Don't pull the plug! the Drosophila mating plug preserves fertility

Reproductive behavior: Decrypting cryptic female choice

Females in many species bias fertilization success and paternity after mating with multiple males. Two new studies uncover the mechanisms of this phenomenon, cryptic female choice, in Drosophila, linking it to pheromone-stimulated ejection of sperm and mating plug.

Gone but not forgotten: dynamics of sperm storage and potential ejaculate digestion in the black soldier fly Hermetia illucens

Understanding the dynamics of sperm storage is essential to unravel the complexity of post-copulatory sexual selection processes in internally fertilized species. This physiological process goes from sperm transfer during copulation to its use for fertilization. In this context, the spatiotemporal dynamics of sperm storage were described in the black soldier fly (BSF) with fluorescence and transmission electron microscopy (TEM). BSF females have compartmentalized spermathecae with a transfer compartment, the fishnet canals, and a storage compartment, the reservoirs. Spermatozoa were counted both during and after mating in the two compartments. In addition to seminal fluids, the male transfers a mass of sperm in the fishnet canals, then only 49% of the transferred spermatozoa reach the reservoirs over two days. TEM observations of the fishnet canals revealed potential digestive functions, explaining the decline in the number and viability of spermatozoa in this compartment but not in the reservoirs. After one mating, females laid up to three fertile clutches, showing no constraints on sperm quantity or quality. Spermatic and ultrastructural investigations strongly suggest that BSF ejaculate acts both as a sperm plug and as a nuptial gift, reinforcing the interest in studying this farming insect as a new model for sexual selection.

Females translate male mRNA transferred during mating

Although RNA is found in the seminal fluid of diverse organisms, it is unknown whether it is functional within females. We developed a proteomic method (VESPA, Variant Enabled SILAC Proteomic Analysis) to test the hypothesis that Drosophila male seminal fluid RNA is translated by females. We found 67 male-derived, female-translated proteins (mdFTPs) in female lower reproductive tracts, many with predicted functions relevant to reproduction. Knockout experiments indicate that mdFTPs play diverse roles in postmating interactions, affecting fertilization success, and the formation/persistence of the insemination reaction mass, a trait hypothesized to be involved in sexual conflict. These findings advance our understanding of reproduction by revealing a mechanism of postmating molecular interactions between the sexes that strengthens and extends male influences on reproduction in previously unrecognized ways. Given the diverse species that carry RNA in seminal fluid, this discovery has broad significance for understanding molecular mechanisms of cooperation and conflict during reproduction.

O-Glycosylation of a male seminal fluid protein influences sperm binding and female postmating behavior

Glycoproteins are abundant within the human reproductive system and alterations in glycosylation lead to reproductive disorders, suggesting that glycans play an important role in reproductive function. In this study, we used the Drosophila reproductive system as a model to investigate the biological functions of O-glycosylation. We found that O-glycosylation in the male accessory glands, an organ responsible for secreting seminal fluid proteins, plays important roles in female postmating behavior. The loss of one O-glycosyltransferase, PGANT9, in the male reproductive system resulted in decreased egg production in mated females. We identified one substrate of PGANT9, lectin-46Ca (CG1656), which is known to affect female postmating responses. We further show that the loss of lectin-46Ca O-glycosylation affects its ability to associate with sperm tails, resulting in reduced transfer within the female reproductive system. Our results provide the first example that O-glycosylation of a seminal fluid protein affects its ability to associate with sperm in vivo. These studies may shed light on the biological function of O-glycans in mammalian reproduction.

Proteomic diversification of spermatostyles among six species of whirligig beetles

Seminal fluid protein composition is complex and commonly assumed to be rapidly divergent due to functional interactions with both sperm and the female reproductive tract (FRT), both of which evolve rapidly. In addition to sperm, seminal fluid may contain structures, such as mating plugs and spermatophores. Here, we investigate the evolutionary diversification of a lesser-known ejaculate structure: the spermatostyle, which has independently arisen in several families of beetles and true bugs. We characterized the spermatostyle proteome, in addition to spermatostyle and FRT morphology, in six species of whirligig beetles (family Gyrinidae). Spermatostyles were enriched for proteolytic enzymes, and assays confirmed they possess proteolytic activity. Sperm-leucylaminopeptidases (S-LAPs) were particularly abundant, and their localization to spermatostyles was confirmed by immunohistochemistry. Although there was evidence for functional conservation of spermatostyle proteomes across species, phylogenetic regressions suggest evolutionary covariation between protein composition and the morphology of both spermatostyles and FRTs. We postulate that S-LAPs (and other proteases) have evolved a novel structural role in spermatostyles and discuss spermatostyles as adaptations for delivering male-derived materials to females.

