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chloroplast genome

Julia Bally, Glen J McIntyre, Rachel L Doran, Karen Lee, Alicia Perez, Hyungtaek Jung, Fatima Naim, Ignacio M Larrinua, Kenneth E Narva, Peter M Waterhouse
Expressing double-stranded RNA (dsRNA) in transgenic plants to silence essential genes within herbivorous pests is referred to as trans-kingdom RNA interference (TK-RNAi) and has emerged as a promising strategy for crop protection. However, the dicing of dsRNA into siRNAs by the plant's intrinsic RNAi machinery may reduce this pesticidal activity. Therefore, genetic constructs, encoding ∼200 nt duplex-stemmed-hairpin (hp) RNAs, targeting the acetylcholinesterase gene of the cotton bollworm, Helicoverpa armigera, were integrated into either the nuclear or the chloroplast genome of Nicotiana benthamiana...
2016: Frontiers in Plant Science
Marlene Teubner, Janina Fuß, Kristina Kühn, Kirsten Krause, Christian Schmitz-Linneweber
Chloroplast RNA metabolism depends on a multitude of nuclear-encoded RNA binding proteins (RBPs). Most known chloroplast RBPs address specific RNA targets and RNA-processing functions. However, members of the small chloroplast ribonucleoprotein family (cpRNPs) play a global role in processing and stabilizing chloroplast RNAs. Here, we show that the cpRNP, CP33A, localizes to a distinct sub-chloroplastic domain and is essential for chloroplast development. The loss of CP33A yields albino seedlings that exhibit aberrant leaf development and can only survive in the presence of an external carbon source...
October 15, 2016: Plant Journal: for Cell and Molecular Biology
Pedro Marcus Pereira Vidigal, Alexandre Siqueira Guedes Coelho, Evandro Novaes, Márcio Henrique Pereira Barbosa, Luiz Alexandre Peternelli
Here, we present the chloroplast genome sequence of the Saccharum hybrid cultivar RB867515, the most planted sugarcane cultivar in Brazil.
October 13, 2016: Genome Announcements
Luciana Cristina Vitorino, Matheus S Lima-Ribeiro, Levi Carina Terribile, Rosane G Collevatti
BACKGROUND: We studied the phylogeography and demographical history of Tabebuia serratifolia (Bignoniaceae) to understand the disjunct geographical distribution of South American seasonally dry tropical forests (SDTFs). We specifically tested if the multiple and isolated patches of SDTFs are current climatic relicts of a widespread and continuously distributed dry forest during the last glacial maximum (LGM), the so called South American dry forest refugia hypothesis, using ecological niche modelling (ENM) and statistical phylogeography...
October 13, 2016: BMC Evolutionary Biology
Hasan Awad Aljohi, Wanfei Liu, Qiang Lin, Yuhui Zhao, Jingyao Zeng, Ali Alamer, Ibrahim O Alanazi, Abdullah O Alawad, Abdullah M Al-Sadi, Songnian Hu, Jun Yu
Coconut (Cocos nucifera L.), a member of the palm family (Arecaceae), is one of the most economically important crops in tropics, serving as an important source of food, drink, fuel, medicine, and construction material. Here we report an assembly of the coconut (C. nucifera, Oman local Tall cultivar) mitochondrial (mt) genome based on next-generation sequencing data. This genome, 678,653bp in length and 45.5% in GC content, encodes 72 proteins, 9 pseudogenes, 23 tRNAs, and 3 ribosomal RNAs. Within the assembly, we find that the chloroplast (cp) derived regions account for 5...
2016: PloS One
Joana F Costa, Showe-Mei Lin, Erasmo C Macaya, Cindy Fernández-García, Heroen Verbruggen
BACKGROUND: Obtaining strongly supported phylogenies that permit confident taxonomic and evolutionary interpretations has been a challenge in algal biology. High-throughput sequencing has improved the capacity to generate data and yields more informative datasets. We sequenced and analysed the chloroplast genomes of 22 species of the order Nemaliales as a case study in the use of phylogenomics as an approach to achieve well-supported phylogenies of red algae. RESULTS: Chloroplast genomes of the order Nemaliales are highly conserved, gene-dense and completely syntenic with very few cases of gene loss...
