Identification of distinct YX-like loci for sex determination and self-incompatibility in an androdioecious shrub
Genetic mapping of sex and self-incompatibility determinants in the androdioecious plant Phillyrea angustifolia
Recommendation: posted 07 July 2021, validated 20 July 2021
Giraud, T. and Rodríguez de la Vega, R. (2021) Identification of distinct YX-like loci for sex determination and self-incompatibility in an androdioecious shrub. Peer Community in Genomics, 100011. 10.24072/pci.genomics.100011
A wide variety of systems have evolved to control mating compatibility in sexual organisms. Their genetic determinism and the factors controlling their evolution represent fascinating questions in evolutionary biology and genomics. The plant Phillyrea angustifolia (Oleaeceae family) represents an exciting model organism, as it displays two distinct and rare mating compatibility systems : 1) males and hermaphrodites co-occur in populations of this shrub (a rare system called androdioecy), while the evolution and maintenance of purely hermaphroditic plants or mixtures of females and hermaphrodites (a system called gynodioecy) are easier to explain ; 2) a homomorphic diallelic self-incompatibility system acts in hermaphrodites, while such systems are usually multi-allelic, as rare alleles are advantageous, being compatible with all other alleles. Previous analyses of crosses brought some interesting answers to these puzzles, showing that males benefit from the ability to mate with all hermaphrodites regardless of their allele at the self-incompatibility system, and suggesting that both sex and self incompatibility are determined by XY-like genetic systems, i.e. with each a dominant allele; homozygotes for a single allele and heterozygotes therefore co-occur in natural populations at both sex and self-incompatibility loci .
Here, Carré et al. used genotyping-by-sequencing to build a genome linkage map of P. angustifolia . The elegant and original use of a probabilistic model of segregating alleles (implemented in the SEX-DETector method) allowed to identify both the sex and self-incompatibility loci , while this tool was initially developed for detecting sex-linked genes in species with strictly separated sexes (dioecy) . Carré et al.  confirmed that the sex and self-incompatibility loci are located in two distinct linkage groups and correspond to XY-like systems. A comparison with the genome of the closely related Olive tree indicated that their self-incompatibility systems were homologous. Such a XY-like system represents a rare genetic determination mechanism for self-incompatibility and has also been recently found to control mating types in oomycetes .
This study  paves the way for identifying the genes controlling the sex and self-incompatibility phenotypes and for understanding why and how self-incompatibility is only expressed in hermaphrodites and not in males. It will also be fascinating to study more finely the degree and extent of genomic differentiation at these two loci and to assess whether recombination suppression has extended stepwise away from the sex and self-incompatibility loci, as can be expected under some hypotheses, such as the sheltering of deleterious alleles near permanently heterozygous alleles . Furthermore, the co-occurrence in P. angustifolia of sex and mating types can contribute to our understanding of the factor controlling their evolution .
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 Billiard S, Husse L, Lepercq P, Godé C, Bourceaux A, Lepart J, Vernet P, Saumitou-Laprade P (2015) Selfish male-determining element favors the transition from hermaphroditism to androdioecy. Evolution, 69, 683–693. https://doi.org/10.1111/evo.12613
 Carre A, Gallina S, Santoni S, Vernet P, Gode C, Castric V, Saumitou-Laprade P (2021) Genetic mapping of sex and self-incompatibility determinants in the androdioecious plant Phillyrea angustifolia. bioRxiv, 2021.04.15.439943, ver. 7 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2021.04.15.439943
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 Jay P, Tezenas E, Giraud T (2021) A deleterious mutation-sheltering theory for the evolution of sex chromosomes and supergenes. bioRxiv, 2021.05.17.444504. https://doi.org/10.1101/2021.05.17.444504
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The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article. The authors declared that they comply with the PCI rule of having no financial conflicts of interest in relation to the content of the article.
Evaluation round #2
DOI or URL of the preprint: 10.1101/2021.04.15.439943
Version of the preprint: 4
Author's Reply, 07 Jul 2021
Decision by Tatiana Giraud and Ricardo C. Rodríguez de la Vega, posted 29 Jun 2021
The authors have throroughly revised the manuscript according to the referees’ comments and we have only a few minor suggestions before we recommend the paper in PCI Genomics.
-L39 : Modes of sexual reproduction are strikingly diverse
-L97 : add a reference
-L99 : italics for « P. angustifolia »
-L108 : explain briefly here what is this stigma test and in details in M&M
-L110 : coma after the bracket
-L115 : unclear what « its » refers to
-L112, L356, 358, 370, 372, 373, 397, 422 and elsewhere : tense should be homogeneous within sentences ; I would keep the past tense all along
-L145 : M allele
-L152 : it has not been clarified that this represents experimental data, and it is unclear as the previous sentence mentions a model
-L177 : delete specific
-L212, L297 : no capital within a sentence even for explaining acronyms
-L234, L244, L723 : no plural when a name is before another name, so either just SNPs or SNP markers
-L277 : it is still not clear what is the principle of this method (ant not only its goal), i.e., how it differs from just classical association genetics
-L321, L323 : give the P values and N
-L325 : no number at the beginning of a sentence or written in full letters
-L331 : revise sentence, the two numbers and two comas are unclear
-L377 : fewer instead of less
-L304 : I would recommend using sequence similarity instead of homology, which has a different meaning in evolution, ie with a notion of shared ancestry
-P11 : is it possible to plot the differentiation between alleles in the scaffold of interest to assess whether the differentiation is much higher at the SI and sex deterining loci than alsewhere, or even if there is a pattern of evolutionary strata ? Even if the contigs cannot be fully ordered, the differentiation levels may add further strong support to the findings and interpretation.
