Duplicated plastid and triplicated cytosolic isozymes of triosephosphate isomerase in maize (Zea mays L.)

We studied electrophoretic variation and inheritance of triosephosphate isomerase (TPI) isozymes in maize (Zea mays L.). In contrast to most diploid plants, in maize, TPI exists as multiple isozymes in both the plastid and cytosolic subcellular compartments. Phenotypes result from the overlay of two independent sets of isozymes and allozymes, representing the plastid (encoded by the nuclear genes Tpi1 and Tpi2) and cytosolic (encoded by Tpi3, Tpi4, and Tpi5) systems. All possible intragenic and intergenic dimeric enzymes are formed between polypeptides within each subcellular compartment. No heterodimers are formed between plastid and cytosolic polypeptides. Extensive surveys of accessions of land races and inbred lines revealed 22 allelic variants for the five loci. Most alleles have been formally validated by segregation analysis. We describe two null alleles at Tpi4, distinguished by their relative abilities to form intergenic heterodimers with polypeptides specified by Tpi3 and Tpi5. Linkage analyses and crosses with B-A translocation stocks were effective in determining the chromosome locations of all five loci. Duplicated genes for both the plastid and cytosolic isozymes were localized to genomic regions that possess numerous other redundant sequences. We placed Tpi1 on the long arm of chromosome 7, approximately 23 centimorgans (cM) distal to g11; we localized its duplicate--Tpi2--17 cM distal to v4 on the long arm of chromosome 2. The triplicate loci encoding cytosolic TPIs reside on chromosomes 3 and 8. Tpi4 is approximately equidistant (11 cM) from d1 and Lg3, near the centromere of chromosome 3. Tpi3 and Tpi5 are located on distal ends of the most poorly marked maize chromosome; Tpi3 is 29 cM distal to Idh 1 on 8L, and Tpi5 is on 8S or near the centromere on 8L. In contrast to most duplicated maize sequences, which often occur in parallel linkages on different chromosomes, Tpi3 and Tpi5 provide an example of intrachromosomal gene duplication. Several of the Tpi loci are located in sparsely mapped regions of the genome, and Tpi1 is the first isozyme marker for chromosome 7.     

INTERGENIC EXCHANGE, GEOGRAPHIC ISOLATION, AND THE EVOLUTION OF BIOLUMINESCENT COLOR FOR PYROPHORUS CLICK BEETLES

Gene duplication is an evolutionary process in which the emergent property of the whole can become greater and different than the sum of its parts. One potential outcome for gene duplication is for loci to evolve different, yet related functions. In this case, intergenic exchange can shuffle blocks of differentiated nucleotides between paralogues to create new alleles and phenotypes rather than simply homogenize loci. Bioluminescent click beetles in the genus Pyrophorus (Coleoptera: Elateridae) provide an opportunity to explore the creative potential of intergenic exchange for gene family evolution. Pyrophorus beetles bioluminesce different light colors from a pair of dorsal light organs and a ventral light organ. The light organs are under the separate genetic control of dorsal and ventral luciferase loci. Here, we report that intergenic exchange is common between dorsal and ventral loci for beetles from Jamaica ( P. plagiophthalamus ), the Dominican Republic ( P. mellifluous ), Belize ( P. luscus ), and Trinidad ( P. noctilucus ). We also present evidence that periods of past geographic isolation for beetles on Jamaica, probably acting in concert with selection, built differentiated blocks of substitutions within dorsal and ventral P. plagiophthalamus luciferase loci. Gene flow and intergenic exchange subsequently shuffled these substitutions between dorsal and ventral loci to produce new color phenotypes on Jamaica, including a yellow–green polymorphism. We discuss the possibility of a previously unrecognized emergent evolutionary property of intergenic exchange for luciferase involving cycles of bioluminescent color change related to differences in selective constrains acting on dorsal versus ventral loci. We also explore whether intergenic exchange may commonly create novel variation and the potential for cyclic evolution in other multigene family systems.     

