Transcriptome and Small RNA Profiling of Potato Virus Y Infected Potato Cultivars, Including Systemically Infected Russet Burbank by Brian T. Ross, Nina Zidack, Rose McDonald, Michelle L. Flenniken

“…To gain greater understanding of the transcriptional changes that occur during the development of systemic PVY-infection, we analyzed Russet Burbank leaf samples one week and four weeks post-inoculation and identified similarities and differences, including higher expression of genes involved in chloroplast function, photosynthesis, and secondary metabolite production, and lower expression of defense response genes at those time points. …”
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Comparative Analysis of <i>Apopellia endiviifolia</i> Plastomes Reveals a Strikingly High Level of Differentiation between Its Terrestrial and Water Form by Jakub Sawicki, Katarzyna Krawczyk, Monika Ślipiko, Kamil Szandar, Monika Szczecińska

“…Newly sequenced, assembled and annotated chloroplast genomes of six European specimens belonging to the two cryptic lineages occupying different microhabitats, revealed the structure typical for liverworts and previously sequenced reference. …”
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Genetic structure and bio-climatic modeling support allopatric over parapatric speciation along a latitudinal gradient by Rossetto Maurizio, Allen Chris B, Thurlby Katie AG, Weston Peter H, Milner Melita L

“…Seven nuclear microsatellites (nSSR) and six chloroplast microsatellites (cpSSR) were amplified across all populations. …”
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Comparative systematics and phylogeography of Quercus Section Cerris in western Eurasia: inferences from plastid and nuclear DNA variation by Marco Cosimo Simeone, Simone Cardoni, Roberta Piredda, Francesca Imperatori, Michael Avishai, Guido W. Grimm, Thomas Denk

“…Cerris using plastid (trnH-psbA) and nuclear (5S-IGS) DNA variation with a dense intra-specific and geographic sampling. Chloroplast haplotypes primarily reflected phylogeographic patterns originating from interspecific cytoplasmic gene flow within sect. …”
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Genomic Sequence of Canadian <i>Chenopodium berlandieri</i>: A North American Wild Relative of Quinoa by Mark E. Samuels, Cassandra Lapointe, Sara Halwas, Anne C. Worley

“…To this end, we first optimized barcode markers in two chloroplast genes, <i>rbcL</i> and <i>matK</i>. Together these markers can distinguish <i>C. berlandieri</i> from the morphologically similar Eurasian invasive <i>C. album</i> (lamb’s quarters). …”
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A phylogenetic analysis of Bromus (Poaceae: Pooideae: Bromeae) based on nuclear ribosomal and plastid data, with a focus on Bromus sect. Bromus by Akram Nasiri, Shahrokh Kazempour-Osaloo, Behnam Hamzehee, Roger D. Bull, Jeffery M. Saarela

“…We infer these species may have obtained their plastomes via chloroplast capture from species of B. sect. Bromus and B. sect. …”
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Effects of the repression of GIGANTEA gene StGI.04 on the potato leaf transcriptome and the anthocyanin content of tuber skin by Khongorzul Odgerel, Jeny Jose, Flóra Karsai-Rektenwald, Gitta Ficzek, Gergely Simon, György Végvári, Zsófia Bánfalvi

“…This protein is involved in flowering, circadian clock control, chloroplast biogenesis, carbohydrate metabolism, stress responses, and volatile compound synthesis. …”
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Genome-Wide Identification and Expression Analysis of the RADIALIS-like Gene Family in <i>Camellia sinensis</i> by Shaoying Wang, Beibei Wen, Yun Yang, Shanshan Long, Jianjun Liu, Meifeng Li

“…According to protein functional interaction networks, CsaRL1a was well connected with WIN1-like, lysine histidine transporter-1-like, β-amylase 3 chloroplastic-like, carbonic anhydrase-2-like (CA2), and carbonic anhydrase dnaJC76 (DJC76). …”
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Zinc oxide nanoparticles alleviates the adverse effects of cadmium stress on Oryza sativa via modulation of the photosynthesis and antioxidant defense system by Mohammad Faizan, Javaid Akhter Bhat, Kamel Hessini, Fangyuan Yu, Parvaiz Ahmad

“…Moreover, the ZnO-NPs supplement has also positive effects on photosynthesis related parameters, SPAD value (40%), chloroplast structure, and qualitatively high fluorescence observed by confocal microscopy even under Cd stress. …”
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Extrapolating plot-scale CO2 and ozone enrichment experimental results to novel conditions and scales using mechanistic modeling by Eric J. Gustafson, Mark E. Kubiske, Brian R. Miranda, Yasutomo Hoshika, Elena Paoletti

“…We added novel algorithms to the model to mechanistically simulate the effects of ozone on photosynthesis through ozone-induced impairment of stomatal control (i.e., stomatal sluggishness) and damage of photosynthetic capacity at the chloroplast level. Results We calibrated the model to empirical observations of competitive interactions on the elevated CO2 and O3 plots of the Aspen-FACE experiment and successfully validated it on the combined factor plots. …”
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Simultaneous determination of protoporphyrin IX and magnesium protoporphyrin IX in Arabidopsis thaliana and Camellia sinensis using UPLC-MS/MS by Chenyu Zhang, Chunlei Ma, Li Zhu, Mingzhe Yao

