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https://www.readbyqxmd.com/read/28429321/euglena-transcript-processing
#1
David C McWatters, Anthony G Russell
RNA transcript processing is an important stage in the gene expression pathway of all organisms and is subject to various mechanisms of control that influence the final levels of gene products. RNA processing involves events such as nuclease-mediated cleavage, removal of intervening sequences referred to as introns and modifications to RNA structure (nucleoside modification and editing). In Euglena, RNA transcript processing was initially examined in chloroplasts because of historical interest in the secondary endosymbiotic origin of this organelle in this organism...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28428810/recent-achievements-obtained-by-chloroplast-transformation
#2
REVIEW
Muhamed Adem, Dereje Beyene, Tileye Feyissa
Chloroplasts play a great role for sustained wellbeing of life on the planet. They have the power and raw materials that can be used as sophisticated biological factories. They are rich in energy as they have lots of pigment-protein complexes capable of collecting sunlight, in sugar produced by photosynthesis and in minerals imported from the plant cell. Chloroplast genome transformation offers multiple advantages over nuclear genome which among others, include: integration of the transgene via homologus recombination that enables to eliminate gene silencing and position effect, higher level of transgene expression resulting into higher accumulations of foreign proteins, and significant reduction in environmental dispersion of the transgene due to maternal inheritance which helps to minimize the major critic of plant genetic engineering...
2017: Plant Methods
https://www.readbyqxmd.com/read/28428552/divergent-copies-of-the-large-inverted-repeat-in-the-chloroplast-genomes-of-ulvophycean-green-algae
#3
Monique Turmel, Christian Otis, Claude Lemieux
The chloroplast genomes of many algae and almost all land plants carry two identical copies of a large inverted repeat (IR) sequence that can pair for flip-flop recombination and undergo expansion/contraction. Although the IR has been lost multiple times during the evolution of the green algae, the underlying mechanisms are still largely unknown. A recent comparison of IR-lacking and IR-containing chloroplast genomes of chlorophytes from the Ulvophyceae (Ulotrichales) suggested that differential elimination of genes from the IR copies might lead to IR loss...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28422071/comparative-analysis-of-the-complete-chloroplast-genome-of-four-endangered-herbals-of-notopterygium
#4
Jiao Yang, Ming Yue, Chuan Niu, Xiong-Feng Ma, Zhong-Hu Li
Notopterygium H. de Boissieu (Apiaceae) is an endangered perennial herb endemic to China. A good knowledge of phylogenetic evolution and population genomics is conducive to the establishment of effective management and conservation strategies of the genus Notopterygium. In this study, the complete chloroplast (cp) genomes of four Notopterygium species (N. incisum C. C. Ting ex H. T. Chang, N. oviforme R. H. Shan, N. franchetii H. de Boissieu and N. forrestii H. Wolff) were assembled and characterized using next-generation sequencing...
April 19, 2017: Genes
https://www.readbyqxmd.com/read/28421090/comparative-genomics-and-phylogenomics-of-east-asian-tulips-amana-liliaceae
#5
Pan Li, Rui-Sen Lu, Wu-Qin Xu, Tetsuo Ohi-Toma, Min-Qi Cai, Ying-Xiong Qiu, Kenneth M Cameron, Cheng-Xin Fu
The genus Amana Honda (Liliaceae), when it is treated as separate from Tulipa, comprises six perennial herbaceous species that are restricted to China, Japan and the Korean Peninsula. Although all six Amana species have important medicinal and horticultural uses, studies focused on species identification and molecular phylogenetics are few. Here we report the nucleotide sequences of six complete Amana chloroplast (cp) genomes. The cp genomes of Amana range from 150,613 bp to 151,136 bp in length, all including a pair of inverted repeats (25,629-25,859 bp) separated by the large single-copy (81,482-82,218 bp) and small single-copy (17,366-17,465 bp) regions...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28420746/the-mitochondrial-dna-mtdna-associated-protein-swib5-influences-mtdna-architecture-and-homologous-recombination
#6
Jonas Blomme, Olivier Van Aken, Jelle Van Leene, Teddy Jégu, Riet Maria De Rycke, Michiel De Bruyne, Jasmien Vercruysse, Jonah Nolf, Twiggy Van Daele, Liesbeth De Milde, Mattias Vermeersch, Catherine Colas des Francs-Small, Geert De Jaeger, Moussa Benhamed, A Harvey Millar, Dirk Inzé, Nathalie Gonzalez
In addition to the nucleus, mitochondria and chloroplasts in plant cells also contain genomes. Efficient DNA repair pathways are crucial in these organelles to fix damage resulting from endogenous and exogenous factors. Plant organellar genomes are complex compared to their animal counterparts and although several plant-specific mediators of organelle DNA repair have been reported, many regulators remain to be identified. Here, we show that a mitochondrial SWI/SNF (nucleosome remodeling) complex B protein, SWIB5, is capable of associating with mitochondrial DNA (mtDNA) in Arabidopsis thaliana...
