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      Exploring Supernumeraries - A New Marker for Screening of B-Chromosomes Presence in the Yellow Necked Mouse Apodemus flavicollis

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          Abstract

          Since the density of simple sequence repeats (SSRs) may vary between different chromosomes of the same species in eukaryotic genomes, we screened SSRs of the whole genome of the yellow necked mouse, Apodemus flavicollis, in order to reveal SSR profiles specific for animals carrying B chromosomes. We found that the 2200 bp band was amplified by primer (CAG) 4AC to a highly increased level in samples with B chromosomes. This quantitative difference (B-marker) between animals with (+B) and without (0B) B chromosomes was used to screen 20 populations (387 animals). The presence/absence of Bs was confirmed in 96.5% of 342 non mosaic individuals, which recommends this method for noninvasive B-presence detection. A group of 45 animals with mosaic and micro B (μB) karyotypes was considered separately and showed 55.6% of overall congruence between karyotyping and molecular screening results. Relative quantification by qPCR of two different targeted sequences from B-marker indicated that these B-specific fragments are multiplied on B chromosomes. It also confirms our assumption that different types of Bs with variable molecular composition may exist in the same individual and between individuals of this species. Our results substantiate the origin of Bs from the standard chromosomal complement. The B-marker showed 98% sequence identity with the serine/threonine protein kinase VRK1 gene, similarly to findings reported for Bs from phylogenetically highly distant mammalian species. Evolutionarily conserved protein-coding genes found in Bs, including this one in A. flavicollis, could suggest a common evolutionary pathway.

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          Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification.

          E Zietkiewicz, A. Rafalski, D Labuda (1994)
          Simple sequence repeats (SSR), or microsatellites, are ubiquitous in eukaryotic genomes. Here we demonstrate the utility of microsatellite-directed DNA fingerprinting by polymerase chain reaction (PCR) amplification of the interrepeat region. No sequencing is required to design the oligonucleotide primers. We tested primers anchored at 3' or 5' termini of the (CA)n repeats, extended into the flanking sequence by 2 to 4 nucleotide residues [3'-anchored primers: (CA)8RG, (CA)8RY, and (CA)7RTCY; and 5'-anchored primers: BDB(CA)7C, DBDA(CA)7, VHVG(TG)7 and HVH(TG)7T]. Radioactively labeled amplification products were analyzed by electrophoresis, revealing information on multiple genomic loci in a single gel lane. Complex, species-specific patterns were obtained from a variety of eukaryotic taxa. Intraspecies polymorphisms were also observed and shown to segregate as Mendelian markers. Inter-SSR PCR provides a novel fingerprinting approach applicable for taxonomic and phylogenetic comparisons and as a mapping tool in a wide range of organisms. This application of (CA)n repeats may be extended to different microsatellites and other common dispersed elements.
          Article 0 comments Cited 381 times – based on 0 reviews     Review now
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            Differential distribution of simple sequence repeats in eukaryotic genome sequences.

            M Katti, P. Ranjekar, V Gupta (2001)
            Complete chromosome/genome sequences available from humans, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, and Saccharomyces cerevisiae were analyzed for the occurrence of mono-, di-, tri-, and tetranucleotide repeats. In all of the genomes studied, dinucleotide repeat stretches tended to be longer than other repeats. Additionally, tetranucleotide repeats in humans and trinucleotide repeats in Drosophila also seemed to be longer. Although the trends for different repeats are similar between different chromosomes within a genome, the density of repeats may vary between different chromosomes of the same species. The abundance or rarity of various di- and trinucleotide repeats in different genomes cannot be explained by nucleotide composition of a sequence or potential of repeated motifs to form alternative DNA structures. This suggests that in addition to nucleotide composition of repeat motifs, characteristic DNA replication/repair/recombination machinery might play an important role in the genesis of repeats. Moreover, analysis of complete genome coding DNA sequences of Drosophila, C. elegans, and yeast indicated that expansions of codon repeats corresponding to small hydrophilic amino acids are tolerated more, while strong selection pressures probably eliminate codon repeats encoding hydrophobic and basic amino acids. The locations and sequences of all of the repeat loci detected in genome sequences and coding DNA sequences are available at http://www.ncl-india.org/ssr and could be useful for further studies.
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              Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences.

