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Advances in Chloroplast Genomics and Proteostasis
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Advances in Chloroplast Genomics and Proteostasis

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (25 July 2023) | Viewed by 6411

Special Issue Editors

Dr. Saroj Kanta Barik

E-Mail Website
Guest Editor
CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
Interests: chloroplast genome sequence; phylogeny of angiosperms; taxon delimitation using genome sequences, proteomics and drought adaptation; ecology and micro-evolution
Dr. Satya Narayan Jena

E-Mail Website
Guest Editor
CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
Interests: comparative plastomics; metabolic pathways and cross talk; quantitative genetics; phylogenetic studies; molecular breeding of plants

Special Issue Information

Dear Colleagues,

Complete chloroplast genome sequencing has expanded our knowledge on the biology, evolutionary history, and diversity of plants. The chloroplast genome sequences differ greatly between and within plant species in terms of both sequence and structural variations. The genomic information obtained from chloroplasts has been extremely useful in identifying closely related wild species of economically important crops for breeding purposes. The chloroplast genomes are particularly helpful in deciphering the evolutionary lineages of the desired taxa and understanding the evolutionary trends. Thus, chloroplast genomics will be one of the focus areas of this Special Issue.

The changing needs of the cell in response to various developmental and environmental stimuli lead to alterations in the cellular proteome and its underlying structural and regulatory networks. Proteostasis involves a group of mechanisms that regulate the protein complement of the cell, and includes protein synthesis, modification, localization, and destruction. The focus of this Special Issue is on protein breakdown in relation to chloroplast, where we shall emphasize the varied ways in which plant proteostasis affects agronomic traits, offers opportunities and methods for modifying different proteostatic systems for crop development, as well as environmental stresses and proteostasis. Under normal conditions, the proteostasis network detects and corrects proteome disruptions to store basal homeostasis, but in stress, cells reprogram the expression of various genes (i.e., the stimulation of a few molecular chaperones, the suppression of protein translation) to bring proteostasis to a different state suited to cope with difficulties. To deal with folding stress, chloroplast uses a variety of mechanisms, including chaperone-mediated refolding, proteolytic destruction, and the regulated production of stress granules. The molecular identification of novel proteostasis pathways will aid the development of stress-tolerant chloroplast, which will boost crop output in harsh conditions. This Special Issue will also cover optimal chloroplast activity based on the coordinated expression of genes from both chloroplast and nuclear genomes.

Dr. Saroj Kanta Barik
Dr. Satya Narayan Jena
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. Genes is an international peer-reviewed open access monthly 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 2600 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 genome assembly
  • phylo-genomics and evolution
  • species lineages
  • chaperone-mediated refolding
  • signaling in chloroplast proteostasis: ubiquitin signaling and autophagy
  • cross-talk between signaling pathways

Published Papers (4 papers)

