Chloroplast genome: Need to close 2 gaps (~2Kbp), any suggestions?
This is a chloroplast genome and I am trying to find a way to close these gaps and finalize my assembly. I have a significant ... This project is my masters thesis and I would like to start running some analyzes on the complete chloroplast genome once I ... Assembly next-gen sequence genome • 1.7k views ADD COMMENT • link 6.6 years ago by lizgzara ▴ 10 ... I have had good results using Abyss at a range of k-mer values to assemble a mitochondrial genome. If these methods fail, you ...
Cellular and transcriptomic analyses reveal two-staged chloroplast biogenesis underpinning photosynthesis build-up in the wheat...
The second phase is marked by the development of photosynthetic chloroplasts which occupy the available cellular space. Using a ... It reveals functionally distinct plastid and chloroplast development stages, identifies processes occurring in each of them, ... which limits the value of transcriptome data to understand the process of chloroplast development. Taking advantage of the ... we provide a simultaneous quantitative analysis for the development of mesophyll cells and of chloroplasts as a cellular ...
"The Chloroplast Genome Sequence of the Marattioid Fern Angiopteris" by J. M. Roper, S. K. Hansen et al.
Chloroplast genome assembly
This tutorial shows genome assembly for a smaller data set - the plant chloroplast genome - a single circular chromosome which ... misc{assembly-chloroplast-assembly, author = "Anna Syme", title = "Chloroplast genome assembly (Galaxy Training Materials)", ... "Reference genome to display": Use a genome from history. *"Select a reference genome": polished-assembly.fasta. ... "Reference genome to display": Use a genome from history. *"Select a reference genome": polished-assembly.fasta. ...
OPUS 4 | A circular chloroplast genome of fagus sylvatica reveals high conservation between two individuals from Germany and...
The chloroplast genome of Bhaga and of the individual from Poland both have only two mismatches as well as three and two indels ... The chloroplast genome of Bhaga was 158,458 bp, and that of Jamy was 158,462 bp long. Using long-read mapping on the ... However, once chloroplast genomes become available from Pleistocene refugia, where a high degree of variation has been reported ... In an attempt to elucidate the orientation of the single-copy regions and to find suitable loci for chloroplast single ...
![Whole Chloroplast Genome Characterization and Comparison of Two Sympatric Species in Genus Hippophae (Elaeagnaceae)[v1] |...](data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAA0AAAAQCAMAAAD6fQULAAAAS1BMVEVHcEz/vwD1yyf9vwf/vgD+vgH5wRP/vgAABzj+vwj7whIABzj7vw3+vgT+vgX+0hX+vwsAADr9vwf8wA38vwYAAD6mfSKMfDT/vgBFulgmAAAAGHRSTlMA+g6x890j7bGGN2p61MkWkE6bbkko3Rhzgv8fAAAAc0lEQVQImV2OSRbEIAgFQTHG2Qzd4f4nDair1Ip6/z8AQIn3bWDRWanbkMKXBLFyFMnc4EjpB9Zr1GFXjsbSdeFraTRpmPk/uoXKzFAvWDubJl85B0c4jUnwXs12g36Acm87l2EYrzWWmdiut0N15Yzw5QXqAAXjnm3RwAAAAABJRU5ErkJggg==)
Whole Chloroplast Genome Characterization and Comparison of Two Sympatric Species in Genus Hippophae (Elaeagnaceae)[v1] |...
After comparing the chloroplast genomes, we found 1302 base difference loci, and 63.29% are located in the intergenic region or ... It is an important reference for studies on the general characteristics and evolution of the Hippophae chloroplast genome. ... In this study, we assembled and annotated chloroplast genomes of sympatric Hippophae gyantsensis and H. rhamnoides subsp. ... yunnanensis chloroplast protein-coding genes, there are 20 and 16 optimal codons, respectively. Most of the optimal codons were ...
Towards Improved Molecular Identification Tools in Fine Fescue (Festuca L., Poaceae) Turfgrasses: Nuclear Genome Size, Ploidy,...
... we used flow cytometry to estimate genome size and ploidy level and sequenced the chloroplast genome of all five taxa. Fine ... we used flow cytometry to estimate genome size and ploidy level and sequenced the chloroplast genome of all five taxa. Fine ... we used flow cytometry to estimate genome size and ploidy level and sequenced the chloroplast genome of all five taxa. Fine ... we used flow cytometry to estimate genome size and ploidy level and sequenced the chloroplast genome of all five taxa. Fine ...
A systematic comparison of chloroplast genome assembly tools
Potato genome decoded | Max-Planck-Gesellschaft
... have for the first time decoded the highly complex genome of the potato. This technically demanding study lays the ... More than 20 years after the first release of the human genome, scientists at the Ludwig-Maximilians-Universität München and ... Under cold conditions, not only the mother plant but also the father plant can pass on its chloroplasts to the offspring ... In the present study, genomes from individual pollen grains were analysed to produce the first, complete map of a potato genome ...
