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Chloroplast genome

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Complete chloroplast genome sequence of Barleria prionitis, comparative chloroplast genomics and phylogenetic relationships among Acanthoideae

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Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots. The chloroplast genome sequence of the medicinal plant Andrographis paniculata.. Phylogenetic studies and comparative chloroplast genome analyses elucidate the basal position of halophyte Nitraria sibirica (Nitrariaceae) in the Sapindales.. Complete chloroplast genome of the multifunctional crop globe artichoke and.

Comparative chloroplast genomes: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia

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Comparative chloroplast genomes: insights into the evolution of the chloroplast. Here, we determined the chloroplast genome of the first natural triploid Chinary type tea. Further, the evolutionary mechanism of the chloroplast genome of Camellia sinensis and the relationships of Camellia species based on chloroplast genome were discussed..

The complete chloroplast genome of greater duckweed (Spirodela polyrhiza 7498) using PacBio long reads: Insights into the chloroplast evolution and transcription regulation

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The chloroplast genome of S.polyrhiza was assembled using a Perl-based software named “Organelle_PBA”. The chloroplast genome was annotated with the tool GeSeq (https://chlorobox.mpimp-golm.mpg.de/. A circular map of the annotated genome was illustrated by using Organellar Genome DRAW (OGDRAW) (https://.

Comparison of chloroplast genomes of Gynura species: Sequence variation, genome rearrangement and divergence studies

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The whole chloroplast genome sequences of 16 Senecio- neae species were aligned by the MAFFT program to find sequence variation. This result shows that this region is not conserved, similar to other regions of the chloroplast genome. For further analysis of the re- sults, the chloroplast genome sequences of four Gynura. 1 Chloroplast genome map of Gynura divaricata.

Decoding first complete chloroplast genome of toothbrush tree (Salvadora persica L.): Insight into genome evolution, sequence divergence and phylogenetic relationship within Brassicales

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Table 3 Codon Usage in this chloroplast genome. persica cp genome with the cp genome of related species. persica cp genome was compared with other eleven cp genomes (A. per- sica cp genome coding region and related species. persica cp genome about 153 SSRs were Table 3 Codon Usage in this chloroplast genome (Continued). persica chloroplast genome and compared it with 11 others cp genome genomes (Fig. persica and related cp genomes (a) Analysis of simple sequence repeats in the twelve chloroplast

The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China

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Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Complete chloroplast genome of Sedum sarmentosum and chloroplast genome evolution in Saxifragales. Complete chloroplast genome of Nicotiana otophora and its comparison with related species.

The chloroplast genome of Amygdalus L. (Rosaceae) reveals the phylogenetic relationship and divergence time

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Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae). doi.org/10.3390/molecules22020249.. doi.org/10.1007/s y.. Phylogenetic relationships of the Fern Cyrtomium falcatum (Dryopteridaceae) from Dokdo Island based on chloroplast genome sequencing. https://doi.org/10.3390/. Molecular phylogeny of the genus Amygdalus (Rosaceae) based on nrDNA ITS and cpDNA trnS-trnG sequences. https://doi.org/10.1038/.

Comparison of different annotation tools for characterization of the complete chloroplast genome of Corylus avellana cv Tombul

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Characterization of the complete chloroplast genomes of five Populus species from the western Sichuan plateau, southwest China: comparative and phylogenetic analyses.. The complete chloroplast genome sequence of the wild Chinese chestnut (Castanea mollissima). The complete sequence of the Acacia ligulata chloroplast genome reveals a highly divergent clpP1 gene. The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza..

Complete chloroplast genome sequence of Betula platyphylla: Gene organization, RNA editing, and comparative and phylogenetic analyses

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The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. SMRT sequencing only de novo assembly of the sugar beet (Beta vulgaris) chloroplast genome. An evaluation of the PacBio. organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. ChloroSeq, an optimized chloroplast RNA-Seq Bioinformatic pipeline, reveals remodeling of the Organellar transcriptome under heat stress.

Taxonomic scheme of the order Chaetophorales (Chlorophyceae, Chlorophyta) based on chloroplast genomes

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The complete chloroplast DNA sequences of the charophycean green algae Staurastrum and Zygnema reveal that the chloroplast genome underwent extensive changes during the evolution of the Zygnematales. The chloroplast genome sequence of the green alga Leptosira terrestris: multiple losses of the inverted repeat and extensive genome rearrangements within the Trebouxiophyceae.