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13 pages, 2342 KiB  
Article
The First Complete Chloroplast Genome of Cordia monoica: Structure and Comparative Analysis
by Rana M. Alshegaihi, Hassan Mansour, Shouaa A. Alrobaish, Najla A. Al Shaye and Diaa Abd El-Moneim
Genes 2023, 14(5), 976; https://doi.org/10.3390/genes14050976 - 26 Apr 2023
Cited by 3 | Viewed by 1466
Abstract
Cordia monoica is a member of the Boraginaceae family. This plant is widely distributed in tropical regions and has a great deal of medical value as well as economic importance. In the current study, the complete chloroplast (cp) genome of C. monoica was [...] Read more.
Cordia monoica is a member of the Boraginaceae family. This plant is widely distributed in tropical regions and has a great deal of medical value as well as economic importance. In the current study, the complete chloroplast (cp) genome of C. monoica was sequenced, assembled, annotated, and reported. This circular chloroplast genome had a size of 148,711 bp, with a quadripartite structure alternating between a pair of repeated inverted regions (26,897–26,901 bp) and a single copy region (77,893 bp). Among the 134 genes encoded by the cp genome, there were 89 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. A total of 1387 tandem repeats were detected, with the hexanucleotides class making up 28 percent of the repeats. Cordia monoica has 26,303 codons in its protein-coding regions, and leucine amino acid was the most frequently encoded amino acid in contrast to cysteine. In addition, 12 of the 89 protein-coding genes were found to be under positive selection. The phyloplastomic taxonomical clustering of the Boraginaceae species provides further evidence that chloroplast genome data are reliable not only at family level but also in deciphering the phylogeny at genus level (e.g., Cordia). Full article
(This article belongs to the Special Issue Advances in Chloroplast Genomics and Proteostasis)
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18 pages, 4003 KiB  
Article
The Complete Chloroplast Genomes of Gynostemma Reveal the Phylogenetic Relationships of Species within the Genus
by Jiaxia Gan, Ying Li, Deying Tang, Baolin Guo, Doudou Li, Feng Cao, Chao Sun, Liying Yu and Zhuyun Yan
Genes 2023, 14(4), 929; https://doi.org/10.3390/genes14040929 - 17 Apr 2023
Cited by 2 | Viewed by 1466
Abstract
Gynostemma is an important medicinal and food plant of the Cucurbitaceae family. The phylogenetic position of the genus Gynostemma in the Cucurbitaceae family has been determined by morphology and phylogenetics, but the evolutionary relationships within the genus Gynostemma remain to be explored. The [...] Read more.
Gynostemma is an important medicinal and food plant of the Cucurbitaceae family. The phylogenetic position of the genus Gynostemma in the Cucurbitaceae family has been determined by morphology and phylogenetics, but the evolutionary relationships within the genus Gynostemma remain to be explored. The chloroplast genomes of seven species of the genus Gynostemma were sequenced and annotated, of which the genomes of Gynostemma simplicifolium, Gynostemma guangxiense and Gynostemma laxum were sequenced and annotated for the first time. The chloroplast genomes ranged from 157,419 bp (Gynostemma compressum) to 157,840 bp (G. simplicifolium) in length, including 133 identical genes: 87 protein-coding genes, 37 tRNA genes, eight rRNA genes and one pseudogene. Phylogenetic analysis showed that the genus Gynostemma is divided into three primary taxonomic clusters, which differs from the traditional morphological classification of the genus Gynostemma into the subgenus Gynostemma and Trirostellum. The highly variable regions of atpH-atpL, rpl32-trnL, and ccsA-ndhD, the repeat unilts of AAG/CTT and ATC/ATG in simple sequence repeats (SSRs) and the length of overlapping regions between rps19 and inverted repeats(IRb) and between ycf1 and small single-copy (SSC) were found to be consistent with the phylogeny. Observations of fruit morphology of the genus Gynostemma revealed that transitional state species have independent morphological characteristics, such as oblate fruit and inferior ovaries. In conclusion, both molecular and morphological results showed consistency with those of phylogenetic analysis. Full article
(This article belongs to the Special Issue Advances in Chloroplast Genomics and Proteostasis)
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15 pages, 3735 KiB  
Article
Analysis of Complete Chloroplast Genome: Structure, Phylogenetic Relationships of Galega orientalis and Evolutionary Inference of Galegeae
by Junjie Feng, Yi Xiong, Xiaoli Su, Tianqi Liu, Yanli Xiong, Junming Zhao, Xiong Lei, Lijun Yan, Wenlong Gou and Xiao Ma
