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Genetics, Genomics and Biotechnology of Plant Cytoplasmic Organelles
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Genetics, Genomics and Biotechnology of Plant Cytoplasmic Organelles

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Molecular Biology".

Deadline for manuscript submissions: closed (28 February 2021) | Viewed by 22424

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editors

Dr. Nunzia Scotti

E-Mail Website
Guest Editor
CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici, NA, Italy
Interests: organelle genome analyses; genetic diversity; gene expression; retrograde signaling; cytoplasmic male sterility; plant biotechnology; molecular farming; model and crop species
Special Issues, Collections and Topics in MDPI journals
Dr. Rachele Tamburino

E-Mail Website
Guest Editor
CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici, NA, Italy
Interests: chloroplast; mitochondrion; proteomics; abiotic stress; retrograde signaling; NGS technology; crops

Special Issue Information

Dear Colleagues,

Chloroplasts and mitochondria are essential plant organelles involved in many fundamental processes (photosynthesis, energy production, metabolism, cell homeostasis, etc.). They are semi-autonomous organelles; hence, their function is dependent upon cross-talk between nuclear and organelle genetic systems. Chloroplasts and mitochondria are also known as stress sensors, since any dysfunction in their activity, caused by both biotic and abiotic factors, leads to a global defense response of the plant involving hormone, ROS, and other metabolic pathways’ activation. Although in recent decades, the new technologies have given a huge boost to genetic, genomic, and biotechnology studies to understand several aspects of molecular mechanisms involved in fundamental processes, there are still many points not fully understood especially in crops.

The goal of this Special Issue is to provide new advances in the field of the genetics, genomics, and biotechnology of plant cytoplasmic organelles. Particularly, this issue is open to research articles and reviews focused on:

- Sequencing of organellar genomes/transcriptomes aimed at providing insight into the evolution of plant species, developing new molecular markers suitable for the study of genetic diversity, analyzing gene expression and maturation, etc.;

- Discovering novel gene functions and deciphering unknown mechanisms, as well as uncovering the molecular mechanisms at the basis of important processes in which chloroplasts or mitochondria are somehow involved (e.g., retrograde signaling, cytoplasmic male sterility);

- Engineering of plastid DNA aiming to evaluate genes able to sustain crop performance (e.g., photosynthesis) or produce recombinant proteins.

Dr. Nunzia Scotti
Dr. Rachele Tamburino
Guest Editors

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. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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

  • chloroplast
  • mitochondria
  • crops
  • gene expression
  • stress response
  • inter-organelle crosstalk
  • signaling networks
  • photosynthesis
  • phylogeny
  • molecular marker
  • barcode
  • NGS
  • genetic engineering
  • recombinant proteins
  • agronomic traits
  • sustainable agriculture

Published Papers (7 papers)

