Polymorphism of Aeromonas spp. tRNA intergenic spacers

We investigated the length polymorphism of the intergenic spacers lying between tRNA genes of Aeromonas spp. A total of 69 strains representing all known genomic species of Aeromonas were used in the study. tDNA-PCR patterns were examined by Dice coefficient (S(D)) and unweighted pair group method of clustering (UPGMA). The strains were allocated into 15 groups at a similarity level of 70%. The strains belonging to seven genomic species: A. hydrophila (HG 1), A. caviae (HG 4), A. sobria (HG 7), A. veronii (HG 8/10), A. encheleia (HG 16), A. popoffii (HG 17), and A. culicicola (HG 18) formed distinct clusters. Our study revealed a genetic heterogeneity of the following species: A. bestiarum, A. salmonicida, A. media, A. eucrenophila, A. jandaei, A. schubertii, and A. allosaccharophila.     

Nucleotide sequence of intergenic and external transcribed spacers of rDNA of diploid wheat Triticum urartu Thum. ex Candil

The primary structure of intergenic non-transcribed and external transcribed spacers of rDNA of diploid wheat Triticum urartu, cloned in pTu3 plasmid 2402 b.p. long was determined. The intergenic non-transcribed rDNA spacer of Tr. urartu was shown to consist of 8 subrepeats with an average of 133 b.p. long, heterogeneous in length and nucleotide sequence. A number of repeated sequences was revealed within each subrepeat. While comparing nucleotide sequences of rDNA subrepeats of Tr. urartu and Tr. aestivum a high homology was found (up to 82%). A high similarity between these plant species was also found in the promoter region and in the external transcribed rDNA spacer. Suppression of the nucleolar organizer of 1A chromosome in the presence of 1B and 6B chromosomes of Tr. aestivum is supposed to be connected with the existence of a great number of subrepeats in the intergenic non-transcribed rDNA spacer of B genome donors in polyploid wheat species of turgidum-aestivum row.     

The distribution of diploids and polyploids of the Scilla scilloides complex in Korea

A total of 3 384 individuals of Scilla scilloides Druce were sampled from 40 natural populations at 35 different localities over the Korean Peninsula and analysed cytogenetically. The following cytogenetic types were found: AA (19.6%), AABB (72.4%), ABBB (4.3%), AABBB (3.0%) and aneuploids (0.8%). Of these, AA was found in 9 populations along the west side of the Korean Peninsula facing the Yellow Sea and on Yeongdo and Jeju Islands. Type AABB, the most common type in the complex, was found in 33 natural populations on the Korean Peninsula and Jeju Island. The distributions of ABBB and AABBB are restricted to the southern part of the Korean Peninsula and Jeju Island; they were found in 8 natural populations. In southern Korea the above four types showed overlapping distribution and two or three were often found growing together.Genome A, occurring in the three allopolyploids in the Korean Peninsula, was the same as that in allopolyploids in Japan. However, genome A occurring as AA diploids was karyotypically different from that in the allopolyploids. On the basis of distribution patterns and cytological features, the origin of the allopolyploids is discussed.     

Coevolution of A and B genomes in allotetraploid Triticum dicoccoides.

Data is presented on the coevolution of A and B genomes in allotetraploid wheat Triticum dicoccoides (2n = 4x = 28, genome AABB) obtained by genomic in situ hybridization (GISH). Probing chromosomes of T. dicoccoides with DNA from the proposed A/B diploid genome ancestors shows evidence of enriching A-genome with repetitive sequences of B-genome type. Thus, ancestral S-genome sequences have spread throughout the AB polyploid genome to a greater extent than have ancestral A-genome sequences. The substitution of part of the A-genome heterochromatin clusters by satellite DNA of the B genome is detected by using the molecular banding technique. The cause may be interlocus concerted evolution and (or) colonization. We propose that the detected high level of intergenomic invasion in old polyploids might reflect general tendencies in speciation and stabilization of the allopolyploid genome.     

The distribution of diploids and polyploids of theScilla scilloides complex in the northeastern district of China

A cytological analysis was made of 1504 individuals ofScilla scilloides Druce from the northeastern district of China. In terms of genome combination four cytotypes were found: AA (90.95%), AAAA (0.07%), AABB (8.92%) and AABB+2 (0.07%). In the cytotypes A and B denote genome A (x=8) and genome B (x=9), respectively. Most of 18 natural populations examined consist of one cytotype: indeed, all individuals examined of 15 of the populations are AA diploids, those of one population AABB allotetraploids, and individuals examined of two other populations have two cytotypes each, AA and AAAA, and AABB and AABB+2. In karyotype the genome A of the AA and AAAA was different from that of the AABB, and a direction of morphological change of chromosomes in the genome A is discussed in light of results of hybridization experiments reported elsewhere. Taken together with information available for the distribution of different cytotypes in China, Korea and Japan, the results of the present study support the view of Maekawa thatScilla scilloides was native to mainland China and lately introduced to Japan.     

