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Fine organization of genomic regions tagged to the 5S rDNA locus of the bread wheat 5B chromosome.
BMC Plant Biol. 2017 Nov 14; 17(Suppl 1):183.BP

Abstract

BACKGROUND

The multigene family encoding the 5S rRNA, one of the most important structurally-functional part of the large ribosomal subunit, is an obligate component of all eukaryotic genomes. 5S rDNA has long been a favored target for cytological and phylogenetic studies due to the inherent peculiarities of its structural organization, such as the tandem arrays of repetitive units and their high interspecific divergence. The complex polyploid nature of the genome of bread wheat, Triticum aestivum, and the technically difficult task of sequencing clusters of tandem repeats mean that the detailed organization of extended genomic regions containing 5S rRNA genes remains unclear. This is despite the recent progress made in wheat genomic sequencing. Using pyrosequencing of BAC clones, in this work we studied the organization of two distinct 5S rDNA-tagged regions of the 5BS chromosome of bread wheat.

RESULTS

Three BAC-clones containing 5S rDNA were identified in the 5BS chromosome-specific BAC-library of Triticum aestivum. Using the results of pyrosequencing and assembling, we obtained six 5S rDNA- containing contigs with a total length of 140,417 bp, and two sets (pools) of individual 5S rDNA sequences belonging to separate, but closely located genomic regions on the 5BS chromosome. Both regions are characterized by the presence of approximately 70-80 copies of 5S rDNA, however, they are completely different in their structural organization. The first region contained highly diverged short-type 5S rDNA units that were disrupted by multiple insertions of transposable elements. The second region contained the more conserved long-type 5S rDNA, organized as a single tandem array. FISH using probes specific to both 5S rDNA unit types showed differences in the distribution and intensity of signals on the chromosomes of polyploid wheat species and their diploid progenitors.

CONCLUSION

A detailed structural organization of two closely located 5S rDNA-tagged genomic regions on the 5BS chromosome of bread wheat has been established. These two regions differ in the organization of both 5S rDNA and the neighboring sequences comprised of transposable elements, implying different modes of evolution for these regions.

Authors+Show Affiliations

The Federal Research Center "Institute of Cytology and Genetics SB RAS", Novosibirsk, Russia.The Federal Research Center "Institute of Cytology and Genetics SB RAS", Novosibirsk, Russia. atos@bionet.nsc.ru.The Federal Research Center "Institute of Cytology and Genetics SB RAS", Novosibirsk, Russia.The Federal Research Center "Institute of Cytology and Genetics SB RAS", Novosibirsk, Russia.The Federal Research Center "Fundamentals of Biotechnology RAS", Moscow, Russia.The Federal Research Center "Fundamentals of Biotechnology RAS", Moscow, Russia.The Federal Research Center "Fundamentals of Biotechnology RAS", Moscow, Russia.The Federal Research Center "Fundamentals of Biotechnology RAS", Moscow, Russia. Faculty of Biology, Moscow State University, Moscow, Russia.The Federal Research Center "Institute of Cytology and Genetics SB RAS", Novosibirsk, Russia.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

29143604

Citation

Sergeeva, Ekaterina M., et al. "Fine Organization of Genomic Regions Tagged to the 5S rDNA Locus of the Bread Wheat 5B Chromosome." BMC Plant Biology, vol. 17, no. Suppl 1, 2017, p. 183.
Sergeeva EM, Shcherban AB, Adonina IG, et al. Fine organization of genomic regions tagged to the 5S rDNA locus of the bread wheat 5B chromosome. BMC Plant Biol. 2017;17(Suppl 1):183.
Sergeeva, E. M., Shcherban, A. B., Adonina, I. G., Nesterov, M. A., Beletsky, A. V., Rakitin, A. L., Mardanov, A. V., Ravin, N. V., & Salina, E. A. (2017). Fine organization of genomic regions tagged to the 5S rDNA locus of the bread wheat 5B chromosome. BMC Plant Biology, 17(Suppl 1), 183. https://doi.org/10.1186/s12870-017-1120-5
Sergeeva EM, et al. Fine Organization of Genomic Regions Tagged to the 5S rDNA Locus of the Bread Wheat 5B Chromosome. BMC Plant Biol. 2017 Nov 14;17(Suppl 1):183. PubMed PMID: 29143604.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Fine organization of genomic regions tagged to the 5S rDNA locus of the bread wheat 5B chromosome. AU - Sergeeva,Ekaterina M, AU - Shcherban,Andrey B, AU - Adonina,Irina G, AU - Nesterov,Michail A, AU - Beletsky,Alexey V, AU - Rakitin,Andrey L, AU - Mardanov,Andrey V, AU - Ravin,Nikolai V, AU - Salina,Elena A, Y1 - 2017/11/14/ PY - 2017/11/17/entrez PY - 2017/11/17/pubmed PY - 2018/3/2/medline KW - 5BS chromosome KW - 5S rDNA KW - BAC-clones KW - FISH KW - Polyploid wheat SP - 183 EP - 183 JF - BMC plant biology JO - BMC Plant Biol VL - 17 IS - Suppl 1 N2 - BACKGROUND: The multigene family encoding the 5S rRNA, one of the most important structurally-functional part of the large ribosomal subunit, is an obligate component of all eukaryotic genomes. 5S rDNA has long been a favored target for cytological and phylogenetic studies due to the inherent peculiarities of its structural organization, such as the tandem arrays of repetitive units and their high interspecific divergence. The complex polyploid nature of the genome of bread wheat, Triticum aestivum, and the technically difficult task of sequencing clusters of tandem repeats mean that the detailed organization of extended genomic regions containing 5S rRNA genes remains unclear. This is despite the recent progress made in wheat genomic sequencing. Using pyrosequencing of BAC clones, in this work we studied the organization of two distinct 5S rDNA-tagged regions of the 5BS chromosome of bread wheat. RESULTS: Three BAC-clones containing 5S rDNA were identified in the 5BS chromosome-specific BAC-library of Triticum aestivum. Using the results of pyrosequencing and assembling, we obtained six 5S rDNA- containing contigs with a total length of 140,417 bp, and two sets (pools) of individual 5S rDNA sequences belonging to separate, but closely located genomic regions on the 5BS chromosome. Both regions are characterized by the presence of approximately 70-80 copies of 5S rDNA, however, they are completely different in their structural organization. The first region contained highly diverged short-type 5S rDNA units that were disrupted by multiple insertions of transposable elements. The second region contained the more conserved long-type 5S rDNA, organized as a single tandem array. FISH using probes specific to both 5S rDNA unit types showed differences in the distribution and intensity of signals on the chromosomes of polyploid wheat species and their diploid progenitors. CONCLUSION: A detailed structural organization of two closely located 5S rDNA-tagged genomic regions on the 5BS chromosome of bread wheat has been established. These two regions differ in the organization of both 5S rDNA and the neighboring sequences comprised of transposable elements, implying different modes of evolution for these regions. SN - 1471-2229 UR - https://www.unboundmedicine.com/medline/citation/29143604/Fine_organization_of_genomic_regions_tagged_to_the_5S_rDNA_locus_of_the_bread_wheat_5B_chromosome_ L2 - https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-017-1120-5 DB - PRIME DP - Unbound Medicine ER -