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Chloroplast 2.0
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Chloroplast 2.0

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 (21 July 2019) | Viewed by 28523

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 colleague,

This Special Issue is the continuation of our previous special issue "Chloroplast".

Chloroplasts are at the front line of many advances in molecular biology, ranging from evolutionary biology to the mechanism of energy transduction, and also includes stress responses and programmed leaf death. In addition to the relevance of basic knowledge, advances are unveiling promising insights to improve plant productivity, disease resistance, and environmental control. The production of secondary metabolites and proteins by transformed chloroplasts adds further excitement to applied investigations of chloroplasts.

The new issue focused on chloroplasts is intended to continue with the successful quantity and quality of papers in the previous issue. Papers submitted to the second Special Issue must report high novelty results and/or plausible and testable new models. The molecular basis of the conversion of light to chemical energy in photosystems is a reference topic. In addition, the structure and function of other components of the photosynthesis machinery, plastid genomic, plastid biogenesis and senescence, metabolism, reactive oxygen species and membrane transport are also of interest, with a special emphasis on the gene level and evolutionary comparisons. Significant advances in chloroplast transformation are also welcome.

Prof. Dr. Bartolome Sabater
Guest Editor

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Keywords

  • electron transport
  • endosymbiosis
  • photosynthesis
  • photosystems
  • plants
  • plastid DNA
  • reactive oxygen species (ROS)
  • thylakoid

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Related Special Issue

Published Papers (7 papers)

