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https://www.readbyqxmd.com/read/28230734/deep%C3%A2-transcriptome%C3%A2-sequencing%C3%A2-of%C3%A2-two%C3%A2-green%C3%A2-algae-chara%C3%A2-vulgaris%C3%A2-and%C3%A2-chlamydomonas%C3%A2-reinhardtii-%C3%A2-provides%C3%A2-no%C3%A2-evidence%C3%A2-of%C3%A2-organellar%C3%A2-rna%C3%A2-editing
#1
A Bruce Cahoon, John A Nauss, Conner D Stanley, Ali Qureshi
Nearly all land plants post-transcriptionally modify specific nucleotides within RNAs, a process known as RNA editing. This adaptation allows the correction of deleterious mutations within the asexually reproducing and presumably non-recombinant chloroplast and mitochondrial genomes. There are no reports of RNA editing in any of the green algae so this phenomenon is presumed to have originated in embryophytes either after the invasion of land or in the now extinct algal ancestor of all land plants. This was challenged when a recent in silico screen for RNA edit sites based on genomic sequence homology predicted edit sites in the green alga Chara vulgaris, a multicellular alga found within the Streptophyta clade and one of the closest extant algal relatives of land plants...
February 20, 2017: Genes
https://www.readbyqxmd.com/read/28228773/import-of-soluble-proteins-into-chloroplasts-and-potential-regulatory-mechanisms
#2
REVIEW
Inga Sjuts, Jürgen Soll, Bettina Bölter
Chloroplasts originated from an endosymbiotic event in which a free-living cyanobacterium was engulfed by an ancestral eukaryotic host. During evolution the majority of the chloroplast genetic information was transferred to the host cell nucleus. As a consequence, proteins formerly encoded by the chloroplast genome are now translated in the cytosol and must be subsequently imported into the chloroplast. This process involves three steps: (i) cytosolic sorting procedures, (ii) binding to the designated receptor-equipped target organelle and (iii) the consecutive translocation process...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28224490/predicting-beta-barrel-transmembrane-proteins-using-hmms
#3
Georgios N Tsaousis, Stavros J Hamodrakas, Pantelis G Bagos
Transmembrane beta-barrels (TMBBs) constitute an important structural class of membrane proteins located in the outer membrane of gram-negative bacteria, and in the outer membrane of chloroplasts and mitochondria. They are involved in a wide variety of cellular functions and the prediction of their transmembrane topology, as well as their discrimination in newly sequenced genomes is of great importance as they are promising targets for antimicrobial drugs and vaccines. Several methods have been applied for the prediction of the transmembrane segments and the topology of beta barrel transmembrane proteins utilizing different algorithmic techniques...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28224056/evaluation-and-comparison-of-fta-card-and-ctab-dna-extraction-methods-for-non-agricultural-taxa
#4
Chloe S Siegel, Florence O Stevenson, Elizabeth A Zimmer
PREMISE OF THE STUDY: An efficient, effective DNA extraction method is necessary for comprehensive analysis of plant genomes. This study analyzed the quality of DNA obtained using paper FTA cards prepared directly in the field when compared to the more traditional cetyltrimethylammonium bromide (CTAB)-based extraction methods from silica-dried samples. METHODS: DNA was extracted using FTA cards according to the manufacturer's protocol. In parallel, CTAB-based extractions were done using the automated AutoGen DNA isolation system...
February 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28220432/genome-wide-analysis-of-chromatin-accessibility-in-arabidopsis-infected-with-pseudomonas-syringae
#5
Yogendra Bordiya, Hong-Gu Kang
Changes in chromatin accessibility are an important aspect of the molecular changes that occur in eukaryotic cells responding to stress, and they appear to play a critical role in stress-induced transcriptional activation/reprogramming and epigenetic changes. In plants, pathogen infection has been shown to induce rapid and drastic transcriptional reprogramming; growing evidence suggests that chromatin remodeling plays an essential role in this phenomenon. The recent development of genomic tools to assess chromatin accessibility presents a significant opportunity to investigate the relationship between chromatin dynamicity and gene expression...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28218791/development-and-validation-of-the-first-ssr-markers-for-mimosa-scabrella-benth
#6
F A Saiki, A P Bernardi, M S Reis, H Faoro, E M Souza, F O Pedrosa, A Mantovani, A F Guidolin
Mimosa scabrella Benth., popularly known as ''bracatinga'', is a pioneer and endemic species of Brazil, occurring in Mixed Ombrophilous Forest associated with Brazilian Atlantic Rainforest biomes. It is a fast-growing tree of the Fabaceae family that facilitates the dynamics of ecological succession. SSR development, when there is no genome sequence, is time and labor intensive and there are no molecular markers for M. scabrella. We developed and validated the first microsatellite markers for this tetraploid species, evaluating mother trees and progenies...
