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https://www.readbyqxmd.com/read/28530408/authentication-markers-for-five-major-panax-species-developed-via-comparative-analysis-of-complete-chloroplast-genome-sequences
#1
Van Binh Nguyen, Hyun-Seung Park, Sang-Choon Lee, Junki Lee, Jee Young Park, Tae-Jin Yang
Ginseng represents a set of high-value medicinal plants of different species: Panax ginseng (Asian ginseng), P. quinquefolius (American ginseng), P. notoginseng (Chinese ginseng), P. japonicus (Bamboo ginseng), and P. vietnamensis (Vietnamese ginseng). Each species is pharmacologically and economically important, with differences in efficacy and price. Accordingly, an authentication system is needed to combat economically motivated adulteration of Panax products. We conducted comparative analysis of the chloroplast genome sequences of these five species, identifying 34-124 indels and 141-560 SNPs...
May 22, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28529836/chloroplast-and-mitochondrial-microsatellites-for-millettia-pinnata-fabaceae-and-cross-amplification-in-related-species
#2
Yanling Wang, Hongxian Xie, Yi Yang, Yelin Huang, Jianwu Wang, Fengxiao Tan
PREMISE OF THE STUDY: Chloroplast and mitochondrial microsatellites were identified to study the population genetics of Millettia pinnata (Fabaceae). METHODS AND RESULTS: Based on publicly available plastid genome sequence data of M. pinnata, 42 primer pairs were developed, of which 17 displayed polymorphisms across 89 individuals from four populations. For chloroplast loci, two to six alleles were recovered and the unbiased haploid diversity per locus ranged from 0...
May 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28529832/application-of-a-simplified-method-of-chloroplast-enrichment-to-small-amounts-of-tissue-for-chloroplast-genome-sequencing
#3
Shota Sakaguchi, Saneyoshi Ueno, Yoshihiko Tsumura, Hiroaki Setoguchi, Motomi Ito, Chie Hattori, Shogo Nozoe, Daiki Takahashi, Riku Nakamasu, Taishi Sakagami, Guillaume Lannuzel, Bruno Fogliani, Adrien S Wulff, Laurent L'Huillier, Yuji Isagi
PREMISE OF THE STUDY: High-throughput sequencing of genomic DNA can recover complete chloroplast genome sequences, but the sequence data are usually dominated by sequences from nuclear/mitochondrial genomes. To overcome this deficiency, a simple enrichment method for chloroplast DNA from small amounts of plant tissue was tested for eight plant species including a gymnosperm and various angiosperms. METHODS: Chloroplasts were enriched using a high-salt isolation buffer without any step gradient procedures, and enriched chloroplast DNA was sequenced by multiplexed high-throughput sequencing...
May 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28500291/the-complete-chloroplast-genome-sequence-of-tung-tree-vernicia-fordii-organization-and-phylogenetic-relationships-with-other-angiosperms
#4
Ze Li, Hongxu Long, Lin Zhang, Zhiming Liu, Heping Cao, Mingwang Shi, Xiaofeng Tan
Tung tree (Vernicia fordii) is an economically important tree widely cultivated for industrial oil production in China. To better understand the molecular basis of tung tree chloroplasts, we sequenced and characterized its genome using PacBio RS II sequencing platforms. The chloroplast genome was sequenced with 161,528 bp in length, composed with one pair of inverted repeats (IRs) of 26,819 bp, which were separated by one small single copy (SSC; 18,758 bp) and one large single copy (LSC; 89,132 bp)...
May 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28500267/impaired-mitochondrial-transcription-termination-disrupts-the-stromal-redox-poise-in-chlamydomonas
#5
Andreas Uhmeyer, Matteo Ballottari, Michela Cecchin, Lutz Wobbe
In photosynthetic eukaryotes, the metabolite exchange between chloroplast and mitochondria ensures efficient photosynthesis under saturating light conditions. The C. reinhardtii mutant stm6 is devoid of the mitochondrial transcription termination factor (mTERF) MOC1 and aberrantly expresses the mitochondrial genome, resulting in enhanced photosynthetic hydrogen production and diminished light tolerance. We analyzed the modulation of mitochondrial and chlororespiration during the acclimation of stm6 and the MOC1-complemented strain to excess light...
May 12, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28486635/geseq%C3%A2-versatile-and-accurate-annotation-of-organelle-genomes
#6
Michael Tillich, Pascal Lehwark, Tommaso Pellizzer, Elena S Ulbricht-Jones, Axel Fischer, Ralph Bock, Stephan Greiner
We have developed the web application GeSeq (https://chlorobox.mpimp-golm.mpg.de/geseq.html) for the rapid and accurate annotation of organellar genome sequences, in particular chloroplast genomes. In contrast to existing tools, GeSeq combines batch processing with a fully customizable reference sequence selection of organellar genome records from NCBI and/or references uploaded by the user. For the annotation of chloroplast genomes, the application additionally provides an integrated database of manually curated reference sequences...
