Target Capture Sequencing Unravels Rubus Evolution by Katherine A. Carter, Aaron Liston, Nahla V. Bassil, Lawrence A. Alice, Jill M. Bushakra, Brittany L. Sutherland, Todd C. Mockler, Douglas W. Bryant, Kim E. Hummer

“…Our objectives were to estimate the phylogeny of 94 taxonomically and geographically diverse species and three cultivars using chloroplast DNA sequences and target capture of approximately 1,000 low copy nuclear genes; estimate divergence times between major Rubus clades; and examine the historical biogeography of species diversification. …”
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Genome-wide identification and expression analysis of the ftsH protein family and its response to abiotic stress in Nicotiana tabacum L by Tianxiunan Pu, Zejun Mo, Long Su, Jing Yang, Ke Wan, Linqi Wang, Renxiang Liu, Yang Liu

“…Studies have shown that it is a key gene for plant chloroplast development and photosynthesis regulation. …”
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Genome-wide survey of the phosphofructokinase family in cassava and functional characterization in response to oxygen-deficient stress by Haiyan Wang, Pingjuan Zhao, Xu Shen, Zhiqiang Xia, Xincheng Zhou, Xin Chen, Cheng Lu, WenquanWang

“…We confirmed by green fluorescent protein fusion protein expression that MePFK03 and MePFPA1 were localised in the chloroplast and cytoplasm, respectively. The expression profiles of the 13 MePFKs detected by quantitative reverse transcription polymerase chain reaction revealed that MePFK02, MePFK03, MePFPA1, MePFPB1 displayed higher expression in leaves, root and flower. …”
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Genome-wide analysis and functional validation reveal the role of late embryogenesis abundant genes in strawberry (Fragaria × ananassa) fruit ripening by Yuanxiu Lin, Musha She, Mantong Zhao, Hong Yu, Wenfei Xiao, Yunting Zhang, Mengyao Li, Qing Chen, Yong Zhang, Yan Wang, Wen He, Xiaorong Wang, Haoru Tang, Ya Luo

“…Subcellular localization prediction indicated that they were mostly localized in chloroplast, cytoplasm and nucleus. Duplication events detection revealed that whole genome duplication or segmental was the main driver for the expansion of LEA family in strawberry. …”
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The AP2 Transcription Factor <i>BrSHINE3</i> Regulates Wax Accumulation in Nonheading Chinese Cabbage by Zhaoyan Huo, Yang Xu, Song Yuan, Jiang Chang, Shuhao Li, Jinwei Wang, Huanhuan Zhao, Ru Xu, Fenglin Zhong

“…The analysis of the subcellular localization showed that <i>BrSHINE3</i> is mainly located in the nucleus and chloroplast of tobacco leaves, suggesting that the gene may function as a transcription factor. …”
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RNA-seq analysis reveals narrow differential gene expression in MEP and MVA pathways responsible for phytochemical divergence in extreme genotypes of Thymus daenensis Celak by Hosein Ahmadi, Reza Fatahi, Zabihollah Zamani, Majid Shokrpour, Morteza Sheikh-Assadi, Peter Poczai

“…These results suggest that an active cytosolic mevalonate (MVA) pathway may be linked to higher levels of sesquiterpenes, triterpenic acids, and carvacrol in ‘Zagheh-11’. The chloroplastic pathway of methyl erythritol phosphate (MEP) may have also contributed to a higher accumulation of thymol in Malayer-21. …”
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Analysis of Genetic Diversity and Phylogenetic Relationships of Wheat (<i>Triticum aestivum</i> L.) Genotypes Using Phenological, Molecular and DNA Barcoding Markers by Mohamed A. El-Esawi, Mohamed M. A. Elashtokhy, Sahar A. M. Shamseldin, Enas M. El-Ballat, Ehab M. Zayed, Yasmin M. Heikal

“…Moreover, based on the two chloroplast DNA regions (<i>rbcL</i> and <i>matK</i>), <i>MatK</i> was found to be more reliable for differentiating among <i>T. aestivum</i> genotypes. …”
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Transcriptome Analysis Reveals Changes in Whole Gene Expression, Biological Process, and Molecular Functions Induced by Nickel in Jack Pine (<i>Pinus banksiana</i>) by Alistar Moy, Karolina Czajka, Paul Michael, Kabwe Nkongolo

“…Of these genes, 21.7% were found in the plasma membrane, 16.1% in the cytosol, 12.4% with the chloroplast and 11.9% in the extracellular region. Nickel ions induced changes in gene expression, resulting in the emergence of differentially regulated categories. …”
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Genome-Wide Identification and Expression Analysis of Heat Shock Protein 70 (<i>HSP70</i>) Gene Family in Pumpkin (<i>Cucurbita moschata</i>) Rootstock under Drought Stress Suggest... by Marzieh Davoudi, Jinfeng Chen, Qunfeng Lou

“…These genes were mostly localized in the cytoplasm, chloroplast, mitochondria, nucleus, and endoplasmic reticulum (ER). …”
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Physio-ultrastructural footprints and iTRAQ-based proteomic approach unravel the role of Piriformospora indica-colonization in counteracting cadmium toxicity in rice by Tichaona Sagonda, Muhammad Faheem Adil, Shafaque Sehar, Adeela Rasheed, Heren Issaka Joan, Younan Ouyang, Imran Haider Shamsi

