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https://www.readbyqxmd.com/read/28097059/the-complete-chloroplast-genome-sequence-of-an-endemic-monotypic-genus-hagenia-rosaceae-structural-comparative-analysis-gene-content-and-microsatellite-detection
#1
Andrew W Gichira, Zhizhong Li, Josphat K Saina, Zhicheng Long, Guangwan Hu, Robert W Gituru, Qingfeng Wang, Jinming Chen
Hagenia is an endangered monotypic genus endemic to the topical mountains of Africa. The only species, Hagenia abyssinica (Bruce) J.F. Gmel, is an important medicinal plant producing bioactive compounds that have been traditionally used by African communities as a remedy for gastrointestinal ailments in both humans and animals. Complete chloroplast genomes have been applied in resolving phylogenetic relationships within plant families. We employed high-throughput sequencing technologies to determine the complete chloroplast genome sequence of H...
2017: PeerJ
https://www.readbyqxmd.com/read/28078742/taxonomic-revision-of-the-agaraceae-with-a-description-of-neoagarum-gen-nov-and-reinstatement-of-thalassiophyllum
#2
Hiroshi Kawai, Takeaki Hanyuda, Gao Xu, Makoto Terauchi, Masahiko Miyata, Sandra C Lindstrom, Nina G Klochkova, Kathy Ann Miller
We confirmed the monophyly of the Agaraceae based on phylogenetic analyses of 6 mitochondrial and 6 chloroplast gene sequences from Agarum, Costaria, Dictyoneurum and Thalassiophyllum species as well as representative species from other laminarialean families. However, the genus Agarum was paraphyletic, comprising two independent clades, A. clathratum/A. turneri and A. fimbriatum/A. oharaense. The latter clade was genetically most closely related to Dictyoneurum spp., and morphologically the species shared a flattened stipe bearing fimbriae (potential secondary haptera) in the mid to upper portion...
January 12, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28076891/comparative-genomics-of-mortierella-elongata-and-its-bacterial-endosymbiont-mycoavidus-cysteinexigens
#3
J Uehling, A Gryganskyi, K Hameed, T Tschaplinski, P K Misztal, S Wu, A Desirò, N Vande Pol, Z Du, A Zienkiewicz, K Zienkiewicz, E Morin, E Tisserant, R Splivallo, M Hainaut, B Henrissat, R Ohm, A Kuo, J Yan, A Lipzen, M Nolan, K LaButti, K Barry, A H Goldstein, J Labbé, C Schadt, G Tuskan, I Grigoriev, F Martin, R Vilgalys, G Bonito
Endosymbiosis of bacteria by eukaryotes is a defining feature of cellular evolution. In addition to well known bacterial origins for mitochondria and chloroplasts, multiple origins of bacterial endosymbiosis are known within the cells of diverse animals, plants, and fungi. Early-diverging lineages of terrestrial fungi harbor endosymbiotic bacteria belonging to the Burkholderiaceae. We sequenced the metagenome of the soil-inhabiting fungus Mortierella elongata and assembled the complete circular chromosome of its endosymbiont, Mycoavidus cysteinexigens, which we place within in a lineage of endofungal symbionts that are sister clade to Burkholderia...
January 11, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28076289/from-bacteria-to-chloroplasts-evolution-of-the-chloroplast-srp-system
#4
Dominik Ziehe, Beatrix Dünschede, Danja Schünemann
Chloroplasts derive from a prokaryotic symbiont that lost most of its genes during evolution. As a result, the great majority of chloroplast proteins are encoded in the nucleus and are posttranslationally imported into the organelle. The chloroplast genome encodes only a few proteins. These include several multispan thylakoid membrane proteins which are synthesized on thylakoid-bound ribosomes and cotranslationally inserted into the membrane. During evolution, ancient prokaryotic targeting machineries were adapted and combined with novel targeting mechanisms to facilitate post- and cotranslational protein transport in chloroplasts...
