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Accumulation of small RNA populations in response to allopolyploidy: analysis of small RNA sequencing data from resynthesized Brassica napus allotetraploid in comparison to their diploid progenitors

ABSTRACT: Evolution and adaptation of living organisms are results of permanent fights against diverse threats, which imply specific responses from the genome itself. Allopolyploidy, combining interspecific hybridization with whole genome duplication, is recognised as an important evolutionary force in plants. Its evolutionary success can be related to the rapid and profound genome reorganizations generated in response to the “Genome Shock” that allow the neo-allopolyploid to adapt efficiently to new environments. While work has focused on the structural and functional consequences of allopolyploidy, studies dedicated to the response of the neo-allopolyploid genome at the level of the functional regulation of genome expression have been rarely conducted. Recently, the hypothesis of a major role for small non coding RNAs (sRNAs) in mediating the immediate functional response of neo-allopolyploid genomes has progressively emerged. Here, we characterize the global response of sRNAs to allopolyploidy in Brassica, using three independent resynthesized B. napus allotetraploids surveyed at two different generations in comparison with their diploid progenitors, by high-throughput sequencing of sRNAs. Our evidence suggests an immediate but transient response of specific sRNA populations, targeting non-coding components of the genome. We identify the early accumulation of both 21- and 24-nt sRNAs involved in the regulation of the same targets, supporting a PTGS-to-TGS shift at the first stages of the neo-allopolyploid formation. We propose that sRNAs are early mobilized in response to allopolyploidy to control the unexpected transcriptional reactivation of various non-coding elements thus, playing the role of guardians of genome integrity during the first steps of neo-allopolyploid formation.

ORGANISM(S): Brassica rapa subsp. oleifera Brassica napus Brassica rapa Brassica oleracea var. botrytis Brassica oleracea

PROVIDER: GSE94076 | GEO | 2017/09/15

SECONDARY ACCESSION(S): PRJNA368726

REPOSITORIES: GEO

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Project description:Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina x townsendii and Spartina anglica (Poaceae) Allopolyploidy results from two events: the merger of divergent genomes and genome duplication. Both events have important functional consequences for the evolution and adaption of newly formed allopolyploid species. In spite of significant progress made the last years, a few studies have decoupled the effects of hybridization from genome duplication in the observed patterns of expression changes accompanying allopolyploidy in natural conditions. We used Agilent Rice oligo-microarrays to explore gene expression changes following allopolyploidy in Spartina that includes a classical example of recent allopolyploid speciation, S. anglica formed during the 19th century following genome duplication of the hybrid S. x townsendii. Our data indicate important, thought different effects of hybridization and genome duplication in the expression patterns of the hybrid and allopolyploid. Deviation from parental additivity was most important following hybridization and was accompanied by maternal expression dominance, although transgressively expressed genes were also encountered. Maternal dominance is attenuated following genome duplication in S. anglica while this species exhibits an increased number of transgressively over expressed genes. These results reflect the decoupled effects of the “genomic shock” following hybridization and genome redundancy, on the genetic, epigenetic and regulatory mechanisms characterizing transcriptomic evolution in allopolyploids. We used Agilent Rice oligo-microarrays to explore gene expression changes among Spartina species, following interspesific hybridization and genome duplication (allopolyploidy). The analysed species included the parents S. maritima & S.alterniflora, the hybrid F1 S x. towensendii and the allopolyploid S.anglica. A total of 20 slides (five replicates per species) were hybridized on a 44 K Rice Agilent array using a one color desgin.

Project description:How allopolyploids are able not only to cope but profit from their condition is a question that remain elusive, but of great importance within the wide context of successful hybrid polyploid evolution. One outstanding example of successful allopolyploidy is the endemic Iberian S. alburnoides fish complex. Previously, based on the evaluation of 7 genes, it was reported that the transcription levels between diploid and triploid hybrid S. alburnoides were similar. If this phenomenon would occur on a full genomic scale, a wide functional diploidization could be related to the success of polyploids. We generated RNA-seq data from whole juvenile fish and from an adult tissue, to perform the first comparative quantitative transcriptomic analysis between ploidy levels of a vertebrate allopolyploid. We found 64% in juvenilesM-b full body samples and 44% in liver samples of similar expression between diploid and triploid hybrids, and those genes are mostly involved in processes of basal biological maintenance of the cells. Yet, respectively only 29% and 15% of transcripts presented accurate dosage compensation. Therefore, an exact functional diploidization of the triploid genome does not occur, but globally a significant down regulation of gene expression in triploids was observed. We find that for those genes which show similar expression levels in diploids and triploids, expression in triploids is not globally strictly proportional to gene dosage nor is it set to a perfect diploid level. This quantitative flexibility of expression may be a strong contributor to overcome the 'genomic shock', and be an immediate evolutionary advantage of allopolyploids. Genotypes: Squalius alburnoides is an allopolyploid cyprinid, resulting from interspecific hybridization between females of Squalius pyrenaicus (P genome) and males of a now extinct species related to Anaecypris hispanica (A genome). S. alburnoides natural populations arecomposed of animals of different ploidy levels and genomic constitutions (different genotypes). The predominant S. alburnoides complex intervenients in the Iberian Peninsula southern rivers are the hybrid triploid PAA, diploid PA, the parental-like diploid AA and the parental species S. pyrenaicus PP.

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Accumulation of small RNA populations in response to allopolyploidy: analysis of small RNA sequencing data from resynthesized Brassica napus allotetraploid in comparison to their diploid progenitors

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