May 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28484234/inferring-the-evolutionary-mechanism-of-the-chloroplast-genome-size-by-comparing-whole-chloroplast-genome-sequences-in-seed-plants
#7
Zheng Xiao-Ming, Wang Junrui, Feng Li, Liu Sha, Pang Hongbo, Qi Lan, Li Jing, Sun Yan, Qiao Weihua, Zhang Lifang, Cheng Yunlian, Yang Qingwen
The chloroplast genome originated from photosynthetic organisms and has retained the core genes that mainly encode components of photosynthesis. However, the causes of variations in chloroplast genome size in seed plants have only been thoroughly analyzed within small subsets of spermatophytes. In this study, we conducted the first comparative analysis on a large scale to examine the relationship between sequence characteristics and genome size in 272 seed plants based on cross-species and phylogenetic signal analysis...
May 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28482814/novel-mutant-alleles-of-the-starch-synthesis-gene-tassivb-d-result-in-the-reduction-of-starch-granule-number-per-chloroplast-in-wheat
#8
Huijun Guo, Yunchuan Liu, Xiao Li, Zhihui Yan, Yongdun Xie, Hongchun Xiong, Linshu Zhao, Jiayu Gu, Shirong Zhao, Luxiang Liu
BACKGROUND: Transient starch provides carbon and energy for plant growth, and its synthesis is regulated by the joint action of a series of enzymes. Starch synthesis IV (SSIV) is one of the important starch synthase isoforms, but its impact on wheat starch synthesis has not yet been reported due to the lack of mutant lines. RESULTS: Using the TILLING approach, we identified 54 mutations in the wheat gene TaSSIVb-D, with a mutation density of 1/165 Kb. Among these, three missense mutations and one nonsense mutation were predicted to have severe impacts on protein function...
May 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28465666/challenges-to-genome-sequence-dissection-in-sweetpotato
#9
REVIEW
Sachiko Isobe, Kenta Shirasawa, Hideki Hirakawa
The development of next generation sequencing (NGS) technologies has enabled the determination of whole genome sequences in many non-model plant species. However, genome sequencing in sweetpotato (Ipomoea batatas (L.) Lam) is still difficult because of the hexaploid genome structure. Previous studies suggested that a diploid wild relative, I. trifida (H.B.K.) Don., is the most possible ancestor of sweetpotato. Therefore, the genetic and genomic features of I. trifida have been studied as a potential reference for sweetpotato...
January 2017: Breeding Science
https://www.readbyqxmd.com/read/28458683/full-chloroplast-genome-assembly-of-11-diverse-watermelon-accessions
#10
Chao Shi, Shuo Wang, Fei Zhao, Hua Peng, Chun-Lei Xiang
No abstract text is available yet for this article.
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28450857/the-functional-roles-of-the-cis-acting-elements-in-bamboo-mosaic-virus-rna-genome
#11
REVIEW
I-Hsuan Chen, Ying-Wen Huang, Ching-Hsiu Tsai
Bamboo mosaic virus (BaMV), which belongs to the genus Potexvirus in the family Alphaflexiviridae, has a single-stranded positive-sense RNA genome that is approximately 6400 nucleotides (nts) in length. Positive-sense RNA viruses can use genomic RNA as a template for translation and replication after entering a suitable host cell. Furthermore, such viral RNA is recognized by capsid protein for packaging and by viral movement protein(s) or the movement protein complex for cell-to-cell and systemic movement. Hence, viral RNA must contain signals for different functions to complete the viral infection cycle...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28432803/sequencing-and-functional-validation-of-the-jgi-brachypodium-distachyon-t-dna-collection
#12
Mon Mandy Hsia, Ronan O'Malley, Amy Cartwright, Rita Nieu, Sean P Gordon, Sandra Kelly, Tina G Williams, Delilah F Wood, Yunjun Zhao, Jennifer Bragg, Mark Jordan, Markus Pauly, Joseph R Ecker, Yong Gu, John P Vogel
Due to a large and growing collection of genomic and experimental resources, Brachypodium distachyon has emerged as a powerful experimental model for the grasses. To add to these resources we sequenced 21,165 T-DNA lines, 15,569 of which were produced in this study. This increased the number of unique insertion sites in the T-DNA collection by 21,078 bringing the overall total to 26,112. Thirty seven percent (9,754) of these insertion sites are within genes (including UTRs and introns) and 28% (7,217) are within 500 bp of a gene...
April 22, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28429321/euglena-transcript-processing
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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 1, 2017: Journal of Experimental Botany
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