January 10, 2017: Biological Chemistry
https://www.readbyqxmd.com/read/28075225/plants-contain-small-families-of-upf0016-proteins-including-the-photosynthesis-affected-mutant71-transporter
#5
Natalie Hoecker, Dario Leister, Anja Schneider
PHOTOSYNTHESIS AFFECTED MUTANT71 (PAM71) is an integral thylakoid membrane protein that functions in manganese uptake into the lumen. Manganese is needed in the thylakoid lumen to build up the inorganic Mn4CaO5 cluster, the catalytic center for water oxidation, and is hence indispensable for oxygen evolution. A recent study revealed that PAM71 is well conserved in plants and shares homology to GCR1 DEPENDENT TRANSLATION FACTOR1 (GDT1) and TRANSMEMBRANE PROTEIN 165 (TMEM165) in Saccharomyces cerevisiae and Homo sapiens, respectively...
January 11, 2017: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/28072865/reading-the-evolution-of-compartmentalization-in-the-ribosome-assembly-toolbox-the-yrg-protein-family
#6
Pablo Mier, Antonio J Pérez-Pulido, Emmanuel G Reynaud, Miguel A Andrade-Navarro
Reconstructing the transition from a single compartment bacterium to a highly compartmentalized eukaryotic cell is one of the most studied problems of evolutionary cell biology. However, timing and details of the establishment of compartmentalization are unclear and difficult to assess. Here, we propose the use of molecular markers specific to cellular compartments to set up a framework to advance the understanding of this complex intracellular process. Specifically, we use a protein family related to ribosome biogenesis, YRG (YlqF related GTPases), whose evolution is linked to the establishment of cellular compartments, leveraging the current genomic data...
2017: PloS One
https://www.readbyqxmd.com/read/28061749/organelle_pba-a-pipeline-for-assembling-chloroplast-and-mitochondrial-genomes-from-pacbio-dna-sequencing-data
#7
Aboozar Soorni, David Haak, David Zaitlin, Aureliano Bombarely
BACKGROUND: The development of long-read sequencing technologies, such as single-molecule real-time (SMRT) sequencing by PacBio, has produced a revolution in the sequencing of small genomes. Sequencing organelle genomes using PacBio long-read data is a cost effective, straightforward approach. Nevertheless, the availability of simple-to-use software to perform the assembly from raw reads is limited at present. RESULTS: We present Organelle-PBA, a Perl program designed specifically for the assembly of chloroplast and mitochondrial genomes...
January 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28061748/complete-chloroplast-genome-of-gracilaria-firma-gracilariaceae-rhodophyta-with-discussion-on-the-use-of-chloroplast-phylogenomics-in-the-subclass-rhodymeniophycidae
#8
Poh-Kheng Ng, Showe-Mei Lin, Phaik-Eem Lim, Li-Chia Liu, Chien-Ming Chen, Tun-Wen Pai
BACKGROUND: The chloroplast genome of Gracilaria firma was sequenced in view of its role as an economically important marine crop with wide industrial applications. To date, there are only 15 chloroplast genomes published for the Florideophyceae. Apart from presenting the complete chloroplast genome of G. firma, this study also assessed the utility of genome-scale data to address the phylogenetic relationships within the subclass Rhodymeniophycidae. The synteny and genome structure of the chloroplast genomes across the taxa of Eurhodophytina was also examined...
January 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28056496/chloroplast-the-trojan-horse-in-plant-virus-interaction
#9
REVIEW
Dhriti Bhattacharyya, Supriya Chakraborty
Chloroplast is one of the most dynamic organelle of a plant cell. It carries out photosynthesis, synthesizes major phytohormones, takes active part in defence response, and is crucial for inter-organelle signaling. Viruses, on the other hand, are extremely strategic in manipulating the internal environment of the host cell. Chloroplast, a prime target for viruses, undergoes enormous structural and functional damage during viral infection. In fact, large proportions of affected gene products in a virus infected plant are closely associated to chloroplast and photosynthesis process...
January 5, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28042823/identification-and-analysis-of-rna-editing-sites-in-the-chloroplast-transcripts-of-aegilops-tauschii-l
#10
Mengxing Wang, Hui Liu, Lingqiao Ge, Guangwei Xing, Meng Wang, Song Weining, Xiaojun Nie
RNA editing is an important way to convert cytidine (C) to uridine (U) at specific sites within RNA molecules at a post-transcriptional level in the chloroplasts of higher plants. Although it has been systematically studied in many plants, little is known about RNA editing in the wheat D genome donor Aegilops tauschii L. Here, we investigated the chloroplast RNA editing of Ae. tauschii and compared it with other wheat relatives to trace the evolution of wheat. Through bioinformatics prediction, a total of 34 C-to-U editing sites were identified, 17 of which were validated using RT-PCR product sequencing...