April 18, 2017: Plant Cell
https://www.readbyqxmd.com/read/28420220/the-maximal-c%C3%A2-self-complementary-trinucleotide-circular-code-x-in-genes-of-bacteria-archaea-eukaryotes-plasmids-and-viruses
#7
Christian J Michel
In 1996, a set X of 20 trinucleotides was identified in genes of both prokaryotes and eukaryotes which has on average the highest occurrence in reading frame compared to its two shifted frames. Furthermore, this set X has an interesting mathematical property as X is a maximal C 3 self-complementary trinucleotide circular code. In 2015, by quantifying the inspection approach used in 1996, the circular code X was confirmed in the genes of bacteria and eukaryotes and was also identified in the genes of plasmids and viruses...
April 18, 2017: Life
https://www.readbyqxmd.com/read/28419381/enhancing-faba-bean-vicia-faba-l-genome-resources
#8
James W Cooper, Michael H Wilson, Martijn F L Derks, Sandra Smit, Karl J Kunert, Christopher Cullis, Christine H Foyer
Grain legume improvement is currently impeded by a lack of genomic resources. The paucity of genome information for faba bean can be attributed to the intrinsic difficulties of assembling/annotating its giant (~13 Gb) genome. In order to address this challenge, RNA-sequencing analysis was performed on faba bean (cv. Wizard) leaves. Read alignment to the faba bean reference transcriptome identified 16 300 high quality unigenes. In addition, Illumina paired-end sequencing was used to establish a baseline for genomic information assembly...
April 17, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28419256/chloromitocu-codon-patterns-across-organelle-genomes-for-functional-genomics-and-evolutionary-applications
#9
Gaurav Sablok, Ting-Wen Chen, Chi-Ching Lee, Chi Yang, Ruei-Chi Gan, Jill L Wegrzyn, Nicola L Porta, Kinshuk C Nayak, Po-Jung Huang, Claudio Varotto, Petrus Tang
Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes...
April 17, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28414099/molecular-evolution-of-the-plastid-genome-during-diversification-of-the-cotton-genus
#10
Zhiwen Chen, Corrinne E Grover, Pengbo Li, Yumei Wang, Hushuai Nie, Yanpeng Zhao, Meiyan Wang, Fang Liu, Zhongli Zhou, Xingxing Wang, Xiaoyan Cai, Kunbo Wang, Jonathan F Wendel, Jinping Hua
Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups, designated A-G and K, and one tetraploid genomic group, namely AD. To gain insight into the phylogeny of Gossypium and molecular evolution of the chloroplast genome duringdiversification, chloroplast genomes (cpDNA) from 6 D-genome and 2 G-genome species of Gossypium (G. armourianum D2-1, G. harknessii D2-2, G. davidsonii D3-d, G. klotzschianum D3-k, G. aridum D4, G. trilobum D8, and G. australe G2, G. nelsonii G3) were newly reported here...
April 13, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28408315/the-corr-hypothesis-for-genes-in-organelles
#11
John F Allen
Chloroplasts and mitochondria perform energy transduction in photosynthesis and respiration. These processes can be described in physico-chemical terms with no obvious requirement for co-located genetic systems, separated from those of the rest of the cell. Accordingly, biochemists once tended to regard endosymbiosis as untestable evolutionary speculation. Lynn Sagan's seminal 1967 paper "On the Origin of Mitosing Cells" outlined the evolution of eukaryotic cells by endosymbiosis of prokaryotes. The endosymbiont hypothesis is consistent with presence of DNA in chloroplasts and mitochondria, but does not assign it a function...
