Genetic markers for Atlantic salmon (Salmo salar L.): single locus inheritance and joint segregation analyses of minisatellite (VNTR) DNA loci

Relatively few genetic markers are available for detailed studies of Atlantic salmon. The detection of 12 distinct minisatellite DNA loci in this species (by 10 Atlantic salmon and brown trout derived probes) and subsequent inheritance analyses in two half-sib families are reported here. Disomic Mendelian inheritance was confirmed at all loci. Only a single aberrant progeny genotype (at Ssa -A60) was observed among 138 progeny screened. None of the loci was sex-linked. The tight linkage association Str -A22/1 with Str -A22/2, previously reported for brown trout, was found to be conserved in the Atlantic salmon genome. An additional male-specific linkage group, Ssa -A34 with Str -A9/2, was also noted. These highly polymorphic loci should find widespread use as chromosomal, individual, familial and, probably, population markers.     

Natural DNA sequences complementary in the same direction: evidence for parallel biosynthesis?

Based on both the occurrence of families of DNA sequences complementary in the same direction in different genomes and the physical possibility of DNA forming a parallel double helix, we postulate an unusual enzymatic synthesis of parallel DNA on a DNA template from its 5-end. We discuss the assumed evolutionary aspects of this problem and suggest ways to check the hypothesis.     

Genome modifications in protoplast-derived tobacco plants: Contents of repetitive DNA sequences

Plasticity of the tobacco genome was studied by testing the DNAs of protoplast-derived regenerants with three different repetitive DNA sequences by the method of quantitative DNA/DNA hybridizations. A large population of 91 regenerants belonging to 35 different protoclones was analysed and a high degree of heterogeneity in the contents of the different DNA repeats was detected. The contents of middle repetitive sequences of two types were more stable or changed in the same direction, while the highly repetitive sequence varied independently and displayed a significant reduction in comparison with the two other sequences. Comparing the variation within the subpopulations of plants of the same clonal origin and the variation among the protoclones led to a conclusion that the pre-existing DNA variability in the starting plant material and/or thein vitro stress during the very early stages of protoclone regeneration played a decisive role in the formation of modified genomes in regenerants.     

原癌基因ras在玉米中同源序列的检出及其荧光原位杂交定位

原癌基因ｒａｓ是动物中抑制细胞凋亡的重要基因之一。以人的ｒａｓ基因为探针,通过Ｓｏｕｔｈｅｒｎ杂交技术,确证玉米和水稻中均含有ｒａｓ基因的同源序列;同时,运用荧光原位杂交技术,首次对ｒａｓ基因在玉米中的同源序列进行了定位。结果表明：ｒａｓ探针在第２号和第７号染色体上均检出了杂交信号,信号检出率分别为１０．８５％和１４．１５％,杂交信号与着丝粒的百分距离分别为 ５４．９２± １．９０和 ９４．６２± ２．７７。上述研究结果为植物细胞凋亡的进一步研究提供了线索和帮助。     

Phylogenetic Analysis of AA-genome Oryza Species (Poaceae) Based on Chloroplast, Mitochondrial, and Nuclear DNA Sequences

Species in the genus Oryza (Poaceae) contain 10 genomic types and are distributed in pan-tropics of the world. To explore phylogenetic relationships of Oryza species having the AA-genome, DNA sequences of the chloroplast trnL intron and trnL-trnF spacer, mitochondrial nad1 intron 2, and nuclear internal transcribed spacer were analyzed, based on materials from 6 cultivated (O. sativa and O. glaberrima) and 13 wild accessions, in addition to a CC-genome species (O. officinalis) that was used as an outgroup. Analyses of the combined sequence data set from different sources provide a much better resolution of the AA-genome species than the individual data set, indicating the limitation of a single gene in phylogenetic reconstruction. The phylogeny based on the combined data set demonstrated an apparent grouping of the AA-genome Oryza species that was well associated with their geographic origin, although the Australian O. meridionalis showed its affinity with the African species. The geographic pattern of the phylogenetic relationship was probably attributed to the frequent genetic exchange and introgression among the AA-genome species from the same continents. In addition, Asian cultivated rice O. sativa showed its close relation to O. rufipogon and O. nivara, whereas African cultivated rice O. glaberrima was closely linked to O. barthii and O. longistaminata, indicating the independent domestication of the two cultivated species in different geographic locations.     