December 30, 2016: Genes
https://www.readbyqxmd.com/read/28042043/first-plastid-phylogenomic-study-reveals-potential-cyto-nuclear-discordance-in-the-evolutionary-history-of-ficus-l-moraceae
#11
Sam Bruun-Lund, Wendy L Clement, Finn Kjellberg, Nina Rønsted
Standard Sanger chloroplast markers provide limited information to resolve species level relationships within plants, in particular within large genera. Figs (Ficus L., Moraceae) compose one of the 50 largest genera of angiosperms with ∼750 species occurring in the tropics and subtropics worldwide. Figs, in addition to being a keystone food resource in rainforests, are well-known for the mutualistic interactions with their pollinating wasps. It is regarded as a model system for understanding co-evolution dating back more than 75million years...
December 29, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28040673/genome-origin-historical-hybridization-and-genetic-differentiation-in-anthosachne-australasica-triticeae-poaceae-inferred-from-chloroplast-rbcl-trnh-psba-and-nuclear-acc1-gene-sequences
#12
Li-Na Sha, Xing Fan, Xiao-Li Wang, Zhen-Zhen Dong, Jian Zeng, Hai-Qin Zhang, Hou-Yang Kang, Yi Wang, Jin-Qiu Liao, Yong-Hong Zhou
BACKGROUND AND AIMS: Anthosachne Steudel is a group of allopolyploid species that was derived from hexaploidization between the Asian StY genome Roegneria entity and the Australasia W genome Australopyrum species. Polyploidization and apomixis contribute to taxonomic complexity in Anthosachne Here, a study is presented on the phylogeny and evolutionary history of Anthosachne australasica The aims are to demonstrate the process of polyploidization events and to explore the differentiation patterns of the St genome following geographic isolation...
January 2017: Annals of Botany
https://www.readbyqxmd.com/read/28034319/comparative-analysis-of-chloroplast-genomes-of-the-genus-citrus-and-its-close-relatives
#13
Xiaogang Liu, Hongkun Wu, Yan Luo, Wanpeng Xi, Zhiqin Zhou
The genus Citrus and its close relatives are economically and nutritionally important fruit trees. However, the huge controversy over the phylogeny of key wild species, as well as the genetic relationship between the cultivated species and their putative wild progenitors, remains unresolved. Comparative analyses of chloroplast (cp) genomes have been useful in resolving various phylogenetic issues. Thus far, the cp genomes of only two Citrus species have been sequenced. In this study, we sequenced six complete cp genomes, four belonging to the genus Citrus, and two belonging to the genera Fortunella and Poncirus, respectively...
December 30, 2016: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28028020/museomics-resolve-the-systematics-of-an-endangered-grass-lineage-endemic-to-north-western-madagascar
#14
Christian Silva, Guillaume Besnard, Anthony Piot, Jacqueline Razanatsoa, Reyjane P Oliveira, Maria S Vorontsova
BACKGROUND AND AIMS: Recent developments in DNA sequencing, so-called next-generation sequencing (NGS) methods, can help the study of rare lineages that are known from museum specimens. Here, the taxonomy and evolution of the Malagasy grass lineage Chasechloa was investigated with the aid of NGS. METHODS: Full chloroplast genome data and some nuclear sequences were produced by NGS from old herbarium specimens, while some selected markers were generated from recently collected Malagasy grasses...
December 27, 2016: Annals of Botany
https://www.readbyqxmd.com/read/28027000/viroid-quasispecies-revealed-by-deep-sequencing
#15
Joseph R J Brass, Robert A Owens, Jaroslav Matoušek, Gerhard Steger
Viroids are non-coding single-stranded circular RNA molecules that replicate autonomously in infected host plants causing mild to lethal symptoms. Their genomes contain about 250-400 nucleotides, depending on viroid species. Members of the family Pospiviriodeae, like the Potato spindle tuber viroid (PSTVd), replicate via an asymmetric rolling-circle mechanism using the host DNA-dependent RNA-Polymerase II in the nucleus, while members of Avsunviroidae are replicated in a symmetric rolling-circle mechanism probably by the nuclear-encoded polymerase in chloroplasts...