February 16, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28218778/identification-and-cloning-of-golden2-like1-glk1-a-transcription-factor-associated-with-chloroplast-development-in-brassica-napus-l
#7
Y L Pan, Y Pan, C M Qu, C G Su, J H Li, X G Zhang
Photosynthesis is the process by which dry matter accumulates, which affects rapeseed yield. In this study, we identified GOLDEN2-LIKE1 (GLK1), located on chromosome A07 and 59.2 kb away from the single nucleotide polymorphism marker SNP16353A07, which encodes a transcription factor associated with the rate of photosynthesis in leaves. We then identified 96 GLK1 family members from 53 species using a hidden Markov model (HMM) search and found 24 of these genes, which were derived from 17 Brassicaceae species...
February 16, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28211478/ecology-and-genetics-affect-relative-invasion-success-of-two-echium-species-in-southern-australia
#8
Xiaocheng Zhu, Paul A Weston, Dominik Skoneczny, David Gopurenko, Lucie Meyer, Brendan J Lepschi, Ragan M Callaway, Geoff M Gurr, Leslie A Weston
Echium plantagineum and E. vulgare are congeneric exotics first introduced to Australia in the early 1800 s. There, E. plantagineum is now highly invasive, whereas E. vulgare has a limited distribution. Studies were conducted to evaluate distribution, ecology, genetics and secondary chemistry to shed light on factors associated with their respective invasive success. When sampled across geographically diverse locales, E. plantagineum was widespread and exhibited a small genome size (1 C = 0.34 pg), an annual life cycle, and greater genetic diversity as assessed by DNA sequence analysis...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28210266/a-phylogenetic-analysis-of-chloroplast-genomes-elucidates-the-relationships-of-the-six-economically-important-brassica-species-comprising-the-triangle-of-u
#9
Peirong Li, Shujiang Zhang, Fei Li, Shifan Zhang, Hui Zhang, Xiaowu Wang, Rifei Sun, Guusje Bonnema, Theo J A Borm
The Brassica genus comprises many economically important worldwide cultivated crops. The well-established model of the Brassica genus, U's triangle, consists of three basic diploid plant species (Brassica rapa, Brassica oleracea, and Brassica nigra) and three amphidiploid species (Brassica napus, Brassica juncea, and Brassica carinata) that arose through interspecific hybridizations. Despite being extensively studied because of its commercial relevance, several aspects of the origin of the Brassica species and the relationships within and among these six species still remain open questions...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28209812/sequencing-and-de-novo-assembly-of-the-complete-chloroplast-genome-of-the-peruvian-carrot-arracacia-xanthorrhiza-bancroft
#10
Javier Santiago Alvarado, Diane Hinojosa López, Isaury Maldonado Torres, María Margarita Meléndez, Rosalinda Aybar Batista, Vivek K Raxwal, Juan A Negrón Berríos, Alok Arun
Arracacia xanthorrhiza is an important secondary food crop in South America and Puerto Rico. The lack of crop protection and improvement strategies leads to infections damaging the storage roots. Here, we report the annotated complete chloroplast genome sequence of A. xanthorrhiza as a step toward developing genomic resources for this crop.
February 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28191642/complete-mitochondrial-genomes-of-prasinophyte-algae-pyramimonas-parkeae-and-cymbomonas-tetramitiformis
#11
Anchittha Satjarak, John A Burns, Eunsoo Kim, Linda E Graham
Mitochondria are archetypal eukaryotic organelles that were acquired by endosymbiosis of an ancient species of alpha-proteobacteria by the last eukaryotic common ancestor. The genetic information contained within the mitochondrial genome has been an important source of information for resolving relationships among eukaryotic taxa. In this study, we utilized mitochondrial and chloroplast genomes to explore relationships among prasinophytes. Prasinophytes are represented by diverse early-diverging green algae whose physical structures and genomes have the potential to elucidate the traits of the last common ancestor of the Viridiplantae (or Chloroplastida)...
