Characterisation of the cDNA clones of two β-tubulin genes and their expression in the potato plant (Solanum tuberosum L.)

The cDNA clones of two potato -tubulin genes were isolated from a tuberising stolon tip library. Analysis of 20 positive clones showed that they represented one or another of two different but very similar -tubulin genes, designated TUBST1 and TUBST2. The expression pattern of -tubulin genes in the potato plant was investigated by RNA blot analysis and by RT-PCR. Southern analysis of potato genomic DNA with coding and non-coding -tubulin probes revealed that there are multiple -tubulin genes in the potato genome and that there is likely to be considerable divergence in the 3 non-coding sequences. Phylogenetic analysis of plant -tubulin genes is described.     

Phylogenetic analysis of the Glomeromycota by partial β-tubulin gene sequences

The 3’ end of the β-tubulin gene was amplified from 50 isolates of 45 species in Glomeromycota. The analyses included a representative selection of all families except Pacisporaceae and Geosiphonaceae. Phylogenetic analyses excluded three intron regions at the same relative positions in all species due to sequence and length polymorphisms. The β-tubulin gene phylogeny was similar to the 18S rRNA gene phylogeny at the family and species level, but it was not concordant at the order level. Species in Gigasporaceae and Glomeraceae grouped together but without statistical support. Paralogous sequences in Glomus species likely contributed to phylogenetic ambiguity. Trees generated using different fungal phyla as out-groups yielded a concordant topology. Family relationships within the Glomeromycota did not change regardless if the third codon position was included or excluded from the analysis. Multiple clones from three isolates of Scutellospora heterogama yielded divergent sequences. However, phylogenetic patterns suggested that only a single copy of the β-tubulin gene was present, with variation attributed to intraspecific sequence divergence.     

Organization and chromosomal localization ofβ-tubulin genes inLeishmania donovani

The genomic organization and chromosomal location of theβ-tubulin isogenes inLeishmania donovani promastigotes has been studied by nucleic acid hybridization techniques using a cloned β-tubulin gene. We have cloned aβ-tubulin gene fragment, 3.3 kbp long, from genomic DNA ofLeishmania donovani using a heterologousβ-tubulin DNA as probe. Restriction maps of this clone have been prepared. It has been estimated that there are approximately 11–15 copies of theβ-tubulin genes per haploid genome. The majority of these isogenes are arranged in a tandem repeat with a length of 3.5 kbp on a single chromosome. In addition a few dispersed gene copies at different chromosomal loci were detected by pulse field gradient gel electrophoresis. Part of the internal coding region of the gene has been sequenced to confirm the identity of theβ-tubulin clone and is found to be nearly identical to that ofLeishmania mexicana amazonensis.     

Synonymous nucleotide substitution rates of β-tubulin and histone genes conform to high overall genomic rates in rodents but not in sea urchins

Summary Sea urchin and rodent genomes have been posited to evolve rapidly as indicated by divergences in single copy nuclear DNA sequences. We have examined whether the synonymous substitution rates of three highly conserved genes, -tubulin, histone H4, and histone H3, adhere to these high genomic substitution rates by comparing sequences between two sea urchins,Strongylocentrotus purpuratus andLytechinus pictus, and between rodents and humans. Whereas the rate of change between the 3 untranslated regions of the -tubulin cDNA ofS. purpuratus (Sp-1), sequenced in this study, and ofL. pictus (Lp-3) was consistent with the overall rate of change estimated from previous DNA hybridization results between these species, the synonymous substitution rates for the carboxyl domains of these -tubulins, as well as for the late histones H4 and H3, were significantly depressed. In contrast, synonymous nucleotide substitution rates between rodents and between rodent and human for the carboxyl domain proper of identical -tubulin isotypes and for histone H4 and H3.1 did not differ from the overall rate of change for the rodent genomes. Moreover, an analysis of paralogous human and mouse -tubulin sequences supported the conclusion that the synonymous substitution rates in the mouse were higher than those in the human. Differences in constraint on evolutionary change were not evident strictly from the conserved amino acid sequences and base compositions of these genes. Other constraining influences seemed more relevant to the departure of the synonymous substitution rates of the sea urchin -tubulin and histone coding regions from the average genomic rate.     

