Gene action in fish of tetraploid origin. II. Cellular and biochemical parameters in clupeoid and salmonoid fish

By use of cell size, protein and hemoglobin content, and enzyme activities as markers, it becomes apparent that in the course of evolution the gene expression of anciently tetraploid fish of the order Ostariophysi was diploidized, but no such regulatory mechanism has evolved in the phylogenetically tetraploid species of the order Isospondyli. This finding is discussed in terms of possible selective neutrality of tetraploid expression and the phylogenetic age of Isospondyli.     

Gene action in fish of tetraploid origin. III. Ribosomal DNA amount in cyprinid fish

Phylogenetically diploid and tetraploid cyprinid fish species have cells of very similar volumes and protein contents. This finding has prompted us to postulate a regulatory system established during the evolution of the tetraploids leading to a diploid state of genic expression. It was proposed that this might be accounted for by a selective loss of ribosomal genes. RNA-DNA hybridization experiments, however, reveal a clear-cut 1:2 relationship of ribosomal DNA amounts between the diploid and the tetraploid species.This work was supported by the Deutsche Forschungsgemeinschaft.     

Gene action in fish of tetraploid origin. I. Cellular and biochemical parameters in cyprinid fish

In phylogenetically diploid and tetraploid Cyprinid fish species, erythrocyte volumes, protein contents, and mean activities of the enzymes LDH, 6PGD, and PGI per cell per active gene locus decline with increasing DNA contents. These findings are assumed to reflect an evolutionary tendency of polyploids to regulate their genic activity down to the level of the diploids.     

Gene action in fish of tetraploid origin. V. Cellular RNA and protein content and enzyme activities in cyprinid,clupeoid, and salmonoid species

The ratio of cellular RNA and protein content is about 1:1 between phylogenetically diploid and tetraploid species of the teleost family Cyprinidae, but is roughly in proportion to ploidy in species of the teleost order Isospondyli. Enzyme activities do not unequivocally comply with this scheme. These findings are discussed in view of the hypothesis that a regulatory mechanism which reduces genic activity has evolved in the tetraploid cyprinids but not in the tetraploid species of the order Isopondyli.     

DNA reassociation kinetics in diploid and phylogenetically tetraploid cyprinidae.

Four diploid and three phylogenetically tetraploid Cyprinidae (Ostariophysi) have been characterized as for nuclear DNA content, modal chromosome number and DNA reassociation kinetics (hydroxyapatite chromatography). Among the diploid species nuclear DNA content (10(-12) g DNA/2C) was 1.62 for Tinca tinca, 1.87 for Scardinius erythrophthalmus, 2.53 for Leuciscus cephalus and 2.75 for Alburnus alburnus, while the phylogenetically tetraploid species Carassius auratus, Barbus barbus and Cyprinus carpio attained 3.40, 3.66 and 3.80 respectively. Modal chromosome number was 2n = 48-50 for diploid individuals and 2n = 100-104 for phylogenetically tetraploid ones. In all the species 5--8% of the genome is represented by highly repetitive and foldback DNA. In DNA reassociation kinetics of phylogenetically tetraploid Cyprinidae a distinct plateau separates an intermediate reassociating sequence fraction (about 22% of the genome; with average repetition frequencies between 1,000 and 1,400) from a slow reassociating one (unique DNA; about 72% of the genome). These two genome fractions are not clearly distinguishable from each other in Cot curves of the diploid Cyprinidae, where a similar plateau is not evident. Since simple ploidy changes are not expected to affect DNA reassociation kinetics we suggest a different evolution in the genome organization of the two ploidy groups. Some possible hypotheses are discussed.     

苜蓿核糖体基因物理定位及染色体荧光分带

利用核糖体基因为探针对,二倍体和四倍体苜蓿(Medicago sativa)进行原位杂交,结果表明,45s在四倍体、二倍体种中总是以单位点位于核仁组织区,5s则有2～3个位点;以二倍体种的基因组DNA为探针的原位杂交表明,蓝花苜蓿(M.coerulea)和黄花苜蓿(M.falcata)均能与四倍体染色体进行杂交,仅杂交信号强弱的染色体数目有差别;荧光染料DAPI使苜蓿的染色体显示带纹,蓝花苜蓿的DAPI带与C-带基本一致.文章对四倍体苜蓿的可能来源进行了讨论.     