Finishing the egg

Gamete development is a fundamental process that is highly conserved from early eukaryotes to mammals. As germ cells develop, they must coordinate a dynamic series of cellular processes that support growth, cell specification, patterning, the loading of maternal factors (RNAs, proteins, and nutrients), differentiation of structures to enable fertilization and ensure embryonic survival, and other processes that make a functional oocyte. To achieve these goals, germ cells integrate a complex milieu of environmental and developmental signals to produce fertilizable eggs. Over the past 50 years, Drosophila oogenesis has risen to the forefront as a system to interrogate the sophisticated mechanisms that drive oocyte development. Studies in Drosophila have defined mechanisms in germ cells that control meiosis, protect genome integrity, facilitate mRNA trafficking, and support the maternal loading of nutrients. Work in this system has provided key insights into the mechanisms that establish egg chamber polarity and patterning as well as the mechanisms that drive ovulation and egg activation. Using the power of Drosophila genetics, the field has begun to define the molecular mechanisms that coordinate environmental stresses and nutrient availability with oocyte development. Importantly, the majority of these reproductive mechanisms are highly conserved throughout evolution, and many play critical roles in the development of somatic tissues as well. In this chapter, we summarize the recent progress in several key areas that impact egg chamber development and ovulation. First, we discuss the mechanisms that drive nutrient storage and trafficking during oocyte maturation and vitellogenesis. Second, we examine the processes that regulate follicle cell patterning and how that patterning impacts the construction of the egg shell and the establishment of embryonic polarity. Finally, we examine regulatory factors that control ovulation, egg activation, and successful fertilization.

Females translate male mRNA transferred during mating

Although RNA is found in the seminal fluid of diverse organisms, it is unknown whether this RNA is functional within females. Here, we develop an experimental proteomic method called VESPA (Variant Enabled SILAC Proteomic Analysis) to test the hypothesis that Drosophila male seminal fluid RNA is translated by females. We find strong evidence for 67 male-derived, female-translated proteins (mdFTPs) in female lower reproductive tracts at six hours postmating, many with predicted functions relevant to reproduction. Gene knockout experiments indicate that genes coding for mdFTPs play diverse roles in postmating interactions, with effects on fertilization efficiency, and the formation and persistence of the insemination reaction mass, a trait hypothesized to be involved in sexual conflict. These findings advance our understanding of reproduction by revealing a novel mechanism of postmating molecular interactions between the sexes that strengthens and extends male influences on reproductive outcomes in previously unrecognized ways. Given the diverse species known to carry RNA in seminal fluid, this discovery has broad significance for understanding molecular mechanisms of cooperation and conflict during reproduction.

Evolutionary dynamics of sex-biased genes expressed in cricket brains and gonads

Sex-biased gene expression, particularly sex-biased expression in the gonad, has been linked to rates of protein sequence evolution (nonsynonymous to synonymous substitutions, dN/dS) in animals. However, in insects, sex-biased expression studies remain centred on a few holometabolous species. Moreover, other major tissue types such as the brain remain underexplored. Here, we studied sex-biased gene expression and protein evolution in a hemimetabolous insect, the cricket Gryllus bimaculatus. We generated novel male and female RNA-seq data for two sexual tissue types, the gonad and somatic reproductive system, and for two core components of the nervous system, the brain and ventral nerve cord. From a genome-wide analysis, we report several core findings. Firstly, testis-biased genes had accelerated evolution, as compared to ovary-biased and unbiased genes, which was associated with positive selection events. Secondly, although sex-biased brain genes were much less common than for the gonad, they exhibited a striking tendency for rapid protein sequence evolution, an effect that was stronger for the female than male brain. Further, some sex-biased brain genes were linked to sexual functions and mating behaviours, which we suggest may have accelerated their evolution via sexual selection. Thirdly, a tendency for narrow cross-tissue expression breadth, suggesting low pleiotropy, was observed for sex-biased brain genes, suggesting relaxed purifying selection, which we speculate may allow enhanced freedom to evolve adaptive protein functional changes. The findings of rapid evolution of testis-biased genes and male and female-biased brain genes are discussed with respect to pleiotropy, positive selection and the mating biology of this cricket.