Gene mapping of isozyme loci in chum salmon

Recombination values were used to calculate the gene-centromere map distances for four electrophoretically detected loci, Aat3, Idh1, Idh4, and Mpi, in chum salmon (Oncorhynchus keta). We also report the results from 39 pairwise examinations for joint segregation for 10 loci in nine testcross families. Only two loci assorted nonrandomly--either Aat1 or Aat2 with Gpt. Gene-centromere distances for Aat3 and Mpi differed significantly from those reported previously for rainbow trout (Salmo gairdneri), a closely related species. This difference indicates either the presence of chromosome rearrangements or a different rate of recombination between the species. These results contrast with the conservation of linkage distances previously reported within and between other salmonid genera.     

海带(Laminaria japonica)丝状体遗传多样性的比较研究

采用垂直板式聚丙烯酰胺凝胶电泳技术对分别来自中国青岛与日本北海道海带(Laminaria japonica)丝状体的6种酶系统（乙醇脱氢酶、谷氨酸脱氢酶、异柠檬酸脱氢酶、乳酸脱氢酶、山梨醇脱氢酶和超氧化物歧化酶）进行了检测,发现存在22个基因位点,分析了不同来源海带丝状体的遗传多样性与遗传分化程度。结果表明：日本北海道海带丝状体的预期杂合度、每个位点有效等位基因数等遗传参数均大于中国青岛海带丝状体。对日本北海道海带丝状体与中国青岛海带丝状体的遗传相似系数和遗传距离进行了计算分析,显示两者发生了遗传分化。日本北海道海带丝状体的遗传多样性高于中国青岛海带丝状体。研究结果还发现在中国青岛海带丝状体的Idh、Ldh 和Sdh中,以及日本北海道海带丝状体的Adh、Gdh、Idh、Ldh、Sdh和Sod中存在着不同迁移率的不等距双带酶,可能由特殊基因控制,并集中在第3个基因位点上。     

Chromosomal localization of 5S and 18S rDNA in five species of subgenus Strobus and their implications for genome evolution of Pinus

BACKGROUND AND AIMS: Studying the genome structure of pines has been hindered by their large genomes and uniform karyotypes. Consequently our understanding of the genome organization and evolutionary changes in different groups of pines is extremely limited. However, techniques are now available that can surmount these difficulties. The purpose of this study was to exploit some of these techniques to characterize the genome differentiation between the two subgenera of Pinus: Pinus and Strobus. METHODS: Double-probe fluorescence in-situ hybridization (FISH) was used to localize the 5S and 18S rDNA loci on chromosomes of five species from the subgenus Strobus: P. bungeana, P. koraiensis, P. armandii, P. wallichiana and P. strobus. * KEY RESULTS: The rDNA FISH pattern varied considerably among the five species, with P. bungeana being the most distinct. By comparing the results obtained with those of previous rDNA FISH studies of members of the subgenus Pinus, several general features of rDNA loci distribution in the genus Pinus can be discerned: (a) species of subgenus Strobus generally have more rDNA loci than species of subgenus Pinus, correlating with their larger genomes in the subgenus Strobus; (b) there is a clear differentiation in 5S and 18S rDNA loci linkage patterns between the two subgenera; (c) variations in the rDNA FISH pattern correlate with phylogenetic relationships among species within the subgenus; (d) P. bungeana has fewer 18S rDNA sites than other pines investigated to date, but they give intense signals, and may reflect the primary distribution of the 18S-25S rDNA loci in the genus. CONCLUSIONS: The stable differentiation in rDNA FISH pattern between the subgenera suggests that chromosomal rearrangements played a role in the splitting of the two subgenera, and transpositional events rather than major structural changes are likely responsible for the variable rDNA distribution patterns among species of the same subgenus with conserved karyotypes.     

