Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species

<p>Abstract</p> <p>Background</p> <p>The recent determination of complete chloroplast (cp) genomic sequences of various plant species has enabled numerous comparative analyses as well as advances in plant and genome evolutionary studies. In angiosperms, the complete cp genome sequences of about 70 species have been determined, whereas those of only three gymnosperm species, <it>Cycas taitungensis</it>, <it>Pinus thunbergii</it>, and <it>Pinus koraiensis </it>have been established. The lack of information regarding the gene content and genomic structure of gymnosperm cp genomes may severely hamper further progress of plant and cp genome evolutionary studies. To address this need, we report here the complete nucleotide sequence of the cp genome of <it>Cryptomeria japonica</it>, the first in the Cupressaceae sensu lato of gymnosperms, and provide a comparative analysis of their gene content and genomic structure that illustrates the unique genomic features of gymnosperms.</p> <p>Results</p> <p>The <it>C. japonica </it>cp genome is 131,810 bp in length, with 112 single copy genes and two duplicated (<it>trn</it>I-CAU, <it>trn</it>Q-UUG) genes that give a total of 116 genes. Compared to other land plant cp genomes, the <it>C. japonica </it>cp has lost one of the relevant large inverted repeats (IRs) found in angiosperms, fern, liverwort, and gymnosperms, such as <it>Cycas </it>and <it>Gingko</it>, and additionally has completely lost its <it>trn</it>R-CCG, partially lost its <it>trn</it>T-GGU, and shows diversification of <it>acc</it>D. The genomic structure of the <it>C. japonica </it>cp genome also differs significantly from those of other plant species. For example, we estimate that a minimum of 15 inversions would be required to transform the gene organization of the <it>Pinus thunbergii </it>cp genome into that of <it>C. japonica</it>. In the <it>C. japonica </it>cp genome, direct repeat and inverted repeat sequences are observed at the inversion and translocation endpoints, and these sequences may be associated with the genomic rearrangements.</p> <p>Conclusion</p> <p>The observed differences in genomic structure between <it>C. japonica </it>and other land plants, including pines, strongly support the theory that the large IRs stabilize the cp genome. Furthermore, the deleted large IR and the numerous genomic rearrangements that have occurred in the <it>C. japonica </it>cp genome provide new insights into both the evolutionary lineage of coniferous species in gymnosperm and the evolution of the cp genome.</p

Antiplatelet Therapy for Prevention of Thromboembolic Complications Associated with Coil Embolization of Unruptured Cerebral Aneurysms

Background: Antiplatelet agents are used during endovascular treatment of cerebral aneurysms to prevent thromboembolic complications. Objective: The aim of this study was to investigate the efficacy of clopidogrel for the prevention of thromboembolic complications during elective coil embolization of unruptured cerebral aneurysms. Methods: Sixty-three patients prospectively received oral clopidogrel 75mg/day from 3 days before and for 1 day after the procedure at our institute (Kohnan Hospital, Sendai, Japan) during 2007. Results: At 24 hours post-coiling, significantly less high-intensity areas, detected by MRI with diffusion-weighted imaging (MRI-DWI), were observed in clopidogrel-treated patients compared with a historical control cohort of aspirin (acetylsalicylic acid)-treated patients (13/63 [20.6%] vs 27/69 [39.1%]; p = 0.02), primarily due to a statistically significantly lower rate during repair of small (<10mm) lesions (p = 0.008).Also, the rate of periprocedural thromboembolic events was lower in the clopidogrel than the aspirin cohort (2/63 [3.2%] vs 5/69 [7.2%]; p = 0.3). Conclusions: Clopidogrel was generally well tolerated with no signs of hemorrhagic complications or liver dysfunction

A frameshift mutation of the chloroplast matK coding region is associated with chlorophyll deficiency in the Cryptomeria japonica virescent mutant Wogon-Sugi

Wogon-Sugi has been reported as a cytoplasmically inherited virescent mutant selected from a horticultural variety of Cryptomeria japonica. Although previous studies of plastid structure and inheritance indicated that at least some mutations are encoded by the chloroplast genome, the causative gene responsible for the primary chlorophyll deficiency in Wogon-Sugi, has not been identified. In this study, we identified this gene by genomic sequencing of chloroplast DNA and genetic analysis. Chloroplast DNA sequencing of 16 wild-type and 16 Wogon-Sugi plants showed a 19-bp insertional sequence in the matK coding region in the Wogon-Sugi. This insertion disrupted the matK reading frame. Although an indel mutation in the ycf1 and ycf2 coding region was detected in Wogon-Sugi, sequence variations similar to that of Wogon-Sugi were also detected in several wild-type lines, and they maintained the reading frame. Genetic analysis of the 19 bp insertional mutation in the matK coding region showed that it was found only in the chlorophyll-deficient sector of 125 full-sibling seedlings. Therefore, the 19-bp insertion in the matK coding region is the most likely candidate at present for a mutation underlying the Wogon-Sugi phenotype