February 12, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28185042/phylogenomic-relationship-of-feijoa-acca-sellowiana-o-berg-burret-with-other-myrtaceae-based-on-complete-chloroplast-genome-sequences
#12
Lilian Oliveira de Machado, Leila do Nascimento Vieira, Valdir Marcos Stefenon, Fábio de Oliveira Pedrosa, Emanuel Maltempi de Souza, Miguel Pedro Guerra, Rubens Onofre Nodari
Given their distribution, importance, and richness, Myrtaceae species comprise a model system for studying the evolution of tropical plant diversity. In addition, chloroplast (cp) genome sequencing is an efficient tool for phylogenetic relationship studies. Feijoa [Acca sellowiana (O. Berg) Burret; CN: pineapple-guava] is a Myrtaceae species that occurs naturally in southern Brazil and northern Uruguay. Feijoa is known for its exquisite perfume and flavorful fruits, pharmacological properties, ornamental value and increasing economic relevance...
February 9, 2017: Genetica
https://www.readbyqxmd.com/read/28182646/complete-chloroplast-genomes-from-apomictic-taraxacum-asteraceae-identity-and-variation-between-three-microspecies
#13
Rubar Hussein M Salih, Ľuboš Majeský, Trude Schwarzacher, Richard Gornall, Pat Heslop-Harrison
Chloroplast DNA sequences show substantial variation between higher plant species, and less variation within species, so are typically excellent markers to investigate evolutionary, population and genetic relationships and phylogenies. We sequenced the plastomes of Taraxacum obtusifrons Markl. (O978); T. stridulum Trávniček ined. (S3); and T. amplum Markl. (A978), three apomictic triploid (2n = 3x = 24) dandelions from the T. officinale agg. We aimed to characterize the variation in plastomes, define relationships and correlations with the apomictic microspecies status, and refine placement of the microspecies in the evolutionary or phylogenetic context of the Asteraceae...
2017: PloS One
https://www.readbyqxmd.com/read/28179182/chloroplast-and-its-phylogenies-to-understand-the-evolutionary-history-of-southern-south-american-azorella-laretia-and-mulinum-azorelloideae-apiaceae
#14
Martina Fernández, Cecilia Ezcurra, Carolina I Calviño
Azorella, Laretia and Mulinum are taxonomically complex, and good candidates to study evolutionary radiations in the Andes and the importance of hybridizations. Previous phylogenetic studies of subfamily Azorelloideae agree that Azorella and Mulinum as currently conceived are not monophyletic, and hence a revision of their circumscription is necessary. However, these phylogenies were based only on chloroplast DNA sequence data. Here, phylogenetic relationships within Azorelloideae were inferred using sequence data from five chloroplast DNA (rps16 intron, trnQ-rps16, rps16-trnK(UUU) 5' -exon, trnG(GCC)-trnS(GCU) and rpL32-trnL(UAG)), and from nuclear rDNA ITS regions to assess the monophyly of Azorella and Mulinum and discuss generic re-circumscriptions, determine hybridization and radiation events, identify and characterize important lineages, and propose hypotheses on evolution of key morphological characters...
February 4, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28178222/complete-chloroplast-genome-of-medicinal-plant-lonicera-japonica-genome-rearrangement-intron-gain-and-loss-and-implications-for-phylogenetic-studies
#15
Liu He, Jun Qian, Xiwen Li, Zhiying Sun, Xiaolan Xu, Shilin Chen
The complete chloroplast (cp) genome of Lonicera japonica, a common ornamental and medicinal plant in North America and East Asia, was sequenced and analyzed. The length of the L. japonica cp genome is 155,078 bp, contains a pair of inverted repeat regions (IRa and IRb), of 23,774 bp each, as well as large (LSC, 88,858 bp) and small (SSC, 18,672 bp) single-copy regions. A total of 129 genes were identified in the cp genome, 16 of which were duplicated within the IR regions. Relative to other plant cp genomes, the L...