Copulation Song in Drosophila: Do Females Sing to Change Male Ejaculate Allocation and Incite Postcopulatory Mate Choice?

Drosophila males sing a courtship song to achieve copulations with females. Females were recently found to sing a distinct song during copulation, which depends on male seminal fluid transfer and delays female remating. Here, it is hypothesized that female copulation song is a signal directed at the copulating male and changes ejaculate allocation. This may alter female remating and sperm usage, and thereby affect postcopulatory mate choice. Mechanisms of how female copulation song is elicited, how males respond to copulation song, and how remating is modulated, are considered. The potential adaptive value of female signaling during copulation is discussed with reference to vertebrate copulation calls and their proposed function in eliciting mate guarding. Female copulation song may be widespread within the Drosophila genus. This newly discovered behavior opens many interesting avenues for future research, including investigation of how sexually dimorphic neuronal circuits mediate communication between nervous system and reproductive organs.

Evolution of Reproductive Behavior

Behaviors associated with reproduction are major contributors to the evolutionary success of organisms and are subject to many evolutionary forces, including natural and sexual selection, and sexual conflict. Successful reproduction involves a range of behaviors, from finding an appropriate mate, courting, and copulation, to the successful production and (in oviparous animals) deposition of eggs following mating. As a consequence, behaviors and genes associated with reproduction are often under strong selection and evolve rapidly. Courtship rituals in flies follow a multimodal pattern, mediated through visual, chemical, tactile, and auditory signals. Premating behaviors allow males and females to assess the species identity, reproductive state, and condition of their partners. Conflicts between the "interests" of individual males, and/or between the reproductive strategies of males and females, often drive the evolution of reproductive behaviors. For example, seminal proteins transmitted by males often show evidence of rapid evolution, mediated by positive selection. Postmating behaviors, including the selection of oviposition sites, are highly variable and Drosophila species span the spectrum from generalists to obligate specialists. Chemical recognition features prominently in adaptation to host plants for feeding and oviposition. Selection acting on variation in pre-, peri-, and postmating behaviors can lead to reproductive isolation and incipient speciation. Response to selection at the genetic level can include the expansion of gene families, such as those for detecting pheromonal cues for mating, or changes in the expression of genes leading to visual cues such as wing spots that are assessed during mating. Here, we consider the evolution of reproductive behavior in Drosophila at two distinct, yet complementary, scales. Some studies take a microevolutionary approach, identifying genes and networks involved in reproduction, and then dissecting the genetics underlying complex behaviors in D. melanogaster Other studies take a macroevolutionary approach, comparing reproductive behaviors across the genus Drosophila and how these might correlate with environmental cues. A full synthesis of this field will require unification across these levels.

Control of mating plug expelling and sperm storage in Drosophila: A gynandromorph- and mutation-based dissection

INTRODUCTION

In this study, we analyzed gynandromorphs with female terminalia, to dissect mating-related female behaviors in Drosophila.

MATERIALS AND METHODS

We used gynandromorphs, experimentally modified wild-type (Oregon-R) females, and mutant females that lacked different components of the female reproductive apparatus.

RESULTS

Many of the gynandromorphs mated but did not expel the mating plug (MP). Some of these - with thousands of sperm in the uterus - failed to take up sperm into the storage organs. There were gynandromorphs that stored plenty of sperm but failed to release them to fertilize eggs. Expelling the MP, sperm uptake into the storage organs, and the release of stored sperm along egg production are separate steps occurring during Drosophila female fertility. Cuticle landmarks of the gynandromorphs revealed that while the nerve foci that control MP expelling and also those that control sperm uptake reside in the abdominal, the sperm release foci derive from the thoracic region of the blastoderm.

DISCUSSION AND CONCLUSION

The gynandromorph study is confirmed by analyses of (a) mutations that cause female sterility: Fs(3)Avar (preventing egg deposition), Tm2^gs (removing germline cells), and iab-4^DB (eliminating gonad formation) and (b) by experimentally manipulated wild-type females: decapitated or cut through ventral nerve cord.

