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https://www.readbyqxmd.com/read/28637286/structure-seq2-sensitive-and-accurate-genome-wide-profiling-of-rna-structure-in-vivo
#1
Laura E Ritchey, Zhao Su, Yin Tang, David C Tack, Sarah M Assmann, Philip C Bevilacqua
RNA serves many functions in biology such as splicing, temperature sensing, and innate immunity. These functions are often determined by the structure of RNA. There is thus a pressing need to understand RNA structure and how it changes during diverse biological processes both in vivo and genome-wide. Here, we present Structure-seq2, which provides nucleotide-resolution RNA structural information in vivo and genome-wide. This optimized version of our original Structure-seq method increases sensitivity by at least 4-fold and improves data quality by minimizing formation of a deleterious by-product, reducing ligation bias, and improving read coverage...
June 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28626007/establishment-of-photosynthesis-is-controlled-by-two-distinct-regulatory-phases
#2
Carole Dubreuil, Xu Jin, Juan de Dios Barajas-López, Timothy Hewitt Hewitt, Sandra Tanz, Thomas Dobrenel, Wolfgang Schröder, Johannes Hanson, Edouard Pesquet, Andreas Grönlund, Ian D Small, Asa Strand
Chloroplasts develop from undifferentiated proplastids present in meristematic tissue. Chloroplast biogenesis is thus closely connected to leaf development, which restricts our ability to study the process of chloroplast biogenesis per se. As a consequence we know relatively little about the regulatory mechanisms behind the establishment of the photosynthetic reactions and how the activities of the two genomes involved are coordinated during chloroplast development. We developed a single-cell-based experimental system from Arabidopsis with high temporal resolution allowing for investigations of the transition from proplastids to functional chloroplasts...
June 16, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28624520/dissecting-the-chloroplast-proteome-of-chickpea-cicer-arietinum-l-provides-new-insights-into-classical-and-non-classical-functions
#3
Nilesh Vikram Lande, Pratigya Subba, Pragya Barua, Dipak Gayen, T S Keshava Prasad, Subhra Chakraborty, Niranjan Chakraborty
Chloroplast, the energy organelle unique to plant cells, is a dynamic entity which integrates an array of metabolic pathways and serves as first level for energy conversion for the entire ecological hierarchy. Increasing amount of sequence data and evolution of mass spectrometric approaches has opened up new avenues for opportune exploration of the global proteome of this organelle. In our study, we aimed at generation of a comprehensive catalogue of chloroplast proteins in a grain legume, chickpea and provided a reference proteome map...
June 14, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28622761/dated-tribe-wide-whole-chloroplast-genome-phylogeny-indicates-recurrent-hybridizations-within-triticeae
#4
Nadine Bernhardt, Jonathan Brassac, Benjamin Kilian, Frank R Blattner
BACKGROUND: Triticeae, the tribe of wheat grasses, harbours the cereals barley, rye and wheat and their wild relatives. Although economically important, relationships within the tribe are still not understood. We analysed the phylogeny of chloroplast lineages among nearly all monogenomic Triticeae taxa and polyploid wheat species aiming at a deeper understanding of the tribe's evolution. We used on- and off-target reads of a target-enrichment experiment followed by Illumina sequencing...
June 16, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28617867/complete-chloroplast-genome-sequence-of-common-bermudagrass-cynodon-dactylon-l-pers-and-comparative-analysis-within-the-family-poaceae
#5
Ya-Yi Huang, Shu-Ting Cho, Mindia Haryono, Chih-Horng Kuo
Common bermudagrass (Cynodon dactylon (L.) Pers.) belongs to the subfamily Chloridoideae of the Poaceae family, one of the most important plant families ecologically and economically. This grass has a long connection with human culture but its systematics is relatively understudied. In this study, we sequenced and investigated the chloroplast genome of common bermudagrass, which is 134,297 bp in length with two single copy regions (LSC: 79,732 bp; SSC: 12,521 bp) and a pair of inverted repeat (IR) regions (21,022 bp)...