October 10, 2016: BMC Evolutionary Biology
Padma Nimmakayala, Yan R Tomason, Venkata L Abburi, Alejandra Alvarado, Thangasamy Saminathan, Venkata G Vajja, Germania Salazar, Girish K Panicker, Amnon Levi, William P Wechter, James D McCreight, Abraham B Korol, Yefim Ronin, Jordi Garcia-Mas, Umesh K Reddy
Melon (Cucumis melo L.) is a phenotypically diverse eudicot diploid (2n = 2x = 24) has climacteric and non-climacteric morphotypes and show wide variation for fruit firmness, an important trait for transportation and shelf life. We generated 13,789 SNP markers using genotyping-by-sequencing (GBS) and anchored them to chromosomes to understand genome-wide fixation indices (Fst) between various melon morphotypes and genomewide linkage disequilibrium (LD) decay. The FST between accessions of cantalupensis and inodorus was 0...
2016: Frontiers in Plant Science
Monica Colombo, Luca Tadini, Carlotta Peracchio, Roberto Ferrari, Paolo Pesaresi
The GENOMES UNCOUPLED 1 (GUN1) gene has been reported to encode a chloroplast-localized pentatricopeptide-repeat protein, which acts to integrate multiple indicators of plastid developmental stage and altered plastid function, as part of chloroplast-to-nucleus retrograde communication. However, the molecular mechanisms underlying signal integration by GUN1 have remained elusive, up until the recent identification of a set of GUN1-interacting proteins, by co-immunoprecipitation and mass-spectrometric analyses, as well as protein-protein interaction assays...
2016: Frontiers in Plant Science
Ting Wang, Zhen Wang, Guopei Chen, Chunbo Wang, Yingjuan Su
Two fundamental questions on how invasive species are able to rapidly colonize novel habitat have emerged. One asks whether a negative correlation exists between the genetic diversity of invasive populations and their geographic distance from the origin of introduction. The other is whether selection on the chloroplast genome is important driver of adaptation to novel soil environments. Here, we addressed these questions in a study of the noxious invasive weed, Mikania micrantha, which has rapidly expanded in to southern China after being introduced to Hong Kong in 1884...
2016: Frontiers in Plant Science
Nicole Parker, Yixing Wang, David Meinke
Natural accessions of Arabidopsis thaliana differ in their ability to tolerate a loss of chloroplast translation. These differences can be attributed in part to variation in a duplicated nuclear gene (ACC2) that targets homomeric acetyl-CoA carboxylase (ACCase) to plastids. This functional redundancy allows limited fatty acid biosynthesis to occur in the absence of heteromeric ACCase, which is encoded in part by the plastid genome. In the presence of functional ACC2, tolerant alleles of several nuclear genes, not yet identified, enhance the growth of seedlings and embryos disrupted in chloroplast translation...
October 5, 2016: Plant Physiology
X L Ren, L Q Li, L Xu, Y S Guo, L M Lu
Potassium is one of the three main mineral nutrients, and is vital for leaf growth and the quality of tobacco (Nicotiana tabacum) plants. In recent years, the isobaric tags for relative and absolute quantitation (iTRAQ) method has been one of the most popular techniques for quantitative proteomic analysis. In this study, we used iTRAQ to compare protein abundances in the roots of control and low potassium-treated tobacco seedlings, and found that 108 proteins were differentially expressed between the two treatments...
August 29, 2016: Genetics and Molecular Research: GMR
Peng-Cheng Fu, Yan-Zhao Zhang, Hui-Min Geng, Shi-Long Chen
BACKGROUND: The chloroplast (cp) genome is useful in plant systematics, genetic diversity analysis, molecular identification and divergence dating. The genus Gentiana contains 362 species, but there are only two valuable complete cp genomes. The purpose of this study is to report the characterization of complete cp genome of G. lawrencei var. farreri, which is endemic to the Qinghai-Tibetan Plateau (QTP). METHODS: Using high throughput sequencing technology, we got the complete nucleotide sequence of the G...
2016: PeerJ
Karen B Barnard-Kubow, Morgan A McCoy, Laura F Galloway
Although organelle inheritance is predominantly maternal across animals and plants, biparental chloroplast inheritance has arisen multiple times in the angiosperms. Biparental inheritance has the potential to impact the evolutionary dynamics of cytonuclear incompatibility, interactions between nuclear and organelle genomes that are proposed to be among the earliest types of genetic incompatibility to arise in speciation. We examine the interplay between biparental inheritance and cytonuclear incompatibility in Campanulastrum americanum, a plant species exhibiting both traits...
