Patterns of ribosomal gene variation in elite commercial chicken pure line populations

The nucleolus organizer region (NOR) encodes the tandemly repeated 18S, 5.8S and 28S ribosomal (r) RNA genes. The NORs of broiler and layer commercial chicken pure lines were studied to establish the type and extent of genetic variation at this important locus. The parameters studied were gene copy number, repeat size, and diversity of NOR-types. The populations were organized into three groups for analysis including brown-egg broiler (13 lines), brown-egg layer (six lines), and white-egg layer (eight lines). The ribosomal gene copy number average of the white-egg layer populations was significantly lower (329 genes) than that of the brown-egg layers (372 genes); the brown-egg broiler ribosomal gene average was intermediate (350 genes). The white-egg layer populations exhibited a ribosomal repeat unit average size of 36 kb, significantly different from the brown-egg layer and brown-egg broiler average repeat unit size of 32.5 and 33.9 kb, respectively. NOR array size was similar among the three groups (6 mb). The brown-egg broiler populations exhibited polymorphic NOR patterns, intra- and interline, whereas the white-egg layer populations were essentially monomorphic for NOR-type; brown-egg layers exhibited an intermediate level of NOR diversity. Some NOR array characteristics may be a function of breed origin as brown-egg commercial populations, both broilers and layers, have similar breed origins and exhibited similarities for predominant repeat unit size as compared with white-egg layer populations. However, the finding that brown-egg broiler lines typically exhibit a greater number of segregating NOR-types than brown-egg layer lines suggests that the selection schemes of broiler vs. layer pure line populations may also have influenced the degree of variation at this gene complex.     

Molecular evolution of pteridophytes and their relationship to seed plants: Evidence from complete 18S rRNA gene sequences

Complete 18S ribosomal RNA sequence data from representatives of all extant pteridophyte lineages together with RNA sequences from different seed plants were used to infer a molecular phylogeny of vascular plants that included all major land plant lineages. The molecular data indicate that lycopsids are monophyletic and are the earliest diverging group within the vascular land plants, whereasPsilotum nudum is more closely related to the seed plants than to other pteridophyte lineages. The phylogenetic trees based on maximum likelihood, parsimony and distance analyses show substantial agreement with the evolutionary relationships of land plants as interpreted from the fossil record.     

Ambrosiozyma kamigamensis sp. nov. and A. neoplatypodis sp. nov., two new ascomycetous yeasts from ambrosia beetle galleries

Two new yeast species of the genus Ambrosiozyma are described on the basis of comparison of nucleotide sequences of large subunit of ribosomal DNA D1/D2 region. Ambrosiozyma kamigamensis and Ambrosiozyma neoplatypodis differ from Ambrosiozyma ambrosiae by 17 nucleotides (3.0%) and 16 nucleotides (2.8%), respectively, out of 565. The two species differ from each other by 13 nucleotides. Ambrosiozyma kamigamensis was isolated from galleries of the ambrosia beetle, Platypus quercivorus, in specimens of Quercus laurifolia and Castanopsis cuspidata located in the southern part of Kyoto, Japan. Ambrosiozyma neoplatypodis was isolated from similar material, but only in Q. laurifolia. Ambrosiozyma kamigamensis can be distinguished from the other Ambrosiozyma species by the inability to assimilate erythritol, whereas A. neoplatypodis can be distinguished by the ability to assimilate both L: -arabinose and nitrate. The type strains of A. kamigamensis and A. neoplatypodis are JCM 14990(T) (=CBS 10899(T)) and JCM 14992(T) (=CBS 10900(T)), respectively. This is the first report of new Ambrosiozyma species since the genus was proposed.     