Allozyme markers for the identification of Lecithochirium rufoviride and Lecithochirium furcolabiatum (Trematoda: Hemiuridae), parasites of Conger conger and Anguilla anguilla from Atlantic Spanish waters

The allozyme variation between 2 sympatric populations of Lecithochirium furcolabiatum and L. rufoviride was examined with the aim to investigate if the 2, morphologically similar, helminths are reproductively distinct. Three enzyme loci, Gpd, Pgm-1, and Idh were found to be diagnostic for the 2 species. These results support the conclusion that the worms are different biological species. Only the Gpi and Gdh loci showed no differences. Marked genetic subdivision was detected at the Idh locus in the L. rufoviride population. Given that the genotypic distribution at Pgm-I showed no significant deviations from Hardy-Weinberg expectations, it does not appear that the absence of heterozygotes for Idh was caused by the reproductive structure of the population. Although there are several other possible reasons for the deficiency of heterozygotes in natural populations, the existence of a new noninterbreeding group within the population studied constitutes a plausible explanation.     

Cross-species amplification of mitochondrial DNA sequence-tagged-site markers in conifers: the nature of polymorphism and variation within and among species in Picea

Primers previously developed to amplify specific non-coding regions of the mitochondrial genome in Angiosperms, and new primers for additional non-coding mtDNA regions, were tested for their ability to direct DNA amplification in 12 conifer taxa and to detect sequence-tagged-site (STS) polymorphisms within and among eight species in Picea. Out of 12 primer pairs, nine were successful at amplifying mtDNA in most of the taxa surveyed. In conifers, indels and substitutions were observed for several loci, allowing them to distinguish between families, genera and, in some cases, between species within genera. In Picea, interspecific polymorphism was detected for four loci, while intraspecific variation was observed for three of the mtDNA regions studied. One of these (SSU rRNA V1 region) exhibited indel polymorphisms, and the two others ( nad1 intron b/c and nad5 intron1) revealed restriction differences after digestion with Sau3AI (PCR-RFLP). A fourth locus, the nad4L- orf25 intergenic region, showed a multibanding pattern for most of the spruce species, suggesting a possible gene duplication. Maternal inheritance, expected for mtDNA in conifers, was observed for all polymorphic markers except the intergenic region nad4L- orf25. Pooling of the variation observed with the remaining three markers resulted in two to six different mtDNA haplotypes within the different species of Picea. Evidence for intra-genomic recombination was observed in at least two taxa. Thus, these mitotypes are likely to be more informative than single-locus haplotypes. They should be particularly useful for the study of biogeography and the dynamics of hybrid zones.     

Expansion and divergence of the GH locus between spider monkey and chimpanzee

Growth hormone (GH) has been previously described as showing distinct evolutionary stories between primates and other mammals. A burst of changes and successive amplification events took place in the primate lineage giving rise to a multigene family in the three Anthropoidea lineages. Polymerase chain reaction (PCR) was used to obtain the genes and the intergenic regions comprising the GH loci of the spider monkey (Ateles geoffroyi), a New-World primate, and of the chimpanzee (Pan troglodytes), an ape. The intergenic sequences of both species were screened by hybridization to detect copies of the Alu family, which have been implicated in the formation of the human GH locus. The GH locus of the spider monkey contains at least six GH-related genes, four of them were cloned. Likewise, five short intergenic sequences of approximately 3 kb were amplified and cloned. On the other hand, in the chimpanzee four new placental lactogen (PL) genes as well as four intergenic regions were amplified. Consequently, in this ape, six genes (two GHs, previously obtained, and four PLs) are clustered, separated by intergenic sequences of different lengths (two short ones of about 5 kb, and at least two long ones between 9 and 13 kb). The presence of Alu sequences within the intergenic regions of both GH loci corroborates the current hypothesis that they acted as a driving force for the locus expansion. GH sequence comparisons reveal that several gene-conversion events might have occurred during the formation of this genome region, which has undergone independent evolution in the three Anthropoidea branches. To establish the GH's evolutionary history may prove to be a difficult task due to these gene-conversion events.     