September 30, 2016: New Phytologist
Karen B Barnard-Kubow, Nina So, Laura F Galloway
Genetic incompatibility is a hallmark of speciation. Cytonuclear incompatibilities are proposed to be among the first genetic barriers to arise during speciation. Accordingly, reproductive isolation within species should be heavily influenced by interactions between the organelle and nuclear genomes. However, there are few clear examples of cytonuclear incompatibility within a species. Here we show substantial postzygotic reproductive isolation in first-generation hybrids between differentiated populations of an herbaceous plant (up to 92% reduction in fitness)...
September 28, 2016: Evolution; International Journal of Organic Evolution
Lindsay Chaney, Ryan Mangelson, Thiruvarangan Ramaraj, Eric N Jellen, Peter J Maughan
PREMISE OF THE STUDY: The amaranth genus contains many important grain and weedy species. We further our understanding of the genus through the development of a complete reference chloroplast genome. METHODS AND RESULTS: A high-quality Amaranthus hypochondriacus (Amaranthaceae) chloroplast genome assembly was developed using long-read technology. This reference genome was used to reconstruct the chloroplast genomes for two closely related grain species (A. cruentus and A...
September 2016: Applications in Plant Sciences
Jessica N C Francisco, Alison G Nazareno, Lúcia G Lohmann
PREMISE OF THE STUDY: In this study, we developed chloroplast microsatellite markers (cpSSRs) for Pachyptera kerere (Bignoniaceae) to investigate the population structure and genetic diversity of this species. METHODS AND RESULTS: We used Illumina HiSeq data to reconstruct the chloroplast genome of P. kerere by a combination of de novo and reference-guided assembly. We then used the chloroplast genome to develop a set of cpSSRs from intergenic regions. Overall, 24 primer pairs were designed, 21 of which amplified successfully and were polymorphic, presenting three to nine alleles per locus...
September 2016: Applications in Plant Sciences
Han Miao, Shengping Zhang, Min Wang, Ye Wang, Yiqun Weng, Xingfang Gu
Leaf color mutants are common in higher plants that can be used as markers in crop breeding or as an important tool in understanding regulatory mechanisms in chlorophyll biosynthesis and chloroplast development. In virescent leaf mutants, young leaves are yellow in color, which gradually return to normal green when the seedlings grow large. In the present study, we conducted phenotypic characterization and genetic mapping of the cucumber virescent leaf mutant 9110Gt conferred by the v-1 locus. Total chlorophyll and carotenoid content in 9110Gt was reduced by 44% and 21%, respectively, as compared with its wild type parental line 9110G...
2016: International Journal of Molecular Sciences
Kai Bernd Stadermann, Daniela Holtgräwe, Bernd Weisshaar
A publicly available data set from Pacific Biosciences was used to create an assembly of the chloroplast genome sequence of the Arabidopsis thaliana genotype Landsberg erecta The assembly is solely based on single-molecule, real-time sequencing data and hence provides high resolution of the two inverted repeat regions typically contained in chloroplast genomes.
2016: Genome Announcements
Charles S P Foster, Hervé Sauquet, Marlien van der Merwe, Hannah McPherson, Maurizio Rossetto, Simon Y W Ho
The evolutionary timescale of angiosperms has long been a key question in biology. Molecular estimates of this timescale have shown considerable variation, being influenced by differences in taxon sampling, gene sampling, fossil calibrations, evolutionary models, and choices of priors. Here, we analyse a data set comprising 76 protein-coding genes from the chloroplast genomes of 195 taxa spanning 86 families, including novel genome sequences for 11 taxa, to evaluate the impact of models, priors, and gene sampling on Bayesian estimates of the angiosperm evolutionary timescale...
September 20, 2016: Systematic Biology
Y Zhou, L Duvaux, G Ren, L Zhang, O Savolainen, J Liu
Genetic variation shared between closely related species may be due to retention of ancestral polymorphisms because of incomplete lineage sorting (ILS) and/or introgression following secondary contact. It is challenging to distinguish ILS and introgression because they generate similar patterns of shared genetic diversity, but this is nonetheless essential for inferring accurately the history of species with overlapping distributions. To address this issue, we sequenced 33 independent intron loci across the genome of two closely related pine species (Pinus massoniana Lamb...
September 21, 2016: Heredity
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