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Chloroplast data notes

Guest Editors:
Ertugrul Filiz: Department of Crop and Animal Production, Duzce University, Turkey
Yong Zhou: King Abdullah University of Science and Technology, Saudi Arabia


Chloroplasts are active metabolic centers that play a key contribution to life on earth by converting solar energy into carbohydrates via photosynthesis and thus releasing oxygen. These organelles are considered to be endosymbiotic cyanobacteria and thus have bacterial origin and are genetically semi-autonomous although they are in constant close relationship with the nucleus. Many chloroplast genes have been transferred to the nucleus but the proteins that are essential for photosynthesis have been retained in the nucleus. With this collection, BMC Genomic Data contributed to the generation of more chloroplast genomes and data sets for the community and thus increased the general knowledge of this important organelle.

Meet the Guest Editors

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Ertugrul Filiz: Department of Crop and Animal Production , Duzce University, Turkey

Dr Filiz obtained his PhD in the field plant genetics. Dr Filiz has dedicated years to conducting cutting-edge scientific research in the field of plant biotechnology. In recent times, his focus has shifted towards exploring the bioinformatic applications in plants. Dr Filiz is currently engaged in extensive studies involving the identification of gene families across plant genomes, as well as conducting bioinformatics analyses and investigating molecular responses under stress conditions.

Yong Zhou: King Abdullah University of Science and Technology, Saudi Arabia

Dr Zhou is a research scientist at King Abdullah University of Science and Technology (KAUST) in Saudi Arabia. His primary focus is using plant genetics and genomic tools to enhance food security. He utilizes next-gen and long-read sequencing techniques to explore genome assembly, genetic diversity, and whole genome variation, including Chloroplast. His research investigates the impact of variations on biodiversity, agricultural traits, and coevolution processes. Dr Zhou's work encompasses fieldwork, lab experiments (DNA, RNA, molecular genetics), computational biology (bioinformatics for large sequence datasets), and incorporates artificial intelligence (AI) methods like machine learning. His goal is to advance applied genomics by integrating ongoing research with AI strategies.

About the collection

Chloroplasts are active metabolic centers that play a key contribution to life on earth by converting solar energy into carbohydrates via photosynthesis and thus releasing oxygen. These organelles are considered to be endosymbiotic cyanobacteria and thus have bacterial origin and are genetically semi-autonomous although they are in constant close relationship with the nucleus. Many chloroplast genes have been transferred to the nucleus but the proteins that are essential for photosynthesis have been retained in the nucleus.

The first chloroplast genomes were sequenced 37 years ago and since then, the evolution of the sequencing techniques have facilitated the sequencing of more chloroplast’s genomes. Third generation sequencing is now widely used for chloroplast genome sequencing and facilitates de novo genome assembly thanks to its long reads, especially in the four chloroplast junctions between the inverted repeat (IR) and single-copy regions.

The availability of more chloroplasts genomes has enabled insights into plant biology and diversity, the phylogeny of plant families as well as helped resolve evolutionary relationships. This information has helped our understanding of adaptation of important crops to the climate for example and has led to translational applications such as conferring them protection against different stresses. The availability of more chloroplast genomes has indeed improved our understanding of intracellular gene transfers, conservation and changes that occurred during domestication. Chloroplast genomes are particularly helpful in the identification of closely related species. They are also useful in modern biotechnology to introduce desirable traits from unrelated species as they are materially inherited in most cultivated crops thus preventing transgene escape via pollen.

With this collection, BMC Genomic Data would like to contribute to the generation of more chloroplast genomes and data sets for the community and thus increase the general knowledge of this important organelle.

Image credit: blueringmedia / Stock.adobe.com

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Submission Guidelines

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This Collection welcomes submission of Data Notes primarily. In addition, original Research Articles and Database Articles will also be considered if they fit the scope of the Collection. Should you wish to submit a different article type, please read our submission guidelines to confirm that type is accepted by the journal. Articles for this Collection should be submitted via our submission system, Snapp. During the submission process you will be asked whether you are submitting to a Collection, please select "Chloroplast data notes" from the dropdown menu.

Articles will undergo the journal’s standard peer-review process and are subject to all of the journal’s standard policies. Articles will be added to the Collection as they are published.

The Editors have no competing interests with the submissions which they handle through the peer review process. The peer review of any submissions for which the Editors have competing interests is handled by another Editorial Board Member who has no competing interests.