Identification of microsatellite loci based on BAC sequencing data and their physical mapping into the soft wheat 5B chromosome

Nesterov, M. A.; Afonnikov, D. A.; Sergeeva, E. M.; Miroshnichenko, L. A.; Bragina, M. K.; Bragin, A. O.; Vasiliev, Gennady V.; Салина, Е. А.

doi:10.1134/s2079059716070078

Cited by 5 publications

(5 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…BAC clones marked by 5S rDNA were included in the pool of 134 BAC-clones belonging to different locations of chromosome 5BS, and were collectively sequenced as one sample on an IonTorrent platform (Thermo Fisher Scientific). The sequencing and assembly were described in Nesterov et al [ 23 ].…”

Section: Methodsmentioning

confidence: 99%

Fine organization of genomic regions tagged to the 5S rDNA locus of the bread wheat 5B chromosome

et al. 2017

View full text Add to dashboard Cite

BackgroundThe 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.ResultsThree 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.ConclusionA 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.Electronic supplementary materialThe online version of this article (doi: 10.1186/s12870-017-1120-5) contains supplementary material, which is available to authorized users.

show abstract

Section: Methodsmentioning

confidence: 99%

Fine organization of genomic regions tagged to the 5S rDNA locus of the bread wheat 5B chromosome

et al. 2017

View full text Add to dashboard Cite

show abstract

“…In order to increase the number of contigs anchored on the chromosome, 134 BAC clones from the middle part of non-anchored contigs were end sequenced and using the Ion Torrent platform. This gave 158 BAC-end sequences and 17,770 Ion Torrent contigs with a total length of 25,879,921 bp [ 23 ], which were used further in GenomeZipper analysis. The collinearity regions between the wheat, Brachypodium, rice, and sorghum were detected based on local collinearity of their already sequenced genomes related to the wheat genome and the positions of some wheat genes localized earlier on deletion bins [ 37 ].…”

Section: Resultsmentioning

confidence: 99%

“…For the Ion Torrent contigs, the markers specific for the studied DNA sequences (referred to as zipper markers; Additional file 6 ), were designed. These markers, along with SSR markers published previously [ 23 ] were used to find correspondence between the Ion Torrent and BAC contigs, as well as to localize the BAC contigs on the genetic and cytogenetic maps (Fig 1 ). The combination of these approaches made it possible to localize an additional number of BAC contigs and increase the coverage length by 54,527 kb, which together with the first stage covered 185,974 kb.…”

Section: Resultsmentioning

confidence: 99%

“…Primer sequences for the designed ISBPs are presented in Additional file 1 . We also used published SSR markers available in the GrainGenes database ( https://wheat.pw.usda.gov/GG3/ ), in our previously publication [ 23 ] and the newly designed SSR markers for 5BS, included in this study (Additional file 1 ).…”

Section: Methodsmentioning

confidence: 99%

“…BAC DNA was isolated using NucleoSpin 96 Flash (Macherey-Nagel) kit. The sequencing on the Ion Torrent platform and assembled with the MIRA program were described previously [ 23 ].…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Features of the organization of bread wheat chromosome 5BS based on physical mapping

et al. 2018

View full text Add to dashboard Cite

BackgroundThe IWGSC strategy for construction of the reference sequence of the bread wheat genome is based on first obtaining physical maps of the individual chromosomes. Our aim is to develop and use the physical map for analysis of the organization of the short arm of wheat chromosome 5B (5BS) which bears a number of agronomically important genes, including genes conferring resistance to fungal diseases.ResultsA physical map of the 5BS arm (290 Mbp) was constructed using restriction fingerprinting and LTC software for contig assembly of 43,776 BAC clones. The resulting physical map covered ~ 99% of the 5BS chromosome arm (111 scaffolds, N50 = 3.078 Mb). SSR, ISBP and zipper markers were employed for anchoring the BAC clones, and from these 722 novel markers were developed based on previously obtained data from partial sequencing of 5BS. The markers were mapped using a set of Chinese Spring (CS) deletion lines, and F2 and RICL populations from a cross of CS and CS-5B dicoccoides.Three approaches have been used for anchoring BAC contigs on the 5BS chromosome, including clone-by-clone screening of BACs, GenomeZipper analysis, and comparison of BAC-fingerprints with in silico fingerprinting of 5B pseudomolecules of T. dicoccoides. These approaches allowed us to reach a high level of BAC contig anchoring: 96% of 5BS BAC contigs were located on 5BS. An interesting pattern was revealed in the distribution of contigs along the chromosome. Short contigs (200–999 kb) containing markers for the regions interrupted by tandem repeats, were mainly localized to the 5BS subtelomeric block; whereas the distribution of larger 1000–3500 kb contigs along the chromosome better correlated with the distribution of the regions syntenic to rice, Brachypodium, and sorghum, as detected by the Zipper approach.ConclusionThe high fingerprinting quality, LTC software and large number of BAC clones selected by the informative markers in screening of the 43,776 clones allowed us to significantly increase the BAC scaffold length when compared with the published physical maps for other wheat chromosomes. The genetic and bioinformatics resources developed in this study provide new possibilities for exploring chromosome organization and for breeding applications.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4470-y) contains supplementary material, which is available to authorized users.

show abstract

Chromosome genomics uncovers plant genome organization and function

Zwyrtková

Šimková

Doležel

2021

Biotechnology Advances

View full text Add to dashboard Cite

Identification of microsatellite loci based on BAC sequencing data and their physical mapping into the soft wheat 5B chromosome

Cited by 5 publications

References 32 publications

Fine organization of genomic regions tagged to the 5S rDNA locus of the bread wheat 5B chromosome

Fine organization of genomic regions tagged to the 5S rDNA locus of the bread wheat 5B chromosome

Features of the organization of bread wheat chromosome 5BS based on physical mapping

Chromosome genomics uncovers plant genome organization and function

Contact Info

Product

Resources

About