Monomorphism of isozyme loci in natural and cultivated amaranth (<Emphasis Type="Italic">Amaranthus</Emphasis> L.) populations

Electrophoretic spectra of alcohol dehydrogenase (ADH), glutamate dehydrogenase (GDH), malate dehydrogenase (MDH), isocitrate dehydrogenase (IDH), and malic enzyme (ME) in different amaranth populations has been studied using a starch gel electrophoresis. 93 populations and 4 cultivars of amaranth have been analyzed. Some populations have been proved to be polymorphic that provided a possibility of a genetic control of the above-mentioned enzymes. The isozyme variability of the studied amaranth populations is low; all studied loci are found to be monomorphic for 73 populations and 4 cultivars. Some populations demonstrate a polymorphism in separate loci (Adh, Mdh 2, Gdh, Idh 1, Idh 2, and Mod 2). The obtained results evidence the presence of a genetic monomorphism in amaranth concerning the loci studied.     

DNA sequence analysis of the defective interfering particles of bacteriophage f1.

Restriction mapping and nucleotide sequence analysis of several defective, interfering particles of bacteriophage f1 are described. These particles contain the nucleotide sequences corresponding to the carboxyl terminus of gene IV and the amino-terminus of gene II and the intergenic space between them. Tandem duplication of a portion of this intergenic space generates defective particles with novel nucleotide sequences not found in wild-type f1. This duplication is shown to contain the origin of complementary strand synthesis. Our results suggest that the duplication occurs at the site of gene II protein action, i.e. the origin of viral strand synthesis. A model is presented for the generation of these duplications in defective particles.     

Rapid expansion of microsatellite sequences in pines

Microsatellite persistence time and evolutionary change was studied among five species of pines, which included a pair of closely related species (Pinus sylvestris and Pinus resinosa) in the subgenus Pinus, their relative Pinus radiata, and another closely related species pair (Pinus strobus and Pinus lambertiana) in the subgenus Strobus. The effective population sizes of these species are known to have ranged from the very small bottlenecks of P. resinosa to vast populations of P. sylvestris. This background allowed us to place the microsatellite evolution in a well-defined phylogenetic setting. Of 30 loci originating from P. strobus and P. radiata, we were able to consistently amplify 4 in most of the these pine species. These priming sites had been conserved for over 100 Myr. The four microsatellites were sequenced in the five species. Flanking sequences were compared to establish that the loci were orthologous. All microsatellites had persisted in these species, despite very different population sizes. We found a recent microsatellite duplication: a closely related pair of loci in P. strobus, where the other four species had just one locus. On two independent occasions, the repeat area of this same microsatellite (locus RPS 105a/b) had grown from a very low repeat number to 15 or 17 in the last 10-25 Myr. Other parts of the same compound microsatellite had remained virtually unchanged. Locus PR 4.6 is known to be polymorphic in both P. radiata and P. sylvestris, but the polymorphism in the two species is due to different motifs. The very large pine genomes are highly repetitive, and microsatellite loci also occur as gene families.     

Correlation between the size of the intergenic regulatory region, the status of cytosine methylation of rRNA genes and nucleolar expression in wheat

Summary A large number of wheat rRNA genes are methylated at all the CCGG sites that are present in the intergenic regions. A smaller number of rRNA genes are not methylated at one or more CCGG sites. A subset of genes was found unmethylated at a specific CCGG site just downstream of the array of 135 by A repeats in the intergenic region. In all the genotypes studied, the rDNA loci with larger intergenic regions between their genes also possess a greater number of rRNA genes that are unmethylated at one or more CCGG sites in the intergenic regions than do the loci with shorter intergenic regions. In four genotypes (for which data were available), rDNA loci with longer intergenic regions had larger secondary constrictions on metaphase chromosomes, a measure of relative locus activity, than the loci with shorter intergenic regions. The results have been integrated into a model for the control of rDNA expression based on correlations between cytosine methylation patterns and the number of upstream 135 by repeats in intergenic regions. According to this model the 135 by repeats play a part in the control of gene activity by binding a protein(s) that is in limiting supply, thereby predisposing the neighbouring gene to become active preferentially.     