April 10, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28407383/msh1-maintains-organelle-genome-stability-and-genetically-interacts-with-reca-and-recg-in-the-moss-physcomitrella-patens
#12
Masaki Odahara, Yoshihito Kishita, Yasuhiko Sekine
Chloroplast and mitochondrial DNA encodes genes essential for photosynthesis and respiration, respectively. Thus, loss of organelle genomic DNA integrity leads to a decline in organelle function and to alteration of organelle genetic information. RECA (RECA1 and RECA2) and RECG, which are homologs of bacterial homologous recombination repair (HRR) factors RecA and RecG, respectively, play an important role in the maintenance of organelle genome integrity by suppressing aberrant recombination between short dispersed repeats (SDRs) in the moss Physcomitrella patens...
April 13, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28396831/cryptochrome-2-extensively-regulates-transcription-of-the-chloroplast-genome-in-tomato
#13
Paolo Facella, Fabrizio Carbone, Antonio Placido, Gaetano Perrotta
Light plays a key role in the regulation of many physiological processes required for plant and chloroplast development. Plant cryptochromes (crys) play an important role in monitoring, capturing, and transmitting the light stimuli. In this study, we analyzed the effects of CRY2 overexpression on transcription of tomato chloroplast genome by a tiling array, containing about 90 000 overlapping probes (5-nucleotide resolution). We profiled transcription in leaves of wild-type and CRY2-overexpressing plants grown in a diurnal cycle, to generate a comprehensive map of chloroplast transcription and to monitor potential specific modulations of the chloroplast transcriptome induced by the overexpression of CRY2...
April 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/28395362/phylogenetic-analysis-and-molecular-characterization-of-xanthium-sibiricum-using-dna-barcoding-pcr-rflp-and-specific-primers
#14
Salvatore Tomasello, Günther Heubl
The fruits of Xanthium sibiricum have been widely used in traditional Chinese medicine for the treatment of nasal sinusitis and headaches. The genus Xanthium (cocklebur) is a taxonomically complex genus. Different taxonomic concepts have been proposed, some including several species, others lumping the different taxa in a few extremely polymorphic species. Due to the morphological similarities between species, the correct authentication of X. sibiricum is very difficult. Therefore, we established a polymerase chain reaction-restriction fragment length polymorphism method and diagnostic PCR based on nuclear internal transcribed spacer and chloroplast trnQ-rps16 barcodes to differentiate X...
April 10, 2017: Planta Medica
https://www.readbyqxmd.com/read/28394430/phylogenetic-positioning-of-the-antarctic-alga-prasiola-crispa-trebouxiophyceae-using-organellar-genomes-and-their-structural-analysis
#15
Evelise Leis Carvalho, Gabriel Luz Wallau, Darlene Lopes Rangel, Laís Ceschini Machado, Antonio Batista Pereira, Filipe de Carvalho Victoria, Juliano Tomazzoni Boldo, Paulo Marcos Pinto
Antarctica is one of the most difficult habitats for sustaining life on earth; organisms that live there have developed different strategies for survival. Among these organisms is the green alga Prasiola crispa, belonging to the class Trebouxiophyceae. The literature on P. crispa taxonomy is scarce, and many gaps in the evolutionary relationship with its closest relatives remain. The goal of this study was to analyze the evolutionary relationships of P. crispa and other green algae using plastid and mitochondrial genomes...
April 10, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28394415/phylogenetic-position-of-the-coral-symbiont-ostreobium-ulvophyceae-inferred-from-chloroplast-genome-data
#16
Heroen Verbruggen, Vanessa R Marcelino, Michael D Guiry, M Chiela M Cremen, Christopher J Jackson
The green algal genus Ostreobium is an important symbiont of corals, playing roles in reef decalcification and providing photosynthates to the coral during bleaching events. A chloroplast genome of a cultured strain of Ostreobium was available, but low taxon sampling and Ostreobium's early-branching nature left doubt about its phylogenetic position. Here we generate and describe chloroplast genomes from four Ostreobium strains as well as Avrainvillea mazei and Neomeris sp., strategically sampled early-branching lineages in the Bryopsidales and Dasycladales, respectively...