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Research

14 pages, 3218 KiB  
Article
Chloroplast Genomes and Comparative Analyses among Thirteen Taxa within Myrsinaceae s.str. Clade (Myrsinoideae, Primulaceae)
by Xiaokai Yan, Tongjian Liu, Xun Yuan, Yuan Xu, Haifei Yan and Gang Hao
Int. J. Mol. Sci. 2019, 20(18), 4534; https://doi.org/10.3390/ijms20184534 - 13 Sep 2019
Cited by 19 | Viewed by 3373
Abstract
The Myrsinaceae s.str. clade is a tropical woody representative in Myrsinoideae of Primulaceae and has ca. 1300 species. The generic limits and alignments of this clade are unclear due to the limited number of genetic markers and/or taxon samplings in previous studies. Here, [...] Read more.
The Myrsinaceae s.str. clade is a tropical woody representative in Myrsinoideae of Primulaceae and has ca. 1300 species. The generic limits and alignments of this clade are unclear due to the limited number of genetic markers and/or taxon samplings in previous studies. Here, the chloroplast (cp) genomes of 13 taxa within the Myrsinaceae s.str. clade are sequenced and characterized. These cp genomes are typical quadripartite circle molecules and are highly conserved in size and gene content. Three pseudogenes are identified, of which ycf15 is totally absent from five taxa. Noncoding and large single copy region (LSC) exhibit higher levels of nucleotide diversity (Pi) than other regions. A total of ten hotspot fragments and 796 chloroplast simple sequence repeats (SSR) loci are found across all cp genomes. The results of phylogenetic analysis support the notion that the monophyletic Myrsinaceae s.str. clade has two subclades. Non-synonymous substitution rates (dN) are higher in housekeeping (HK) genes than photosynthetic (PS) genes, but both groups have a nearly identical synonymous substitution rate (dS). The results indicate that the PS genes are under stronger functional constraints compared with the HK genes. Overall, the study provides hypervariable molecular markers for phylogenetic reconstruction and contributes to a better understanding of plastid gene evolution in Myrsinaceae s.str. clade. Full article
(This article belongs to the Special Issue Chloroplast 2.0)
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17 pages, 998 KiB  
Article
Plastid Genomes of Carnivorous Plants Drosera rotundifolia and Nepenthes × ventrata Reveal Evolutionary Patterns Resembling Those Observed in Parasitic Plants
by Eugeny V. Gruzdev, Vitaly V. Kadnikov, Alexey V. Beletsky, Elena Z. Kochieva, Andrey V. Mardanov, Konstantin G. Skryabin and Nikolai V. Ravin
Int. J. Mol. Sci. 2019, 20(17), 4107; https://doi.org/10.3390/ijms20174107 - 22 Aug 2019
Cited by 13 | Viewed by 4012
Abstract
Carnivorous plants have the ability to capture and digest small animals as a source of additional nutrients, which allows them to grow in nutrient-poor habitats. Here we report the complete sequences of the plastid genomes of two carnivorous plants of the order Caryophyllales, [...] Read more.
Carnivorous plants have the ability to capture and digest small animals as a source of additional nutrients, which allows them to grow in nutrient-poor habitats. Here we report the complete sequences of the plastid genomes of two carnivorous plants of the order Caryophyllales, Drosera rotundifolia and Nepenthes × ventrata. The plastome of D. rotundifolia is repeat-rich and highly rearranged. It lacks NAD(P)H dehydrogenase genes, as well as ycf1 and ycf2 genes, and three essential tRNA genes. Intron losses are observed in some protein-coding and tRNA genes along with a pronounced reduction of RNA editing sites. Only six editing sites were identified by RNA-seq in D. rotundifolia plastid genome and at most conserved editing sites the conserved amino acids are already encoded at the DNA level. In contrast, the N. × ventrata plastome has a typical structure and gene content, except for pseudogenization of the ccsA gene. N. × ventrata and D. rotundifolia could represent different stages of evolution of the plastid genomes of carnivorous plants, resembling events observed in parasitic plants in the course of the switch from autotrophy to a heterotrophic lifestyle. Full article
(This article belongs to the Special Issue Chloroplast 2.0)
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15 pages, 4559 KiB  
Article
Comparison and Phylogenetic Analysis of Chloroplast Genomes of Three Medicinal and Edible Amomum Species
by Yingxian Cui, Xinlian Chen, Liping Nie, Wei Sun, Haoyu Hu, Yulin Lin, Haitao Li, Xilong Zheng, Jingyuan Song and Hui Yao
Int. J. Mol. Sci. 2019, 20(16), 4040; https://doi.org/10.3390/ijms20164040 - 19 Aug 2019
Cited by 72 | Viewed by 5383
Abstract
Amomum villosum is an important medicinal and edible plant with several pharmacologically active volatile oils. However, identifying A. villosum from A. villosum var. xanthioides and A. longiligulare which exhibit similar morphological characteristics to A. villosum, is difficult. The main goal of this [...] Read more.
