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

Population biology of Habenaria radiata（Orchidaceae）in Far East Russia and Japan

Demography of Habenaria radiata was studied in the Far East Russia and Japan. The populations of the spe-cies studied in Russia were always bigger in size than those studied in Japan. Nearly 40% of the Russian plants studied reached the generative stage forming consequently flowers within two years, another 14% did so within three years. Their seeds formed seed banks maintained in nature for at least 1.5 years. Seeds took 2―6 months to develop protocorms. Spatial structure of the population was characterized by the dense clone formation by inten-sively vegetative reproduction at rates of 30―80%. Such a population established mainly by ramets in Russia was big and dense, while that in Japan was small and scattered. Vegetatively mature plants dominated in most of the populations studied in Russia and Japan. Externally wounded plants appeared sometimes in Japan after heavy rains

A population study in epiphytic Sarcochilus japonicus（Orchidaceae）

A population biology of Sarcochilus japonicus（Rchb. f．）Miq．（Orchidaceae）is studied. After seeds are dispersed and germinated, they produce protocorms which develop their primary shoot axes elongated and creeped along the surface of substratum and bear firstly tiny scale leaf at the shoot apex and later up to two true-leaves and roots to grow up to a plantlet. Population maintenance and growth of S. japonicus occur mostly by sexual repro-duction and partially by vegetative reproduction with growing lateral buds in the monopodial shoot. Age spec-trum in the population is relatively similar to that of certain terrestrial orchids previously studied. The largest loci of S. japonicus are situated on the host boughs spreading to the north to southwest direction, that may de-pend for further population dynamics on their own ability to use resources of the environment.広島県福富町長圓寺のクロマツ古木に着生するカヤランの個体群について分析した。種子は発芽するとプロトコームを形成した。初期のプロトコームは細長く伸び，樹皮表面に這うように翼状に定着し，先端には微小の鱗片葉を1 枚着け，生長とともに第一本葉と根をだした。1～2 枚の本葉と根を1.5 cmほどに伸ばした幼植物体が形成された最終段階で，プロトコーム本体は枯れた。個体群の維持，生長は有性生殖によるが，一部単軸シュートにでた側芽の生長による栄養繁殖によった。個体群内の相対的年齢構成比率は，すでに報告した地生ラン数種個体群での年齢構成に似ていた。クロマツ樹上のカヤラン密生部位は北～南西面に広がった枝上にあった

A comparison of structural adaptation in three petrophyte ferns

Three petrophyte ferns, Lepisorus thunbergianus and Lemmaphyllum microphyllum（Polypodiaceae）and Crepi-domanes latealatum（Hymenophyllaceae）were compared on the basis of biomorphological, histological and cyto-logical data as well as characteristics of plastid apparatus. They showed xero-, meso-, hygro-, helio-, scio- and cryo-morphous characteristics in combination. Lepisorus thunbergianus was shade tolerant, hydrolabile xeromesophyte, that indicated an intermediate position between homoio- and poikilohydric ferns, an eutroph. Lemmaphyllum microphyllum was shade tolerant, hydrolabile, homoiohydric mesophyte with xeromorphous syn-drome, an oligotroph. Crepidomanes latealatum was a sciophyte, hydrolabile poikilohydric hygrophyte, an oligotroph. They had two alternative strategies of their adaptiogenesis : Lepisorus thunbergianus and Lem. mi-crophyllum performed an enhanced ability of water retention of the tissues and cells and C . latealatum per-formed an ability to endure a deep dehydration of tissues without loss of viability and displayed restoration of the normal hydrature under favorable conditions. They also indicated similar tendency of adaptiogenesis : They were dwarfish, evergreen, showed changes in mesophyll from an increase of cell density and number of cell lay-ers up to reduction in structure ; and secondary poikilohydry and oligotrophy of epilitophytes in function

Phylogenetic analysis of Malagasy Gastrorchis and Phaius （Orchidaceae）based on internal transcribed spacer（ITS）sequence

The molecular phylogenetics among five species of Gastrorchis and Phaius pulchellus all endemic to Madagas-car and additional four species of non-Malagasy Phaius was studied on the basis of the sequence analysis of ITS region of rDNA. The species of Gastrorchis and those of Phaius studied constituted two respective clades, except-ing Malagasy P . pulchellus was placed in the clade of Gastrorchis. This fact suggests that Malagasy P . pulchell-us might be shared and originated from the common ancestor of Gastrorchis

MDM2 is a novel E3 ligase for HIV-1 Vif

The human immunodeficiency virus type 1 (HIV-1) Vif plays a crucial role in the viral life cycle by antagonizing a host restriction factor APOBEC3G (A3G). Vif interacts with A3G and induces its polyubiquitination and subsequent degradation via the formation of active ubiquitin ligase (E3) complex with Cullin5-ElonginB/C. Although Vif itself is also ubiquitinated and degraded rapidly in infected cells, precise roles and mechanisms of Vif ubiquitination are largely unknown. Here we report that MDM2, known as an E3 ligase for p53, is a novel E3 ligase for Vif and induces polyubiquitination and degradation of Vif. We also show the mechanisms by which MDM2 only targets Vif, but not A3G that binds to Vif. MDM2 reduces cellular Vif levels and reversely increases A3G levels, because the interaction between MDM2 and Vif precludes A3G from binding to Vif. Furthermore, we demonstrate that MDM2 negatively regulates HIV-1 replication in non-permissive target cells through Vif degradation. These data suggest that MDM2 is a regulator of HIV-1 replication and might be a novel therapeutic target for anti-HIV-1 drug

Prevention of Adoptively Transferred Diabetes in Nonobese Diabetic Mice with IL-10–Transduced Islet-specific Th1 Lymphocytes A Gene Therapy Model for Autoimmune Diabetes

Four pancreatic islet-specific CD4+ helper T (Th) 1 (Th1) clones and two Th1 clones transduced with an SRα promoter-linked murine IL-10 (mIL-10) cDNA of 2.0–6.0×10[6] cells were adoptively transferred to nonobese diabetic (NOD) mice at age 8 d. Cyclophosphamide (CY) was administered at age 37 d (plus CY), and the incidence of diabetes and the histological grade of insulitis were examined at age 47 d. After the adoptive transfer of IL-10–transduced Th1 cells, polymerase chain reaction (PCR) and reversetranscription (RT)-PCR detected the neo gene and the retrovirus vector-mediated IL-10 mRNA in situ in recipient islets, respectively. RT-PCR detected the decrease of IFN-γ mRNA relative to IL-10 mRNA in IL-10–transduced Th1 clones in vitro and also in recipient islets. All four wild type Th1 clones plus CY induced the insulitis grade of 2.75 and diabetes in 66% of recipient NOD mice. IL-10–transduced two Th1 clones plus CY induced periinsulitis with the grade of 1.43 and diabetes in 8.0%. The 1:1 mixture of wild type Th1 cells and IL-10–transduced Th1 cells plus CY induced periinsulitis with the grade of 1.85 and diabetes in 20%. The suppression of diabetes through decreasing IFN-γ mRNA by the tissue-specific delivery of IL-10 to pancreatic islets with IL-10–transduced Th1 cells affords us the starting basis to develop the gene therapy for autoimmune diabetes