Genital coupling, morphology and evolution of male holding structures in Cicadinae (Hemiptera: Cicadidae)

Male and female genitalia include some of the most complex and morphologically diverse structures in Metazoa. Ornamentations in genitalia have been studied in several groups, and a variety of functional roles have been proposed. Although complex features of the genitalia have been observed in internal genitalia in cicadas, their functions have not yet been elucidated. These ornamentations, together with precopulatory sexual selection, make cicadas good models for evolutionary studies on genital coupling. We explore the structural interaction of male and female genitalia in Guyalna bonaerensis (Berg) (Cicadinae) and the morphology of male ornamentations in Cicadinae generally. We group these ornamentations into two traits according to their inferred function: anchoring or gripping. We analyse the theca and vesica of 24 species and perform ancestral trait reconstruction under maximum likelihood and stochastic mapping on a Bayesian tree. Ornamentations of the male vesica and the female seminal ampoule possibly ensure male attachment by working as an active lock to avoid the premature termination of intercourse. These ornamentations emerged independently in different lineages in Cicadinae, reinforcing the suggestion that they are important adaptations to achieve complete copulation. Our results foster questions for the field of sexual selection and associated mechanisms shaping the evolution of male and female genitalia.

Genetic Factors Influencing Sperm Competition

Females of many different species often mate with multiple males, creating opportunities for competition among their sperm. Although originally unappreciated, sperm competition is now considered a central form of post-copulatory male–male competition that biases fertilization. Assays of differences in sperm competitive ability between males, and interactions between females and males, have made it possible to infer some of the main mechanisms of sperm competition. Nevertheless, classical genetic approaches have encountered difficulties in identifying loci influencing sperm competitiveness while functional and comparative genomic methodologies, as well as genetic variant association studies, have uncovered some interesting candidate genes. We highlight how the systematic implementation of approaches that incorporate gene perturbation assays in experimental competitive settings, together with the monitoring of progeny output or sperm features and behavior, has allowed the identification of genes unambiguously linked to sperm competitiveness. The emerging portrait from 45 genes (33 from fruit flies, 8 from rodents, 2 from nematodes, and 2 from ants) is their remarkable breadth of biological roles exerted through males and females, the non-preponderance of sperm genes, and their overall pleiotropic nature.

Selection shapes turnover and magnitude of sex-biased expression in Drosophila gonads

BACKGROUND

Sex-biased gene expression is thought to drive the phenotypic differences in males and females in metazoans. Drosophila has served as a primary model for studying male-female differences in gene expression, and its effects on protein sequence divergence. However, the forces shaping evolution of sex-biased expression remain largely unresolved, including the roles of selection and pleiotropy. Research on sex organs in Drosophila, employing original approaches and multiple-species contrasts, provides a means to gain insights into factors shaping the turnover and magnitude (fold-bias) of sex-biased expression.

RESULTS

Here, using recent RNA-seq data, we studied sex-biased gonadal expression in 10,740 protein coding sequences in four species of Drosophila, D. melanogaster, D. simulans, D. yakuba and D. ananassae (5 to 44 My divergence). Using an approach wherein we identified genes with lineage-specific transitions (LSTs) in sex-biased status (amongst testis-biased, ovary-biased and unbiased; thus, six transition types) standardized to the number of genes with the ancestral state (S-LSTs), and those with clade-wide expression bias status, we reveal several key findings. First, the six categorical types of S-LSTs in sex-bias showed disparate rates of turnover, consistent with differential selection pressures. Second, the turnover in sex-biased status was largely unrelated to cross-tissue expression breadth, suggesting pleiotropy does not restrict evolution of sex-biased expression. Third, the fold-sex-biased expression, for both testis-biased and ovary-biased genes, evolved directionally over time toward higher values, a crucial finding that could be interpreted as a selective advantage of greater sex-bias, and sexual antagonism. Fourth, in terms of protein divergence, genes with LSTs to testis-biased expression exhibited weak signals of elevated rates of evolution (than ovary-biased) in as little as 5 My, which strengthened over time. Moreover, genes with clade-wide testis-specific expression (44 My), a status not observed for any ovary-biased genes, exhibited striking acceleration of protein divergence, which was linked to low pleiotropy.