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Research

17 pages, 5941 KiB  
Article
Comparative Analysis of Chloroplast Genomes of Four Medicinal Capparaceae Species: Genome Structures, Phylogenetic Relationships and Adaptive Evolution
by Dhafer A. Alzahrani, Enas J. Albokhari, Samaila S. Yaradua and Abidina Abba
Plants 2021, 10(6), 1229; https://doi.org/10.3390/plants10061229 - 17 Jun 2021
Cited by 11 | Viewed by 2796
Abstract
This study presents for the first time the complete chloroplast genomes of four medicinal species in the Capparaceae family belonging to two different genera, Cadaba and Maerua (i.e., C. farinosa, C. glandulosa, M. crassifolia and M. oblongifolia), to investigate their evolutionary process [...] Read more.
This study presents for the first time the complete chloroplast genomes of four medicinal species in the Capparaceae family belonging to two different genera, Cadaba and Maerua (i.e., C. farinosa, C. glandulosa, M. crassifolia and M. oblongifolia), to investigate their evolutionary process and to infer their phylogenetic positions. The four species are considered important medicinal plants, and are used in the treatment of many diseases. In the genus Cadaba, the chloroplast genome ranges from 156,481 bp to 156,560 bp, while that of Maerua ranges from 155,685 bp to 155,436 bp. The chloroplast genome of C. farinosa, M. crassifolia and M. oblongifolia contains 138 genes, while that of C. glandulosa contains 137 genes, comprising 81 protein-coding genes, 31 tRNA genes and 4 rRNA genes. Out of the total genes, 116–117 are unique, while the remaining 19 are replicated in inverted repeat regions. The psbG gene, which encodes for subunit K of NADH dehydrogenase, is absent in C. glandulosa. A total of 249 microsatellites were found in the chloroplast genome of C. farinosa, 251 in C. glandulosa, 227 in M. crassifolia and 233 in M. oblongifolia, the majority of which are mononucleotides A/T found in the intergenic spacer. Comparative analysis revealed variable hotspot regions (atpF, rpoC2, rps19 and ycf1), which can be used as molecular markers for species authentication and as regions for inferring phylogenetic relationships among them, as well as for evolutionary studies. The monophyly of Capparaceae and other families under Brassicales, as well as the phylogenetic positions of the studied species, are highly supported by all the relationships in the phylogenetic tree. The cp genomes reported in this study will provide resources for studying the genetic diversity of Capparaceae, as well as resolving phylogenetic relationships within the family. Full article
(This article belongs to the Special Issue Genetics, Genomics and Biotechnology of Plant Cytoplasmic Organelles)
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20 pages, 4118 KiB  
Article
Mitochondrial mRNA Processing in the Chlorophyte Alga Pediastrum duplex and Streptophyte Alga Chara vulgaris Reveals an Evolutionary Branch in Mitochondrial mRNA Processing
by Grayson C. R. Proulex, Marcus J. Meade, Kalina M. Manoylov and A. Bruce Cahoon
Plants 2021, 10(3), 576; https://doi.org/10.3390/plants10030576 - 18 Mar 2021
Viewed by 2973
Abstract
Mitochondria carry the remnant of an ancestral bacterial chromosome and express those genes with a system separate and distinct from the nucleus. Mitochondrial genes are transcribed as poly-cistronic primary transcripts which are post-transcriptionally processed to create individual translationally competent mRNAs. Algae post-transcriptional processing [...] Read more.
Mitochondria carry the remnant of an ancestral bacterial chromosome and express those genes with a system separate and distinct from the nucleus. Mitochondrial genes are transcribed as poly-cistronic primary transcripts which are post-transcriptionally processed to create individual translationally competent mRNAs. Algae post-transcriptional processing has only been explored in Chlamydomonas reinhardtii (Class: Chlorophyceae) and the mature mRNAs are different than higher plants, having no 5′ UnTranslated Regions (UTRs), much shorter and more variable 3′ UTRs and polycytidylated mature mRNAs. In this study, we analyzed transcript termini using circular RT-PCR and PacBio Iso-Seq to survey the 3′ and 5′ UTRs and termini for two green algae, Pediastrum duplex (Class: Chlorophyceae) and Chara vulgaris (Class: Charophyceae). This enabled the comparison of processing in the chlorophyte and charophyte clades of green algae to determine if the differences in mitochondrial mRNA processing pre-date the invasion of land by embryophytes. We report that the 5′ mRNA termini and non-template 3′ termini additions in P. duplex resemble those of C. reinhardtii, suggesting a conservation of mRNA processing among the chlorophyceae. We also report that C. vulgaris mRNA UTRs are much longer than chlorophytic examples, lack polycytidylation, and are polyadenylated similar to embryophytes. This demonstrates that some mitochondrial mRNA processing events diverged with the split between chlorophytic and streptophytic algae. Full article
(This article belongs to the Special Issue Genetics, Genomics and Biotechnology of Plant Cytoplasmic Organelles)
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20 pages, 15223 KiB  
Article
A Core Module of Nuclear Genes Regulated by Biogenic Retrograde Signals from Plastids
by Björn Grübler, Carolina Cozzi and Thomas Pfannschmidt
Plants 2021, 10(2), 296; https://doi.org/10.3390/plants10020296 - 4 Feb 2021
Cited by 7 | Viewed by 2820
Abstract
Chloroplast biogenesis during seedling development of angiosperms is a rapid and highly dynamic process that parallels the light-dependent photomorphogenic programme. Pre-treatments of dark-grown seedlings with lincomyin or norflurazon prevent chloroplast biogenesis upon illumination yielding albino seedlings. A comparable phenotype was found for the [...] Read more.
