Evolution of ribosomal DNA-derived satellite repeat in tomato genome

<p>Abstract</p> <p>Background</p> <p>Tandemly repeated DNA, also called as satellite DNA, is a common feature of eukaryotic genomes. Satellite repeats can expand and contract dramatically, which may cause genome size variation among genetically-related species. However, the origin and expansion mechanism are not clear yet and needed to be elucidated.</p> <p>Results</p> <p>FISH analysis revealed that the satellite repeat showing homology with intergenic spacer (IGS) of rDNA present in the tomato genome. By comparing the sequences representing distinct stages in the divergence of rDNA repeat with those of canonical rDNA arrays, the molecular mechanism of the evolution of satellite repeat is described. Comprehensive sequence analysis and phylogenetic analysis demonstrated that a long terminal repeat retrotransposon was interrupted into each copy of the 18S rDNA and polymerized by recombination rather than transposition via an RNA intermediate. The repeat was expanded through doubling the number of IGS into the 25S rRNA gene, and also greatly increasing the copy number of type I subrepeat in the IGS of 25-18S rDNA by segmental duplication. Homogenization to a single type of subrepeat in the satellite repeat was achieved as the result of amplifying copy number of the type I subrepeat but eliminating neighboring sequences including the type II subrepeat and rRNA coding sequence from the array. FISH analysis revealed that the satellite repeats are commonly present in closely-related <it>Solanum </it>species, but vary in their distribution and abundance among species.</p> <p>Conclusion</p> <p>These results represent that the dynamic satellite repeats were originated from intergenic spacer of rDNA unit in the tomato genome. This result could serve as an example towards understanding the initiation and the expansion of the satellite repeats in complex eukaryotic genome.</p

Marker-Assisted Evaluation of Two Powdery Mildew Resistance Candidate Genes in Korean Cucumber Inbred Lines

Two genes, CsLRR-RPK2 (CsGy5G015660) and CsaMLO8 (Csa5G623470), have been considered as powdery mildew (PM) resistance genes in cucumbers. In this study, we evaluated the involvement of the alleles of these two genes in PM resistance in 100 commercial Korean cucumber inbred lines. To achieve this, we developed cleaved amplified polymorphic sequences (CAPS) and InDel markers from CsLRR-RPK2 and CsaMLO8. Genotyping analysis indicated that the CsLRR-RPK2-CAPS marker showed a stronger correlation with the PM-resistant phenotype, with an 84% consistency compared to the CsaMLO8-InDel marker. The use of the CsaMLO8-InDel marker showed a 70% consistency between phenotype and genotype results. It was proposed that the CsLRR-RPK2-CAPS marker successfully eliminated PM-susceptible inbred lines, since both genotype and phenotype results were 100% identical. Furthermore, the present study revealed that the introduction of one of these alleles is probably enough to confer PM resistance in cucumbers. However, seven PM-resistant inbred lines harbored either CsaMLO8 or CsLRR-RPK2 alleles, indicating that there is another PM-resistant resource(s) besides CsaMLO8- and CsLRR-RPK2&ndash;originated resistance in the commercial Korean inbred lines. Our results provide reliable evidence confirming two PM-resistant candidate genes for the detection of PM resistance resources in cucumber inbred lines

Taxonomic notes on Phyllocnistis citrella (Lepidoptera: Gracillariidae) with genital structures and DNA barcode from Korea

Until now, only one species, Phyllocnistis citrella Stainton, of the genus Phyllocnistis belonging to the family Gracillariidae is listed in Korea, without available information on its identification and morphology, which is now a very serious and important insect pest species in southern area. This study was carried out to provide the illustration with genital structure and DNA barcode data for rapid monitoring, which has not been presented in this country to date

Preliminary survey of indigenous parasites associated with Phyllocnistis citrella Stainton (Lepidoptera, Gracillariidae) in Jeju, Korea

In order to identify the parasitoids of Phyllocnistis citrella Stainton [commonly known as the citrus leafminer (CLM)], we collected CLM larvae and pupae in the Seogwipo area of Jeju-do, identified parasitoid species, and determined parasitism rates. In May 2014, nine parasitoids were identified from the CLM larvae and pupae that infested 300 fresh citrus leaves, yielding a parasitism rate of 3.03%. In August 2014, 53 parasitoid wasps emerged from 203 collected CLM larvae and pupae, indicating that the parasitism rate rose to 25.84%. The parasitoid wasps observed in May 2014 consisted of five individuals of Sympiesis sp. 1 (Eulophidae), one Pnigalio sp. 1 (Eulophidae), and three Aphelinus sp. 1 (Aphelinidae). The highest proportion of the parasitic wasps that emerged in August 2014 were Sympiesis sp. 1 (n = 49), followed by Quadrastichus sp. 1 (Eulophidae; n = 4). This study documents the seasonal parasitism rate of parasitic wasps and basic characteristics of each parasitoid in Korea

Integration of Cytogenetic and Genetic Linkage Maps Unveils the Physical Architecture of Tomato Chromosome 2

We report the integration of the linkage map of tomato chromosome 2 with a high-density bacterial artificial chromosome fluorescence in situ hybridization (BAC–FISH)-based cytogenetic map. The euchromatic block of chromosome 2 resides between 13 and 142 cM and has a physical length of 48.12 μm, with 1 μm equivalent to 540 kb. BAC–FISH resolved a pair of loci that were 3.7–3.9 Mb apart and were not resolved on the linkage map. Most of the regions had crossover densities close to the mean of ∼200 kb/cM. Relatively hot and cold spots of recombination were unevenly distributed along the chromosome. The distribution of centimorgan/micrometer values was similar to the previously reported recombination nodule distribution along the pachytene chromosome. FISH-based physical maps will play an important role in advanced genomics research for tomato, including map-based cloning of agronomically important traits and whole-genome sequencing