CONCLUSIONS

By studying LSTs and clade-wide sex-biased gonadal expression in a multi-species clade of Drosophila, we describe evidence that interspecies turnover and magnitude of sex-biased expression have been influenced by selection. Further, whilst pleiotropy was not connected to turnover in sex-biased gonadal expression, it likely explains protein sequence divergence.

Dynamic changes in ejaculatory bulb size during Drosophila melanogaster aging and mating

The ejaculatory bulb of Drosophila melanogaster males produces proteins and pheromones that play important roles in reproduction. This tissue is also the final mixing site for the ejaculate before transfer to the female. The ejaculatory bulb's dynamics remain largely unstudied. By microscopy of the ejaculatory bulb in maturing adult males, we observed that the ejaculatory bulb expands in size as males age. Moreover, we document that when males mate, their ejaculatory bulb expands further as ejaculate transfer begins, and then contracts halfway through the course of mating as ejaculate transfer finishes. Although there is some male-to-male variation in the timing of these changes, ultimately the tissue changes in a predictable pattern that gives insight into the active mating process in Drosophila.

Evolutionary Dynamics of Male Reproductive Genes in the Drosophila virilis Subgroup

Postcopulatory sexual selection (PCSS) is a potent evolutionary force that can drive rapid changes of reproductive genes within species, and thus has the potential to generate reproductive incompatibilities between species. Male seminal fluid proteins (SFPs) are major players in postmating interactions, and are important targets of PCSS in males. The virilis subgroup of Drosophila exhibits strong interspecific gametic incompatibilities, and can serve as a model to study the genetic basis of PCSS and gametic isolation. However, reproductive genes in this group have not been characterized. Here we utilize short-read RNA sequencing of male reproductive organs to examine the evolutionary dynamics of reproductive genes in members of the virilis subgroup: D. americana, D. lummei, D. novamexicana, and D. virilis. We find that the majority of male reproductive transcripts are testes-biased, accounting for ∼15% of all annotated genes. Ejaculatory bulb (EB)-biased transcripts largely code for lipid metabolic enzymes, and contain orthologs of the D. melanogaster EB protein, Peb-me, which is involved in mating-plug formation. In addition, we identify 71 candidate SFPs, and show that this gene set has the highest rate of nonsynonymous codon substitution relative to testes- and EB-biased genes. Furthermore, we identify orthologs of 35 D. melanogaster SFPs that have conserved accessory gland expression in the virilis group. Finally, we show that several of the SFPs that have the highest rate of nonsynonymous codon substitution reside on chromosomal regions, which contributes to paternal gametic incompatibility between species. Our results show that SFPs rapidly diversify in the virilis group, and suggest that they likely play a role in PCSS and/or gametic isolation.

Cleavage of the Drosophila seminal protein Acp36DE in mated females enhances its sperm storage activity

Sperm storage in the mated female reproductive tract (RT) is required for optimal fertility in numerous species with internal fertilization. In Drosophila melanogaster, sperm storage is dependent on female receipt of seminal fluid proteins (SFPs) during mating. The seminal fluid protein Acp36DE is necessary for the accumulation of sperm into storage. In the female RT, Acp36DE localizes to the anterior mating plug and also to a site in the common oviduct, potentially "corralling" sperm near the entry sites into the storage organs. Genetic studies showed that Acp36DE is also required for a series of conformational changes of the uterus that begin at the onset of mating and are hypothesized to move sperm towards the entry sites of the sperm storage organs. After Acp36DE is transferred to the female RT, the protein is cleaved by the astacin-metalloprotease Semp1. However, the effect of this cleavage on Acp36DE's function in sperm accumulation into storage is unknown. We used mass spectrometry to identify the single cleavage site in Acp36DE. We then mutated this site and tested the effects on sperm storage. Mutations of Acp36DE's cleavage site that slowed or prevented cleavage of the protein slowed the accumulation of sperm into storage, although they did not affect uterine conformational changes in mated females. Moreover, the N-terminal cleavage product of Acp36DE was sufficient to mediate sperm accumulation in storage, and it did so faster than versions of Acp36DE that could not be cleaved or were only cleaved slowly. These results suggest that cleavage of Acp36E may increase the number of bioactive molecules within the female RT, a mechanism similar to that hypothesized for Semp1's other substrate, the seminal fluid protein ovulin.

