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91 results for “chloroplast genome”
The chloroplast genomes of Sanicula (Apiaceae): plastome structure, comparative analyses, and phylogenetic relationships
<p><em>Sanicula</em> (Apiaceae subfamily Saniculoideae) is a taxonomically difficult genus of medicinal value. Its distribution center is in China, where there are 18 species (11 of which are endemic). To provide plastid genome resources, whole chloroplast genomes of five <em>Sanicula</em> species (<em>S. flavovirens</em>, <em>S. giraldii</em>, <em>S. lamelligera</em>, <em>S. odorata</em>, and <em>S. rubriflora</em>) were sequenced and compared to the previously published <em>S. orthacantha</em> plastome. These genomes exhibit a typical quadripartite structure. All contain 129 different genes, including 84 protein-coding, 37 tRNA, and 8 rRNA genes. Loci <em>rpl2</em>, <em>matK</em>, <em>psbA</em>, and <em>ycf1</em> are the most variable. Results of maximum likelihood analysis of 90 whole plastome sequences from Apioideae and Saniculoideae and the outgroup <em>Hydrocotyle</em> (Araliaceae) reveal sectional relationships in <em>Sanicula</em> different from the traditional classification system, support the monophyly of Apioideae and its sister group relationship to Saniculoideae, and show concordant topologies to nrDNA ITS and other plastome-based phylogenies. <em>Sanicula orthacantha</em> and <em>S. chinensis</em> form a clade sister group to <em>S. lamelligera</em> and <em>S. odorata</em>, consecutively. These four species comprise a clade sister group to the clade of <em>S. rubriflora</em> and <em>S. flavovirens</em>, with this entire group sister to <em>S. giraldii</em>. The plastid genome resources provided herein will be important for future systematic, evolutionary, phylogenomic, and population-level studies of <em>Sanicula</em>.</p>
Figure 1 in An investigation on the chloroplast and nuclear genomes of taxa belong to the subgenus Dracunculus (Bess.) Rydb. of Artemisia L. (Asteraceae) in Turkey
Figure 1. Geographic distribution of four species of the subgenus Dracunculus in Turkey (A. campestris (), A. marschalliana (), A. araratica () and A. scoparia () (Civelek et al., 2010, Kursat 2010).
Fig. 3 in Chloroplast genome of the conserved Aster altaicus var. uchiyamae B2015-0044 as genetic barcode
Fig. 3. The variable sites in the chloroplast genomes of Aster altaicus var. uchiyamae. Variable sequences are marked in red. GG: Yeoju, Gyeonggi Province, CB: Cheongju, Chungcheongbuk Province.
Fig. 2 in Chloroplast genome of the conserved Aster altaicus var. uchiyamae B2015-0044 as genetic barcode
Fig. 2. The sequence alignment of variable sites in the chloroplast genomes of Aster altaicus var. uchiyamae. Variable sequences are marked in red. GG: Yeoju, Gyeonggi Province, CB: Cheongju, Chungcheongbuk Province.
Fig. 2 in Chloroplast genome of white wild chrysanthemum, Dendranthema sp. K247003, as genetic barcode
Fig. 2. Comparison of chloroplast genomes of Dendranthema sp. K247003 and D. boreale IT121002 using mVISTA program. Grey arrows and thick black lines above the alignment indicate genes with their orientation and the position of the IRs, respectively. The Yscale represents the percent identity between 50-100%. Genome regions are color-coded: Coding regions in blue; noncoding sequences (CNS) in red.