Chloroplast biogenesis during seedling development of angiosperms is a rapid and highly dynamic process that parallels the light-dependent photomorphogenic programme. Pre-treatments of dark-grown seedlings with lincomyin or norflurazon prevent chloroplast biogenesis upon illumination yielding albino seedlings. A comparable phenotype was found for the Arabidopsis mutant plastid-encoded polymerase associated protein 7 (pap7) being defective in the prokaryotic-type plastid RNA polymerase. In all three cases the defect in plastid function has a severe impact on the expression of nuclear genes representing the influence of retrograde signaling pathway(s) from the plastid. We performed a meta-analysis of recently published genome-wide expression studies that investigated the impact of the aforementioned chemical and genetic blocking of chloroplast biogenesis on nuclear gene expression profiles. We identified a core module of 152 genes being affected in all three conditions. These genes were classified according to their function and analyzed with respect to their implication in retrograde signaling and chloroplast biogenesis. Our study uncovers novel genes regulated by retrograde biogenic signals and suggests the action of a common signaling pathway that is used by signals originating from plastid transcription, translation and oxidative stress. Full article
(This article belongs to the Special Issue Genetics, Genomics and Biotechnology of Plant Cytoplasmic Organelles)
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13 pages, 5863 KiB  
Article
Transmission of Engineered Plastids in Sugarcane, a C4 Monocotyledonous Plant, Reveals that Sorting of Preprogrammed Progenitor Cells Produce Heteroplasmy
by Ghulam Mustafa and Muhammad Sarwar Khan
Plants 2021, 10(1), 26; https://doi.org/10.3390/plants10010026 - 24 Dec 2020
Cited by 4 | Viewed by 2448
Abstract
We report here plastid transformation in sugarcane using biolistic transformation and embryogenesis-based regeneration approaches. Somatic embryos were developed from unfurled leaf sections, containing preprogrammed progenitor cells, to recover transformation events on antibiotic-containing regeneration medium. After developing a proficient regeneration system, the FLARE-S (fluorescent [...] Read more.
We report here plastid transformation in sugarcane using biolistic transformation and embryogenesis-based regeneration approaches. Somatic embryos were developed from unfurled leaf sections, containing preprogrammed progenitor cells, to recover transformation events on antibiotic-containing regeneration medium. After developing a proficient regeneration system, the FLARE-S (fluorescent antibiotic resistance enzyme, spectinomycin and streptomycin) expression cassette that carries species-specific homologous sequence tails was used to transform plastids and track gene transmission and expression in sugarcane. Plants regenerated from streptomycin-resistant and genetically confirmed shoots were subjected to visual detection of the fluorescent enzyme using a fluorescent stereomicroscope, after genetic confirmation. The resultant heteroplasmic shoots remained to segregate on streptomycin-containing MS medium, referring to the unique pattern of division and sorting of cells in C4 monocotyledonous compared to C3 monocotyledonous and dicotyledonous plants since in sugarcane bundle sheath and mesophyll cells are distinct and sort independently after division. Hence, the transformation of either mesophyll or bundle sheath cells will develop heteroplasmic transgenic plants, suggesting the transformation of both types of cells. Whilst developed transgenic sugarcane plants are heteroplasmic, and selection-based regeneration protocol envisaging the role of division and sorting of cells in the purification of transplastomic demands further improvement, the study has established many parameters that may open up exciting possibilities to express genes of agricultural or pharmaceutical importance in sugarcane. Full article
(This article belongs to the Special Issue Genetics, Genomics and Biotechnology of Plant Cytoplasmic Organelles)
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15 pages, 1822 KiB  
Article
Cultivated Tomato (Solanum lycopersicum L.) Suffered a Severe Cytoplasmic Bottleneck during Domestication: Implications from Chloroplast Genomes
by Rachele Tamburino, Lorenza Sannino, Donata Cafasso, Concita Cantarella, Luigi Orrù, Teodoro Cardi, Salvatore Cozzolino, Nunzio D’Agostino and Nunzia Scotti
Plants 2020, 9(11), 1443; https://doi.org/10.3390/plants9111443 - 26 Oct 2020
Cited by 13 | Viewed by 3380
Abstract
In various crops, genetic bottlenecks occurring through domestication can limit crop resilience to biotic and abiotic stresses. In the present study, we investigated nucleotide diversity in tomato chloroplast genome through sequencing seven plastomes of cultivated accessions from the Campania region (Southern Italy) and [...] Read more.
