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.     

Egg release in gametophytes of Laminaria saccharina: Induction by darkness and inhibition by blue light and u.v.

Gametophytes of Laminaria saccharina cultivated from zoospores in a light-dark regime (16:8), release eggs exclusively during the dark cycles, 8–10 days after seeding of the zoospores, and mainly during the first 30 min of darkness. The inhibiting effects of light during the light cycle of 16 h per day is also apparent in gametophytes which have experienced only two dark cycles prior to day 8, when egg release begins. Egg release can be shifted to any time during the light cycle by prolonging the irradiation with white fluorescent light and by subsequent darkening for 1 h. In gametophytes cultivated in continuous white fluorescent light eggs are also released from day 8–10, so in this case no inhibiting activity of light is apparent. Egg release is inhibited by blue light and u.v., with peak wavelengths for inhibition at 372, 413, 438 and 481 nm. No inhibition occurs at wavelengths above 513 nm. The light requirement for inhibition is very low. A photon fluence rate of 1·4 μE m^-2s^-1, given for 45 min at 449 nm, inhibits egg release in 50% of the mature gametophytes. There is some evidence that a circadian rhythm is involved, primarily since in gametophytes which are transferred at the beginning of day 8 from 16:8 to constant conditions (darkness, continuous red or green light) the diel rhythm of egg release persists until day 11.     

Phylogenetic Relationships of the Marine Nematode Family Comesomatidae

The phylogenetic relationships of the Comesomatidae have remained unresolved at the family level because they have diagnostic morphological features of both the Monhysterida and the Chromadorida. A comparison of the partial sequence of 18S rDNA from representative taxa of Comesomatidae and of morphological data, analyzed in conjunction with molecular and morphological data from monhysterids and chromadorids, suggests a closer relationship of the Comesomatidae with Monhysterida than with Chromadorida.     

Relationships among orders and families of marsupials based on 12S ribosomal DNA sequences and the timing of the marsupial radiation

Part of the mitochondrial 12S ribosomal RNA gene was amplified and sequenced for 26 marsupials. Multiple alignments for these sequences as well as seven additional sequences taken from GenBank were obtained using CLUSTAL. PAUP was used for phylogenetic analysis and to obtain random tree-length distributions. Analyses were performed with and without phylogenetic constraints. Our results clearly show that 12S rDNA contains phylogenetic signal at and above the ordinal level and is thus appropriate for addressing phylogenetic questions deep in the mammalian tree. Standard parsimony analyses provide some support for a clade containing diprotodontians, dasyurids,Dromiciops, andNotoryctes; transversion parsimony analysis suggests the possible inclusion of peramelids as well. Within the Diprotodontia, vombatids and phascolarctids cluster together on transversion parsimony and phalangerids may be associated with this clade. The enigmatic tarsipedids are apparently part of a clade that also contains pseudocheirids, petaurids, and acrobatids. The 12S sequences suggest that the origination of extant marsupial orders peaked 15 million years later than the equivalent taxonomic diversification of extant placental orders and may be entirely post-Cretaceous. Families of diprotodontian marsupials originated during the Eocene and early Oligocene, which is consistent with previous single-copy DNA hybridization results.     

Phylogeny of Agavaceae based on ITS rDNA sequence variation

Several systems of classification have been proposed for the family Agavaceae. A distinctive bimodal karyotype and similarities of fruits and seeds strongly support close relationships among Yucca, Hesperaloë, Beschorneria, Furcraea, Agave, Manfreda, Polianthes, Prochnyanthes, and perhaps Hosta. However, Dasylirion, Beaucamea, Nolina, Calibanus, Dracaena, and Sansevieria differ in so many cytological and morphological features that many have concluded they should be excluded from Agavaceae and separated into two families, Nolinaceae and Dracaenaceae. Chloroplast DNA restriction site data support these separations and indicate that Nolinaceae and Dracaenaceae are very close to Convallariaceae (Maianthemum, Convallaria, Aspidistra, Liriope, etc.). In this paper we report the results of an ITS rDNA sequencing study of 40 taxa in Agavaceae sensu lato and related groups in the order Asparagales. Sequence alignments were optimized using the Consistency Index, Retention Index, and Rescaled Consistency Index to find the alignment that exhibited the least amount of homoplasy. The results of our study are congruent with the conclusions drawn from cytological, immunological, cpDNA, and rbcL studies, which support a narrow interpretation of Agavaceae and a close relationship among Convallariaceae, Dracaenaceae, and Nolinaceae. In addition, the ITS sequence data provide evidence for some interesting relationships within these families.     

Molecular phylogenetics of Uvaria (Annonaceae): relationships with Balonga,Dasoclema and Australian species of Melodorum

An extended molecular phylogenetic analysis of Uvaria (Annonaceae) is presented, using maximum parsimony, maximum likelihood and Bayesian methods, based on sequences of four plastid DNA regions (matK, psbA‐trnH spacer, rbcL and trnL‐F). The additional taxa include the monotypic West African genus Balonga, the monotypic South‐East Asian genus Dasoclema and seven Australian representatives of the genus Melodorum. The results indicate that all of these taxa are nested within a well‐supported clade otherwise consisting of Uvaria species, indicating that their taxonomic treatment needs to be reassessed. The distinguishing morphological characteristics of the taxa are re‐evaluated and interpreted as specialized adaptations of the basic Uvaria structure. The genus Uvaria is accordingly extended following the transfer of these species, necessitating six new nomenclatural combinations and two replacement names. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 163 , 33–43.     

