Possible mechanisms responsible for absence of a retrotransposon family on a plant <scp>Y</scp> chromosome

Kubát, Zdeněk; Žlůvová, Jitka; Vogel, Ivan; Kováčová, Viera; Čermák, Tomáš; Čegan, Radim; Hobza, Roman; Vyskot, Boris; Kejnovský, Eduard

doi:10.1111/nph.12669

Cited by 34 publications

(24 citation statements)

References 75 publications

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“…We also demonstrate specific regions in Ogre elements with higher female coverage suggesting their dominant presence on the X chromosome. Our data confirm previous cytogenetic observations by Cermak et al [2008] and Kubat et al [2014]. The Retand element, like specific Ogre regions, suggests female (X)-biased abundance.…”

Section: Resultssupporting

confidence: 82%

The X Chromosome Is Necessary for Somatic Development in the Dioecious Silene latifolia: Cytogenetic and Molecular Evidence and Sequencing of a Haploid Genome

Soukupova

Nevrtalova

Čížková

et al. 2014

Cytogenet Genome Res

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Silene latifolia (or white campion) possesses a well-established sex determination system with a dominant Y chromosome in males (the mammalian type). The heteromorphic sex chromosomes X and Y in S. latifolia largely stopped recombination; thus, we can expect a gradual genetic degeneration of the Y chromosome. It is well proven that neither diploid nor polyploid S. latifolia sporophytes can survive without at least one X, so the only life stage possessing the Y as the sole sex chromosome is the male gametophyte (pollen tube), while the female gametophyte seems to be X-dependent. Previous studies on anther-derived plants of this species showed that the obtained plants (largely haploid or dihaploid) were phenotypically and cytologically female. In this paper, we provide molecular evidence for the inviability of plants lacking the X chromosome. Using sex-specific PCR primers, we show that all plantlets and plants derived from anther cultures are female. In studying anther-derived diploid females by sequencing of X-linked markers, we demonstrate that these plants are really homozygous dihaploids. A haploid regenerant plant was sequenced (8× genome coverage) using Illumina technology. Genome data are disposable in the EMBL database as a standard for full genome and X chromosome assembly in this model species. Homozygous dihaploids were back-crossed with males to yield a progeny useful for the study of the evolution of the Y chromosome.

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Section: Resultssupporting

confidence: 82%

The X Chromosome Is Necessary for Somatic Development in the Dioecious Silene latifolia: Cytogenetic and Molecular Evidence and Sequencing of a Haploid Genome

Soukupova

Nevrtalova

Čížková

et al. 2014

Cytogenet Genome Res

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“…For example, Rumex acetosa belongs to a clade that may have been dioecious for 15–16 MYA (Navajas‐Pérez et al ., ), but X–Y divergence has not been estimated. Its Y chromosomes are heterochromatic (Shibata et al ., ; Mariotti et al ., ), unlike those of other cytologically well‐studied plants, such as S. latifolia and S. dioica (Grabowska‐Joachimiak & Joachimiak, ; Kubat et al ., ), which are estimated to be younger (Section III). However, heterochromatin can evolve rapidly, as in papaya.…”

Section: Old Established Sex Chromosome Systemsmentioning

confidence: 99%

Plant contributions to our understanding of sex chromosome evolution

2015

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52I.53II.53III.54IV.55V.55VI.56VII.57VIII.58IX.59X.59XI.61XII.6262References62 Summary A minority of angiosperms have male and female flowers separated in distinct individuals (dioecy), and most dioecious plants do not have cytologically different (heteromorphic) sex chromosomes. Plants nevertheless have several advantages for the study of sex chromosome evolution, as genetic sex determination has evolved repeatedly and is often absent in close relatives. I review sex‐determining regions in non‐model plant species, which may help us to understand when and how (and, potentially, test hypotheses about why) recombination suppression evolves within young sex chromosomes. I emphasize high‐throughput sequencing approaches that are increasingly being applied to plants to test for non‐recombining regions. These data are particularly illuminating when combined with sequence data that allow phylogenetic analyses, and estimates of when these regions evolved. Together with comparative genetic mapping, this has revealed that sex‐determining loci and sex‐linked regions evolved independently in many plant lineages, sometimes in closely related dioecious species, and often within the past few million years. In reviewing recent progress, I suggest areas for future work, such as the use of phylogenies to allow the informed choice of outgroup species suitable for inferring the directions of changes, including testing whether Y chromosome‐like regions are undergoing genetic degeneration, a predicted consequence of losing recombination.

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“…Surprisingly, the copy number is lower in the male (6,765) than in the female (7,145) genome, which can reflect absence of Athila in the Y chromosome and slight enrichment in the X chromosome. Retand and Ogre elements that are underrepresented in the Y chromosome of S. latifolia also show lower copy numbers in male than female genomes in contrast to other TEs with uniform chromosomal distribution [Kubat et al, 2014].…”

Section: Athila Elements Are Overrepresented In the Female Genomementioning

confidence: 99%

Identification of a Novel Retrotransposon with Sex Chromosome-Specific Distribution in Silene latifolia

Králová

Čegan

Kubát

et al. 2014

Cytogenet Genome Res

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Silene latifolia is a dioecious plant species with chromosomal sex determination. Although the evolution of sex chromosomes in S. latifolia has been the subject of numerous studies, a global view of X chromosome structure in this species is still missing. Here, we combine X chromosome microdissection and BAC library screening to isolate new X chromosome-linked sequences. Out of 8 identified BAC clones, only BAC 86M14 showed an X-preferential signal after FISH experiments. Further analysis revealed the existence of the Athila retroelement which is enriched in the X chromosome and nearly absent in the Y chromosome. Based on previous data, the Athila retroelement belongs to the CL3 group of most repetitive sequences in the S. latifolia genome. Structural, transcriptomics and phylogenetic analyses revealed that Athila CL3 represents an old clade in the Athila lineage. We propose a mechanism responsible for Athila CL3 distribution in the S. latifolia genome.

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Possible mechanisms responsible for absence of a retrotransposon family on a plant Y chromosome

Cited by 34 publications

References 75 publications

The X Chromosome Is Necessary for Somatic Development in the Dioecious <b><i>Silene latifolia</i></b>: Cytogenetic and Molecular Evidence and Sequencing of a Haploid Genome

The X Chromosome Is Necessary for Somatic Development in the Dioecious <b><i>Silene latifolia</i></b>: Cytogenetic and Molecular Evidence and Sequencing of a Haploid Genome

Plant contributions to our understanding of sex chromosome evolution

Identification of a Novel Retrotransposon with Sex Chromosome-Specific Distribution in <b><i>Silene latifolia</i></b>

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