Phylogenetic reconstruction of Aegilops section Sitopsis and the evolution of tandem repeats in the diploids and derived wheat polyploids.

The evolution of 2 tandemly repeated sequences Spelt1 and Spelt52 was studied in Triticum species representing 2 evolutionary lineages of wheat and in Aegilops sect. Sitopsis, putative donors of their B/G genomes. Using fluorescence in situ hybridization we observed considerable polymorphisms in the hybridization patterns of Spelt1 and Spelt52 repeats between and within Triticum and Aegilops species. Between 2 and 28 subtelomeric sites of Spelt1 probe were detected in Ae. speltoidies, depending on accession. From 8 to 12 Spelt1 subtelomeric sites were observed in species of Timopheevi group (GAt genome), whereas the number of signals in emmer/aestivum accessions was significantly less (from 0 to 6). Hybridization patterns of Spelt52 in Ae. speltoides, Ae. longissima, and Ae. sharonensis were species specific. Subtelomeric sites of Spelt52 repeat were detected only in T. araraticum (T. timopheevii), and their number and chromosomal location varied between accessions. Superimposing copy number data onto our phylogenetic scheme constructed from RAPD data suggests 2 major independent amplifications of Spelt52 and 1 of Spelt1 repeats in Aegilops divergence. It is likely that the Spelt1 amplification took place in the ancient Ae. speltoides before the divergence of polyploid wheats. The Spelt52 repeat was probably amplified in the lineage of Ae. speltoides prior to divergence of the allopolyploid T. timopheevii but after the divergence of T. durum. In a separate amplification event, Spelt52 copy number expanded in the common ancestor of Ae. longissima and Ae. sharonensis.     

Evolution of the rpoB-psbZ region in fern plastid genomes: notable structural rearrangements and highly variable intergenic spacers

Background  

The rpoB-psbZ (BZ) region of some fern plastid genomes (plastomes) has been noted to go through considerable genomic changes. Unraveling its evolutionary dynamics across all fern lineages will lead to clarify the fundamental process shaping fern plastome structure and organization.     

Selective constraint in intergenic regions of human and mouse genomes.

We aligned and analyzed 100 pairs of complete, orthologous intergenic regions from the human and mouse genomes (average length approximately 12 000 nucleotides). The alignments alternate between highly similar segments and dissimilar segments, indicating a wide variation of selective constraint. The average number of selectively constrained nucleotides within a mammalian intergenic region is at least 2000. This is threefold higher than within a nematode intergenic region and at least twofold higher than the number of selectively constrained nucleotides coding for an average protein. Because mammals possess only two- to threefold more proteins than Caenorhabditis elegans, the higher complexity of mammals might be primarily because of the functioning of intergenic DNA.     

Nor loci analysis in progenies of plants regenerated from the scutellar callus of bread-wheat

Summary Progenies of plants regenerated from scutellar callus of bread wheat (Triticum aestivum L.) were analysed for the organization of the intergenic spacer of the rRNA genes, located at the sites of the nucleolar organizer region (Nor loci). Sexual progenies derived from the regenerated plants of three wheat cultivars were subjected to this analysis. The respective DNAs were digested with the restriction endonuclease TaqI, and probed with a specific rDNA fragment by Southern blothybridization. The intergenic rDNA spacer could thus be characterized for each of the three cultivars. Thirty-eight progeny plants of the cultivars Chinese Spring and Miriam were found to be stable in their organisation of the Nor loci: no changes relative to the Nor of control plants from these cultivars were revealed. On the other hand, three progeny plants of ND7532 showed reduction in the number of the rDNA spacers. Since no variability in the Nor loci could be revealed among control ND7532 plants, this seems to indicate that the changes in the progeny of regenerated plants resulted from the in vitro culture of the scutellar callus. Grain glutenin and gliadin profiles of sexual progenyplants derived from scutellar calli of Chinese Spring, of Miriam as well as of ND7532 were identical to the respective control plants of these cultivars, indicating low (or no) somaclonal variation in these grain proteins in the analyzed plants.     