“…However, the lack of systematic study of the detection method and the metabolic difference between species have caused the research on chloroplast retrograde signaling controversial for a long time. …”
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Differential genetic responses to the stress revealed the mutation-order adaptive divergence between two sympatric ginger species by Bing-Hong Huang, Yuan-Chien Lin, Chih-Wei Huang, Hsin-Pei Lu, Min-Xin Luo, Pei-Chun Liao

“…For understanding when and how these two species diverged, intraspecific variation was estimated from three chloroplast DNA fragments (cpDNA) and interspecific genome-wide SNPs and expression differences after saline treatment were examined by transcriptomic analyses. …”
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Transcriptomic Determination of the Core Genes Regulating the Growth and Physiological Traits of <i>Quercus mongolica</i> Fisch. ex Ledeb by Xinman Li, Min Jiang, Junjie Ren, Zhaohua Liu, Wanying Zhang, Guifen Li, Jinmao Wang, Minsheng Yang

“…The co-expression network also indicated key roles for genes related to the stress response (SDH, WAK5, APA1), metabolic processes (UGT76A2, HTH, At5g42100, PEX11C), signal transduction (INPS1, HSD1), and chloroplast biosynthesis (CAB13, PTAC16, PNSB5). Functional annotation of these core genes implies that <i>Q. mongolica</i> can adapt to different environments by regulating photosynthesis, plant hormone signal transduction, the stress response, and other key physiological and biochemical processes. …”
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Aspectos anatômicos de plântulas Foeniculum vulgare Mill. Anatomical aspects of the Foeniculum vulgare Mill. seedling by C.F. Azevedo, Z.G.M. Quirino, E.R. Rego, R.L.A. Bruno, G.Z. Silva

“…The cotyledons and the leaves have photosynthetic and nutrition functions, as indicated by the presence of large numbers of stomata, chloroplast and starch. The anatomical characterization of the F. vulgare seedling aids in specie identification and knowledge of cellular organization, providing information that assists in physiological, taxonomic and ecological studies.…”
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<named-content content-type="genus-species">Ralstonia solanacearum</named-content> Type III Effector RipAY Is a Glutathione-Degrading Enzyme That Is Activated by Plant Cytosolic Th... by Takafumi Mukaihara, Tadashi Hatanaka, Masahito Nakano, Kenji Oda

“…Interestingly, RipAY was activated by plant h-type thioredoxins that exist in large amounts in the plant cytosol, but not by chloroplastic m-, f-, x-, y- and z-type thioredoxins, in a thiol-independent manner. …”
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Development of a High-Quality/Yield Long-Read Sequencing-Adaptable DNA Extraction Method for Crop Seeds by Naohiro Shioya, Eri Ogiso-Tanaka, Masanori Watanabe, Toyoaki Anai, Tomoki Hoshino

“…DNA extracted from seeds using the IMP Boom method showed an increase in the percentage of the nuclear genome with a decrease in the relative ratio of chloroplast DNA. These results suggested that the proposed IMP Boom method can extract high-quality and high-concentration DNA that can be used for long-read sequencing, which cannot be achieved from plant seeds using other conventional DNA extraction methods. …”
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Comparative phylogeographic analysis of Cuscuta campestris and Cuscuta reflexa in Kenya: Implications for management of highly invasive vines by Joel Masanga, Richard Oduor, Amos Alakonya, Mathew Ngugi, Patroba Ojola, Emily S. Bellis, Steven Runo

“…A comparative phylogeographic analysis, based on chloroplast and nuclear ribosomal DNA, was performed to determine genetic diversities, population structure, and isolation of C. campestris and C. reflexa in Kenya. …”
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Identification of DNA Markers Linked to Blooming Time in Almond by Mousa Rasouli, Mohammad Reza Fattahi Moghaddam, Ali Imani, Zabihollah Zamani, Pedro Martínez-Gómez

“…A modified-bulk segregant analysis in combination with the application of the 140 RAPD primers, 87 nuclear SSR markers spanning the whole almond genome and 5 chloroplast SSR markers, were used to identify molecular markers linked to flowering time. …”
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Phenotypic Variability and Genetic Diversity of <i>Phragmites australis</i> in Quebec and Kashmir Reveal Contrasting Population Structure by Gowher A. Wani, Manzoor A. Shah, Honoré Tekeu, Zafar A. Reshi, Alain R. Atangana, Damase P. Khasa

“…Herbarium-based information sources from 2005 onwards about nativity and distributional range of <i>Phragmites australis</i> were used to survey putative native populations of the species in Quebec, and chloroplast DNA (cpDNA) PCR-RFLP analyses identified only one native population, whereas the same analyses revealed that the Kashmir populations are invasive. …”
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Comprehensive proteome analyses of lysine acetylation in tea leaves by sensing nitrogen nutrition by Jutang Jiang, Zhongshuai Gai, Yu Wang, Kai Fan, Litao Sun, Hui Wang, Zhaotang Ding

“…The most of the identified lysine acetylation proteins were located in the chloroplast (39%) and cytoplasm (29%). The largest group of acetylated proteins consisted of many enzymes, such as ATP synthase, ribosomal proteins and malate dehydrogenase [NADP], which were related to metabolism (38%) in the biological process. …”
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