Amomum villosum is an important medicinal and edible plant with several pharmacologically active volatile oils. However, identifying A. villosum from A. villosum var. xanthioides and A. longiligulare which exhibit similar morphological characteristics to A. villosum, is difficult. The main goal of this study, therefore, is to mine genetic resources and improve molecular methods that could be used to distinguish these species. A total of eight complete chloroplasts (cp) genomes of these Amomum species which were collected from the main producing areas in China were determined to be 163,608–164,069 bp in size. All genomes displayed a typical quadripartite structure with a pair of inverted repeat (IR) regions (29,820–29,959 bp) that separated a large single copy (LSC) region (88,680–88,857 bp) from a small single copy (SSC) region (15,288–15,369 bp). Each genome encodes 113 different genes with 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. More than 150 SSRs were identified in the entire cp genomes of these three species. The Sanger sequencing results based on 32 Amomum samples indicated that five highly divergent regions screened from cp genomes could not be used to distinguish Amomum species. Phylogenetic analysis showed that the cp genomes could not only accurately identify Amomum species, but also provide a solid foundation for the establishment of phylogenetic relationships of Amomum species. The availability of cp genome resources and the comparative analysis is beneficial for species authentication and phylogenetic analysis in Amomum. Full article
(This article belongs to the Special Issue Chloroplast 2.0)
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15 pages, 2527 KiB  
Article
Development of Plastid Genomic Resources for Discrimination and Classification of Epimedium wushanense (Berberidaceae)
by Mengyue Guo, Li Ren, Yanqin Xu, Baosheng Liao, Jingyuan Song, Ying Li, Nitin Mantri, Baolin Guo, Shilin Chen and Xiaohui Pang
Int. J. Mol. Sci. 2019, 20(16), 4003; https://doi.org/10.3390/ijms20164003 - 16 Aug 2019
Cited by 10 | Viewed by 2639
Abstract
Epimedium wushanense (Berberidaceae) is recorded as the source plant of Epimedii Wushanensis Folium in the Chinese Pharmacopoeia. However, controversies exist on the classification of E. wushanense and its closely related species, namely, E. pseudowushanense, E. chlorandrum, E. mikinorii, E. [...] Read more.
Epimedium wushanense (Berberidaceae) is recorded as the source plant of Epimedii Wushanensis Folium in the Chinese Pharmacopoeia. However, controversies exist on the classification of E. wushanense and its closely related species, namely, E. pseudowushanense, E. chlorandrum, E. mikinorii, E. ilicifolium, and E. borealiguizhouense. These species are often confused with one another because of their highly similar morphological characteristics. This confusion leads to misuse in the medicinal market threatening efficiency and safety. Here, we studied the plastid genomes of these Epimedium species. Results show that the plastid genomes of E. wushanense and its relative species are typical circular tetramerous structure, with lengths of 156,855–158,251 bp. A total of 112 genes were identified from the Epimedium plastid genomes, including 78 protein-coding, 30 tRNA, and 4 rRNA genes. A loss of rpl32 gene in E. chlorandrum was found for the first time in this study. The phylogenetic trees constructed indicated that E. wushanense can be distinguished from its closely related species. E. wushanense shows a closer relationship to species in ser. Dolichocerae. In conclusion, the use of plastid genomes contributes useful genetic information for identifying medicinally important species E. wushanense and provides new evidence for understanding phylogenetic relationships within the Epimedium genus. Full article
(This article belongs to the Special Issue Chloroplast 2.0)
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14 pages, 1566 KiB  
Article
UMP Kinase Regulates Chloroplast Development and Cold Response in Rice
by Qing Dong, Ying-Xin Zhang, Quan Zhou, Qun-En Liu, Dai-Bo Chen, Hong Wang, Shi-Hua Cheng, Li-Yong Cao and Xi-Hong Shen
Int. J. Mol. Sci. 2019, 20(9), 2107; https://doi.org/10.3390/ijms20092107 - 29 Apr 2019
Cited by 14 | Viewed by 3496
Abstract
Pyrimidine nucleotides are important metabolites that are building blocks of nucleic acids, which participate in various aspects of plant development. Only a few genes involved in pyrimidine metabolism have been identified in rice and the majority of their functions remain unclear. In this [...] Read more.
Pyrimidine nucleotides are important metabolites that are building blocks of nucleic acids, which participate in various aspects of plant development. Only a few genes involved in pyrimidine metabolism have been identified in rice and the majority of their functions remain unclear. In this study, we used a map-based cloning strategy to isolate a UMPK gene in rice, encoding the UMP kinase that phosphorylates UMP to form UDP, from a recessive mutant with pale-green leaves. In the mutant, UDP content always decreased, while UTP content fluctuated with the development of leaves. Mutation of UMPK reduced chlorophyll contents and decreased photosynthetic capacity. In the mutant, transcription of plastid-encoded RNA polymerase-dependent genes, including psaA, psbB, psbC and petB, was significantly reduced, whereas transcription of nuclear-encoded RNA polymerase-dependent genes, including rpoA, rpoB, rpoC1, and rpl23, was elevated. The expression of UMPK was significantly induced by various stresses, including cold, heat, and drought. Increased sensitivity to cold stress was observed in the mutant, based on the survival rate and malondialdehyde content. High accumulation of hydrogen peroxide was found in the mutant, which was enhanced by cold treatment. Our results indicate that the UMP kinase gene plays important roles in regulating chloroplast development and stress response in rice. Full article