Single-copy DNA relationships between diploid and tetraploid teleostean fish species

The degree of single-copy DNA relatedness among nine Salmonid, Osmerid, and Clupeid species (teleosts, order Isospondyli) was explored by interspecific DNA hybridization and the determination of the thermal stability of these hybrids. It is shown that the extent of base substitution and the amount of shared sequences is largely consistent with the systematic interrelationship of the species compared. A tentative estimate of the average base substitution rate is about 0.1–0.25% per million years, which is in the range typical for animal and plant nuclear genomes. The results are also discussed in view of the phylogenetically tetraploid state of the Salmonid genomes. A comparison of the amount of intra-genomic and inter-genomic divergence in the tetraploids suggests that a polyploidization event occurred recently in Salmonid evolution.     

Ribosomal RNA structure in the diploid and phylogenetically polyploid amphibian species Hyla and Odontophrynus

Ribosomal RNA of the diploid amphibian species Hyla chrysoscelis and Odontophrynus americanus is structurally modified by hidden breaks. Phylogenetically polyploid related species like the tetraploid Hyla versicolor, the tetraploid Odontophrynus americanus and the octoploid Ceratophrys ornata do not show hidden breaks in ribosomal RNA. Structural modifications of rRNA molecules in diploid amphibians has no detectable effect on the ribosomal activity in vitro.     

Characterization of the ribosomal DNA units in two related Prunus species (P. Cerasifera and P. Spinosa)

Summary The genetic relationships between two Prunus species, involved in rootstock breeding, were examined at the level of the ribosomal RNA genes. Twenty clones of P. cerasifera, a diploid species, and 12 clones of P. spinosa, a tetraploid wild species, were studied. The use of three heterologous ribosomal DNA probes covering different regions of the ribosomal tandem repeats enabled us to construct restriction maps for EcoRI and BamHI. We identified two unit types (unit I and unit II) in P. cerasifera. In P. spinosa, P. cerasifera units were present in addition to a third ribosomal unit type (unit III). These results appeared to confirm previous cytological studies (Salesses 1973) indicating that one of the genomes in P.spinosa has homology with the one from P. cerasifera.     

Amount of repeated and non-repeated DNA in the genomes of closely related fish species with varying genome sizes.

1. Within the teleostean family Cyprinidae, diploid species occur with wide variation in genome size. There also exist species which were anciently tetraploid. 2. The quantitative changes of DNA content in the diploids are primarily due to differences in the amount of intermediately repeated DNA. DNA sequence composition of the ancient tetraploid genomes suggests that the species derived from diploid ancestors of small genome size. 3. The average base composition and the base compositional heterogeneity are similar in all the species examined.     

GENETIC VARIATION IN TRAGOPOGON SPECIES: ADDITIONAL ORIGINS OF THE ALLOTETRAPLOIDS T. MIRUS AND T. MISCELLUS (COMPOSITAE)

Genetic diversity in the introduced diploids Tragopogon dubius, T. porrifolius, and T. pratensis and their neoallotetraploid derivatives T. mirus and T. miscellus was estimated to assess the numbers of recurrent, independent origins of the two tetraploid species in the Palouse region of eastern Washington and adjacent Idaho. These tetraploid species arose in this region, probably within the past 50–60 yr, and provide one of the best models for the study of polyploidy in plants. The parental species of both T. mirus and T. miscellus have been well documented, and each tetraploid species has apparently formed multiple times. However, a recent survey of the distributions of these allotetraploids revealed that both tetraploid species have expanded their ranges considerably during the past 50 yr, and several new populations of each species were discovered. Therefore, to evaluate the possibility that these recently discovered populations are of recent independent origin, a broad analysis of genetic diversity in T. mirus, T. miscellus, and their diploid progenitors was conducted. Analyses of allozymic and DNA restriction site variation in all known populations of T. mirus and T. miscellus in the Palouse and several populations of each parental diploid species revealed several distinct genotypes in each tetraploid species. Four isozymic multilocus genotypes were observed in T. mirus, and seven were detected in T. miscellus. Tragopogon mirus possesses a single chloroplast genome, that of T. porrifolius, and two distinct repeat types of the 18S-26S ribosomal RNA genes. Populations of T. miscellus from Pullman, Washington, have the chloroplast genome of T. dubius; all other populations of T. miscellus have the chloroplast DNA of T. pratensis. All populations of T. miscellus combine the ribosomal RNA repeat types of T. dubius and T. pratensis, as demonstrated previously. When all current and previously published data are considered, both T. mirus and T. miscellus appear to have formed numerous times even within the small geographic confines of the Palouse, with estimates of five to nine and two to 21 independent origins, respectively. Such recurrent polyploidization appears to characterize most polyploid plant species investigated to date (although this number is small) and may contribute to the genetic diversity and ultimate success of polyploid species.     