Genes 2023, 14(1), 176; https://doi.org/10.3390/genes14010176 - 09 Jan 2023
Cited by 4 | Viewed by 1911
Abstract
Galega orientalis, a leguminous herb in the Fabaceae family, is an ecologically and economically important species widely cultivated for its strong stress resistance and high protein content. However, genomic information of Galega orientalis has not been reported, which limiting its evolutionary analysis. [...] Read more.
Galega orientalis, a leguminous herb in the Fabaceae family, is an ecologically and economically important species widely cultivated for its strong stress resistance and high protein content. However, genomic information of Galega orientalis has not been reported, which limiting its evolutionary analysis. The small genome size makes chloroplast relatively easy to obtain genomic sequence for phylogenetic studies and molecular marker development. Here, the chloroplast genome of Galega orientalis was sequenced and annotated. The results showed that the chloroplast genome of G. orientalis is 125,280 bp in length with GC content of 34.11%. A total of 107 genes were identified, including 74 protein-coding genes, 29 tRNAs and four rRNAs. One inverted repeat (IR) region was lost in the chloroplast genome of G. orientalis. In addition, five genes (rpl22, ycf2, rps16, trnE-UUC and pbf1) were lost compared with the chloroplast genome of its related species G. officinalis. A total of 84 long repeats and 68 simple sequence repeats were detected, which could be used as potential markers in the genetic studies of G. orientalis and related species. We found that the Ka/Ks values of three genes petL, rpl20, and ycf4 were higher than one in the pairwise comparation of G. officinalis and other three Galegeae species (Calophaca sinica, Caragana jubata, Caragana korshinskii), which indicated those three genes were under positive selection. A comparative genomic analysis of 15 Galegeae species showed that most conserved non-coding sequence regions and two genic regions (ycf1 and clpP) were highly divergent, which could be used as DNA barcodes for rapid and accurate species identification. Phylogenetic trees constructed based on the ycf1 and clpP genes confirmed the evolutionary relationships among Galegeae species. In addition, among the 15 Galegeae species analyzed, Galega orientalis had a unique 30-bp intron in the ycf1 gene and Tibetia liangshanensis lacked two introns in the clpP gene, which is contrary to existing conclusion that only Glycyrrhiza species in the IR lacking clade (IRLC) lack two introns. In conclusion, for the first time, the complete chloroplast genome of G. orientalis was determined and annotated, which could provide insights into the unsolved evolutionary relationships within the genus Galegeae. Full article
(This article belongs to the Special Issue Advances in Chloroplast Genomics and Proteostasis)
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10 pages, 2424 KiB  
Brief Report
The First Complete Chloroplast Genome of Campanula carpatica: Genome Characterization and Phylogenetic Diversity
by Won-Sub Yoon, Chang-Kug Kim and Yong-Kab Kim
Genes 2023, 14(8), 1597; https://doi.org/10.3390/genes14081597 - 07 Aug 2023
Viewed by 1093
Abstract
Campanula carpatica is an ornamental flowering plant belonging to the family Campanulaceae. The complete chloroplast genome of C. carpatica was obtained using Illumina HiSeq X and Oxford Nanopore (Nanopore GridION) platforms. The chloroplast genome exhibited a typical circular structure with a total length [...] Read more.
Campanula carpatica is an ornamental flowering plant belonging to the family Campanulaceae. The complete chloroplast genome of C. carpatica was obtained using Illumina HiSeq X and Oxford Nanopore (Nanopore GridION) platforms. The chloroplast genome exhibited a typical circular structure with a total length of 169,341 bp, comprising a large single-copy region of 102,323 bp, a small single-copy region of 7744 bp, and a pair of inverted repeats (IRa/IRb) of 29,637 bp each. Out of a total 120 genes, 76 were protein-coding genes, 36 were transfer RNA genes, and eight were ribosomal RNA genes. The genomic characteristics of C. carpatica are similar to those of other Campanula species in terms of repetitive sequences, sequence divergence, and contraction/expansion events in the inverted repeat regions. A phylogenetic analysis of 63 shared genes in 16 plant species revealed that Campanula zangezura is the closest relative of C. carpatica. Phylogenetic analysis indicated that C. carpatica was within the Campanula clade, and C. pallida occupied the outermost position of that clade. Full article
(This article belongs to the Special Issue Advances in Chloroplast Genomics and Proteostasis)
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