In various crops, genetic bottlenecks occurring through domestication can limit crop resilience to biotic and abiotic stresses. In the present study, we investigated nucleotide diversity in tomato chloroplast genome through sequencing seven plastomes of cultivated accessions from the Campania region (Southern Italy) and two wild species among the closest (Solanum pimpinellifolium) and most distantly related (S. neorickii) species to cultivated tomatoes. Comparative analyses among the chloroplast genomes sequenced in this work and those available in GenBank allowed evaluating the variability of plastomes and defining phylogenetic relationships. A dramatic reduction in genetic diversity was detected in cultivated tomatoes, nonetheless, a few de novo mutations, which still differentiated the cultivated tomatoes from the closest wild relative S. pimpinellifolium, were detected and are potentially utilizable as diagnostic markers. Phylogenetic analyses confirmed that S. pimpinellifolium is the closest ancestor of all cultivated tomatoes. Local accessions all clustered together and were strictly related with other cultivated tomatoes (S. lycopersicum group). Noteworthy, S. lycopersicum var. cerasiforme resulted in a mixture of both cultivated and wild tomato genotypes since one of the two analyzed accessions clustered with cultivated tomato, whereas the other with S. pimpinellifolium. Overall, our results revealed a very reduced cytoplasmic variability in cultivated tomatoes and suggest the occurrence of a cytoplasmic bottleneck during their domestication. Full article
(This article belongs to the Special Issue Genetics, Genomics and Biotechnology of Plant Cytoplasmic Organelles)
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19 pages, 3319 KiB  
Article
Mitochondrial Genome of Fagus sylvatica L. as a Source for Taxonomic Marker Development in the Fagales
by Malte Mader, Hilke Schroeder, Thomas Schott, Katrin Schöning-Stierand, Ana Paula Leite Montalvão, Heike Liesebach, Mirko Liesebach, Barbara Fussi and Birgit Kersten
Plants 2020, 9(10), 1274; https://doi.org/10.3390/plants9101274 - 27 Sep 2020
Cited by 11 | Viewed by 3743
Abstract
European beech, Fagus sylvatica L., is one of the most important and widespread deciduous tree species in Central Europe and is widely managed for its hard wood. The complete DNA sequence of the mitochondrial genome of Fagus sylvatica L. was assembled and annotated [...] Read more.
European beech, Fagus sylvatica L., is one of the most important and widespread deciduous tree species in Central Europe and is widely managed for its hard wood. The complete DNA sequence of the mitochondrial genome of Fagus sylvatica L. was assembled and annotated based on Illumina MiSeq reads and validated using long reads from nanopore MinION sequencing. The genome assembled into a single DNA sequence of 504,715 bp in length containing 58 genes with predicted function, including 35 protein-coding, 20 tRNA and three rRNA genes. Additionally, 23 putative protein-coding genes were predicted supported by RNA-Seq data. Aiming at the development of taxon-specific mitochondrial genetic markers, the tool SNPtax was developed and applied to select genic SNPs potentially specific for different taxa within the Fagales. Further validation of a small SNP set resulted in the development of four CAPS markers specific for Fagus, Fagaceae, or Fagales, respectively, when considering over 100 individuals from a total of 69 species of deciduous trees and conifers from up to 15 families included in the marker validation. The CAPS marker set is suitable to identify the genus Fagus in DNA samples from tree tissues or wood products, including wood composite products. Full article
(This article belongs to the Special Issue Genetics, Genomics and Biotechnology of Plant Cytoplasmic Organelles)
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13 pages, 987 KiB  
Article
Mitochondrial Genome of Fagopyrum esculentum and the Genetic Diversity of Extranuclear Genomes in Buckwheat
by Maria D. Logacheva, Mikhail I. Schelkunov, Aleksey N. Fesenko, Artem S. Kasianov and Aleksey A. Penin
Plants 2020, 9(5), 618; https://doi.org/10.3390/plants9050618 - 12 May 2020
Cited by 15 | Viewed by 3418
Abstract
Fagopyrum esculentum (common buckwheat) is an important agricultural non-cereal grain plant. Despite extensive genetic studies, the information on its mitochondrial genome is still lacking. Using long reads generated by single-molecule real-time technology coupled with circular consensus sequencing (CCS) protocol, we assembled the buckwheat [...] Read more.
Fagopyrum esculentum (common buckwheat) is an important agricultural non-cereal grain plant. Despite extensive genetic studies, the information on its mitochondrial genome is still lacking. Using long reads generated by single-molecule real-time technology coupled with circular consensus sequencing (CCS) protocol, we assembled the buckwheat mitochondrial genome and detected that its prevalent form consists of 10 circular chromosomes with a total length of 404 Kb. In order to confirm the presence of a multipartite structure, we developed a new targeted assembly tool capable of processing long reads. The mitogenome contains all genes typical for plant mitochondrial genomes and long inserts of plastid origin (~6.4% of the total mitogenome length). Using this new information, we characterized the genetic diversity of mitochondrial and plastid genomes in 11 buckwheat cultivars compared with the ancestral subspecies, F. esculentum ssp. ancestrale. We found it to be surprisingly low within cultivars: Only three to six variations in the mitogenome and one to two in the plastid genome. In contrast, the divergence with F. esculentum ssp. ancestrale is much higher: 220 positions differ in the mitochondrial genome and 159 in the plastid genome. The SNPs in the plastid genome are enriched in non-synonymous substitutions, in particular in the genes involved in photosynthesis: psbA, psbC, and psbH. This presumably reflects the selection for the increased photosynthesis efficiency as a part of the buckwheat breeding program. Full article
(This article belongs to the Special Issue Genetics, Genomics and Biotechnology of Plant Cytoplasmic Organelles)
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