genodive version 3.0: Easy‐to‐use software for the analysis of genetic data of diploids and polyploids

genodive version 3.0 is a user‐friendly program for the analysis of population genetic data. This version presents a major update from the previous version and now offers a wide spectrum of different types of analyses. genodive has an intuitive graphical user interface that allows direct manipulation of the data through transformation, imputation of missing data, and exclusion and inclusion of individuals, population and/or loci. Furthermore, genodive seamlessly supports 15 different file formats for importing or exporting data from or to other programs. One major feature of genodive is that it supports both diploid and polyploid data, up to octaploidy (2n = 8x) for some analyses, but up to hexadecaploidy (2n = 16x) for other analyses. The different types of analyses offered by genodive include multiple statistics for estimating population differentiation (φ_ST, F_ST, F?_ST, G_ST, G?_ST, G??_ST, D_est, R_ST, ρ), analysis of molecular variance‐based K‐means clustering, Hardy–Weinberg equilibrium, hybrid index, population assignment, clone assignment, Mantel test, Spatial Autocorrelation, 23 ways of calculating genetic distances, and both principal components and principal coordinates analyses. A unique feature of genodive is that it can also open data sets with nongenetic variables, for example environmental data or geographical coordinates that can be included in the analysis. In addition, genodive makes it possible to run several external programs (lfmm , structure , instruct and vegan ) directly from its own user interface, avoiding the need for data reformatting and use of the command line. genodive is available for computers running Mac OS X 10.7 or higher and can be downloaded freely from: http://www.patrickmeirmans.com/software .     

Highly rearranged and size‐variable chloroplast genomes in conifers II clade (cupressophytes): evolution towards shorter intergenic spacers

Although conifers are of immense ecological and economic value, bioengineering of their chloroplasts remains undeveloped. Understanding the chloroplast genomic organization of conifers can facilitate their bioengineering. Members of the conifer II clade (or cupressophytes) are highly diverse in both morphologic features and chloroplast genomic organization. We compared six cupressophyte chloroplast genomes (cpDNAs) that represent four of the five cupressophyte families, including three genomes that are first reported here (Agathis dammara, Calocedrus formosana and Nageia nagi). The six cupressophyte cpDNAs have lost a pair of large inverted repeats (IRs) and vary greatly in size, organization and tRNA copies. We demonstrate that cupressophyte cpDNAs have evolved towards reduced size, largely due to shrunken intergenic spacers. In cupressophytes, cpDNA rearrangements are capable of extending intergenic spacers, and synonymous mutations are negatively associated with the size and frequency of rearrangements. The variable cpDNA sizes of cupressophytes may have been shaped by mutational burden and genomic rearrangements. On the basis of cpDNA organization, our analyses revealed that in gymnosperms, cpDNA rearrangements are phylogenetically informative, which supports the ‘gnepines’ clade. In addition, removal of a specific IR influences the minimal rearrangements required for the gnepines and cupressophyte clades, whereby Pinaceae favours the removal of IRB but cupressophytes exclusion of IRA. This result strongly suggests that different IR copies have been lost from conifers I and II. Our data help understand the complexity and evolution of cupressophyte cpDNAs.     

Phylogenetic analysis of C, M, N, and U genomes and their relationships with Triticum and other related genomes as revealed by LMW-GS genes at Glu-3 loci

Phylogenetic relationships between the C, U, N, and M genomes of Aegilops species and the genomes of common wheat and other related species were investigated by using three types of low-molecular-weight glutenin subunit (LMW-GS) genes at Glu-3 loci. A total of 20 LMW-GS genes from Aegilops and Triticum species were isolated, including 11 LMW-m type and 9 LMW-i type genes. Particularly, four LMW-m type and three LMW-i type subunits encoded by the genes on the C, N, and U genomes possessed an extra cysteine residue at conserved positions, which could provide useful information for understanding phylogenetic relationships among Aegilops and Triticum genomes. Phylogenetic trees constructed by using either LMW-i or the combination of LMW-m and LMW-s, as well as analysis of all the three types of LMW-GS genes together, demonstrated that the C and U genomes were closely related to the A genome, whereas the N and M genomes were closely related to the D genome. Our results support previous findings that the A genome was derived from Triticum uratu, the B genome was from Aegilops speltoides, and the D genome was from Aegilops tauschii. In addition, phylogenetic relationships among different genomes analysed in this study support the concept that Aegilops is not monophyletic.     

Chromosomal localization and characterization of rDNA loci in the Brassica A and C genomes.