“…P. indica colonization sustained chloroplast integrity and reduced Cd translocation (46% and 64%), significantly lowering malondialdehyde (MDA) content (11.3% and 50.4%) compared to uninoculated roots under Cd stress in IR8 and ZX1H, respectively. …”
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Recent Trends in Research on the Genetic Diversity of Plants: Implications for Conservation by Yasmin G. S. Carvalho, Luciana C. Vitorino, Ueric J. B. de Souza, Layara A. Bessa

“…In plants, indices of genetic diversity (e.g., <i>k</i>, <i>h</i> and <i>&#960;</i>) and structure (e.g., F_ST) are typically inferred from sequences of chloroplast markers. Given the recent advances and popularization of molecular techniques for research in population genetics, phylogenetics, phylogeography, and ecology, we adopted a scientometric approach to compile evidence on the recent trends in the use of cpDNA sequences as markers for the analysis of genetic diversity in botanical studies, over the years. …”
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Effects of high CO2 treatment on green-ripening and peel senescence in banana and plantain fruits by Mu-bo SONG, Lu-ping TANG, Xue-lian ZHANG, Mei BAI, Xue-qun PANG, Zhao-qi ZHANG

“…Compared to the effect on plantains, 20% CO2 treatment delayed the decline in the chlorophyll florescence (Fv/Fm) values and in the mRNA levels of a gene coding small subunit of Rubisco (SSU), and postponed the disruption of the ultrastructure of chloroplast in the peel tissue of bananas, indicating that the senescence of the green cells in the exocarp layer was delayed by 20% CO2, to more extent in bananas than in plantains. …”
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Bacterial communities in the gut of wild and mass-reared Zeugodacus cucurbitae and Bactrocera dorsalis revealed by metagenomic sequencing by Ashok B. Hadapad, Suresh K. G. Shettigar, Ramesh S. Hire

“…Higher relative abundance of Phylum Firmicutes was observed in mass-reared fruit fly than wild adults. Cyanobacteria/Chloroplast and Actinobacteria were also present with very low relative abundance in both wild as well as mass-reared melon fly and Oriental fruit fly. …”
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Intestinal Microbiota Differences in <i>Litopenaeus vannamei</i> Shrimp between Greenhouse and Aquaponic Rearing by Yabin Dou, Mengying Wen, Hui Shen, Sheng Zhang, Ge Jiang, Yi Qiao, Jie Cheng, Xiaohui Cao, Xihe Wan, Xiaoman Sun

“…In addition, pathways such as sulfate, chloroplast, phototrophy, and the nitrogen metabolism were significantly different between the WE and YE samples. …”
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Physiological and Ultrastructural Changes in <i>Dendranthema morifolium</i> Cultivars Exposed to Different Cadmium Stress Conditions by Luqman Muhammad, Salahuddin, Asif Khan, Yunwei Zhou, Miao He, Abdulwahed Fahad Alrefaei, Murtaza Khan, Sajid Ali

“…Additionally, ultrastructure changes also occurred with the increase in the Cd stress, i.e., 20 mg L⁻¹ to 100 mg L⁻¹, and these changes caused alterations in cell organelles, including in the chloroplast, grana, lamella, thylakoid, and stroma. …”
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QTL mapping and transcriptome analysis identify candidate genes regulating pericarp thickness in sweet corn by Xiaming Wu, Bo Wang, Fugui Xie, Liping Zhang, Jie Gong, Wei Zhu, Xiaoqin Li, Faqiang Feng, Jun Huang

“…GRMZM2G143352 and GRMZM2G143402 have been annotated as AUX/IAA transcription factor and ZIM transcription factor, respectively, while GRMZM2G143389 has been annotated as FATTY ACID EXPORT 2, chloroplastic. Conclusions This study identified a major QTL and candidate genes that could accelerate breeding for the thin pericarp thickness variety of sweet corn, and these results established the basis for map-based cloning and further functional research.…”
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Crossability and genetic analyses of Andrographis paniculata nees. populations using phenotypic and molecular markers by Valdiani, Alireza

“…Phylogenetic analysis was performed using three chloroplast genes consisting of Internal Transcribed Spacer Region (ITS), Plastid matK regions, rps16 gene and trnL-F intron region along with phytochemical markers. …”
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Isolation of transketolase gene, subcellular localization, and transketolase protein structure studies of sugarcane (Saccharum officinarum. L) by Kalhori, Nahid

“…Analysis by Target P 1.1 followed by Chloro P revealed that sugarcane transketolase is localised in the chloroplast which is 85 amino acids are plant plastid target sequence. …”
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Systematics and cuttings rooting performance of cempaka (Magnolia spp.plum. ex L., Magnoliaceae) in Peninsular Malaysia by Hoong, Tan Sin

“…Dendrogram generated showed similar relationships with previous studies based on chloroplast DNA sequences. The number of ISSR markers informative for discrimination of infraspecific variation in M. champaca, M. alba, M. macklottii var. …”
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Genetic diversities in wild and cultivated populations of the two closely-related medical plants species, Tripterygium Wilfordii and T. Hypoglaucum (Celastraceae) by Chao Liu, Jingyi Wang, Ya-Zhu Ko, Meng-Shin Shiao, Yiheng Wang, Jiahui Sun, Qingjun Yuan, Lisong Wang, Yu-Chung Chiang, Lanping Guo

“…Results In this study, we investigated the genetic diversity and population structure of the two traditional medicinal semiwoody vines plant species, Tripterygium wilfordii and T. hypoglaucum, including wild and cultivated populations using chloroplast DNA (cpDNA) sequences and microsatellite loci. …”
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