A novel inversion in the chloroplast genome of marama (Tylosema esculentum). - PacBio
... the chloroplast genome has been assembled from next-generation sequencing using both Illumina and Pac-Bio data. The genome is ... These data extend the range of variability of legume chloroplast genomes. The sequencing of multiple individuals has identified ... even in the closest relatives for which the complete chloroplast genome is available, and two complete copies of the ycf1 gene ... leaving open the question of legume chloroplast genomes adapted to particular arid environments.© The Author 2017. Published by ...
Complete chloroplast genome sequence of Clematis calcicola (Ranunculaceae), a species endemic to Korea
In the present study, the complete chloroplast genome (chloroplast genome) of C. calcicola is reported for the first time, to ... 7,417 of which corresponded to the chloroplast genome (depth 5.4). The complete chloroplast genome sequence of C. calcicola was ... The complete chloroplast genome (cp genome) sequence of Clematis calcicola J. S. Kim (Ranunculaceae) is 159,655 bp in length. ... 2). The chloroplast genome of C. calcicola was 11 bp longer than that of C. macropetala (159,647 bp, NC_041477). Nevertheless, ...
Peaches Preceded Humans: Fossil Evidence from SW China | Scientific Reports
The chloroplast genome of Amygdalus L. (Rosaceae) reveals the phylogenetic relationship and divergence time *Zhongyu Du ... Genome structure variation analyses of peach reveal population dynamics and a 1.67 Mb causal inversion for fruit shape *Jiantao ... The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and ... A high-quality assembled genome of a representative peach landrace, Feichenghongli, and analysis of distinct late florescence ...
RuBisCO - Wikipedia
"10.The Chloroplast Genome". The Cell: A Molecular Approach (2nd ed.). Washington, D.C: ASM Press. ISBN 978-0-87893-106-4. , one ... so it is noteworthy that one of its subunits is encoded by the chloroplast genome. Dhingra A, Portis AR, Daniell H (April 2004 ... and the small chains are imported to the stromal compartment of chloroplasts from the cytosol by crossing the outer chloroplast ... The chloroplast gene rbcL, which codes for the large subunit of RuBisCO has been widely used as an appropriate locus for ...
Genetic differentiation of Liquidambar Orientalis Mill. varieties with respect to matK region of chloroplast genome
varieties with respect to matK region of chloroplast genome," M.S. - Master of Science, Middle East Technical University, 2007. ... analysis of pinus nigra arnold subspecies pallasiana varieties with respect to non-coding trn regions of chloroplast genome. ... For this purpose, 18 different populations were sampled throughout the species range and matK region of chloroplast DNA (cpDNA ...
Characterization of the Complete Chloroplast Genome Sequence of Dalbergia Species And Its Phylogenetic Implications - CD...
... we sequenced and compared the chloroplast genomes of nine species of Dalbergia. We found that these chloroplast genomes were ... Based on comparison of chloroplast genomes, we identified a set of highly variable markers that can be developed as specific ... Phylogenetic analyses based on whole chloroplast genome data provided the best resolution of Dalbergia, and phylogenetic ... Characterization of the Complete Chloroplast Genome Sequence of Dalbergia Species And Its Phylogenetic Implications. ...
De novo assembly of transcriptome and draft chloroplast genome from RNAseq data of Bacopa monnieri L. (Bramhi)
... of chloroplast genome has been assembled and in progress. The draft chloroplast genome will also help in shedding light towards ... De novo assembly of transcriptome and draft chloroplast genome from RNAseq data of Bacopa monnieri L. (Bramhi). Uncategorized ... An attempt was made to assemble the draft chloroplast genome from the assembled transcriptome data and ~65% ... Pathway mapping of the unigenes using Kyoto encyclopedia of genes and genomes revealed 14,816 transcripts involved in 143 ...
How guard cell chloroplasts obtain energy | ScienceDaily
Earlier studies suggested that guard cell chloroplasts (GCCs) cannot fix CO2 but later studies argued otherwise. Until recently ... A Genome of Photosynthetic Animals Decoded. July 15, 2021 Some sea slugs take up chloroplasts from the algae that they consume ... How guard cell chloroplasts obtain energy. Date:. February 10, 2022. Source:. The University of Hong Kong. Summary:. Whether ... "How guard cell chloroplasts obtain energy." ScienceDaily. www.sciencedaily.com. /. releases. /. 2022. /. 02. /. 220210084945. ...
Category:Genomes - Wikimedia Commons
genome entirety of an organisms hereditary information; genome of organism (encoded by the genomic DNA) is the (biological) ... genome; 基因組; genoma; genom; genoma; genom; genomas; genom; Genome; Géanóm; जीनोम; จีโนม; genom; ജീനോം; 基因組; Genom; Геном; ... Media in category "Genomes". The following 200 files are in this category, out of 334 total. ... Genome map of the bacteriophage ΦX174 showing overlapping genes.svg 1,040 × 1,117; 437 KB. ...