Feeding of Chinese fir (<em>Cunninghamia lanceolate</em>) seedling by Japanese hare (<em>Lepus brachyurus</em>)_Influence of seedling size

To elucidate the size of Chinese fir seedlings, of which mainstem is fed by the Japanese hare, we observed the feeding damage for seedlings planted from February 2020 to February 2021 in a stand in Tarumizu City, Kagoshima Prefecture, Japan. We planted 60 seedlings of various heights (82–197 cm) and recorded the situation of the seedling in February, March, May, August, November 2020, and February 2021. [Data contents] D0: Stem diameter at base D20: Stem diameter at 20 cm height D40: Stem diameter at 40 cm height D60: Stem diameter at 60 cm height D80: Stem diameter at 80 cm height D100: Stem diameter at 100 cm height Height: Seedling height Length: Length of mainstem Condition: Dead or Live of seedling Feeding_mainstem: Feeding damage of mainstem (1: fed mainstem) Diameter_cutting: Stem diameter in a part with feeding damage Feeding_branch: Feeding damage of branch (1: fed branch) Height_IntactBranch: Height of branch without feeding damage on November 2020 Height_FedBranch: Height of branch with feeding damage on November 2020 Number_sprout: Number of sprout, which emerged from a part with feeding damage Feeding_sprout: Feeding damage of sprout (1: fed sprout) Please see RELATED MATERIALS 1 for more detail.</p

Complete nucleotide sequence of the D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species-1

Ty. Numbers at the C-terminal ends indicate the length of the amino acid sequences in each species.<p><b>Copyright information:</b></p><p>Taken from "Complete nucleotide sequence of the D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species"</p><p>http://www.biomedcentral.com/1471-2229/8/70</p><p>BMC Plant Biology 2008;8():70-70.</p><p>Published online 23 Jun 2008</p><p>PMCID:PMC2443145.</p><p></p

Complete nucleotide sequence of the D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species-6

He relevant regions of LSC (Large Single Copy), SSC (Small Single Copy) and IR (Inverted Repeat) regions in the (A), (B), (C), (D), and (E) cp genomes, respectively. In the (F) and (G) cp genomes, gray, blue and orange boxes show the relevant regions of the SSC and IR regions of the cp genome. Red boxes in the cp genome show the defined IR in the cp genome. In the cp genome, the black and white arrows show duplicated genes; I-CAU (black arrows), Q-UUG (white arrows).<p><b>Copyright information:</b></p><p>Taken from "Complete nucleotide sequence of the D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species"</p><p>http://www.biomedcentral.com/1471-2229/8/70</p><p>BMC Plant Biology 2008;8():70-70.</p><p>Published online 23 Jun 2008</p><p>PMCID:PMC2443145.</p><p></p

Complete nucleotide sequence of the D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species-3

He amino acid length of the D gene product in is approximately twice that of the other five plant cp genomes.<p><b>Copyright information:</b></p><p>Taken from "Complete nucleotide sequence of the D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species"</p><p>http://www.biomedcentral.com/1471-2229/8/70</p><p>BMC Plant Biology 2008;8():70-70.</p><p>Published online 23 Jun 2008</p><p>PMCID:PMC2443145.</p><p></p

Complete nucleotide sequence of the D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species-8

N the direction of transcription. The colored boxes indicate the same gene units among the seven cp genomes, including . The tRNA anti-codon is abbreviated in the six plant cp genomes excluding . The character highlighted in red represents the duplicated Q-UUG in the cp genome. The pseudogene is indicated by ψ (pseudo-).<p><b>Copyright information:</b></p><p>Taken from "Complete nucleotide sequence of the D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species"</p><p>http://www.biomedcentral.com/1471-2229/8/70</p><p>BMC Plant Biology 2008;8():70-70.</p><p>Published online 23 Jun 2008</p><p>PMCID:PMC2443145.</p><p></p

Complete nucleotide sequence of the D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species-2

F the T-GGU gene in each cp genome is shown above each sequence. The secondary structure of the T-GGU gene is described at the top.<p><b>Copyright information:</b></p><p>Taken from "Complete nucleotide sequence of the D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species"</p><p>http://www.biomedcentral.com/1471-2229/8/70</p><p>BMC Plant Biology 2008;8():70-70.</p><p>Published online 23 Jun 2008</p><p>PMCID:PMC2443145.</p><p></p