<i>SlWUS1</i>; An X-linked Gene Having No Homologous Y-Linked Copy in<i>Silene latifolia</i>

Kazama, Yusuke; Nishihara, Kenji; Bergero, Roberta; Fujiwara, Makoto; Abe, Tomoko; Charlesworth, Deborah; Kawano, Shigeyuki

doi:10.1534/g3.112.003749

Cited by 18 publications

(20 citation statements)

References 70 publications

(94 reference statements)

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“…Our new map includes 11 genes whose X-linked copies have been genetically mapped: seven by Bergero et al 25 and four by Kazama et al 43 . The orders of these genes on the Y chromosome in Fig.…”

Section: Resultsmentioning

confidence: 99%

A new physical mapping approach refines the sex-determining gene positions on the Silene latifolia Y-chromosome

Kazama

Ishii

Aonuma

et al. 2016

Sci Rep

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Sex chromosomes are particularly interesting regions of the genome for both molecular genetics and evolutionary studies; yet, for most species, we lack basic information, such as the gene order along the chromosome. Because they lack recombination, Y-linked genes cannot be mapped genetically, leaving physical mapping as the only option for establishing the extent of synteny and homology with the X chromosome. Here, we developed a novel and general method for deletion mapping of non-recombining regions by solving “the travelling salesman problem”, and evaluate its accuracy using simulated datasets. Unlike the existing radiation hybrid approach, this method allows us to combine deletion mutants from different experiments and sources. We applied our method to a set of newly generated deletion mutants in the dioecious plant Silene latifolia and refined the locations of the sex-determining loci on its Y chromosome map.

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Section: Resultsmentioning

confidence: 99%

A new physical mapping approach refines the sex-determining gene positions on the Silene latifolia Y-chromosome

Kazama

Ishii

Aonuma

et al. 2016

Sci Rep

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“…When these studies were done, very few validated X-hemizygous genes were available in S. latifolia . Only two fully degenerated Y-linked genes in S. latifolia have so far been documented [ 27 , 28 ]. Two recent studies used segregation analysis in large families and inferred further X-hemizygous genes, one being a segregation analysis using RadSeq data [ 5 , 29 ]; however comparing these genes with the sex-linked contigs from RNA-seq studies reveals that ~57 % might be X/Y gene pairs, so we cannot use them as well-validated X-hemizygous genes (see the list of genes with X-hemizygous segregation patterns in Additional file 4 : Table S4).…”

Section: Resultsmentioning

confidence: 99%

Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia

Blavet

Muyle

et al. 2015

BMC Genomics

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BackgroundSilene latifolia represents one of the best-studied plant sex chromosome systems. A new approach using RNA-seq data has recently identified hundreds of new sex-linked genes in this species. However, this approach is expected to miss genes that are either not expressed or are expressed at low levels in the tissue(s) used for RNA-seq. Therefore other independent approaches are needed to discover such sex-linked genes.ResultsHere we used 10 well-characterized S. latifolia sex-linked genes and their homologs in Silene vulgaris, a species without sex chromosomes, to screen BAC libraries of both species. We isolated and sequenced 4 Mb of BAC clones of S. latifolia X and Y and S. vulgaris genomic regions, which yielded 59 new sex-linked genes (with S. vulgaris homologs for some of them). We assembled sequences that we believe represent the tip of the Xq arm. These sequences are clearly not pseudoautosomal, so we infer that the S. latifolia X has a single pseudoautosomal region (PAR) on the Xp arm. The estimated mean gene density in X BACs is 2.2 times lower than that in S. vulgaris BACs, agreeing with the genome size difference between these species. Gene density was estimated to be extremely low in the Y BAC clones. We compared our BAC-located genes with the sex-linked genes identified in previous RNA-seq studies, and found that about half of them (those with low expression in flower buds) were not identified as sex-linked in previous RNA-seq studies. We compiled a set of ~70 validated X/Y genes and X-hemizygous genes (without Y copies) from the literature, and used these genes to show that X-hemizygous genes have a higher probability of being undetected by the RNA-seq approach, compared with X/Y genes; we used this to estimate that about 30 % of our BAC-located genes must be X-hemizygous. The estimate is similar when we use BAC-located genes that have S. vulgaris homologs, which excludes genes that were gained by the X chromosome.ConclusionsOur BAC sequencing identified 59 new sex-linked genes, and our analysis of these BAC-located genes, in combination with RNA-seq data suggests that gene losses from the S. latifolia Y chromosome could be as high as 30 %, higher than previous estimates of 10-20 %.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1698-7) contains supplementary material, which is available to authorized users.

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“…2012 ). The X-hemizygous gene SlWUS1 in Silene latifolia was shown (using qRT-PCR) to have lower expression levels in males than in females and to have both X copies expressed in females ( Kazama et al. 2012 ), therefore, the study concluded that there was no evidence that this gene was dosage compensated or X-inactivated.…”

Section: Introductionmentioning

confidence: 98%

“…From these four studies ( Bergero et al. 2015 ; Chibalina and Filatov 2011 ; Kazama et al. 2012 ; Muyle et al.…”

Section: Introductionmentioning

confidence: 99%

The Evolution of Sex Chromosomes and Dosage Compensation in Plants

Muyle

Shearn

Marais

2017

Genome Biology and Evolution

106

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Plant sex chromosomes can be vastly different from those of the few historical animal model organisms from which most of our understanding of sex chromosome evolution is derived. Recently, we have seen several advancements from studies on green algae, brown algae, and land plants that are providing a broader understanding of the variable ways in which sex chromosomes can evolve in distant eukaryotic groups. Plant sex-determining genes are being identified and, as expected, are completely different from those in animals. Species with varying levels of differentiation between the X and Y have been found in plants, and these are hypothesized to be representing different stages of sex chromosome evolution. However, we are also finding that sex chromosomes can remain morphologically unchanged over extended periods of time. Where degeneration of the Y occurs, it appears to proceed similarly in plants and animals. Dosage compensation (a phenomenon that compensates for the consequent loss of expression from the Y) has now been documented in a plant system, its mechanism, however, remains unknown. Research has also begun on the role of sex chromosomes in sexual conflict resolution, and it appears that sex-biased genes evolve similarly in plants and animals, although the functions of these genes remain poorly studied. Because the difficulty in obtaining sex chromosome sequences is increasingly being overcome by methodological developments, there is great potential for further discovery within the field of plant sex chromosome evolution.

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SlWUS1; An X-linked Gene Having No Homologous Y-Linked Copy inSilene latifolia

Cited by 18 publications

References 70 publications

A new physical mapping approach refines the sex-determining gene positions on the Silene latifolia Y-chromosome

A new physical mapping approach refines the sex-determining gene positions on the Silene latifolia Y-chromosome

Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia

The Evolution of Sex Chromosomes and Dosage Compensation in Plants

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