Data from: Chloroplast genomes of six Colocasia species (Araceae) including taro
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The chloroplast genomes of Sanicula (Apiaceae): plastome structure, comparative analyses, and phylogenetic relationships
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Chloroplast genome sequencing reads from snow gum
<p>Tutorial data for chloroplast genome assembly: fastq reads from illumina and nanopore sequencing for the snow gum, <em>Eucalyptus pauciflora</em>.</p> <p>Data from: Wang, W., Schalamun, M., Morales-Suarez, A. et al. Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case. BMC Genomics 19, 977 (2018) doi:10.1186/s12864-018-5348-8</p> <p>Data hosted at NCBI under accession numbers: illumina (SRR7153063) and nanopore (SRR7153095). Additional illumina file SRR7153071 not used here. </p> <p>This is how the files have been changed from the original datasets: </p> <p>Using the Galaxy platform (usegalaxy.org): </p> <ul> <li> <p>Each dataset was separately mapped to the NCBI Reference Sequence for <em>Eucalyptus pauciflora </em>chloroplast NC_039597.1, using BWA-MEM. </p> </li> <li> <p>Unmapped reads were filtered out using a SAMtools flag. </p> </li> <li> <p>Bam files were converted to fastq files.</p> </li> <li> <p>Each fastq file was then reduced in size:</p> </li> <li> <p>snow-gum-illumina-cp-reduced: has the first 62,500 reads only. Note that original pairing of reads has not been preserved so consider these to be unpaired reads for this tutorial.</p> </li> <li> <p>snow-gum-nanopore-cp-reduced: has only reads that are longer than 90,000 bp.</p> </li> </ul>
1,825 Oryza chloroplast genomes
<p>1,825 complete or near-complete chloroplast genomes of Oryza species.</p> <p>Reconstruction based on previously published data (PRJEB2829; PRJEB2578; PRJEB2052; PRJEB6180).</p> <p>Includes O. rufipogon, O. sativa (temperate japonica, tropical japonica, indica, aus, aromatic).</p> <p>Reference: Civan P, Brown T. Genetic origins of cultivated rice (<em>Oryza sativa</em> L.) and the role of gene flow during its domestication. <em>In preparation.</em></p>
The alignments of chloroplast genome sequences and nuclear ribosomal DNA fragments of six oak species sampled in the hot-dry valley of the Jinsha River, southwestern China
<p>Both chloroplast (cp) genome sequences and nuclear ribosomal (nr) DNA were assembled using GetOrganelle v.1.7.6.1 for 18 oak trees sampled in the Panzhihua Cycad National Nature Reserve, Sichuan Province, China. These trees belong to six oak species, including Quercus cocciferoides, Q. dolicholepis, Q. franchetii, Q. griffithii, Q. longispica, and Q. variabilis. We used PhyloSuite v.1.1.152 to extract coding sequences (CDSs), tRNA genes, rRNA genes, introns, and intergenic spacers (IGSs) of the 18 oak cp genomes. These sequences were aligned separately using MAFFT v.7.3.13 and manually adjusted with BioEdit v.7.2.5. Length variations in mononucleotide repeats were excluded and inversions were replaced with their reverse complements because of their tendency for homoplasy. Other indels were coded as binary characters according to the simple gap coding method using GapCoder. Separate assignments were concatenated according to their respective positions in the cp genome to obtain the alignments of LSC, SSC, IRb, and the whole cp genome.</p>
The complete chloroplast genome of Mimusops elengi (Sapotaceae)
<p><span>The first complete chloroplast genome sequences of <i><span>Mimusops elengi</span></i> (Sapotaceae) were reported in this study. The cpDNA of <i><span>M</span></i><i><span>.</span></i><i><span> elengi</span></i> is 159,719 bp in length, contains a large single-copy region (LSC) of 88,935 bp and a small single-copy region (SSC) of 18,606 bp, which were separated by a pair of inverted repeat (IR) regions of 26,089 bp. The genome contains 132 genes, including 87 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 36.8%. Phylogenetic analysis of 12 chloroplast genomes within the family Sapotaceae suggests that the sister relationship of <i><span>Autranella</span></i> and <i><span>Tieghemella</span></i><span> is strongly supported. </span><i><span>Minusops</span></i> genus is close to <i><span>Autranella</span></i> and <i><span>Tieghemella</span></i>, although the support value is still low.</span></p>
Supplementary Materials from the article Characterization and molecular evolution analysis of Periploca forrestii inferred from its complete chloroplast genome sequence
<p>Table S1. Base composition of chloroplast genome in <em>P. forrestii</em>, Table S2. The lengths of introns and exons for the splitting genes, Table S3. The GC content of the codons from <em>P. forrestii </em>chloroplast genome, Table S4. Preferred codons in chloroplast genome of <em>P. forrestii</em>, Table S5. Long repeat sequences in the <em>P. forrestii </em>chloroplast genome, Figure S1. Codon bias analysis of P. forrestii chloroplast genome. (A) Neutrality plot analysis; (B) Analysis of PR2 bias plot; (C) Analysis on ENC and GC3 relationship.</p>
Comparative analysis of chloroplast genomes of Sanguisorba species and insights into phylogenetic implications and molecular dating
