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Non-random expression of ribosomal DNA units in a grasshopper showing high intragenomic variation for the ITS2 region.
Insect Mol Biol. 2015 Jun; 24(3):319-30.IM

Abstract

We analyse intragenomic variation of the ITS2 internal transcribed spacer of ribosomal DNA (rDNA) in the grasshopper Eyprepocnemis plorans, by means of tagged PCR 454 amplicon sequencing performed on both genomic DNA (gDNA) and RNA-derived complementary DNA (cDNA), using part of the ITS2 flanking coding regions (5.8S and 28S rDNA) as an internal control for sequencing errors. Six different ITS2 haplotypes (i.e. variants for at least one nucleotide in the complete ITS2 sequence) were found in a single population, one of them (Hap4) being specific to a supernumerary (B) chromosome. The analysis of both gDNA and cDNA from the same individuals provided an estimate of the expression efficiency of the different haplotypes. We found random expression (i.e. about similar recovery in gDNA and cDNA) for three haplotypes (Hap1, Hap2 and Hap5), but significant underexpression for three others (Hap3, Hap4 and Hap6). Hap4 was the most extremely underexpressed and, remarkably, it showed the lowest sequence conservation for the flanking 5.8-28S coding regions in the gDNA reads but the highest conservation (100%) in the cDNA ones, suggesting the preferential expression of mutation-free rDNA units carrying this ITS2 haplotype. These results indicate that the ITS2 region of rDNA is far from complete homogenization in this species, and that the different rDNA units are not expressed at random, with some of them being severely downregulated.

Authors+Show Affiliations

Departamento de Genética, Universidad de Granada, Granada, Spain.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

25565136

Citation

Ruiz-Estévez, M, et al. "Non-random Expression of Ribosomal DNA Units in a Grasshopper Showing High Intragenomic Variation for the ITS2 Region." Insect Molecular Biology, vol. 24, no. 3, 2015, pp. 319-30.
Ruiz-Estévez M, Ruiz-Ruano FJ, Cabrero J, et al. Non-random expression of ribosomal DNA units in a grasshopper showing high intragenomic variation for the ITS2 region. Insect Mol Biol. 2015;24(3):319-30.
Ruiz-Estévez, M., Ruiz-Ruano, F. J., Cabrero, J., Bakkali, M., Perfectti, F., López-León, M. D., & Camacho, J. P. (2015). Non-random expression of ribosomal DNA units in a grasshopper showing high intragenomic variation for the ITS2 region. Insect Molecular Biology, 24(3), 319-30. https://doi.org/10.1111/imb.12158
Ruiz-Estévez M, et al. Non-random Expression of Ribosomal DNA Units in a Grasshopper Showing High Intragenomic Variation for the ITS2 Region. Insect Mol Biol. 2015;24(3):319-30. PubMed PMID: 25565136.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Non-random expression of ribosomal DNA units in a grasshopper showing high intragenomic variation for the ITS2 region. AU - Ruiz-Estévez,M, AU - Ruiz-Ruano,F J, AU - Cabrero,J, AU - Bakkali,M, AU - Perfectti,F, AU - López-León,M D, AU - Camacho,J P M, Y1 - 2015/01/07/ PY - 2015/1/8/entrez PY - 2015/1/8/pubmed PY - 2016/3/19/medline KW - Amplicon sequencing KW - B chromosomes KW - ITS2 KW - rDNA expression SP - 319 EP - 30 JF - Insect molecular biology JO - Insect Mol Biol VL - 24 IS - 3 N2 - We analyse intragenomic variation of the ITS2 internal transcribed spacer of ribosomal DNA (rDNA) in the grasshopper Eyprepocnemis plorans, by means of tagged PCR 454 amplicon sequencing performed on both genomic DNA (gDNA) and RNA-derived complementary DNA (cDNA), using part of the ITS2 flanking coding regions (5.8S and 28S rDNA) as an internal control for sequencing errors. Six different ITS2 haplotypes (i.e. variants for at least one nucleotide in the complete ITS2 sequence) were found in a single population, one of them (Hap4) being specific to a supernumerary (B) chromosome. The analysis of both gDNA and cDNA from the same individuals provided an estimate of the expression efficiency of the different haplotypes. We found random expression (i.e. about similar recovery in gDNA and cDNA) for three haplotypes (Hap1, Hap2 and Hap5), but significant underexpression for three others (Hap3, Hap4 and Hap6). Hap4 was the most extremely underexpressed and, remarkably, it showed the lowest sequence conservation for the flanking 5.8-28S coding regions in the gDNA reads but the highest conservation (100%) in the cDNA ones, suggesting the preferential expression of mutation-free rDNA units carrying this ITS2 haplotype. These results indicate that the ITS2 region of rDNA is far from complete homogenization in this species, and that the different rDNA units are not expressed at random, with some of them being severely downregulated. SN - 1365-2583 UR - https://www.unboundmedicine.com/medline/citation/25565136/Non_random_expression_of_ribosomal_DNA_units_in_a_grasshopper_showing_high_intragenomic_variation_for_the_ITS2_region_ L2 - https://doi.org/10.1111/imb.12158 DB - PRIME DP - Unbound Medicine ER -