Phylogenetics and biogeography of eastern Asian-North American disjunct genus Pachysandra （Buxaceae） inferred from nucleotide sequences

Pachysandra is an eastern Asian-North American disjtunct genus with three species, two in eastern Asia （Pachysandra axillaris and Pachysandra terminalis） and one in eastern North America （Pachysandra procurnbens）. Although morphological and cytological studies suggest a close affinity of Pprocumbens with P axillaris, molecular data from nuclear and chloroplast DNA regions have provided conflicting signals. In this study, we tested previous phylogenetic hypotheses using sequences of nuclear ribosomal DNA internal transcribed spacers and chloroplast ndhF gene from multiple individuals of each of the three species. We also estimated the time of divergence between eastem Asia and eastern North America. Our results support the morphological and cytological conclusion that P procumbens is more closely related to P axillaris than to P terminalis. The estimated time of divergence of P axillaris and P procumbens was 14.6±5.5 mya, consistent with estimates from many other eastern Asian-North American disjunct genera. The migration of Pachysandra populations from eastern Asia to North America might have occurred by way of the North Atlantic land bridge.     

Monophyletic groups within the Parmeliaceae identified by ITS rDNA, β-tubulin and GAPDH sequences

Phylogenetic relationships within the Parmeliaceae are analysed cladistically on the basis of DNA characters from partial β-tubulin, partial glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and ITS sequences. 100 taxa representing 73 of the 88 genera currently recognised are included in the analyses. Eight monophyletic groups including two or more genera were identified in the tree calculated from the combined data matrix. Three of the groups cover almost half of the species of the family. The largest and strongest supported group includes seven genera with their distribution centres in the Southern Hemisphere: Almbornia, Chondropsis, Karoowia, Namakwa, Neofuscelia, Xanthomaculina and Xanthoparmelia. The second group is a clade of four essentially tropical genera: Concamerella, Flavoparmelia, Parmotrema and Rimelia. The third large group with strong support is the core of cetrarioid lichens, distributed primarily in cold areas of the Northern Hemisphere. The genus Parmelia sensu Hale is not closely related with most of its segregates. One new combination, Cetrariella commixta, is proposed. Coelopogon abraxas is reported from South America for the first time.     

Cloning,characterisation and expression of the α-tubulin genes of the leech,Hirudo medicinalis

We have isolated two α-tubulin cDNAs from the leech, Hirudo medicinalis. Both encode putative proteins of 451 amino-acids which differ from each other at only two positions. Southern blotting suggests that there are only two α-tubulin genes in the leech. The genes contain two introns and, because of the extremely high homology of the nucleotide sequence from the second intron to the end of the genes, we have inferred that a gene conversion event about 9.5 million years ago has homogenised the Hirudo α-tubulin sequences. Using in situ hybridisation to tissue sections, we have shown that the two genes are probably expressed in all neurons of the leech ganglia and that their spatial distribution remains unchanged during neuronal regeneration. The deduced amino-acid sequences of the leech α-tubulins show that they have greatest similarity to those from a platyhelminth, echiuran and mollusc with rather less to arthropod α-tubulins. The protein sequences of the leech α-tubulins have been compared with representatives of those from across all phyla to determine if any specific feature labels certain isotypes of tubulin for neuronal expression.     

Physicochemical measurement of the base composition of mRNA-related sequences of the human α and β globin genes

Hybrids formed between human and globin cDNA and total human cellular DNA have been studied by thermal denaturation and cesium chloride density gradient centrifugation. From these studies, the weight average G+C content of human globin cDNA has been determined to be 62%±2% and that of human globin cDNA 51%±2%. These values correlate well with the results of G+C content of the human and globin cDNAs as determined by direct nucleotide sequence analysis of the cDNAs. Thermal denaturation and cesium chloride density gradient centrifugation of DNA-cDNA hybrids can therefore provide accurate information on the base composition of mRNA related sequences of any single copy gene for which a relatively pure cDNA can be obtained, without the necessity for direct nucleotide sequence analysis.     

