Number of the records: 1
The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, Homoploid Hybrids, and Cryptic Introgressants
- 1.
SYSNO ASEP 0524236 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, Homoploid Hybrids, and Cryptic Introgressants Author(s) Garcia, Sonia (BFU-R)
Wendel, J. F. (US)
Borowska-Zuchowska, N. (PL)
Ainouche, M. (FR)
Kuderová, Alena (BFU-R) ORCID
Kovařík, Aleš (BFU-R) RID, ORCIDNumber of authors 6 Article number 41 Source Title Frontiers in Plant Science. - : Frontiers Research Foundation - ISSN 1664-462X
Roč. 11, FEB 10 2020 (2020)Number of pages 14 s. Publication form Online - E Language eng - English Country CH - Switzerland Keywords concerted evolution ; rdna loci ; thinopyrum-intermedium Subject RIV EF - Botanics OECD category Plant sciences, botany R&D Projects GA19-03442S GA ČR - Czech Science Foundation (CSF) Method of publishing Open access Institutional support BFU-R - RVO:68081707 UT WOS 000517318500001 EID SCOPUS 85079769944 DOI 10.3389/fpls.2020.00041 Annotation Introduction
Ribosomal DNA (rDNA) loci have been widely used for identification of allopolyploids and hybrids, although few of these studies employed high-throughput sequencing data. Here we use graph clustering implemented in the RepeatExplorer (RE) pipeline to analyze homoeologous 5S rDNA arrays at the genomic level searching for hybridogenic origin of species. Data were obtained from more than 80 plant species, including several well-defined allopolyploids and homoploid hybrids of different evolutionary ages and from widely dispersed taxonomic groups.
Results
(i) Diploids show simple circular-shaped graphs of their 5S rDNA clusters. In contrast, most allopolyploids and other interspecific hybrids exhibit more complex graphs composed of two or more interconnected loops representing intergenic spacers (IGS). (ii) There was a relationship between graph complexity and locus numbers. (iii) The sequences and lengths of the 5S rDNA units reconstituted in silico from k-mers were congruent with those experimentally determined. (iv) Three-genomic comparative cluster analysis of reads from allopolyploids and progenitor diploids allowed identification of homoeologous 5S rRNA gene families even in relatively ancient (c. 1 Myr) Gossypium and Brachypodium allopolyploids which already exhibit uniparental partial loss of rDNA repeats. (v) Finally, species harboring introgressed genomes exhibit exceptionally complex graph structures.
Conclusion
We found that the cluster graph shapes and graph parameters (k-mer coverage scores and connected component index) well-reflect the organization and intragenomic homogeneity of 5S rDNA repeats. We propose that the analysis of 5S rDNA cluster graphs computed by the RE pipeline together with the cytogenetic analysis might be a reliable approach for the determination of the hybrid or allopolyploid plant species parentage and may also be useful for detecting historical introgression events.Workplace Institute of Biophysics Contact Jana Poláková, polakova@ibp.cz, Tel.: 541 517 244 Year of Publishing 2021 Electronic address http://apps.webofknowledge.com/InboundService.do?customersID=Alerting&mode=FullRecord&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=Alerting&SrcAuth=Alerting&SID=D6NcDKQSChJd2p47yqF&UT=WOS%3A000517318500001
Number of the records: 1