February 7, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28177839/phylogenetic-relationships-among-low-ploidy-poa-species-using-chloroplast-sequences
#16
Alpana Joshi, Shaun Bushman, Brandon D Pickett, Matthew Darwin Robbins, Jack Staub, Paul G Johnson
Species in the Poa genus are taxonomically and genetically difficult to delineate due to high and variable polyploidy, aneuploidy, and challenging breeding systems. Approximately 5% of the proposed species in Poa are considered to include or comprise diploids, but very few of those diploids are represented in seed collections. Recent phylogenetic studies of Poa have included some diploid species to elucidate Poa genome relationships. In this study we build upon that foundation of diploid Poa relationships with additional confirmed diploid species and accessions, and with additional chloroplast sequences...
November 23, 2016: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28163587/comparative-analysis-of-single-nucleotide-polymorphisms-in-the-nuclear-chloroplast-and-mitochondrial-genomes-in-identification-of-phylogenetic-association-among-seven-melon-cucumis-melo-l-cultivars
#17
Qianglong Zhu, Peng Gao, Shi Liu, Sikandar Amanullah, Feishi Luan
A variety of melons are cultivated worldwide, and their specific biological properties make them an attractive model for molecular studies. This study aimed to investigate the single nucleotide polymorphisms (SNPs) from the mitochondrial, chloroplast, and nuclear genomes of seven melon accessions (Cucumis melo L.) to identify the phylogenetic relationships among melon cultivars with the Illumina HiSeq 2000 platform and bioinformatical analyses. The data showed that there were a total of 658 mitochondrial SNPs (207-295 in each), while there were 0-60 chloroplast SNPs among these seven melon cultivars, compared to the reference genome...
December 2016: Breeding Science
https://www.readbyqxmd.com/read/28163584/parental-diagnosis-of-satsuma-mandarin-citrus-unshiu-marc-revealed-by-nuclear-and-cytoplasmic-markers
#18
Hiroshi Fujii, Satoshi Ohta, Keisuke Nonaka, Yuichi Katayose, Toshimi Matsumoto, Tomoko Endo, Terutaka Yoshioka, Mitsuo Omura, Takehiko Shimada
Satsuma mandarins (Citrus unshiu Marc.) are the predominant cultivated citrus variety in Japan. Clarification of its origin would prove valuable for citrus taxonomy and mandarin breeding programs; however, current information is limited. We applied genome-wide genotyping using a 384 citrus single nucleotide polymorphism (SNP) array and MARCO computer software to investigate the satsuma mandarin parentage. Genotyping data from 206 validated SNPs were obtained to evaluate 67 citrus varieties and lines. A total of five parent-offspring relationships were newly found by MARCO based on the 206 SNP genotypes, indicating that 'Kishuu mikan' type mandarins (Citrus kinokuni hort...
December 2016: Breeding Science
https://www.readbyqxmd.com/read/28158587/a-novel-inversion-in-the-chloroplast-genome-of-marama-tylosema-esculentum
#19
Yunsoo Kim, Christopher Cullis
No abstract text is available yet for this article.
January 31, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28158318/the-first-complete-chloroplast-genome-sequences-of-ulmus-species-by-de-novo-sequencing-genome-comparative-and-taxonomic-position-analysis
#20
Li-Hui Zuo, Ai-Qin Shang, Shuang Zhang, Xiao-Yue Yu, Ya-Chao Ren, Min-Sheng Yang, Jin-Mao Wang
Elm (Ulmus) has a long history of use as a high-quality heavy hardwood famous for its resistance to drought, cold, and salt. It grows in temperate, warm temperate, and subtropical regions. This is the first report of Ulmaceae chloroplast genomes by de novo sequencing. The Ulmus chloroplast genomes exhibited a typical quadripartite structure with two single-copy regions (long single copy [LSC] and short single copy [SSC] sections) separated by a pair of inverted repeats (IRs). The lengths of the chloroplast genomes from five Ulmus ranged from 158,953 to 159,453 bp, with the largest observed in Ulmus davidiana and the smallest in Ulmus laciniata...
2017: PloS One
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