The nucleotide and deduced amino acid sequences of a cDNA encoding a new species of Pregnancy-Specific β1-Glycoprotein (PSβG)

We screened a cDNA library of a human placenta with cDNA for nonspecific cross-reacting antigen, a member of the carcinoembryonic antigen gene family. One of the positive clones, PS34, was found to encode a 426 amino acid protein belonging to pregnancy-specific β₁-glycoprotein (PSβG). The mature PS34 protein consisted of domains, N, A1, A2, B2 and C. The domain-N of PS34 showed sequence similarities of 79.8–83.5% to those of the PSβG members so far reported, indicating PS34 is a new member of PSβG and also of the carcinoembryonic antigen gene family.     

A nucleotide substitution in one of the β-tubulin genes of Trichoderma viride confers resistance to the antimitotic drug methyl benzimidazole-2-yl-carbamate

We characterized a Trichoderma viride strain that is resistant to the antimitotic drug methyl benzimidazole-2-yl-carbamate (MBC). This species has two β-tubulin genes (tub1 and tub2) and by reverse genetics we showed that a mutation in the tub2 gene confers MBC resistance in this strain. Comparison of the tub2 sequence of the mutant strain with that of the wild type revealed that a single amino acid substitution of tyrosine for histidine at position 6 is responsible for the MBC tolerance. Furthermore, we showed that this gene can be used as a homologous dominant selectable marker in T. viride transformation. Both tubulin genes were completely sequenced. They differ by 48 residues and the degree of identity between their deduced amino acid sequences is 86.3%.     

cDNA cloning of β-tubulin gene and organization of tubulin genes in Vigna radiata (mung bean) genome

We isolated an almost full-length cDNA clone containing -tubulin gene from a partial cDNA library of mung bean using chicken cDNA as probe. Cross-hybridization with chicken -tubulin cDNA and positive hybridization-selection and translation of mung bean mRNA established that this clone contains -tubulin sequences. We studied the organization of tubulin genes in mung bean. In this plant tubulin genes are organized in tandem repeats of alternating - and -tubulin genes. The 5.6 kb basis repeat unit which contains both - and -tubulin genes is repeated twenty times per haploid genome.Abbreviations SDS sodium dodecyl sulphate - 1×SSPE 150 mM NaCl, 10 mM NaH₂PO₄ and 1 mM EDTA, pH 7.4     

Origin and early evolution of eukaryotes inferred from the amino acid sequences of translation elongation factors 1α/Tu and 2/G

Phylogenetic placements of archaebacteria and protozoa are important in understanding the origin and early evolution of eukaryotes. These problems have been analyzed mainly by comparisons of small subunit ribosomal RNA (SrRNA) sequences. However, the SrRNA phylogeny may sometimes be unreliable, especially when base compositions are biased among species. Because it is difficult to take full account of the bias in inferring the SrRNA tree, alternative examinations using protein sequence data have been very much desired. We analyzed the phylogenetic relationship among eukaryotes, archaebacteria, and eubacteria by the ML method of protein phylogeny using amino acid sequence data of EF-1α/Tu and 2/G. The unrooted tree analyses of both the EF-1α/Tu and 2/G consistently demonstrated that the ‘eocyte’ tree, in which archaebacteria are not monophyletic but eocytes are closer to eukaryotes than to other archaebacteria, is very likely. Further analysis using a composite tree of EF-1α/Tu and 2/G suggested that archaebacteria are closer to eukaryotes than to eubacteria but are not monophyletic. These results clearly support the hypothesis that eukaryotes have evolved from the eocyte-like organism. We also analyzed a protozoan phylogeny including mitochondrion-lacking species by the ML method using EF-1α and EF-2 data sets, and demonstrated (a) that two mitochondrion-lacking species, G. plecoglossi (Microsporidians) and G. lamblia (Diplomonads) probably represent the first and the second earliest offshoots of eukaryotes, respectively; (b) that Trypanosoma is not likely to have diverged next to Giardia as suggested by the SrRNA tree, but shows high affinity with higher eukaryotes; and (c) that protein phylogeny would give a robust estimation because amino acid compositions of conservative proteins do not differ significantly among species.     

