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Plastids

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 10366

Special Issue Editor

Prof. Dr. Bartolome Sabater

E-Mail Website
Guest Editor
Department of Life Sciences (Ciencias de la Vida), University of Alcalá, Alcalá de Henares, 28805 Madrid, Spain
Interests: genetic machinery of chloroplasts; molecular mechanisms of plant senescence; molecular mechanisms of stress responses; organism entropy; regulation of photosynthetic electron transport
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue, focusing on plastids, will continue with the successful quantity and quality of papers in the previous chloroplast issues extending them to chloroplast-like organelles sharing similar DNA. It aims to include investigations from chloroplasts to leucoplasts, chromoplasts, and plastid-related organelles of protozoa. Manuscripts submitted to the “Plastids” Special Issue must report high-quality and novel investigations dealing with the molecular biology of all plastid types. Energy conversion in chloroplasts; biogenesis and interconversions of non-photosynthetic plastids; metabolism; reactive oxygen species; membrane biogenesis; and transport, structure, and evolutionary relations will be warmly welcomed. Molecular insights on genetic machinery, regulatory mechanisms, evolution, development, or senescence are mandatory over descriptive reports. With this invitation, I hope that your contributions make the “Plastids” Special Issue a new reference milestone.

Prof. Dr. Bartolome Sabater
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • chloroplasts
  • non-photosynthetic plastids
  • photosynthesis
  • plastid evolution
  • plastid genomics
  • reactive oxygen species

Published Papers (3 papers)

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Research

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19 pages, 1462 KiB  
Article
Chloroplast Genome Annotation Tools: Prolegomena to the Identification of Inverted Repeats
by Ante Turudić, Zlatko Liber, Martina Grdiša, Jernej Jakše, Filip Varga and Zlatko Šatović
Int. J. Mol. Sci. 2022, 23(18), 10804; https://doi.org/10.3390/ijms231810804 - 16 Sep 2022
Cited by 6 | Viewed by 2718
Abstract
The development of next-generation sequencing technology and the increasing amount of sequencing data have brought the bioinformatic tools used in genome assembly into focus. The final step of the process is genome annotation, which works on assembled genome sequences to identify the location [...] Read more.
The development of next-generation sequencing technology and the increasing amount of sequencing data have brought the bioinformatic tools used in genome assembly into focus. The final step of the process is genome annotation, which works on assembled genome sequences to identify the location of genome features. In the case of organelle genomes, specialized annotation tools are used to identify organelle genes and structural features. Numerous annotation tools target chloroplast sequences. Most chloroplast DNA genomes have a quadripartite structure caused by two copies of a large inverted repeat. We investigated the strategies of six annotation tools (Chloë, Chloroplot, GeSeq, ORG.Annotate, PGA, Plann) for identifying inverted repeats and analyzed their success using publicly available complete chloroplast sequences of taxa belonging to the asterid and rosid clades. The annotation tools use two different approaches to identify inverted repeats, using existing general search tools or implementing stand-alone solutions. The chloroplast sequences studied show that there are different types of imperfections in the assembled data and that each tool performs better on some sequences than the others. Full article
(This article belongs to the Special Issue Plastids)
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19 pages, 9267 KiB  
Article
Comparative Analysis of Chloroplast Genome in Saccharum spp. and Related Members of ‘Saccharum Complex’
by Sicheng Li, Weixing Duan, Jihan Zhao, Yanfen Jing, Mengfan Feng, Bowen Kuang, Ni Wei, Baoshan Chen and Xiping Yang
Int. J. Mol. Sci. 2022, 23(14), 7661; https://doi.org/10.3390/ijms23147661 - 11 Jul 2022
Cited by 7 | Viewed by 2116
Abstract
High ploids of the sugarcane nuclear genome limit its genomic studies, whereas its chloroplast genome is small and conserved, which is suitable for phylogenetic studies and molecular marker development. Here, we applied whole genome sequencing technology to sequence and assemble chloroplast genomes of [...] Read more.
High ploids of the sugarcane nuclear genome limit its genomic studies, whereas its chloroplast genome is small and conserved, which is suitable for phylogenetic studies and molecular marker development. Here, we applied whole genome sequencing technology to sequence and assemble chloroplast genomes of eight species of the ‘Saccharum Complex’, and elucidated their sequence variations. In total, 19 accessions were sequenced, and 23 chloroplast genomes were assembled, including 6 species of Saccharum (among them, S. robustum, S. sinense, and S. barberi firstly reported in this study) and 2 sugarcane relative species, Tripidium arundinaceum and Narenga porphyrocoma. The plastid phylogenetic signal demonstrated that S. officinarum and S. robustum shared a common ancestor, and that the cytoplasmic origins of S. sinense and S. barberi were much more ancient than the S. offcinarum/S. robustum linage. Overall, 14 markers were developed, including 9 InDel markers for distinguishing Saccharum from its relative species, 4 dCAPS markers for distinguishing S. officinarum from S. robustum, and 1 dCAPS marker for distinguishing S. sinense and S. barberi from other species. The results obtained from our studies will contribute to the understanding of the classification and plastome evolution of Saccharinae, and the molecular markers developed have demonstrated their highly discriminatory power in Saccharum and relative species. Full article
(This article belongs to the Special Issue Plastids)
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Review

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16 pages, 1411 KiB  
Review
LHC-like Proteins: The Guardians of Photosynthesis
by Guy Levin and Gadi Schuster
Int. J. Mol. Sci. 2023, 24(3), 2503; https://doi.org/10.3390/ijms24032503 - 28 Jan 2023
Cited by 10 | Viewed by 4418
Abstract
The emergence of chlorophyll-containing light-harvesting complexes (LHCs) was a crucial milestone in the evolution of photosynthetic eukaryotic organisms. Light-harvesting chlorophyll-binding proteins form complexes in proximity to the reaction centres of photosystems I and II and serve as an antenna, funnelling the harvested light [...] Read more.
The emergence of chlorophyll-containing light-harvesting complexes (LHCs) was a crucial milestone in the evolution of photosynthetic eukaryotic organisms. Light-harvesting chlorophyll-binding proteins form complexes in proximity to the reaction centres of photosystems I and II and serve as an antenna, funnelling the harvested light energy towards the reaction centres, facilitating photochemical quenching, thereby optimizing photosynthesis. It is now generally accepted that the LHC proteins evolved from LHC-like proteins, a diverse family of proteins containing up to four transmembrane helices. Interestingly, LHC-like proteins do not participate in light harvesting to elevate photosynthesis activity under low light. Instead, they protect the photosystems by dissipating excess energy and taking part in non-photochemical quenching processes. Although there is evidence that LHC-like proteins are crucial factors of photoprotection, the roles of only a few of them, mainly the stress-related psbS and lhcSR, are well described. Here, we summarize the knowledge gained regarding the evolution and function of the various LHC-like proteins, with emphasis on those strongly related to photoprotection. We further suggest LHC-like proteins as candidates for improving photosynthesis in significant food crops and discuss future directions in their research. Full article
(This article belongs to the Special Issue Plastids)
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