2017: PloS One
https://www.readbyqxmd.com/read/28611359/chloroplast-genomic-resource-of-paris-for-species-discrimination
#6
Yun Song, Shaojun Wang, Yuanming Ding, Jin Xu, Ming Fu Li, Shuifang Zhu, Naizhong Chen
Paris is famous in China for its medicinal value and has been included in the Chinese Pharmacopoeia. Inaccurate identification of these species could confound their effective exploration, conservation, and domestication. Due to the plasticity of the morphological characteristics, correct identification among Paris species remains problematic. In this regard, we report the complete chloroplast genome of P. thibetica and P. rugosa to develop highly variable molecular markers. Comparing three chloroplast genomes, we sought out the most variable regions to develop the best cpDNA barcodes for Paris...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28608849/the-complete-chloroplast-genome-sequences-of-fritillaria-ussuriensis-maxim-and-fritillaria-cirrhosa-d-don-and-comparative-analysis-with-other-fritillaria-species
#7
Inkyu Park, Wook Jin Kim, Sang-Min Yeo, Goya Choi, Young-Min Kang, Renzhe Piao, Byeong Cheol Moon
The genus Fritillaria belongs to the widely distributed Liliaceae. The bulbs of Fritillaria, F. ussuriensis and F. cirrhosa are valuable herbaceous medicinal ingredients. However, they are still used indiscriminately in herbal medicine. Identification and molecular phylogenic analysis of Fritillaria species are therefore required. Here, we report the complete chloroplast (CP) genome sequences of F. ussuriensis and F. cirrhosa. The two Fritillaria CP genomes were 151,524 and 151,083 bp in length, respectively, and each included a pair of inverted repeated regions (52,678 and 52,156 bp) that was separated by a large single copy region (81,732 and 81,390 bp), and a small single copy region (17,114 and 17,537 bp)...
June 13, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28601077/structure-of-plastid-genomes-of-photosynthetic-eukaryotes
#8
REVIEW
N P Yurina, L S Sharapova, M S Odintsova
This review presents current views on the plastid genomes of higher plants and summarizes data on the size, structural organization, gene content, and other features of plastid DNAs. Special emphasis is placed on the properties of organization of land plant plastid genomes (nucleoids) that distinguish them from bacterial genomes. The prospects of genetic engineering of chloroplast genomes are discussed.
June 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/28592987/an-efficient-protocol-for-perennial-ryegrass-mesophyll-protoplast-isolation-and-transformation-and-its-application-on-interaction-study-between-lpnol-and-lpnyc1
#9
Guohui Yu, Qiang Cheng, Zheni Xie, Bin Xu, Bingru Huang, Bingyu Zhao
BACKGROUND: Perennial ryegrass (Lolium perenne L.) is an important temperate grass used for turf and forage purposes. With the increasing accumulation of genomic and transcriptomic data of perennial ryegrass, an efficient protoplast and transient gene expression protocol is highly desirable for in vivo gene functional studies in its homologous system. RESULTS: In this report, a highly efficient protoplast isolation (5.6 × 10(7) protoplasts per gram of leaf material) and transient expression (plasmid transformation efficiency at 55...
2017: Plant Methods
https://www.readbyqxmd.com/read/28592899/origin-and-evolutionary-history-of-freshwater-rhodophyta-further-insights-based-on-phylogenomic-evidence
#10
Fangru Nan, Jia Feng, Junping Lv, Qi Liu, Kunpeng Fang, Chaoyan Gong, Shulian Xie
Freshwater representatives of Rhodophyta were sampled and the complete chloroplast and mitochondrial genomes were determined. Characteristics of the chloroplast and mitochondrial genomes were analyzed and phylogenetic relationship of marine and freshwater Rhodophyta were reconstructed based on the organelle genomes. The freshwater member Compsopogon caeruleus was determined for the largest chloroplast genome among multicellular Rhodophyta up to now. Expansion and subsequent reduction of both the genome size and GC content were observed in the Rhodophyta except for the freshwater Compsopogon caeruleus...