-P12 : it could be interesting to discuss the mating-type system in oomycetes that also resembles XY sex-determining systems (DOI:https://doi.org/10.1016/j.cub.2020.07.057)
-L471, L484, L493, 497, 530 : I would use the term homologous instead of orthologous ; Orthologous is used for genes, to distinguish paralogous and orthologous genes among homologous genes, but you have not studied or found paralogs here, and it cannot be used with « functionnally » to my understanding
-L478-479 : I do not understand this sentence, it seems to have a syntax issue
-L493 : sexes or sexual morphs instead of sex
-L496 : « such as » is redundant with « eg »
-L14 : I find frustrating not to have some speculations about what can cause this distortion… meiotic drive ? more complex genetic system than a single locus ? selection for balanced male and female functions in the population, which can be different from the sexual morph census numbers ?
Tatiana Giraud and Ricardo Rodriguez de la Vega
Evaluation round #1
DOI or URL of the preprint: 10.1101/2021.04.15.439943
Version of the preprint: 3
Author's Reply, 28 Jun 2021
Decision by Tatiana Giraud, posted 09 Jun 2021
The manuscript has been evaluated by two referees, who agree that this manuscript on the genetic mapping of sex and self-incompatibility determinants in an androdioecious plant is sound, elegant and interesting for the evolutionary biology community. Both referees nevertheless provide a list of excellent suggestions and questions, such as testing the new version of sex-DETector, providing the list of candidate genes and their predicted functions, and comparing genetic maps between sexes. I would encourage resubmission if you are able to revise the manuscript along all these lines.
In addition, please also address the comments below:
-L33-34: I would delete the two occurrences of “more” here
-All along the text, I would avoid abbreviations (such as DSI); abbreviations are rarely useful for readers and only render the text harder to read. In addition, some syntax using DSI is incorrect, eg L89, it should be DSI system or determinant?
-L76-77: clarify, are S- and L-morph flowers the same as “pin” and “thrum”?
-L82: there is no such thing as a “basal” clade in a phylogenetic tree, see for example: https://doi.org/10.1111/j.0307-6970.2004.00262.x
-L83: clarify, is the diallelic self-incompatibility the expected system for heterostyled phenotypes?
-L87-88: clarify, not clear if this applies only to dioecious sex systems or to all three. What’s “x” in “2n=2x=46”?
-L97-98, L167: explain what is the “stigma test” also clarify if the “more distant species” are in different tribes.
-L103: not all orthologs are “identical by descend”, I reckon you want to test whether they are orthologs (here a locus already committed to this function in the last common ancestor) and if so whether they have remained identically positioned (see comment on use of “syntenic” below).
-L111: name some examples of lineages in which separate sexes have unfolded independently of diallelic self-incompatibility
-L117: here and elsewhere use common names at first mention (here European olive)
-L132: is “segregates” rightly used here? I would think that alleles segregate in a progeny but a progeny does not “segregate”?
-L135: is this really an “observation” as the sentence suggests, or a result or the model as the previous sentences let think?
-L138: a reference is missing for the observed “departure”.
-L164, L171, L255: “sex” usually means genetic mixing, here shouldn’t it be “gender”?
-L166: no number at a beginning of a sentence, or spell it out.
-L185-188: I found too cursory the description of how the “de novo catalog” was created. I’m not sure what “catalog” means here.
-L193: Make sure the “custom script” is available as supplemental or in the public domain. Same at L203.
-L193-194: correct typo and split the sentence “(..), after removal of SNPs markers with read cover <5.The script combines(...)”.
-L195: homogenize the typography of “Lep-Map3” (written as “Lep-MAP3” elsewhere).
-L218: correct the typo, should be “hemizygous”.
-L221: explain briefly the principle of the method.
-L241: justify why 110bp was considered enough to determine whether the (reciprocal?) hit is syntenic.
-L268: remind the reader that this logarithm of odds score was chosen so 23 linkage groups are obtained.
-L277 no plural when a name qualifies another by being before it, so either “locus identification” or “identification of loci”
-L285 and L297-298: I reckon the loci showing “autosomal inheritance” are worth discussing, how these could be in a region where other loci follow a “XY segregation” pattern?
-L313-314: loci do not “find” homology between genomes, a more precise wording would be “365 loci have good/non ambiguous matches in the European olive tree assembly”.
-L350: comment, is the olive tree’s S-locus less confidentially assembled? e.g. is it scaffolded with long/many N tracks?
-L373-374: I think “Identification of sequences that have remained linked over these” reads better.
-In the discussion, I am not sure “syntenic” is rightly used and clear (L344, 347, L364): I do not see how synteny (i.e. similar gene order) provides support for the hypothesis that the two systems are orthologous? Do you mean instead that the two studies mapped the locus genomic regions with orthologous genes? Unclear L344 what is “identified” (add “as the region controlling SI)?
-L408, it is unclear what “fully aligned” means here?
-L416: missing closing parenthesis.
-L418: it is unclear what “sexual specialization” means here? Separate sexes? Sexual dimorphism? Anisogamy?
-L419-420: unclear what you mean within brackets, make a separate sentence and explain the logical relationship with the preceding sentence
-The following reference may be cited in the last paragraph on P18: 10.1111/j.1469-185X.2010.00153.x.
-Figure 1: Remove the lines framing the figure.
-Figure 2: Lines are colored according to the linkage map, right?
-Figure 3: Adding as scale of SNP density to the points (e.g. color by factor, color= in ggplot2’s aes). Could you comment on the interwoven forward and reverse synteny between olive tree Chr18 and LG18?
-Figure 4: lines are blue, not green.
- Could you comment if the non-recombining region around the sex and self-incompatibility loci have been extended in P. angustifolia? Do the small contigs of olive tree match other regions in P. angustifolia?