              Klaus Mayer, Nils Stein, Marie Kubaláková … (2012)
              Supernumerary B chromosomes are optional additions to the basic set of A chromosomes, and occur in all eukaryotic groups. They differ from the basic complement in morphology, pairing behavior, and inheritance and are not required for normal growth and development. The current view is that B chromosomes are parasitic elements comparable to selfish DNA, like transposons. In contrast to transposons, they are autonomously inherited independent of the host genome and have their own mechanisms of mitotic or meiotic drive. Although B chromosomes were first described a century ago, little is known about their origin and molecular makeup. The widely accepted view is that they are derived from fragments of A chromosomes and/or generated in response to interspecific hybridization. Through next-generation sequencing of sorted A and B chromosomes, we show that B chromosomes of rye are rich in gene-derived sequences, allowing us to trace their origin to fragments of A chromosomes, with the largest parts corresponding to rye chromosomes 3R and 7R. Compared with A chromosomes, B chromosomes were also found to accumulate large amounts of specific repeats and insertions of organellar DNA. The origin of rye B chromosomes occurred an estimated ∼1.1-1.3 Mya, overlapping in time with the onset of the genus Secale (1.7 Mya). We propose a comprehensive model of B chromosome evolution, including its origin by recombination of several A chromosomes followed by capturing of additional A-derived and organellar sequences and amplification of B-specific repeats.
              Article 0 comments Cited 89 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Andreas Houben: Role: Editor
                Journal
                Journal ID (nlm-ta): PLoS One
                Journal ID (iso-abbrev): PLoS ONE
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosone
                Title: PLoS ONE
                Publisher: Public Library of Science (San Francisco, CA USA )
                ISSN (Electronic): 1932-6203
                Publication date (Electronic): 23 August 2016
                Publication date Collection: 2016
                Volume: 11
                Issue: 8
                Electronic Location Identifier: e0160946
                Affiliations
                [1 ]Department of Genetic Research, Institute for Biological Research “Siniša Stanković”, University of Belgrade, Belgrade, Serbia
                [2 ]Molekulare Zytogenetik, Institut für Humangenetik und Anthropologie, Universitätsklinikum, Jena, Germany
                Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), GERMANY
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                • Conceptualization: VB GS.

                • Formal analysis: VB GS JB.

                • Funding acquisition: MV.

                • Investigation: MR NK TL.

                • Methodology: GS VB.

                • Project administration: MV.

                • Resources: MV TL.

                • Supervision: MV.

                • Validation :MV JB.

                • Visualization: JB.

                • Writing – original draft: VB GS.

                • Writing – review & editing: VB GS.

                Article
                Publisher ID: PONE-D-16-02016
                DOI: 10.1371/journal.pone.0160946
                PMC ID: 4994964
                PubMed ID: 27551940
                SO-VID: 902deac9-1ca5-4ad4-a26a-6faafefe84a5
                Copyright © © 2016 Bugarski-Stanojević et al
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                Date received : 18 January 2016
                Date accepted : 27 July 2016
                Page count
                Figures: 6, Tables: 1, Pages: 18
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100004564, Ministarstvo Prosvete, Nauke i Tehnolokog Razvoja;
                Award ID: 173003
                Award Recipient :
                This work was supported by the Ministry of Education and Science of Serbia ( http://www.mpn.gov.rs/nauka), Contract No. 173003. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Research Article
                Subject: Biology and Life Sciences
                Subject: Cell Biology
                Subject: Chromosome Biology
                Subject: Chromosomes
                Subject: Biology and Life Sciences
                Subject: Genetics
                Subject: Cytogenetics
                Subject: Karyotypes
                Subject: Biology and life sciences
                Subject: Molecular biology
                Subject: Molecular biology techniques
                Subject: Sequencing techniques
                Subject: Sequence analysis
                Subject: DNA sequence analysis
                Subject: Research and analysis methods
                Subject: Molecular biology techniques
                Subject: Sequencing techniques
                Subject: Sequence analysis
                Subject: DNA sequence analysis
                Subject: Biology and Life Sciences
                Subject: Computational Biology
                Subject: Genome Analysis
                Subject: Sequence Assembly Tools
                Subject: Biology and Life Sciences
                Subject: Genetics
                Subject: Genomics
                Subject: Genome Analysis
                Subject: Sequence Assembly Tools
                Subject: Biology and Life Sciences
                Subject: Molecular Biology
                Subject: Molecular Biology Techniques
                Subject: Artificial Gene Amplification and Extension
                Subject: Polymerase Chain Reaction
                Subject: Research and Analysis Methods
                Subject: Molecular Biology Techniques
                Subject: Artificial Gene Amplification and Extension
                Subject: Polymerase Chain Reaction
                Subject: Biology and Life Sciences
                Subject: Biochemistry
                Subject: Enzymology
                Subject: Enzymes
                Subject: Protein Kinases
                Subject: Serine-Threonine Kinases
                Subject: Biology and Life Sciences
                Subject: Biochemistry
                Subject: Proteins
                Subject: Enzymes
                Subject: Protein Kinases
                Subject: Serine-Threonine Kinases
                Subject: Research and Analysis Methods
                Subject: Cytogenetic Techniques
                Subject: Fluorescent in Situ Hybridization
                Subject: Biology and Life Sciences
                Subject: Molecular Biology
                Subject: Molecular Biology Techniques
                Subject: Molecular Probe Techniques
                Subject: Probe Hybridization
                Subject: Fluorescent in Situ Hybridization
                Subject: Research and Analysis Methods
                Subject: Molecular Biology Techniques
                Subject: Molecular Probe Techniques
                Subject: Probe Hybridization
                Subject: Fluorescent in Situ Hybridization
                Subject: Research and Analysis Methods
                Subject: Database and Informatics Methods
                Subject: Database Searching
                Subject: Sequence Similarity Searching
                Custom metadata
                Data Availability All relevant data are within the paper and its Supporting Information files.

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