June 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28588587/a-dynamic-tandem-repeat-in-monocotyledons-inferred-from-a-comparative-analysis-of-chloroplast-genomes-in-melanthiaceae
#11
Hoang Dang Khoa Do, Joo-Hwan Kim
Chloroplast genomes (cpDNA) are highly valuable resources for evolutionary studies of angiosperms, since they are highly conserved, are small in size, and play critical roles in plants. Slipped-strand mispairing (SSM) was assumed to be a mechanism for generating repeat units in cpDNA. However, research on the employment of different small repeated sequences through SSM events, which may induce the accumulation of distinct types of repeats within the same region in cpDNA, has not been documented. Here, we sequenced two chloroplast genomes from the endemic species Heloniopsis tubiflora (Korea) and Xerophyllum tenax (USA) to cover the gap between molecular data and explore "hot spots" for genomic events in Melanthiaceae...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28579999/development-of-chloroplast-and-nuclear-dna-markers-for-chinese-oaks-quercus-subgenus-quercus-and-assessment-of-their-utility-as-dna-barcodes
#12
Jia Yang, Lucía Vázquez, Xiaodan Chen, Huimin Li, Hao Zhang, Zhanlin Liu, Guifang Zhao
Chloroplast DNA (cpDNA) is frequently used for species demography, evolution, and species discrimination of plants. However, the lack of efficient and universal markers often brings particular challenges for genetic studies across different plant groups. In this study, chloroplast genomes from two closely related species (Quercus rubra and Castanea mollissima) in Fagaceae were compared to explore universal cpDNA markers for the Chinese oak species in Quercus subgenus Quercus, a diverse species group without sufficient molecular differentiation...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28578201/correlated-evolutionary-rates-across-genomic-compartments-in-annonaceae
#13
Paul H Hoekstra, Jan J Wieringa, Erik Smets, Rita D Brandão, Jenifer de Carvalho Lopes, Roy H J Erkens, Lars W Chatrou
The molecular clock hypothesis is an important concept in biology. Deviations from a constant rate of nucleotide substitution have been found widely among lineages, genomes, genes and individual sites. Phylogenetic research can accommodate for these differences in applying specific models of evolution. Lineage-specific rate heterogeneity however can generate bi- or multimodal distributions of substitution rates across the branches of a tree and this may mislead phylogenetic inferences with currently available models...
May 31, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28575004/comparative-chloroplast-genomes-of-eleven-schima-theaceae-species-insights-into-dna-barcoding-and-phylogeny
#14
Xiang-Qin Yu, Bryan T Drew, Jun-Bo Yang, Lian-Ming Gao, De-Zhu Li
Schima is an ecologically and economically important woody genus in tea family (Theaceae). Unresolved species delimitations and phylogenetic relationships within Schima limit our understanding of the genus and hinder utilization of the genus for economic purposes. In the present study, we conducted comparative analysis among the complete chloroplast (cp) genomes of 11 Schima species. Our results indicate that Schima cp genomes possess a typical quadripartite structure, with conserved genomic structure and gene order...
2017: PloS One
https://www.readbyqxmd.com/read/28573928/diversity-of-mitochondrial-plastid-dnas-mtpts-in-seed-plants
#15
Xin-Cun Wang, Haimei Chen, Dan Yang, Chang Liu
Mitochondrial plastid DNAs (MTPTs) refer to plastid-derived DNA fragments in mitochondrial genomes. While the MTPTs have been described for numerous species, its overall patterns have not been examined in details. Here, we carried out a systematic analysis of MTPTs among 73 plant species, including 28 algae, 1 liverwort, 2 moss, 1 lycophyte, 1 gymnosperm, 1 magnoliid, 12 monocots, 26 eudicots and 1 relic angiosperm Amborella trichopoda. A total of 300 MTPT gene clusters were found in 39 seed plants, which represented 144 MTPT gene cluster types...
