Transposable Elements and Genome Expansion in Cultivated and Wild Potato and Tomato Species

Gantuz, Magdalena; Marfil, Carlos Federico; Masuelli, Ricardo Williams

doi:10.1007/978-3-030-30343-3_11

Cited by 2 publications

(3 citation statements)

References 79 publications

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“…and Solanum sp. ; Gaiero et al, 2019;Gantuz et al, 2021;Michael, 2014;Zedek et al, 2010), pointing to a particularly strong impact of repeats (i.e., LTR retrotransposons) on beet genome sizes. Specific amplification and elimination of repeats may explain why the genome size of B. nana rather resembles those of the section Beta, even though this species is repeatedly considered a member of the section Corollinae (Frese & Ford-Lloyd, 2020;Kadereit et al, 2006;Sielemann et al, 2022).…”

Section: Beet and Wild Beet Genome Size Variation Results From Repeat...mentioning

confidence: 99%

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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

The Plant Journal

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SUMMARYSugar beet and its 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 DNAs are among the fastest evolving parts of the genome, we investigated, if repeatome innovations and losses are linked to chromosomal differentiation and speciation. We traced genome and chromosome‐wide evolution across 13 beet species comprising all sections of the genera Beta and Patellifolia. For this, we combined short and long read sequencing, flow cytometry, and cytogenetics to build a comprehensive framework that spans the complete scale from DNA to chromosome to genome. Genome sizes and repeat profiles reflect the separation into three gene pools with contrasting evolutionary patterns. Among all repeats, satellite DNAs harbor most genomic variability, leading to fundamentally different centromere architectures, ranging from chromosomal uniformity in Beta and Patellifolia to the formation of patchwork chromosomes in Corollinae/Nanae. We show that repetitive DNAs are causal for the genome expansions and contractions across the beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite DNAs in particular vary considerably between beet genomes, leading to the evolution of distinct chromosomal setups in the three gene pools, likely contributing to the barriers in beet breeding. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal system for studying the link between repeats, genomic variability, and chromosomal differentiation and provide a theoretical fundament for understanding barriers in any crop breeding effort.

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Section: Beet and Wild Beet Genome Size Variation Results From Repeat...mentioning

confidence: 99%

“…and Solanum sp. ; Gaiero et al., 2019; Gantuz et al., 2021; Michael, 2014; Zedek et al., 2010), pointing to a particularly strong impact of repeats (i.e., LTR retrotransposons) on beet genome sizes.…”

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

The Plant Journal

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“…compared to Eleocharis sp., Solanum sp., Hesperis -clade sp. ; Zedek et al ., 2010; Michael, 2014; Gaiero et al ., 2019; Hloušková et al ., 2019; Gantuz et al ., 2021), pointing to a particularly strong impact of repeats (i.e. LTR retrotransposons) on beet genome sizes.…”

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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Transposable Elements and Genome Expansion in Cultivated and Wild Potato and Tomato Species

Cited by 2 publications

References 79 publications

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

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

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

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