Ribosomal RNA gene variation in diploid and tetraploid Tolmiea menziesii

Evidence from gross morphology, karyology and flavonoid chemistry suggests that Tolmiea menziesii is one of the clearest examples of autopolyploidy in natural populations. To provide additional data regarding the origin of the tetraploid cytotype of Tolmiea, both the 5S and 18S-25S ribosomal RNA genes were studied at the restriction enzyme level. Using restriction enzymes that cut once per repeat, the lengths of the 5S and 18S-25S ribosomal genes were estimated in diploids and tetraploid plants. There appear to be no consistent differences between diploids and tetraploids for the repeat length of the 18S-25S ribosomal genes. Furthermore, there is no significant repeat length heterogeneity within tetraploid plants for these genes. In addition, no differences in repeat length of the 5S genes were observed among the diploid and tetraploid plants analysed. The homogeneity observed among diploid and tetraploid plants for repeat length of the 5S and 18S-25S ribosomal genes is consistent with the hypothesis that the tetraploid cytotype is of autopolyploid origin.     

Studies on the origin and evolution of tetraploid wheats based on the internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA

In this study, the internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA in the tetraploid wheats, Triticum turgidum (AABB) and Triticum timopheevii (AAGG), their possible diploid donors, i.e., Triticum monococcum (AA), Triticum urartu (AA), and five species in Aegilops sect. Sitopsis (SS genome), and a related species Aegilops tauschii were cloned and sequenced. ITS1 and ITS2 regions of 24 clones from the above species were compared. Phylogenetic analysis demonstrated that Aegilops speltoides was distinct from other species in Aegilops sect. Sitopsis and was the most-likely donor of the B and G genomes to tetraploid wheats. Two types of ITS repeats were cloned from Triticum turgidum ssp. dicoccoides, one markedly similar to that from T. monococcum ssp. boeoticum (AA), and the other to that from Ae. speltoides (SS). The former might have resulted from a recent integression event. The results also indicated that T. turgidum and T. timopheevii might have simultaneously originated from a common ancestral tetraploid species or be derived from two hybridization events but within a very short interval time. ITS paralogues in tetraploid wheats have not been uniformly homogenized by concerted evolution, and high heterogeneity has been found among repeats within individuals of tetraploid wheats. In some tetraploid wheats, the observed heterogeneity originated from the same genome (B or G). Three kinds of ITS repeats from the G genome of an individual of T. timopheevii ssp. araraticum were more divergent than that from inter-specific taxa. This study also demonstrated that hybridization and polyploidization might accelerate the evolution rate of ITS repeats in tetraploid wheats.     

Polyploidy in Cupressaceae: Discovery of a new naturally occurring tetraploid,Xanthocyparis vietnamensis

While polyploidy (whole-genome multiplication) is generally considered rare in extant gymnosperms (with the exception of Ephedra, Ephedraceae), the occurrence of sporadic polyploid individuals belonging to various genera in the conifer family Cupressaceae has been reported in the literature. In addition, recent studies have revealed that polyploidy is not uncommon in the genus Juniperus (Cupressaceae), with tetraploid and hexaploid individuals reported in individuals collected from wild populations. Given these findings, we undertook a comprehensive screening of ploidy levels in 32 species belonging to the four genera that are phylogenetically closest to Juniperus (i.e.,Callitropsis, Hesperocyparis, Xanthocyparis, and Cupressus), referred to as the CaHXCu complex. In addition, we also determined the ploidy level of two accessions in the poorly studied tetraploid, Fitzroya cupressoides. Using flow cytometry together with published chromosome counts to assign ploidy levels, we show that all species of the CaHXCu complex are diploid except Xanthocyparis vietnamensis, which is tetraploid, with a genome size of 44.60 pg/2 C. This study opens up new opportunities for studying the impact and consequences of polyploidy on the evolution and adaptation of species in Cupressaceae.     

Abundance and diversity of Archaea in heavy-metal-contaminated soils.

The impact of heavy-metal contamination on archaean communities was studied in soils amended with sewage sludge contaminated with heavy metals to varying extents. Fluorescent in situ hybridization showed a decrease in the percentage of Archaea from 1.3% +/- 0.3% of 4', 6-diamidino-2-phenylindole-stained cells in untreated soil to below the detection limit in soils amended with heavy metals. A comparison of the archaean communities of the different plots by denaturing gradient gel electrophoresis revealed differences in the structure of the archaean communities in soils with increasing heavy-metal contamination. Analysis of cloned 16S ribosomal DNA showed close similarities to a unique and globally distributed lineage of the kingdom Crenarchaeota that is phylogenetically distinct from currently characterized crenarchaeotal species.     