June 2, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28570677/detecting-early-signs-of-heat-and-drought-stress-in-phoenix-dactylifera-date-palm
#16
Omid Safronov, Jürgen Kreuzwieser, Georg Haberer, Mohamed S Alyousif, Waltraud Schulze, Naif Al-Harbi, Leila Arab, Peter Ache, Thomas Stempfl, Joerg Kruse, Klaus X Mayer, Rainer Hedrich, Heinz Rennenberg, Jarkko Salojärvi, Jaakko Kangasjärvi
Plants adapt to the environment by either long-term genome evolution or by acclimatization processes where the cellular processes and metabolism of the plant are adjusted within the existing potential in the genome. Here we studied the adaptation strategies in date palm, Phoenix dactylifera, under mild heat, drought and combined heat and drought by transcriptomic and metabolomic profiling. In transcriptomics data, combined heat and drought resembled heat response, whereas in metabolomics data it was more similar to drought...
2017: PloS One
https://www.readbyqxmd.com/read/28561261/analysis-of-chloroplast-genomes-and-a-supermatrix-inform-reclassification-of-the-rhodomelaceae-rhodophyta
#17
Pilar Díaz-Tapia, Christine A Maggs, John A West, Heroen Verbruggen
With over a thousand species, the Rhodomelaceae is the most species-rich family of red algae. While its genera have been assigned to 14 tribes, the high-level classification of the family has never been evaluated with a molecular phylogeny. Here, we reassess its classification by integrating genome-scale phylogenetic analysis with observations of the morphological characters of clades. In order to resolve relationships among the main lineages of the family we constructed a phylogeny with 55 chloroplast genomes (52 newly determined)...
May 31, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28542519/characterization-of-the-whole-chloroplast-genome-of-chikusichloa-mutica-and-its-comparison-with-other-rice-tribe-oryzeae-species
#18
Zhiqiang Wu, Cuihua Gu, Luke R Tembrock, Dong Zhang, Song Ge
Chloroplast genomes are a significant genomic resource in plant species and have been used in many research areas. The complete genomic information from wild crop species could supply a valuable genetic reservoir for breeding. Chikusichloa mutica is one of the most important wild distant relatives of cultivated rice. In this study, we sequenced and characterized its complete chloroplast (cp) genome and compared it with other species in the same tribe. The whole cp genome sequence is 136,603 bp in size and exhibits a typical quadripartite structure with large and small single-copy regions (LSC, 82,327 bp; SSC, 12,598 bp) separated by a pair of 20,839-bp inverted repeats (IRA, B)...
2017: PloS One
https://www.readbyqxmd.com/read/28539650/the-effect-of-two-amino-acid-residue-substitutions-via-rna-editing-on-dark-operative-protochlorophyllide-oxidoreductase-in-the-black-pine-chloroplasts
#19
Haruki Yamamoto, Junko Kusumi, Hisanori Yamakawa, Yuichi Fujita
Dark-operative protochlorophyllide oxidoreductase (DPOR) is a key enzyme to produce chlorophyll in the dark. Among photosynthetic eukaryotes, all three subunits chlL, chlN, and chlB are encoded by plastid genomes. In some gymnosperms, two codons of chlB mRNA are changed by RNA editing to codons encoding evolutionarily conserved amino acid residues. However, the effect of these substitutions on DPOR activity remains unknown. We first prepared cyanobacterial ChlB variants with amino acid substitution(s) to mimic ChlB translated from pre-edited mRNA...
May 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28533973/plastomes-of-the-green-algae-hydrodictyon-reticulatum-and-pediastrum-duplex-sphaeropleales-chlorophyceae
#20
Hilary A McManus, Daniel J Sanchez, Kenneth G Karol
BACKGROUND: Comparative studies of chloroplast genomes (plastomes) across the Chlorophyceae are revealing dynamic patterns of size variation, gene content, and genome rearrangements. Phylogenomic analyses are improving resolution of relationships, and uncovering novel lineages as new plastomes continue to be characterized. To gain further insight into the evolution of the chlorophyte plastome and increase the number of representative plastomes for the Sphaeropleales, this study presents two fully sequenced plastomes from the green algal family Hydrodictyaceae (Sphaeropleales, Chlorophyceae), one from Hydrodictyon reticulatum and the other from Pediastrum duplex...
2017: PeerJ
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