Two dispersed highly repeated DNA families of Triturus vulgaris meridionalis (Amphibia, Urodela) are widely conserved among Salamandridae

Cloning and genetic variability of a HindIII repetitive DNA in Acrossocheilus paradoxus (Cyprinidae)

Thirty clones of a highly repetitive HindIII fragment of DNA from seven populations of Acrossocheilus paradoxus (Cyprinidae) were isolated and sequenced. The fragment represents a tandemly repeated sequence, with a monomeric unit of 270 bp, amounting to 0.08-0.10% of the fish genome. Higher units of this monomer appear as a ladder in Southern blots. The HindIII satellite DNA family is conserved in three genera of the Cyprinidae. Variation in nucleotide sequences of this repetitive fragment, which is A+T-rich, is distributed both within individuals and among populations. High overall nucleotide divergence (dij = 0.056 +/- 0.001) was detected among clones of the HindIII satellite DNAs of Acrossocheilus paradoxus. Based on the molecular clock hypothesis, the maximum evolutionary rate was estimated to be 5.3 x 10(-7) substitutions per site per year. Lineage sorting may have contributed to the genetic heterogeneity within individuals and populations. Cladistic analyses indicated a closer phylogeographic relationship between populations of the central and south regions in Taiwan.

Variability of DNA methylation pattern in somatic and germ cells in male newt (Amphibia, Urodela) Triturus cristatus carnifex

In a survey of several mammalian genomes, namely humans, rodents and bovines, the differences in the 5-methylcytosine (m5C) content show that repeated DNA sequences from sperm were undermethylated and from various somatic tissues were heavily methylated. This report shows a pattern of methylation in male newt (Amphibia, Urodela) Triturus cristatus carnifex (T. c. c.) unlike that so far described by other authors in mammals. Using methylation sensitive and insensitive enzymes (HpaII and MspI) and successive 3' terminal labelling (fill-in), we found a greater degree of DNA methylation in premeiotic germ and sperm cells compared to somatic tissue such as hepatocytes. Furthermore the degree of total DNA methylation in spermatozoa appears somewhere between premeiotic germ cells and somatic tissue. Blot hybridization shows that two highly conserved repetitive sequences in amphibian T. c. c., pTvm1 and pTvm8, contribute significantly to the degree of DNA methylation, suggesting a function for these sequences, such as a role in transcriptional regulation.

Satellite DNA sequences as taxonomic markers in nematodes of agronomic interest

The success of alternative crop protection practices against plant-parasitic nematodes using host resistance genes depends fundamentally upon identification of the species and pathotypes effectively controlled by these genes. In the same way, biological control of insects by entomopathogenic nematodes will work only if the nematode strains used are indeed active against the pests to be eliminated. For these applications, the accurate interspecific and/or intraspecific identification of nematodes is thus of outstanding importance. Here, Eric Grenier, Philippe Castagnone-Sereno and Pierre Abad discuss the recent use of satellite DNA sequences in nematode taxonomic diagnostics.

A family of centromeric satellite DNAs from the European brown frog Rana graeca italica

Digestion of Rana graeca italica DNA with Asp 718I produces highly repetitive fragments of 281 and 385 bp that were cloned and sequenced. The shorter fragment corresponds to the unit repeat (RgiS1b) of a satellite DNA. The longer fragment was found to be part of a 494-bp repeat of another satellite DNA (RgiS1a) that was cloned intact as an EcoRV fragment. RgiS1b is 97% homologous to RgiS1a, from which it seems to be derived by a single deletion. Among all species tested, only the related brown frog Rana dalmatina contained homologous repetitive DNA. The overall number of RgiS1a and RgiS1b repeats per R. graeca italica haploid genome was estimated to be 2.7 x 10(5). RgiS1a and RgiS1b repeats are organized in separate arrays, but repetitive units formed by various combinations of the two repeats were also observed on Southern blots. The amount of these extra repeats varies greatly among animals from the same population, representing a rare case of individual variability in the satellite DNA organization. FISH with probes specific for both satellites, or for RgiS1a only, labeled the centromeric and pericentromeric heterochromatin of all chromosomes. This indicated that RgiS1a and RgiS1b are interspersed within the same heterochromatic regions of the chromosomes.

Cloning and characterization of a repetitive 1.9 Kb HindIII DNA fragment from Crotalus durissus terrificus genome

Eukaryote genomes are endowed with varying quantities of repeated DNA families. These families show different patterns of conservation among species, copy numbers, chromosomal distribution, and transcription. Characterization of repeated DNA sequences could help to understand the genome anatomy and organization or be used in molecular systematics and molecular evolution studies. We describe here a repetitive DNA sequence of the HindIII family present in the genome of the rattlesnake Crotalus durissus terrificus. In Brazil, the family Crotalus is comprised only by one species durissus, which include several subspecies. The number and distribution of these subspecies are controversial. In the present study, the genomic DNA of a female rattlesnake was digested with HindIII resulting in a strong 1.9 Kb band. A partial genomic library was constructed from the 1.9 Kb DNAs rescued from the agarose gel after HindIII digestion and ligated to the vector pGEM3Zf(+) (Promega). Analysis of 69 clones, 44 hybridized with the 1.9 Kb probe isolated from one of the clones-clone 76, indicating that the DNA isolated from this clone should represent the 1.9 Kb HindIII fragment. This 1.9 Kb HindIII DNA was completely characterized by sequencing.