Role of an N-Terminal Splice Segment in the Activation of the Cation Channel TRPM2 by ADP-Ribose and Hydrogen Peroxide

In the dysfunctional splice variant TRPM2-ΔN, a stretch of 20 amino acids (aa 537–556) is missing within the N-terminal cytosolic tail of the cation channel TRPM2. The ΔN-stretch overlaps with two IQ-like calmodulin-binding domains. Moreover, it contains two PxxP motifs implicated in protein–protein interactions. Here, we constructed variants to test whether any of these motifs may explain why TRPM2-ΔN does not respond to stimulation with either ADP ribose or hydrogen peroxide. Each of the two IQ-motifs could be removed without loss of channel function. Similarly, deletion of either one or both PxxP motifs had no effect. Moreover, the single point mutation D543E associated with bipolar disorder does not change the activation of TRPM2. We conclude that no functional role can be attributed to any of the structural motifs within the ΔN-stretch that may be a spacer segment for other functional sites in the N terminus.     

Matrix-associated DNA from maize is enriched in repetitive sequences

In order to elucidate some features of the topological organization of DNA within the plant nucleus, DNA fragments involved in the attachment of the DNA loops to the nuclear matrix in maize were studied. The matrix-associated DNA from dry embryo and meristematic cells after extensive digestion with DNase I and high salt treatment was about 2% of the total DNA, sized within the range of 50 and 250 bp. This DNA was found to be enriched in repetitive DNA sequences, both for nuclei from dry embryo and meristematic cells. The loop size of the DNA in cells of Zea mays appeared to be between 5 and 25 kbp.Abbreviations EDTA Diamino-ethanetetraacetic acid - EtBr Ethidium bromide - LIS Lithium diiodosalicylate - PMSF Phenylmethylsulfonyl fluoride - SDS Sodium dodecyl sulfate     

The colonization history of Olea europaea L. in Macaronesia based on internal transcribed spacer 1 (ITS-1) sequences, randomly amplified polymorphic DNAs (RAPD), and intersimple sequence repeats (ISSR)

Phylogenetic relationships in the Olea europaea complex and the phylogeography of 24 populations of the Macaronesian olive (O. europaea ssp. cerasiformis) were assessed by using three molecular markers: nuclear ribosomal internal transcribed spacer 1 (ITS-1) sequences, randomly amplified polymorphic DNAs (RAPD), and intersimple sequence repeats (ISSR). Parsimony analysis of the ITS-1 sequences and Neighbour-joining (NJ) analyses of RAPD and ISSR banding variation revealed four major lineages in the O. europaea complex: (1) ssp. cuspidata; (2) ssp. cerasiformis from Madeira; (3) ssp. laperrinei; and (4) ssp. cerasiformis from the Canary Islands plus ssp. europaea. These results provide unequivocal support for two independent dispersal events of Olea to the Madeira and Canary Islands. Molecular and morphological evidence led to recognition of two separate olive taxa in Macaronesia, to date included in ssp. cerasiformis. NJ analyses of the combined RAPD and ISSR data suggest that the colonization of the Canaries by O. europaea may have followed an east to west stepping-stone model. An interisland dispersal sequence can be recognized, starting from the continent to Fuerteventura, Gran Canaria, Tenerife, La Gomera, and finally La Palma. High dispersal activity of the lipid-rich Olea fruits by birds in the Mediterranean region is congruent with multiple dispersal of olives to Macaronesia and successive colonization of the archipelagos. The observation of strong genetic isolation between populations of different islands of the Canary Islands suggests, however, that subsequent interisland dispersal and establishment has been very rare or may not have occurred at all.     

Detection and correction of assembly errors of rice Nipponbare reference sequence

A complete and high‐quality genome reference sequence of an organism provides a solid foundation for a wide research community and determines the outcomes of relevant genomic, genetic, molecular and evolutionary research. Rice is an important food crop and a model plant for grasses, and therefore was the first chosen crop plant for whole genome sequencing. The genome of the japonica representative rice variety, Nipponbare, was sequenced using a gold standard, map‐based clone‐by‐clone strategy. However, although the Nipponbare reference sequence (RefSeq) has the best quality for existing crop genome sequences, it still contains many assembly errors and gaps. To improve the Nipponbare RefSeq, first a robust method is required to detect the hidden assembly errors. Through alignments between BAC‐end sequences (BESs) embedded in the Nipponbare bacterial artificial chromosome (BAC) physical map and the Nipponbare RefSeq, we detected locations on the Nipponbare RefSeq that were inversely matched with BESs and could therefore be candidates for spurious inversions of assembly. We performed further analysis of five potential locations and confirmed assembly errors at those locations; four of them, two on chr4 and two on chr11 of the Nipponbare RefSeq (IRGSP build 5), were found to be caused by reverse repetitive sequences flanking the locations. Our approach is effective in detecting spurious inversions in the Nipponbare RefSeq and can be applied for improving the sequence qualities of other genomes as well.