Comparative chloroplast genomes of Paris Sect. Marmorata: Insights into repeat regions and evolutionary implications

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Insights from the complete chloroplast genome into the evolution of Sesamum indicum L. Complete chloroplast genome of Sedum sarmentosum and chloroplast genome evolution in Saxifragales. Insight into infrageneric circumscription through complete chloroplast genome sequences of two Trillium species. Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes.

Analysis of six chloroplast genomes provides insight into the evolution of Chrysosplenium (Saxifragaceae)

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To get a complete chloroplast genome, which can be used as a reference in assembling chloroplast genome of the other five species, C. Chloroplast genome assembly and annotation. The sequencing of the chloroplast DNA of C. The clean reads were aligned to the complete chloroplast genome of C.. The GC content of the whole chloroplast genome and the third position GC content of codons for all ten species were calculated using an in-house Python script.

Study of spontaneous mutations in the transmission of poplar chloroplast genomes from mother to offspring

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Each of the 47 real datasets of whole-genome shotgun sequencing had chloroplast reads of more than 10 5 (100 k) pairs. We employed four different parameter strategies to assemble a chloroplast genome from each of the 47 chloroplast read datasets, which were isolated from whole-genome sequencing reads from the three poplar clones I45, I69 and NL895. trichocarpa chloroplast genome covered by the assemblies of the simulated short reads under multiple k-mer values.

Assembly of chloroplast genomes with long- and short-read data: A comparison of approaches using Eucalyptus pauciflora as a test case

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For example, short-reads that derive from regions of the nuclear or mitochondrial genome that are similar to the chloroplast genome may map with high probabil- ity to the chloroplast genome, but this mapping is far less likely to occur with long-reads, which in our dataset are a minimum of 5 kb.

Using full chloroplast genomes of ‘red’ and ‘yellow’ Bixa orellana (achiote) for kmer based identification and phylogenetic inference

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The structure of the two chloroplast genomes presented here was effectively identical to that of the previously published chloroplast genome of Bixa orellana (NC_. Complete synteny was maintained, and the size and gene content of the inverted repeats was the same in all three accessions (Table 1).

The chloroplast genomes of four Bupleurum (Apiaceae) species endemic to Southwestern China, a diversity center of the genus, as well as their evolutionary implications and phylogenetic inferences

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The complete chloroplast genome of the hare ’ s ear root, Bupleurum falcatum: Its molecular features.. The first complete chloroplast genome sequence of the medicinal plant Bupleurum marginatum (Apiaceae). Comparative analysis of the complete plastid genome of five Bupleurum species and new insights into DNA barcoding and phylogenetic relationship. Interglacial refugia preserved high genetic diversity of the Chinese mole shrew in the mountains of Southwest China.

Complete chloroplast genomes of all six Hosta species occurring in Korea: Molecular structures, comparative, and phylogenetic analyses

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Inferring the evolutionary mechanism of the chloroplast genome size by comparing whole-chloroplast genome sequences in seed plants. The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Comparative analysis of the complete chloroplast genomes of four Aconitum medicinal species.. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees

Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: Insights into evolutionary divergence and phylogenomic implications

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Origin and evolution of the chloroplast division machinery. The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Complete chloroplast genome sequence and phylogenetic analysis of the medicinal plant Artemisia annua. Two chloroplast DNA inversions originated simultaneously during the early evolution of the sunflower family (Asteraceae). Tribal interrelationships of the Asteraceae.

Chloroplast genome variation and phylogenetic relationships of Atractylodes species

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A total of 265 SSRs were detected in the chloroplast ge- nomes of six Atractylodes species by the GMATA analysis.. Table 1 The basic chloroplast genome information of six Atractylodes species. Percent of chloroplast genome reads. Chloroplast genome coverage(X . SSR events are distributed randomly in the chloroplast genome.

Chloroplast genome sequence of Chongming lima bean (Phaseolus lunatus L.) and comparative analyses with other legume chloroplast genomes

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Fine structural features of the chloroplast genome:. comparison of the sequenced chloroplast genomes. Complete sequence and comparative analysis of the chloroplast genome of coconut palm (Cocos nucifera). A chloroplast DNA inversion as a subtribal character in the Phaseoleae (Leguminosae). Multiple domestications of the Mesoamerican gene pool of lima bean (Phaseolus lunatus L.