Repetitive sequences: cause for variation in genome size and chromosome morphology in the genus Oryza

Large variation in genome size as determined by the nuclear DNA content and the mitotic chromosome size among diploid rice species is revealed using flow cytometry and image analyses. Both the total chromosomal length (r_0.939) and the total chromosomal area (r_0.927) correlated well with the nuclear DNA content. Among all the species examined, Oryza australiensis (E genome) and O. brachyantha (F genome), respectively, were the largest and smallest in genome size. O. sativa (A genome) involving all the cultivated species showed the intermediate genome size between them. The distribution patterns of genome-specific repetitive DNA sequences were physically determined using fluorescence in situ hybridization (FISH). O. brachyantha had limited sites of the repetitive DNA sequences specific to the F genome. O. australiensis showed overall amplification of genome-specific DNA sequences throughout the chromosomes. The amplification of the repetitive DNA sequences causes the variation in the chromosome morphology and thus the genome size among diploid species in the genus Oryza.     

Absence of repetitive DNA sequences associated with sex chromosomes in natural populations of the Trinidad guppy (Poecilia reticulata)

The genus Poecilia has been widely studied as a model for the evolution of sex chromosomes. In the course of molecular studies on population genetic structure and sexual selection in the Trinidad guppy, we examined our preparations for male-linked, repetitive DNA polymorphisms. We have not obtained any evidence of male-specific polymorphisms, in contrast to an earlier study. Our results have significant implications for theories on the evolution of sex chromosomes.Correspondence to: F. Breden     

Lateral transfers of insertion sequences between Wolbachia,Cardinium and Rickettsia bacterial endosymbionts

Various bacteria live exclusively within arthropod cells and collectively act as an important driver of arthropod evolutionary ecology. Whereas rampant intra-generic DNA transfers were recently shown to have a pivotal role in the evolution of the most common of these endosymbionts, Wolbachia, the present study show that inter-generic DNA transfers also commonly take place, constituting a potent source of rapid genomic change. Bioinformatic, molecular and phylogenetic data provide evidence that a selfish genetic element, the insertion sequence ISRpe1, is widespread in the Wolbachia, Cardinium and Rickettsia endosymbionts and experiences recent (and likely ongoing) transfers over long evolutionary distances. Although many ISRpe1 copies were clearly expanding and leading to rapid endosymbiont diversification, degraded copies are also frequently found, constituting an unusual genomic fossil record suggestive of ancient ISRpe1 expansions. Overall, the present data highlight how ecological connections within the arthropod intracellular environment facilitate lateral DNA transfers between distantly related bacterial lineages.     

Nucleus Isthmi Is Required to Sustain Target Pursuit during Visually Guided Prey-Catching

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Characterization of 10 KDA prolamin genes in Phyllostachys aurea (Bambusoideae, Poaceae)

Prolamin is the dominant class of seed storage protein in grasses (Poaceae). Information on the 10 kDa multigene family coding for prolamins characteristic of the bambusoid-oryzoid grasses is limited. Two genes encoding 10 kDa prolamin were cloned and sequenced in the bambusoid species Phyllostachys aurea to assess the sequence diversity of this gene family in the oryzoid-bambusoid grasses. The genes, ~417 bp in length, were 96% similar at the DNA sequence level, differing in 12 base substitutions dispersed throughout the sequence. Eight of these mutations were nonsynonymous, leading to amino acid substitutions in the coding region, and one was nonsense, producing an amber stop codon. One gene had an open reading frame (ORF) of 139 amino acids, while the other gene had a shorter ORF (106 amino acids) due to the presence of a stop codon in the coding region and, thus, represents a pseudogene. Deduced proteins showed amino acid composition similar to that of rice. The study underscores the overall conserved nature of this multigene family and reflects considerable sequence divergence at the DNA and amino acid levels between the Oryza and the Phyllostachys genes. The systematic implication of the data is discussed in light of the inconsistent placement of Oryza in the Bambusoideae or Oryzoideae.     

Genome characterization of glucose-isomerase-producingStreptomyces sp. NCIM 2730: detection of sequences homologous to a rice repeat sequence

Restriction analysis of the genomic DNA from a high glucose/xylose-isomerase-yieldingStreptomyces sp. NCIM 2730 revealed a number of distinct bands on a background smear, indicating the occurrence of repeated DNA sequences in the genome. Optical renaturation analysis indicated that 25% of the genome comprised rapidly reannealing sequences with a copy number of 50 and a kinetic complexity of 3×10³. Hybridization of theStreptomyces genomic library with theStreptomyces DNA, supported the estimate of the repetitive DNA content derived from the re-association kinetics of the DNA. Hybridization of DNA from three differentStreptomyces species with a rice repetitive DNA probe revealed the presence of homologous sequences, which is a unique finding.M.S. Ghatge was and V.V. Deshpande and P.K. Ranjekar are with the Division of Biochemical Sciences, National Chemical Laboratory, Pune -41108, India; M.S. Ghatge is now with the Department of Microbiology & Molecular Biology, The University of Kansas Medical Center, 36th and Rainbow Blvd, Kansas City, Kansas - 66103, USA.     

Effect of carbon and nitrogen sources, pH and temperature on in vitro culture of several isolates of Amanita caesarea (Scop.:Fr.) Pers.

Several isolates were obtained from sporocarps of Amanita caesarea (Scop.: Fr.) Pers. associated with Quercus suber and Castanea sativa coming from the southwest of Spain. Culture conditions were optimized for these isolates. The largest radial growth was obtained at pH 6–7, and optimal growth temperature was 24–28°C depending on the isolate. Albumin bovine and nitrate produced the largest patch size diameters, but the greatest mycelium dry weight yields were obtained with ammonium. Mannitol produced the largest radial growth, and mannitol and glucose yielded the biggest mycelium dry weights. Although variations in growth behaviour between isolates were observed, only one internal spacer sequence–restriction fragment length polymorphism type was obtained.     

四个DNA 片段在山茶属分子系统学研究中的应用

选取山茶属14 个组中的10 组21 种植物对目前常用于属内种间的4 个DNA 片段( ITS、waxy 、trnLF
、rpL16) 进行序列测定。结果表明: ( 1) 来自叶绿体基因组的2 个片段( trnL- F、rpL 16) 其PCR 扩增和
测序都很容易, 但两者的进化速率都非常慢, 序列矩阵只有很少信息位点( trnL-F 含9 个, rpL16 为20
个) , 不能提供必要的系统发育信息。( 2) 来自核基因组的ITS 片段其PCR 产物比较容易获得, 但其序列
的测定存在较多问题。( 3) waxy 是来自核基因组的另一个片段, 其PCR 扩增因受模板DNA 的数量和质量
的影响很大而有一定难度, 但其进化速率较快, 序列矩阵具有较多信息位点( 92 个) , 并且在山茶属是单
拷贝, 这对于解决山茶属这类具有许多近缘物种的类群的系统关系有重要价值。基于tsnL- F、rpL16 和
waxy 三组数据所建分子系统树支持山茶属为一单系, 但属下系统由于取样等原因有待进一步研究。