Rapid Evolution of Ovarian-Biased Genes in the Yellow Fever Mosquito (Aedes aegypti)

Males and females exhibit highly dimorphic phenotypes, particularly in their gonads, which is believed to be driven largely by differential gene expression. Typically, the protein sequences of genes upregulated in males, or male-biased genes, evolve rapidly as compared to female-biased and unbiased genes. To date, the specific study of gonad-biased genes remains uncommon in metazoans. Here, we identified and studied a total of 2927, 2013, and 4449 coding sequences (CDS) with ovary-biased, testis-biased, and unbiased expression, respectively, in the yellow fever mosquito Aedes aegypti The results showed that ovary-biased and unbiased CDS had higher nonsynonymous to synonymous substitution rates (dN/dS) and lower optimal codon usage (those codons that promote efficient translation) than testis-biased genes. Further, we observed higher dN/dS in ovary-biased genes than in testis-biased genes, even for genes coexpressed in nonsexual (embryo) tissues. Ovary-specific genes evolved exceptionally fast, as compared to testis- or embryo-specific genes, and exhibited higher frequency of positive selection. Genes with ovary expression were preferentially involved in olfactory binding and reception. We hypothesize that at least two potential mechanisms could explain rapid evolution of ovary-biased genes in this mosquito: (1) the evolutionary rate of ovary-biased genes may be accelerated by sexual selection (including female-female competition or male-mate choice) affecting olfactory genes during female swarming by males, and/or by adaptive evolution of olfactory signaling within the female reproductive system (e.g., sperm-ovary signaling); and/or (2) testis-biased genes may exhibit decelerated evolutionary rates due to the formation of mating plugs in the female after copulation, which limits male-male sperm competition.

The role of copulatory plugs in the mosquito-parasitic nematode Strelkovimermis spiculatus

The mosquito-parasitic nematode, Strelkovimermis spiculatus (Mermithidae: Nematoda) emerges from hosts and aggregates to form mating clusters characterized by intense male-male competition for females. Successful males deposit an adhesive copulatory plug over the female vulva after insemination. In choice experiments, males strongly preferred virgin females, whereas plugged females were ignored. Males made no attempt to displace copulatory plugs deposited by previous males. Plugged females repelled males without the need for physical contact. The observed chemical repellency was independent of females, since excised plugs alone showed the same negative male response. Removal of the plug shortly after mating reduced fecundity by 90%, presumably due to spermatids leaking from the vulva. The plug as a nutritional gift hypothesis was rejected because there was no post-mating reduction in plug size that would have indicated absorption. Despite being a male adaption to sperm competition, we conclude that the copulatory plug serves the fitness needs of both males and females in multiple roles that include paternity preservation, reduced male harassment, improved male search for mates, increased fecundity, and sperm retention.

The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species

Background

The Mediterranean fruit fly (medfly), Ceratitis capitata, is a major destructive insect pest due to its broad host range, which includes hundreds of fruits and vegetables. It exhibits a unique ability to invade and adapt to ecological niches throughout tropical and subtropical regions of the world, though medfly infestations have been prevented and controlled by the sterile insect technique (SIT) as part of integrated pest management programs (IPMs). The genetic analysis and manipulation of medfly has been subject to intensive study in an effort to improve SIT efficacy and other aspects of IPM control.

Results

The 479 Mb medfly genome is sequenced from adult flies from lines inbred for 20 generations. A high-quality assembly is achieved having a contig N50 of 45.7 kb and scaffold N50 of 4.06 Mb. In-depth curation of more than 1800 messenger RNAs shows specific gene expansions that can be related to invasiveness and host adaptation, including gene families for chemoreception, toxin and insecticide metabolism, cuticle proteins, opsins, and aquaporins. We identify genes relevant to IPM control, including those required to improve SIT.

Conclusions

The medfly genome sequence provides critical insights into the biology of one of the most serious and widespread agricultural pests. This knowledge should significantly advance the means of controlling the size and invasive potential of medfly populations. Its close relationship to Drosophila, and other insect species important to agriculture and human health, will further comparative functional and structural studies of insect genomes that should broaden our understanding of gene family evolution.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-016-1049-2) contains supplementary material, which is available to authorized users.