December 27, 2016: RNA Biology
https://www.readbyqxmd.com/read/28025543/rna-editing-and-its-molecular-mechanism-in-plant-organelles
#16
REVIEW
Mizuho Ichinose, Mamoru Sugita
RNA editing by cytidine (C) to uridine (U) conversions is widespread in plant mitochondria and chloroplasts. In some plant taxa, "reverse" U-to-C editing also occurs. However, to date, no instance of RNA editing has yet been reported in green algae and the complex thalloid liverworts. RNA editing may have evolved in early land plants 450 million years ago. However, in some plant species, including the liverwort, Marchantia polymorpha, editing may have been lost during evolution. Most RNA editing events can restore the evolutionarily conserved amino acid residues in mRNAs or create translation start and stop codons...
December 23, 2016: Genes
https://www.readbyqxmd.com/read/28018385/chloroplast-genome-sequence-of-pigeonpea-cajanus-cajan-l-millspaugh-and-cajanus-scarabaeoides-l-thouars-genome-organization-and-comparison-with-other-legumes
#17
Tanvi Kaila, Pavan K Chaduvla, Swati Saxena, Kaushlendra Bahadur, Santosh J Gahukar, Ashok Chaudhury, T R Sharma, N K Singh, Kishor Gaikwad
Pigeonpea (Cajanus cajan (L.) Millspaugh), a diploid (2n = 22) legume crop with a genome size of 852 Mbp, serves as an important source of human dietary protein especially in South East Asian and African regions. In this study, the draft chloroplast genomes of Cajanus cajan and Cajanus scarabaeoides (L.) Thouars were generated. Cajanus scarabaeoides is an important species of the Cajanus gene pool and has also been used for developing promising CMS system by different groups. A male sterile genotype harboring the C...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28009803/phylogenetic-relationships-of-the-fern-cyrtomium-falcatum-dryopteridaceae-from-dokdo-island-based-on-chloroplast-genome-sequencing
#18
Gurusamy Raman, Kyoung Su Choi, SeonJoo Park
Cyrtomium falcatum is a popular ornamental fern cultivated worldwide. Native to the Korean Peninsula, Japan, and Dokdo Island in the Sea of Japan, it is the only fern present on Dokdo Island. We isolated and characterized the chloroplast (cp) genome of C. falcatum, and compared it with those of closely related species. The genes trnV-GAC and trnV-GAU were found to be present within the cp genome of C. falcatum, whereas trnP-GGG and rpl21 were lacking. Moreover, cp genomes of Cyrtomium devexiscapulae and Adiantum capillus-veneris lack trnP-GGG and rpl21, suggesting these are not conserved among angiosperm cp genomes...
December 2, 2016: Genes
https://www.readbyqxmd.com/read/28008672/the-angulata7-gene-encodes-a-dnaj-like-zinc-finger-domain-protein-involved-in-chloroplast-function-and-leaf-development-in-arabidopsis
#19
Tamara Muñoz-Nortes, José Manuel Pérez-Pérez, María Rosa Ponce, Héctor Candela, José Luis Micol
The characterization of mutants with altered leaf shape and pigmentation has previously allowed the identification of nuclear genes that encode plastid-localized proteins that perform essential functions in leaf growth and development. A large-scale screen previously allowed us to isolate ethyl methanesulfonate-induced mutants with small rosettes and pale green leaves with prominent marginal teeth, which were assigned to a phenotypic class that we dubbed Angulata. The molecular characterization of the twelve genes assigned to this phenotypic class should help us to advance our understanding of the still poorly understood relationship between chloroplast biogenesis and leaf morphogenesis...
December 23, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28007896/the-complete-structure-of-the-chloroplast-70s-ribosome-in-complex-with-translation-factor-py
#20
Philipp Bieri, Marc Leibundgut, Martin Saurer, Daniel Boehringer, Nenad Ban
Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, they still contain their own genome and the machinery for protein biosynthesis. Here, we present the atomic structure of the chloroplast 70S ribosome prepared from spinach leaves and resolved by cryo-EM at 3.4 Å resolution. The complete structure reveals the features of the 4.5S rRNA, which probably evolved by the fragmentation of the 23S rRNA, and all five plastid-specific ribosomal proteins...
December 22, 2016: EMBO Journal
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