Taxonomic position of "Pseudomonas oxalaticus" strain ox14T (DSM 1105T) (Khambata and Bhat, 1953) and its description in the genus Ralstonia as Ralstonia oxalatica comb. nov

"Pseudomonas oxalaticus" strain Ox1T (= DSM 1105T), which was described as an oxalate-decomposing bacterium, was reinvestigated to clarify its taxonomic position. 16S ribosomal DNA sequence comparisons demonstrated that this species is phylogenetically related to the species of the genus Ralstonia. and represents a new species. The result of the DNA-DNA hybridization value was supported in this placement. Strain Ox1T is closely related to Ralstonia eutropha with a less than 60% DNA-DNA hybridization value. The new name Ralstonia oxalatica comb. nov. is proposed to strain Ox1T, on the basis of these results and previously published data for the G+C content of the genomic DNA and the phenotypic characters.     

Chromosomal organization of a sequence related to LTR-like elements of Ty1-copia retrotransposons in Avena species.

A repetitive sequence, pAs17, was isolated from Avena strigosa (As genome) and characterized. The insert was 646 bp in length and showed 54% AT content. Databank searches revealed its high homology to the long terminal repeat (LTR) sequences of the specific family of Ty1-copia retrotransposons represented by WIS2-1A and Bare. It was also found to be 70% identical to the LTR domain of the WIS2-1A retroelement of wheat and 67% identical to the Bare-1 retroelement of barley. Southern hybridizations of pAs17 to diploid (A or C genomes), tetraploid (AC genomes), and hexaploid (ACD genomes) oat species revealed that it was absent in the C diploid species. Slot-blot analysis suggested that both diploid and tetraploid oat species contained 1.3 x 10(4) copies, indicating that they are a component of the A-genome chromosomes. The hexaploid species contained 2.4 x 10(4) copies, indicating that they are a component of both A- and D-genome chromosomes. This was confirmed by fluorescent in situ hybridization analyses using pAs17, two ribosomal sequences, and a C-genome specific sequence as probes. Further, the chromosomes involved in three C-A and three C-D intergenomic translocations in Avena murphyi (AC genomes) and Avena sativa cv. Extra Klock (ACD genomes), respectively, were identified. Based on its physical distribution and Southern hybridization patterns, a parental retrotransposon represented by pAs17 appears to have been active at least once during the evolution of the A genome in species of the Avena genus.     

Characteristics and utility of nuclear-encoded large-subunit ribosomal gene sequences in phylogenetic studies of red algae

Primer sequences are described for amplifying and sequencing a large fragment (approximately 2500 b.p.) of the nuclear-encoded large-subunit ribosomal RNA gene (LSU) from red algae. In comparison to RuBisCo large-subunit gene (rbcL) and nuclear-encoded small-subunit ribosomal RNA gene (SSU) sequence data, LSU sequence data was intermediate in the number of phylogenetically informative positions and sequence divergence. Parsimony analysis of LSU sequences for 16 Gelidiales species resolved some nodes unresolved in rbcL and SSU parsimony trees. An analysis of LSU sequences from 13 species of red algae classified in 11 orders suggests that this gene may be useful in studies of higher-level relationships of red algae.     

Metarhizium brachyspermum sp. nov. (Clavicipitaceae), a new species parasitic on Elateridae from Japan

Ascomata of a Metarhizium species were collected from Tochigi Prefecture, Japan. The ascomata were similar to M. kalasinense in its host preference for elaterids, olive-green clavate stromata, and obliquely immersed perithecia, but the asci and ascospores were significantly shorter in length than those of the latter species. Furthermore, phylogenetic analyses based on the internal transcribed spacer region of nuclear ribosomal DNA and the elongation factor 1-alpha gene showed that the Japanese species was phylogenetically distinctive in the M. anisopliae lineage, including M. kalasinense. Accordingly, we describe a new species, M. brachyspermum. Isolates of this species produced olive-green conidial masses on the surface of the colony. Also, hyphal anastomoses between two metulae were often observed on conidiophores.     

Immunoglobulin heavy chain constant and heavy chain variable region genes in phylogenetically diverse species of bony fish

Summary Genomic DNA from 18 phylogenetically diverse species of bony fish was hybridized with probes specific for the channel catfish immunoglobulin heavy chain constant (CH) gene, as well as with immunoglobulin heavy chain variable (VH) probes specific for five channel catfish VH gene families. The results showed that CH probes strongly hybridized only to genomic fragments from other catfish species. In contrast, restricted DNA from most other species hybridized with at least two channel catfish VH probes. In those species whose DNA hybridized with multiple VH probes, the restriction pattern of hybridizing fragments was probe-dependent. These studies suggest that (1) the CH gene defined in channel catfish appears to share similarity only with CH genes in other catfish species, (2) families of VH genes appear to have diverged in early phylogenetic lineages of teleosts, and (3) VH genes similar to those defined in catfish appear to be widely represented in phylogenetically diverse species of teleosts.