Using fluorescence in situ hybridization, we located ribosomal DNA loci on prometaphase chromosomes of the diploid species Brassica rapa and Brassica oleracea and their amphidiploid Brassica napus. Based on comparisons of chromosome morphology and hybridization patterns, we characterized the individual B. napus rDNA loci according to their presumed origins in the Brassica A and C genomes. As reported in other studies, the sum of rDNA loci observed on B. rapa (AA genome) and B. oleracea (CC genome) chromosomes was one greater than the total number of loci seen in their amphidiploid B. napus (AACC). Evidence is presented that this reduction in B. napus rDNA locus number results from the loss of the smallest A genome rDNA site in the amphidiploid.     

A PCR-based amplification method retaining the quantitative difference between two complex genomes

With the increasing emergence of genome-wide analysis technologies (including comparative genomic hybridization (CGH), expression profiling on microarrays, differential display (DD), subtractive hybridization, and representational difference analysis (RDA)), there is frequently a need to amplify entire genomes or cDNAs by PCR to obtain enough material for comparisons among target and control samples. A major problem with PCR is that amplification occurs in a nonlinear manner and reproducibility is influenced by stray impurities. As a result, when two complex DNA populations are amplified separately, the quantitative relationship between two genes after amplification is generally not the same as their relation before amplification. Here we describe balanced PCR, a procedure that faithfully retains the difference among corresponding amplified genes by using a simple principle. Two distinct genomic DNA samples are tagged with oligonucleotides containing both a common and a unique DNA sequence. The genomic DNA samples are pooled and amplified in a single PCR tube using the common DNA tag. By mixing the two genomes, PCR loses the ability to discriminate among the different alleles and the influence of impurities is eliminated. The PCR-amplified pooled samples can be separated using the DNA tag unique to each individual genomic DNA sample. The principle of this method has been validated with synthetic DNA, genomic DNA, and cDNA applied on microarrays. By removing the bias of PCR, this method allows a balanced amplification of allelic fragments from two complex DNAs even after three sequential rounds of PCR. This balanced PCR approach should allow genetic analysis in minute laser-microdissected tissues, paraffin-embedded archived material, or single cells.     

PCR-based RFLP analysis of an intergenic spacer region in cpDNA of some wild wheat species

Wheat is one of the basic food materials for humans and other animals. Continuing studies into breeding new species, which are suitable for agriculture, are based on the contention that the restricting factors are the effects of the nuclear genes. Such focusing of studies on the nuclear genome leads to restriction on the information on organelle DNAs, although cytoplasmic genetic factors are effective on the morphological, physiological and reproductive features of plants. Restriction fragment length polymorphism analysis (RFLP) of chloroplast DNA (cpDNA) has become a powerful tool for studying phylogenetic relationships. In this study, seven wheat species, belonging to Aegilops and Triticum , were studied. An intergenic spacer region of cpDNA was digested by six different restriction endonuclease enzymes, and fragments so obtained were investigated using the agarose gel electrophoresis technique. Discussion on the phylogenetic relationships among Triticum and Aegilops species is based on the resultant data.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 148 , 305–310.     

Characterization of intergenic spacers in two rrn operons of Enterococcus hirae ATCC 9790.

Two DNA restriction enzyme fragments coding for the 3' termini of 16S rRNA, the 5' termini of 23S rRNA, and the intergenic spaces between them in Enterococcus hirae ATCC 9790 were cloned and sequenced. The intergenic space of one of these genes contains a tRNA(Ala) sequence, whereas the other does not. Nevertheless, the intergenic spaces contain several regions that exhibit high levels of sequence homology and are capable of forming structures with similar base pairs. An analysis of Southern blots of chromosomal DNA cut with one and two restriction enzymes indicated that E. hirae has a total of six rrn operons.     

利用基于PCR的分子标记区分普通小麦-提莫菲维小麦渐渗系

采用定位于小麦2B染色体上的72对分子标记对含小麦抗白粉病基因Pm6的8份普通小麦（T.aestivum L.）-提莫菲维（T.timopheevii zhuk.）渐渗系材料进行分析, 通过分子标记标图确定8份材料中渗入的提莫菲维小麦染色体片段的大小, 同时结合连锁图谱对这些材料进行了遗传和物理标图。参考本研究所用的分子标记在染色体2B上的定位结果, Pm6基因被位于2B 染色体长臂近末端2BL-6区域, 提莫菲维小麦2G染色体渐渗片断长度由短到长排列顺序为: IGV1-465相似文献