Endogenous virus sRNA regulates gene expression following genome shock in tomato hybrids

López-Gomollón, Sara; Mueller, Sebastian Y.; Baulcombe, David C.

doi:10.1101/2021.09.20.461014

Cited by 1 publication

(1 citation statement)

References 22 publications

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“…Since the genomic shock of polyploidisation may stimulate rapid and dynamic genomic changes such as the activation of retrotransposons and viral elements (McClintock, 1984; Lopez-Gomollon et al ., 2021), genome size may subsequently increase. The overall repeat content is indeed greater within the polyploid beet genomes compared to their closest diploid relatives, mainly due to an increased abundance of Ty3- gypsy retrotransposons.…”

Section: Discussionmentioning

confidence: 99%

Repeat turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets

Schmidt,

Sielemann,

Breitenbach

et al. 2023

Preprint

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Background: Sugar beet (Beta vulgarissubsp.vulgaris) and its crop wild relatives share a base chromosome number of nine and similar chromosome morphologies. Yet, interspecific breeding is impeded by chromosome and sequence divergence that is still not fully understood. Since repetitive DNA sequences represent the fastest evolving parts of the genome, they likely impact genomic variability and contribute to the separation of beet gene pools. Hence, we investigated if innovations and losses in the repeatome can be linked to chromosomal differentiation and speciation.Results: We traced genome- and chromosome-wide evolution across sugar beet and twelve wild beets comprising all sections of the beet generaBetaandPatellifolia. For this, we combined data from short and long read sequencing, flow cytometry, and cytogenetics to build a comprehensive data framework for our beet panel that spans the complete scale from DNA sequence to chromosome up to the genome. Genome sizes and repeat profiles reflect the separation of the beet species into three gene pools. These gene pools harbor repeats with contrasting evolutionary patterns: We identified section- and species-specific repeat emergences and losses, e.g. of the retrotransposons causal for genome expansions in the sectionCorollinae/Nanae. Since most genomic variability was found in the satellite DNAs, we focused on tracing the 19 beetSat families across the three beet sections/genera. These taxa harbor evidence for contrasting strategies in repeat evolution, leading to contrasting satellite DNA profiles and fundamentally different centromere architectures, ranging from chromosomal uniformity inBetaandPatellifoliaspecies to the formation of patchwork chromosomes inCorollinae/Nanaespecies.Conclusions: We show that repetitive DNA sequences are causal for genome size expansion and contraction across the beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite DNAs in particular vary considerably among beet taxa, leading to the evolution of distinct chromosomal setups. These differences likely contribute to the barriers in beet breeding between the three gene pools. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal system for studying the link between repeats, genome variability, and chromosomal differentiation/evolution and provide a theoretical basis for understanding barriers in crop breeding.

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Section: Discussionmentioning

confidence: 99%