Genus-wide sequencing supports a two-locus model for sex-determination in <i>Phoenix</i>

Torres, María Fernanda; Mathew, Lisa S.; Ahmed, Ikhlak; Al-Azwani, Iman K.; Krueger, Robert R.; Rivera, Diego; Mohamoud, Yasmin Ali; Clark, Andrew G.; Suhre, Karsten; Malek, Joel A.

doi:10.1101/245514

Cited by 24 publications

(34 citation statements)

References 49 publications

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“…k-mer refers to all the possible substrings of length k that are contained in a genome, and have been useful in identifying sex-specific (Y chromosome) sequence in a range of organisms [90][91][92] , including guppies 23 , by comparing male and female k-mer profiles.…”

Section: Y-mer Miningmentioning

confidence: 99%

Divergence and Remarkable Diversity of the Y Chromosome in Guppies

Almeida

Sandkam

Morris

et al. 2020

Preprint

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The guppy sex chromosomes show an extraordinary diversity in divergence across populations and closely related species. In order to understand the dynamics of the guppy Y chromosome, we used linked-read sequencing to assess Y chromosome evolution and diversity across upstream and downstream population pairs that vary in predator and food abundance in three replicate watersheds. Based on our population-specific genome assemblies, we first confirmed and extended earlier reports of two strata on the guppy sex chromosomes. Stratum I shows significant accumulation of male-specific sequence, consistent with Y divergence, and predates the colonization of Trinidad. In contrast, Stratum II shows divergence from the X, but no Y-specific sequence, and this divergence is greater in three replicate upstream populations compared to their downstream pair. Despite longstanding assumptions that sex chromosome recombination suppression is achieved through inversions, we find no evidence of inversions associated with either Stratum I or Stratum II. Instead, we observe a remarkable diversity in Y chromosome haplotypes within each population, even in the ancestral Stratum I. This diversity is likely due to gradual mechanisms of recombination suppression, which, unlike an inversion, allow for the maintenance of multiple haplotypes. In addition, we show that this Y diversity is dominated by low-frequency haplotypes segregating in the population, suggesting a link between haplotype diversity and female-preference for rare Y-linked colour variation. Our results reveal the complex interplay between recombination suppression and Y chromosome divergence at the earliest stages of sex chromosome divergence.

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Section: Y-mer Miningmentioning

confidence: 99%

Divergence and Remarkable Diversity of the Y Chromosome in Guppies

Almeida

Sandkam

Morris

et al. 2020

Preprint

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“…Over the past decade, impressive progress has been made in unraveling the genetic basis of sex determination in several dioecious plants and the evolutionary history of their sex chromosomes, including papaya (Wang et al , 2012), persimmon (Akagi et al , 2014), asparagus (Harkess et al , 2017), strawberry (Tennessen et al , 2018), date palm (Torres et al , 2018) and kiwifruit (Akagi et al , 2018, 2019). Consistent with the independent origins of sex chromosomes, the sex determination genes identified in these species differ from each another, although most of them function in similar hormone response pathways (Feng et al , 2020).…”

Section: Introductionmentioning

confidence: 99%

A general model to explain repeated turnovers of sex determination in the Salicaceae

Yang

Zhang

Wang

et al. 2020

Preprint

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0Dioecy, the presence of separate sexes on distinct individuals, has evolved repeatedly 3 1 in multiple plant lineages. However, the specific mechanisms through which sex 3 2 systems evolve and their commonalities among plant species remain poorly 3 3 understood. With both XY and ZW sex systems, the family Salicaceae provides a 3 4 system to uncover the evolutionary forces driving sex chromosome turnovers. In this 3 5 study, we performed a genome-wide association study to characterize sex 3 6 determination in two Populus species, P. euphratica and P. alba. Our results reveal an 3 7XY system of sex determination on chromosome 14 of P. euphratica, and a ZW 3 8 system on chromosome 19 of P. alba. We further assembled the corresponding sex 3 9 determination regions, and found that their sex chromosome turnovers may be driven 4 0 by the repeated translocations of a Helitron-like transposon. During the translocation, 4 1 this factor may have captured partial or intact sequences that are orthologous to a 4 2 type-A cytokinin response regulator gene. Based on results from this and other 4 3recently published studies, we hypothesize that this gene may act as a master regulator 4 4 of sex determination for the entire family. We propose a general model to explain how 4 5 the XY and ZW sex systems in this family can be determined by the same RR gene. 6Our study provides new insights into the diversification of incipient sex chromosome 4 7 in flowering plants by showing how transposition and rearrangement of a single gene 4 8 can control sex in both XY and ZW systems. 4 9 5 0

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“…All Phoenix species are dioecious, and the characters of fruits and seeds are used to differentiate some of them, so male individuals are generally more difficult to identify than female individuals (Barrow, ; Rivera & al., ; Torres & al., ). Remarkably, only female individuals of the palm with red‐bluish fruits have been described.…”

Section: Introductionmentioning

confidence: 97%