Community structure of ectomycorrhizal fungi in a Pinus muricata forest: minimal overlap between the mature forest and resistant propagule communities

We have investigated colonization strategies by comparing the abundance and frequency of ectomycorrhizal fungal species on roots in a mature Pinus muricata forest with those present as resistant propagules colonizing potted seedlings grown in the same soil samples. Thirty-seven fungal species were distinguished by internal transcribed spacer (ITS) restriction fragment length polymorphisms (RFLPs); most were identified to species level by sporocarp RFLP matches or to genus/family level by using sequence databases for the mitochondrial and nuclear large-subunit rRNA genes. The below-ground fungal community found in the mature forest contrasted markedly with the resistant propagule community, as only four species were found in both communities. The dominant species in the mature forest were members of the Russulaceae, Thelephorales and Amanitaceae. In contrast, the resistant propagule community was dominated by Rhizopogon species and by species of the Ascomycota. Only one species, Tomentella sublilacina (Thelephorales), was common in both communities. The spatial distribution of mycorrhizae on mature roots and propagules in the soil differed among the dominant species. For example, T. sublilacina mycorrhizae exhibited a unique bias toward the organic horizons, Russula brevipes mycorrhizae were denser and more clumped than those of other species and Cenococcum propagules were localized, whereas R. subcaerulescens propagules were evenly distributed. We suggest that species differences in resource preferences and colonization strategies, such as those documented here, contribute to the maintenance of species richness in the ectomycorrhizal community.     

The mitochondrial genome of the Russian wheat aphid Diuraphis noxia: Large repetitive sequences between trnE and trnF in aphids

To characterize aphid mitochondrial genome (mitogenome) features, we sequenced the complete mitogenome of the Russian wheat aphid, Diuraphis noxia. The 15,784-bp mitogenome with a high A + T content (84.76%) and strong C skew (− 0.26) was arranged in the same gene order as that of the ancestral insect. Unlike typical insect mitogenomes, D. noxia possessed a large tandem repeat region (644 bp) located between trnE and trnF. Sequencing partial mitogenome of the cotton aphid (Aphis gossypii) further confirmed the presence of the large repeat region in aphids, but with different repeat length and copy number. Another motif (58 bp) tandemly repeated 2.3 times in the control region of D. noxia. All repeat units in D. noxia could be folded into stem-loop secondary structures, which could further promote an increase in copy numbers. Characterization of the D. noxia mitogenome revealed distinct mitogenome architectures, thus advancing our understanding of insect mitogenomic diversities and evolution.     

Mechanism of regulating the expression of λN gene by ribosomal protein at translational level

In ribosomal protein S12 mutant or L24 mutant the expression of λN gene was depressed at translational level. To study its mechanism the λN gene region of λN -lacZ gene fusion was trimmed from its 5′ end to 3′ end with DNA exonuclease III (DNA cxoIII) in order to alter the TIR (translational initiation region) and the ding region of λN gene. After DNA sequencing 23 species of different λN-lacZ fused genes were obtained. The β-galactosidase activities of these deletants in ribosomal protein mutant were compared with that in wild type strain. The result indicated that (i) S12 mutant could affect 305 subunit’s binding to the TIR of λN gene messenger and cause the difficulty in forming 30s initiation complex and then decrease the efficiency of translational initiation; (ii) in S12 mutant the coding region of λN gene alw affected the expression λN gene; (iii) in L24 mutant the inhibition of λN gene expression was not related to translational initiation and the 5′ end of the coding region of λN gene, but related to the 3′ end of λN gene. Project supported by the National Natural Science Foundation of China (Grant Nos. 39480014, 39570162) and Chinese Academy of Sciences.     

Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences

Approximately 500 species of ascomycetous yeasts, including members of Candida and other anamorphic genera, were analyzed for extent of divergence in the variable D1/D2 domain of large subunit (26S) ribosomal DNA. Divergence in this domain is generally sufficient to resolve individual species, resulting in the prediction that 55 currently recognized taxa are synonyms of earlier described species. Phylogenetic relationships among the ascomycetous yeasts were analyzed from D1/D2 sequence divergence. For comparison, the phylogeny of selected members of the Saccharomyces clade was determined from 18S rDNA sequences. Species relationships were highly concordant between the D1/D2 and 18S trees when branches were statistically well supported.