April 10, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28388677/the-barley-stripe-mosaic-virus-%C3%AE-b-protein-promotes-chloroplast-targeted-replication-by-enhancing-unwinding-of-rna-duplexes
#17
Kun Zhang, Yongliang Zhang, Meng Yang, Songyu Liu, Zhenggang Li, Xianbing Wang, Chenggui Han, Jialin Yu, Dawei Li
RNA viruses encode various RNA binding proteins that function in many steps of viral infection cycles. These proteins function as RNA helicases, methyltransferases, RNA-dependent RNA polymerases, RNA silencing suppressors, RNA chaperones, movement proteins, and so on. Although many of the proteins bind the viral RNA genome during different stages of infection, our knowledge about the coordination of their functions is limited. In this study, we describe a novel role for the Barley stripe mosaic virus (BSMV) γb as an enhancer of αa RNA helicase activity, and we show that the γb protein is recruited by the αa viral replication protein to chloroplast membrane sites of BSMV replication...
April 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28382528/diverse-origins-of-enzymes-involved-in-the-biosynthesis-of-chloroplast-peptidoglycan
#18
Naoki Sato, Hiroyoshi Takano
Chloroplasts are believed to be descendants of ancestral cyanobacteria that had peptidoglycan layer between the outer and the inner membranes. Historically, the glaucophyte Cyanophora paradoxa and the rhizopod Paulinella chromatophora were believed to harbor symbiotic cyanobacteria having peptidoglycan, which were conventionally named "cyanelles". In addition, the complete set of genes involved in the synthesis of peptidoglycan has been found in the moss Physcomitrella patens and some plants and algae. The presence of peptidoglycan-like structures was demonstrated by a new metabolic labeling technique in P...
April 5, 2017: Journal of Plant Research
https://www.readbyqxmd.com/read/28360398/nucleotide-diversity-and-phylogenetic-relationships-among-gladiolus-cultivars-and-related-taxa-of-family-iridaceae
#19
Niraj Singh, Baleshwar Meena, Ashish Kumar Pal, Roop Kumar Roy, Sri Krishna Tewari, Sushma Tamta, Tikam Singh Rana
The plastid genome regions of two intergenic spacers, psbA-trnH and trnL-trnF, were sequenced to study the nucleotide diversity and phylogenetic relationships among Gladiolus cultivars. Nucleotide diversity of psbA-trnH region was higher than trnL-trnF region of chloroplast. We employed Bayesian, maximum parsimony (MP) and neighbour-joining (NJ) approaches for phylogenetic analysis of Gladiolus and related taxa using combined datasets from chloroplast genome. The psbA-trnH and trnL-trnF intergenic spacers of Gladiolus and related taxa-like Babiana, Chasmanthe, Crocus, Iris, Moraea, Sisyrinchium, Sparaxis and two out group species (Hymenocallis littoralis and Asphodeline lutea) were used in the present investigation...
March 2017: Journal of Genetics
https://www.readbyqxmd.com/read/28356141/genomic-history-of-the-origin-and-domestication-of-common-bean-unveils-its-closest-sister-species
#20
Martha Rendón-Anaya, Josaphat M Montero-Vargas, Soledad Saburido-Álvarez, Anna Vlasova, Salvador Capella-Gutierrez, José Juan Ordaz-Ortiz, O Mario Aguilar, Rosana P Vianello-Brondani, Marta Santalla, Luis Delaye, Toni Gabaldón, Paul Gepts, Robert Winkler, Roderic Guigó, Alfonso Delgado-Salinas, Alfredo Herrera-Estrella
BACKGROUND: Modern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domesticated descendants. Among cultivated plants, common bean (Phaseolus vulgaris L.) is the most important grain legume. Yet, our understanding of the origins and concurrent shaping of the genome of this crop plant is limited. RESULTS: We sequenced the genomes of 29 accessions representing 12 Phaseolus species...
March 29, 2017: Genome Biology
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