;

- Plastid genome from parasitic plant, saprotrophic plant, or plants living in extreme environmental conditions such as drought, cold, high-altitude, high soil salinity environments

- Bioinformatics tools for the annotation and analysis of plastid genomes coming from the above species.

Keywords: plastome, pseudogenes, gene losses, population, comparative study, extreme environmental condition, bioinformatics tool

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