Cloning and characterization of a highly conserved satellite DNA sequence specific for the phytoparasitic nematode Bursaphelenchus xylophilus

The phytoparasitic nematode, Bursaphelenchus xylophilus, contains an unusually abundant satellite DNA which constitutes up to 30% of its genome. It is represented as a tandemly repeated MspI-site-containing sequence with a monomeric unit of 160 bp. Thirteen monomers were cloned and sequenced. The consensus sequence is 62% A+T-rich, with the presence of direct and inverted repeat clusters. Monomers of the sequence are very similar, showing on average 3.9% divergence from the calculated consensus. The results suggest that some homogenizing mechanism is acting to maintain the homogeneity of this satellite DNA despite its abundance and that it is not transcribed.

Conservation of a highly repeated DNA family of Aedes albopictus among mosquito genomes (Diptera: Culicidae)

The genomic organization and chromosomal localization of a cloned 0.79-kb highly repeated DNA fragment, H-115, isolated from Aedes albopictus has been examined. The cloned fragment is a part of a larger unit of 1.86 kb that is tandemly repeated in the Ae. albopictus genome. The H-115 family of sequences are located at the intercalary position on chromosome 1 in Ae. albopictus. Similar patterns of in situ and Southern blot hybridization results are obtained in Ae. aegypti, Ae. seatoi, Ae. flavopictus, Ae. polynesiensis, Ae. Alcasidi, and Ae. katherinensis. The H-115 sequences are widely conserved in Culicidae and are found in Haemagogus equinus, Tripteroides bambusa, and Anopheles quadrimaculatus by hybridization under high stringency conditions. The H-115 sequences are also tandemly repeated in Hg. equinus with a monomer unit of 1.86 kb and in Tp. bambusa with a slightly diverged monomer unit of 1.90kb. In Anopheles quadrimaculatus, the H-115 sequences are dispersed throughout the genome. Partial sequence analysis shows that the H-115 insert is 62% AT and contains two perfect inverted repeats and numerous perfect direct repeats. The occurrence of inverted repeats with potential to form intrastrand palindromic structure suggests that the H-115 family of sequences may be involved in chromatin condensation.

Microdissection and cloning of DNA from landmark loops of amphibian lampbrush chromosomes

Microdissection of the "globular" and "granular" landmark loops of Pleurodeles lampbrush chromosomes and subsequent cloning of their DNA yielded several recombinant clones. The 6.6-kb insert of one of them was subcloned and the 600 bp of one subclone was characterized by Southern and slot hybridizations as well as by sequencing. This sequence, designated p130B, was shown to belong to a class of moderately repetitive DNA. RNA expression of this sequence was investigated by in situ hybridization of p130B to the nascent transcripts of lateral loops. Results showed that: (1) the same transcripts were not always found in matrices of landmarks exhibiting the same morphological features; (2) the same transcripts were expressed in loops of different morphological types. Based on these results we suggest that even if there is a morphological similarity of landmark loops, this does not reflect total similarity of their transcripts.

Characterisation of a short, highly repeated and centromerically localised DNA sequence in crested and marbled newts of the genus Triturus

A 32-33 bp highly repeated DNA sequence, TkS1, has been isolated from genomic DNA of the newt Triturus karelini digested with the restriction endonucleases HaeIII or AluI. TkS1 is known to be localised in the centromeric heterochromatin of all the chromosomes in T. karelini and the related species T. cristatus. TkS1 has been shown to be present in varying amounts in the genomic DNA of a range of species of Triturus, including representatives of the two main subgenera Triturus and Palaeotriton. A programme of sequencing of monomers, dimers and trimers of TkS1 was carried out in order to determine the level of conservation of the sequence within and between species of Triturus. Altogether 204 monomer (32/33 bp) clones were made of TkS1 from three individuals of T. karelini, and one individual each of T. cristatus, T. carnifex, T. dobrogicus and T. marmoratus, all members of the subgenus Triturus and the cristatus species group. A number of dimer (64 bp) and trimer (96 bp) clones were also made from DNA of a single specimen of T. karelini digested with HaeIII or AluI. Three distinct types of TkS1 were identified in all species examined, except for T. marmoratus where only two of the types were found. The types were distinguished on the basis of certain recurring divergent patterns in monomers sequenced from T. karelini. Type 1 is mainly characterised by the presence of an AluI site at positions 24-27 and type 3 mainly by the presence of an additional base (C) at position 14. Type 2 normally lacks the AluI site and the C at position 14, as well as having a number of other distinguishing features. TkS1 and its three types have remained remarkably constant in sequence since before the divergence of T. marmoratus from other species in the cristatus species group, about 10 million years ago. Examination of all 204 monomer clones and comparison with consensus sequences for the three types shows less than 5% divergence at any one position in the sequence. There is good evidence from examination of dimer and trimer clones of TkS1 that the different types are intermingled with each other, and all three types are likely to be present on all chromosomes. Dimeric (64 bp) TkS1 clones constructed from AluI fragments of T. karelini DNA show evidence of a trimeric (96 bp) "supertype" with the pattern type 1-type 3-type 1 that is much more common than would be expected on a random basis.(ABSTRACT TRUNCATED AT 400 WORDS)