Isolation and Characterization of Schizosaccharomyces Pombe Mutants Affected in Mitotic Recombination

A haploid Schizosaccharomyces pombe strain carrying a heteroallelic duplication of the ade6 gene was used to isolate mitotic recombination-deficient mutants. Recombination between the different copies of the ade6 gene can lead to Ade+ segregants. These are observed as growing papillae when colonies of a suitable size are replicated onto selective medium. We isolated mutants which show an altered papillation phenotype. With two exceptions, they exhibit a decrease in the frequency of mitotic recombination between the heteroalleles of the duplication. The two other mutants display a hyper-recombination phenotype. The 12 mutations were allocated to at least nine distinct loci by recombination tests. Of the eight rec mutants analyzed further, six were also affected in mitotic intergenic recombination in the intervals cen2-mat or cen3-arg 1. No effect on mitotic intragenic recombination was observed. These data suggest that mitotic gene conversion and crossing over can be separated mutationally. Meiotic recombination occurs at the wild-type frequency in all mutants investigated.     

Variability and genetic differentiation among Anopheles (Ano.) intermedius Chagas, 1908 and Anopheles (Ano.) mattogrossensis Lutz & Neiva, 1911 (Diptera: Culicidae) from the Brazilian Amazon

Anopheles (Anopheles) intermedius and Anopheles (Ano.) mattogrossensis are Brazilian anopheline species belonging to the scarcely studied Anopheles subgenus. Few studies have been done on the genetic differentiation of these species. Both species have been found infected by Plasmodium and are sympatric with other anopheline species from the Nyssorhynchus subgenus. Eighteen enzymatic loci were analyzed in larval specimens of An. intermedius and An. mattogrossensis aiming to estimate the variability and genetic differentiation between these species. An. mattogrossensis population showed higher genetic variability (P = 44.4 and Ho = 0.081 +/- 0.031) than that of An. intermedius (P = 33.3 and Ho = 0.048 +/- 0.021). Most analyzed loci showed genotypic frequencies according to Hardy-Weinberg equilibrium, except for LAP1 and LAP2 in An. intermedius, and EST1 and PGM loci in An. mattogrossensis. The genetic distance between these species (D = 0.683) was consistent with the inter-specific values reported for Anopheles subgenus. We verified that the polymorphism and heterozygosity percentile values found in both species and compared to those in the literature, showed no relation between the level of isozyme variability and geographical distribution. The low variability found in these two species is probably more related to the niche they occupy than to their geographic distribution.     

Molecular markers for phylogenetic applications derived from comparative plastome analysis of Prunus species

Interspecific and intergeneric relationships of Prunus s.l. are still unclear due to low levels of genetic variation among species, and resulting partially unresolved phylogenetic inferences. Here we sequenced and compared six complete plastomes from two subgenera of Prunus in order to choose molecular markers to increase the amount of genetic variation suitable for inference of Prunus phylogeny. The plastomes range between 157 817 and 158 995 bp in length, and we found different levels of inverted repeat (IR) contraction among the three sampled subgenera of Prunus s.l. Most regions in Prunus plastomes considered individually provide low phylogenetic resolution at the subgenus or species level compared to a tree constructed using all 78 coding regions combined. We compared levels of variation among 206 coding regions and noncoding (intergenic and intron) plastid regions and inferred phylogenies from each region considered individually. We then chose using two regions together for future studies of relationships in Prunus, ycf1 and trnT-L, that display high to moderate levels of variation among coding and intergenic regions, respectively, and that individually permit inference of resolved species-level trees in Prunus with moderate to strong branch support. Considered together, these two regions allow inference of the same topology of Prunus inferred using all coding plastid regions combined, with comparable levels of tree support to the full plastome set. These two loci should therefore be useful as a plastid phylogenetic marker set for further inference of relationships within Prunus s.l.     