(This article belongs to the Special Issue Chloroplast 2.0)
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17 pages, 4982 KiB  
Article
Evolutionary Analysis of Plastid Genomes of Seven Lonicera L. Species: Implications for Sequence Divergence and Phylogenetic Relationships
by Mi-Li Liu, Wei-Bing Fan, Ning Wang, Peng-Bin Dong, Ting-Ting Zhang, Ming Yue and Zhong-Hu Li
Int. J. Mol. Sci. 2018, 19(12), 4039; https://doi.org/10.3390/ijms19124039 - 14 Dec 2018
Cited by 24 | Viewed by 4742
Abstract
Plant plastomes play crucial roles in species evolution and phylogenetic reconstruction studies due to being maternally inherited and due to the moderate evolutionary rate of genomes. However, patterns of sequence divergence and molecular evolution of the plastid genomes in the horticulturally- and economically-important [...] Read more.
Plant plastomes play crucial roles in species evolution and phylogenetic reconstruction studies due to being maternally inherited and due to the moderate evolutionary rate of genomes. However, patterns of sequence divergence and molecular evolution of the plastid genomes in the horticulturally- and economically-important Lonicera L. species are poorly understood. In this study, we collected the complete plastomes of seven Lonicera species and determined the various repeat sequence variations and protein sequence evolution by comparative genomic analysis. A total of 498 repeats were identified in plastid genomes, which included tandem (130), dispersed (277), and palindromic (91) types of repeat variations. Simple sequence repeat (SSR) elements analysis indicated the enriched SSRs in seven genomes to be mononucleotides, followed by tetra-nucleotides, dinucleotides, tri-nucleotides, hex-nucleotides, and penta-nucleotides. We identified 18 divergence hotspot regions (rps15, rps16, rps18, rpl23, psaJ, infA, ycf1, trnN-GUU-ndhF, rpoC2-rpoC1, rbcL-psaI, trnI-CAU-ycf2, psbZ-trnG-UCC, trnK-UUU-rps16, infA-rps8, rpl14-rpl16, trnV-GAC-rrn16, trnL-UAA intron, and rps12-clpP) that could be used as the potential molecular genetic markers for the further study of population genetics and phylogenetic evolution of Lonicera species. We found that a large number of repeat sequences were distributed in the divergence hotspots of plastid genomes. Interestingly, 16 genes were determined under positive selection, which included four genes for the subunits of ribosome proteins (rps7, rpl2, rpl16, and rpl22), three genes for the subunits of photosystem proteins (psaJ, psbC, and ycf4), three NADH oxidoreductase genes (ndhB, ndhH, and ndhK), two subunits of ATP genes (atpA and atpB), and four other genes (infA, rbcL, ycf1, and ycf2). Phylogenetic analysis based on the whole plastome demonstrated that the seven Lonicera species form a highly-supported monophyletic clade. The availability of these plastid genomes provides important genetic information for further species identification and biological research on Lonicera. Full article
(This article belongs to the Special Issue Chloroplast 2.0)
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20 pages, 3648 KiB  
Article
Intergeneric Relationships within the Early-Diverging Angiosperm Family Nymphaeaceae Based on Chloroplast Phylogenomics
by Dingxuan He, Andrew W. Gichira, Zhizhong Li, John M. Nzei, Youhao Guo, Qingfeng Wang and Jinming Chen
Int. J. Mol. Sci. 2018, 19(12), 3780; https://doi.org/10.3390/ijms19123780 - 28 Nov 2018
Cited by 13 | Viewed by 4223
Abstract
The order Nymphaeales, consisting of three families with a record of eight genera, has gained significant interest from botanists, probably due to its position as a basal angiosperm. The phylogenetic relationships within the order have been well studied; however, a few controversial nodes [...] Read more.
The order Nymphaeales, consisting of three families with a record of eight genera, has gained significant interest from botanists, probably due to its position as a basal angiosperm. The phylogenetic relationships within the order have been well studied; however, a few controversial nodes still remain in the Nymphaeaceae. The position of the Nuphar genus and the monophyly of the Nymphaeaceae family remain uncertain. This study adds to the increasing number of the completely sequenced plastid genomes of the Nymphaeales and applies a large chloroplast gene data set in reconstructing the intergeneric relationships within the Nymphaeaceae. Five complete chloroplast genomes were newly generated, including a first for the monotypic Euryale genus. Using a set of 66 protein-coding genes from the chloroplast genomes of 17 taxa, the phylogenetic position of Nuphar was determined and a monophyletic Nymphaeaceae family was obtained with convincing statistical support from both partitioned and unpartitioned data schemes. Although genomic comparative analyses revealed a high degree of synteny among the chloroplast genomes of the ancient angiosperms, key minor variations were evident, particularly in the contraction/expansion of the inverted-repeat regions and in RNA-editing events. Genome structure, and gene content and arrangement were highly conserved among the chloroplast genomes. The intergeneric relationships defined in this study are congruent with those inferred using morphological data. Full article
(This article belongs to the Special Issue Chloroplast 2.0)
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