Genome analysis of mitochondria and chloroplast from red alga dulse: [Open Access] Kumagai et al., 2019, Marine Drugs
Genome analysis of mitochondria and chloroplast from red alga dulse * Mitochondria and Chloroplast genome of Southern Hokkaido ... Genome analysis of mitochondria and chloroplast from red alga dulse and the relation of bioactivity × SDGs ... Genome analysis of mitochondria and chloroplast from red alga dulse and the relation of bioactivity ... Genome analysis of mitochondria and chloroplast from red alga dulse and the relation of bioactivity. ...
Origins of cultivars of <i>Chrysanthemum</i>-Evidence from the chloroplast genome and nuclear ...
Origins of cultivars of Chrysanthemum-Evidence from the chloroplast genome and nuclear LFY gene Yue-Ping Ma1 , Liang Zhao2 , ... Origins of cultivars of Chrysanthemum-Evidence from the chloroplast genome and nuclear LFY gene[J]. J Syst Evol, 2020, 58(6): ... known cultivars and wild species of the genus Chrysanthemum using chloroplast genomes and the nuclear LEAFY gene. Our results ...
Publication : USDA ARS
The objective of this study was to demonstrate multiplex sequencing of Fragaria chloroplast genomes using the Illumina Genome ... Title: Multiplexed Fragaria Chloroplast Genome Sequencing Author. NJUGUNA, WAMBUI - Oregon State University ... Multiplexed Fragaria Chloroplast Genome Sequencing. Acta Horticulturae. 859:315-320.. Interpretive Summary: Relationships among ... Technical Abstract: A method to sequence multiple chloroplast genomes that uses the sequencing depth of ultra high throughput ...
Transfer of chloroplast genomic DNA to mitochondrial genome occurred at least 300 MYA<...
keywords = "Chloroplast genome, Gene transfer, Mitochondrial genome, mtpt, Seed plants",. author = "Daryi Wang and Wu, {Yu Wei ... Transfer of chloroplast genomic DNA to mitochondrial genome occurred at least 300 MYA. / Wang, Daryi; Wu, Yu Wei; Shih, Arthur ... Transfer of chloroplast genomic DNA to mitochondrial genome occurred at least 300 MYA. Molecular Biology and Evolution. 2007 9月 ... Transfer of chloroplast genomic DNA to mitochondrial genome occurred at least 300 MYA. 於: Molecular Biology and Evolution. 2007 ...
Complete chloroplast genome of Stephania tetrandra (Menispermaceae) from Zhejiang Province: insights into molecular structures,...
The complete chloroplast (cp) genome data has become a promising strategy to determine geographical origin and understand ... Complete chloroplast genome of Stephania tetrandra (Menispermaceae) from Zhejiang Province: insights into molecular structures ... Overall, we provided comprehensive and detailed information on the complete chloroplast genome and identified nucleotide ... The cp genome of S. tetrandra voucher ZJ was 157,725 bp, consisting of a large single copy region (89,468 bp), a small single ...
Return of the Lemnaceae: duckweed as a model plant system in the genomics and postgenomics era (Journal Article) | DOE PAGES
High-Throughput Sequencing of Three Lemnoideae (Duckweeds) Chloroplast Genomes from Total DNA journal, September 2011 * Wang, ... Phylogenic study of Lemnoideae (duckweeds) through complete chloroplast genomes for eight accessions journal, January 2017 * ... The complete chloroplast genome of greater duckweed (Spirodela polyrhiza 7498) using PacBio long reads: insights into the ... Complete Sequence of the Duckweed (Lemna minor) Chloroplast Genome: Structural Organization and Phylogenetic Relationships to ...
The total chloroplast genome collection regarding developed mango (Prunus persica var. nectarina curriculum vitae. 'Rui Guang...
The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): Comparative analysis of evolutionary rate with that of grasses...
T1 - The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae). T2 - Comparative analysis of evolutionary rate with that ... The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): Comparative analysis of evolutionary rate with that of grasses ... The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): Comparative analysis of evolutionary rate with that of grasses ... The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): Comparative analysis of evolutionary rate with that of grasses ...
Development of primer pairs from diverse chloroplast genomes for use in plant phylogenetic research | GMR | Genetics and...
However, the number of variable sequences provided by chloroplast DNA for suggested genes or genomic regions in plant ... the complete chloroplast genomic sequences of six plant species (including Oryza sativa, Arabidopsis thaliana, Glycine max, ... Variation in the chloroplast DNA sequence is useful for plant phylogenetic studies. ... Development of primer pairs from diverse chloroplast genomes for use in plant phylogenetic research. * Y.C. Yang ...
PPR-SMRs: ancient proteins with enigmatic functions
Although few in number, they figure prominently in the chloroplast biogenesis and retrograde signaling literature due to their ... Keywords: Arabidopsis thaliana; Zea mays; chloroplast; endonuclease; genomes uncoupled; mitochondria; pentatricopeptide repeat ... Although few in number, they figure prominently in the chloroplast biogenesis and retrograde signaling literature due to their ... while they are limited to species that contain chloroplasts, their presence in algae and early branching land plant lineages ...