<pre class="js_message_plain ng-binding"><em>Sanguisorba</em> is a small genus, which consists of about 15 species widely distributed in North America and Eurasia. Previous studies on <em>Sanguisorba</em> are useful for understanding of phylogeny and chloroplast (cp) genome evolution of <em>Sanguisorba</em>. However, the cp genome resources of <em>Sanguisorba</em> are still limited, and the phylogeny and molecular dating for <em>Sanguisorba</em> and its relatives still need further explored. Here, we reported four cp genomes of <em>Sanguisorba</em> and conducted comparative analysis of the four <em>Sanguisorba</em> cp genomes plus five previously published ones. The nine cp genomes of <em>Sanguisorba</em> have typical tetrad quadripartite structure, with a total length of 154 282 to 155 730 bp, and their gene content, gene structure, and gene order are relatively conservative. The analysis of single copy (SC)/inverted repeat (IR) boundaries shows very slight boundary differences in <em>Sanguisorba</em> cp genomes. Eight variation hotspots were screened as excellent candidate markers of <em>Sanguisorba</em>. Phylogenetic analysis indicated <em>Sanguisorba</em> was monophyletic and was a member of tribe Agrimonieae subtribe Sanguisorbinae. Within <em>Sanguisorba</em>, <em>S. filiformis</em> is a sister group of six other taxa in the present sampling. Estimation of the divergence times indicated that subtribes Agrimoniinae and Sanguisorbinae diverged at the transition between the Oligocene and the Miocene, and divergent times of Agrimonieae genera ranged from the late Miocene to the Middle Pleistocene. This study enriches the available cp genome resources of <em>Sanguisorba</em>, and it is of great significance to further study the phylogeny and evolution of <em>Sanguisorba</em> and its relatives.</pre>
Baraminology of Cucurbitaceae based on chloroplast genome analysis
<p>The gourd family (Cucurbitaceae) is an economically important and diverse group of plants, with approximately 1000 species. Previous analysis of hybridization data and nuclear ITS regions in 70 species of 14 genera of the family Cucurbitaceae identified seven putative holobaramins.</p><p>The present study expands upon this previous analysis by analyzing the sequence similarity of the chloroplast genome between 30 species from Cucurbitaceae. The clustering analysis showed six putative holobaramins: <i>Gynostemma</i>, <i>Gomphogyne</i>+<i>Hemsleya</i>,<i> Cucurbita</i>, <i>Cucumis</i>, <i>Citrullus</i>, <i>Coccinia grandis</i>+<i>Hodgsonia macrocarpa</i>+<i>Lagenaria siceraria</i>+<i>Momordica charantia</i>+<i>Siraitia grosvernorii</i>+<i>Trichosanthes kirilowii</i>. All six groups had a significant p-value except <i>Gomphogyne</i>+<i>Hemsleya</i>. Of these, Gynostemma and <i>Gomphogyne</i>+<i>Hemsleya</i> are two new putative holobaramins. </p><p>The present study is the second of its kind, after an analysis of chloroplast genomes in Liliales. This study used both hybridization data and chloroplast genome sequences that supported each other's results. Future chloroplast genome studies could be performed on plant groups that have enough species with mitochondrial genomes.</p>
Figure 2 in An investigation on the chloroplast and nuclear genomes of taxa belong to the subgenus Dracunculus (Bess.) Rydb. of Artemisia L. (Asteraceae) in Turkey
Figure 2. Maximum Likelyhood tree showing the phylogenetic relationship between individuals.
Fig. 1 in Chloroplast genome of the conserved Aster altaicus var. uchiyamae B2015-0044 as genetic barcode
Fig. 1. Plastid genomic map of Aster altaicus var. uchiyamae.
Fig. 1 in Chloroplast genome of white wild chrysanthemum, Dendranthema sp. K247003, as genetic barcode
Fig. 1. Plastid genomic map of Dendranthema sp. K247003.
Chloroplast genome assemblies and comparative analyses of commercially important Vaccinium berry crops
<p><em>Vaccinium</em> is a large genus of shrubs that includes a handful of economically important berry crops. Given the numerous hybridizations and polyploidization events, the taxonomy of this genus has remained the subject of long debate. In addition, berries and berry-based products are liable to adulteration, either fraudulent or unintentional due to misidentification of species. The availability of more genomic information could help achieve higher phylogenetic resolution for the genus, provide molecular markers for berry crop identification, and a framework for efficient genetic engineering of chloroplasts. Therefore, in this study, we assembled five <em>Vaccinium</em> chloroplast sequences representing the economically relevant berry types: northern highbush blueberry (<em>V. corymbosum</em>), southern highbush blueberry (<em>V. corymbosum</em> hybrids), rabbiteye blueberry (<em>V. virgatum</em>), lowbush blueberry (<em>V. angustifolium</em>), and bilberry (<em>V. myrtillus</em>). Comparative analyses showed that the <em>Vaccinium</em> chloroplast genomes exhibited an overall highly conserved synteny and sequence identity among them. Polymorphic regions included the expansion/contraction of inverted repeats, gene copy number variation, simple sequence repeats, indels, and single nucleotide polymorphisms. Based on their in silico discrimination power, we suggested variants that could be developed into molecular markers for berry crop identification. Phylogenetic analysis revealed multiple origins of highbush blueberry plastomes, likely due to the hybridization events that occurred during northern and southern highbush blueberry domestication.</p>
Chloroplast and mitochondrial genomes of Ulva mutabilis
<p>Annotated chloroplast and mitochondrial genomes of Ulva mutabilis (wild-type). Genbank format.</p>
Chloroplast genome assemblies and comparative analyses of commercially important Vaccinium berry crops
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International Brain Laboratory public data
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