Phylogenetic relationships in West Mediterranean Scaritina (Coleoptera: Carabidae) inferred from mitochondrial COI sequences and karyotype analysis

The phylogenetic relationships of the West Mediterranean lineages of the subtribe Scaritina have been investigated by studying the mitochondrial cytochrome oxidase gene (COI) and the mitotic and meiotic chromosomes, including the localization of rDNA genes by fluorescence in situ hybridization. These sources of data are congruent and suggest the following conclusions: (1) the subgenus Parallelomorphus (genus Scarites ) is a monophyletic group according to molecular and karyotypic data, in agreement with its geographical distribution and morphological characters; (2) in the same genus, the subgenus Scallophorites seems to be monophyletic but includes two well-separated lineages – one represented by Scarites buparius (Forster, 1771) and Scarites occidentalis (Bedel, 1895) (both with multiple sex chromosomes), and one represented by Scarites hespericus (Dejean, 1831); (3) the nominal subgenus Scarites s.s . represented by Scarites eurytus (Fischer, 1828), is cladistically more closely related to subgenus Scallophorites than to subgenus Parallelomorphus ; (4) Distichus planus (Bonelli, 1813) belongs to a distinct clade that is well separated from Scarites, and shows more plesiomorphic states of COI sequence and chromosome number. In addition, the presence of two autapomorphies, such as rDNA sites located in the X chromosome, and an A + T rich intergenic spacer of about 120 bp between the stop codon of the COI gene and the tRNAleu, agree with the ranking of Distichus as a separate genus from Scarites .     

Cross-species amplification of Eucalyptus microsatellite loci

This study examined the interspecific amplification of nuclear microsatellite loci developed mainly for eucalypts in the subgenus Symphyomyrtus across five species within the second most speciose subgenus, subgenus Eucalyptus. A set of eight to 10 loci, depending on taxon, have been identified that are highly variable and easily scored. The successful transfer of microsatellite loci to these eucalypt species sidesteps the expensive and time-consuming development of species-specific microsatellite libraries. This primer set will enable the examination and cross-species comparison of the genetic resources of commercially and ecologically important members of the subgenus Eucalyptus.     

Alcohol dehydrogenase isozymes in grain sorghum (Sorghum bicolor): Evidence for a gene duplication

Two sets of alcohol dehydrogenase (ADH) bands are regularly observed in grain sorghum (Sorghum bicolor): set I is a permanent triplet; set II is variable, as either two or three bands. A faint set III is detected only when extracts from seeds subjected to anerobiosis are run in neutralpH gels. Dissociation-reassociation experiments reveal that the central band of the set I triplet is a heterodimer of the other two. Full-sib progeny analysis from selfed plants shows that the set II bands are doublets, with heterozygotes having only three apparent bands instead of four because of the similar mobilities of the fast-migrating isozyme specified by the slow allele and the slow isozyme specified by the fast allele. We propose a three-locus model as the best explanation of these patterns. Set I consists of the products of two loci and their intergenic heterodimer. Set III is specified by a third locus. Set II isozymes are the intergenic heterodimers of the two set I loci and the set III locus. This explanation is similar to that of Schwartz and Freeling for maize but suggests that the evolution ofSorghum includes a gene duplication of the homologue of theAdh-1 locus inZea. Supported by USDA Grant 59-2063-01522 to NCE and KWF.     

中华稻蝗四个种群的遗传分化

采用水平淀粉凝胶电泳技术研究中华稻蝗(Oxya chinensis)四个种群的12个基因座位,探讨其遗传分化.这四个种群分别采自内蒙古呼和浩特、山西代县、山西太原和陕西西安.Ck和Mdh-2在四个种群中均为单态,其余的基因座位至少在一个种群内有两个以上的等位基因;在Ldh和Mdh-1的等位基因频率呈现梯度分布趋势.多态基因座位百分率(P)和平均每个基因座位的等位基因数目(A)分别为58.3%-66.7%和2.2-2.8,平均杂合度为Ho=0.173-0.240.除Gpi,Hk-2,Idh,Ldh和Mdh-1在部分蝗虫种群符合Hardy-Weinberg平衡外,其余绝大多数基因座位的基因型频率显著偏离Hardy-Weinberg平衡.四个种群间FST平均值不存在显著差异(FST=0.0510,P＞0.05),结合高的Nei's遗传一致度(I＞0.97)可知,种群之间遗传分化不明显.我们认为人类的农业活动可能促进了种群间的基因交流,从而降低了分化程度[动物学报50(2)187-192,2004].