γ-Glutamylcysteine Production by Escherichia coli B Cells Dosed with the γ-Glutamylcysteine Synthetase Gene

Molecular studies on the evolution and systematics of fungi have been established primarily based on the neutral theory by analyzing neutral mutations in some defined segments of housekeeping genes as genetic markers. Such an approach is, however, hardly applicable for analyzing ancient evolutionary radiations. In the present study, we looked for DNA sequences characterizing higher taxa, and discovered a unique macroevolutionary genomic marker, megB1, that specifies the phylum Basidiomycota. megB1 is an approximately 500-bp DNA element, which is defined by terminal sequences and five internal segments conserved throughout the phylum. megB1 resides on the rDNA intergenic spacer 1 (IGS1) from 27 species of 10 Basidiomycota genera examined. While megB1 was not found in IGS1 from the other 92 species of the 27 Basidiomycota genera, several genera representing them carry megB1 in some other genomic regions. No known taxonomic criteria fit into the classification on the basis of whether megB1 resides on rDNA. Neighbor-joining analysis of the megB1 sequence, however, properly assigned species to their respective genera. Thus far, megB1 has not been found in any genomic or genetic databases currently available for other phyla. These results suggest that megB1 may have emerged upon the occurrence of Basidiomycota, and that this phylum evolved thereafter leaving this element conserved throughout their further differentiation. megB1 may be a novel genomic marker useful in the analysis of ancient through the latest evolutionary radiation in Basidiomycota.     

The Constitutional Amine of Antibiotic YA-56

In addition to the previously reported six amino acids and two carbohydrates (one disaccharide), 3-aminopropionamidine was isolated as a constituent from the acid hydrolyzate of the antibiotic YA–56X, one of the major component of antibiotic YA–56 complex. Based on the hitherto found informations, structural comparison of the antibiotic YA–56 X and Y was made with phleomycins, bleomycins, zorbamycin and zorbonomycin B to which antibiotic YA–56 closely related. Among those, zorbamycin was identical with antibiotic YA–56 X.     

叶蝉科昆虫分子系统发育的研究进展

从基因组DNA的提取、研究的基因片段、PCR引物选用、扩增条件以及叶蝉科不同阶元的分子系统发育分析等方面,综述叶蝉科(半翅目:叶蝉科)昆虫分子系统发育的研究进展。目前角顶叶蝉类的研究成果相对较多,大叶蝉亚科次之,其余类群的研究较少或无。线粒体基因与核基因序列联合分析以及线粒体全序列分析以及基因序列与形态数据相结合分析,分子鉴定叶蝉与共生菌之间的协同进化的研究,将是叶蝉分子系统学未来发展的主要研究手段。     

Phylogenetic relationships of New Zealand Asteraceae inferred from ITS sequences

Forty-five sequences from members of all genera of Asteraceae indigenous to New Zealand and 50 published sequences representing the tribal diversity in the family were analyzed to assess the utility of ITS sequences to resolve phylogenetic relationships. Previous studies using chloroplast DNA sequences and morphology provided support for several clades in the Asteraceae, yet the relationships among some of these were uncertain. The results from ITS analysis were largely consistent with these earlier studies. The New Zealand species are included in at least six clades, most of these corresponding to recognized tribes. Our results have also clarified the tribal affinities of a few anomalous genera. Haastia, previously aligned with the Gnaphalieae or the Astereae, is nested in the Senecioneae. Centipeda, previously included in the Astereae or Anthemideae, emerges near the Heliantheae. The relationships of Abrotanella remain unresolved. Received August 8, 2001 Accepted November 6, 2001     

Symbiont diversity in scleractinian corals from tropical reefs and subtropical non-reef communities in Taiwan

We examined zooxanthellae diversity in scleractinian corals from southern Taiwan and the Penghu Archipelago, a tropical coral reef and a subtropical non-reefal community, respectively. Zooxanthellae diversity was investigated in 52 species of scleractinian corals from 26 genera and 13 families, using restriction fragment length polymorphism (RFLP), and phylogenetic analyses of the nuclear small-subunit ribosomal DNA (nssrDNA) and large-subunit ribosomal DNA (nlsrDNA). RFLP and phylogenetic analyses of nuclear-encoded ribosomal RNA genes showed that Symbiodinium clade C was the dominant zooxanthellae in scleractinian corals in the seas around Taiwan; Symbiodinium clade D was also found in some species. Both Symbiodinium clade C and D were found in colonies of seven species of scleractinian corals. Symbiodinium clade D was associated with corals that inhabit either shallow water or the reef edge in deep water, supporting the hypothesis that Symbiodinium clade D is a relatively stress-tolerant zooxanthellae found in marginal habitats.Communicated by Biological Editor H.R. Lasker