Phylogeny and Evolution of Selected Primates as Determined by Sequences of the ε-Globin Locus and 5′ Flanking Regions

We studied phylogenetic relationships of 39 primate species using sequences of the -globin gene. For 13 species, we also included flanking sequences 5 of this locus. Parsimony analyses support the association of tarsiers with the anthropoids. Our analysis of New World monkeys supports the model in which the callitrichines form a clade with Aotus, Cebus, and Saimiri, with Cebus and Saimiri being sister taxa. However, analysis of the 5 flanking sequences did not support grouping the atelines with Callicebus and the pitheciins. Our data support the classification of platyrrhines into three families, Cebidae (consisting of Cebus, Saimiri, Aotus, and the callitrichines; Atelidae—the atelines; and Pitheciidae—Callicebus and the pithiciins. The strepsirhines form well-defined lemuroid and lorisoid clades, with the cheirogaleids (dwarf and mouse lemurs) and Daubentonia (aye-aye) in the lemuroids, and the aye-aye being the most anciently derived. These results support the hypothesis that nonhuman primates of Madagascar descended from a single lineage. Local molecular clock calculations indicate that the divergence of lemuroid and lorisoid lineages, and the earliest diversification of lemuroids, occurred during the Eocene. The divergence of major lorisoid lineages was probably considerably more recent, possibly near the Miocene–Oligocene boundary. Within hominoids some estimated dates differ somewhat from those found with more extensive noncoding sequences in the -globin cluster.     

Karyological knowledge of the Italian vascular flora as inferred by the analysis of “Chrobase.it”

Abstract

Chromosome number knowledge of the Italian vascular flora is stored in the online database Chrobase.it, which includes 6723 records, referable to 3428 taxa, 2799 accepted species and subspecies (about 35% of the national flora), and 3410 different chromosome countings (cytotypes). Appropriate queries to Chrobase.it allowed us to calculate mean, modal and median chromosome numbers for the Italian vascular flora, for geographical subgroups (islands, south, centre, north) and for selected orders, families and genera. Chromosome number data were available for 41 out of 55 orders (74%) and 107 out of 428 families (67%), represented by 664 out of 1297 genera (51%). The most studied administrative regions are Sicily (844 taxa), Tuscany (592 taxa), and Sardinia (390 taxa), while the most studied families are Asteraceae (465 taxa), Fabaceae (266 taxa), Brassicaceae (158 taxa), and Poaceae (144 taxa). Chromosome numbers range from 2n = 6, occurring in several species of Hypochaeris (Asteraceae), to 2n = 240, occurring in Ophioglossum (Ophioglossaceae), Dryopteris (Dryopteridaceae) and Arenaria (Caryophyllaceae) (mode is 2n = 18, and median is 2n = 24). Chromosome number variability was analyzed by frequencies (linear plots) and ANOVA, resulting in significant differences among geographical groups (mean chromosome number increasing from islands-south to centre-north) and selected taxa. B-chromosomes occur in 5.3% of data (148 taxa) and their number is not significantly different among geographical areas, while they occur only in 14 orders, 17 families, and 56 genera. The number of B-chromosomes ranges from 1 to 13 (mode = 1, median = 2).     

Evolution of immunoglobulin V genes: Evidence indicating that recently duplicated human Vκ sequences have diverged by gene conversion

We have analyzed several closely related members of the gene family encoding the variable regions of human immunoglobulin kappa light chains (V_κ genes). Two of these genes differ at a single nucleotide out of 940 bases sequenced, and are believed to be alleles of a locus called HK101. This substitution results in an amino acid replacement in the first complementarity-determining region of the kappa chain. We also compared the structures of two nonallelic human V_κ loci (HK101 and HK137) and found a high degree of sequence homology over a region at least 13.5 kb long. This long block of homology indicates that these two loci arose from a recent gene duplication. The DNA sequences of these two nonallelic V_κ genes exhibit a very unusual distribution of nucleotide substitutions. Seven of the ten substitutions found among 940 bases are clustered in a 39 base stretch encoding the first complementarity-determining region and the second framework region of the protein. We suggest that this cluster of substitutions was generated by a gene conversion in which a small segment of one gene was replaced with the homologous segment from another V_κ gene.