Phylogenetic evidence for multiple independent origins of functional kleptoplasty in Sacoglossa (Heterobranchia, Gastropoda)

A reference genome for the long-term kleptoplast-retaining sea slug Elysia crispata morphotype clarki

Several species of sacoglossan sea slugs possess the incredible ability to sequester chloroplasts from the algae they consume. These "photosynthetic animals" incorporate stolen chloroplasts, called kleptoplasts, into the epithelial cells of tubules that extend from their digestive tracts throughout their bodies. The mechanism by which these slugs maintain functioning kleptoplasts in the absence of an algal nuclear genome is unknown. Here, we report a draft genome of the sacoglossan slug Elysia crispata morphotype clarki, a morphotype native to the Florida Keys that can retain photosynthetically active kleptoplasts for several months without feeding. We used a combination of Oxford Nanopore Technologies long reads and Illumina short reads to produce a 786-Mb assembly (N50 = 0.459 Mb) containing 68,514 predicted protein-coding genes. A phylogenetic analysis found no evidence of horizontal acquisition of genes from algae. We performed gene family and gene expression analyses to identify E. crispata genes unique to kleptoplast-containing slugs that were more highly expressed in fed versus unfed developmental life stages. Consistent with analyses in other kleptoplastic slugs, our investigation suggests that genes encoding lectin carbohydrate-binding proteins and those involved in regulation of reactive oxygen species and immunity may play a role in kleptoplast retention. Lastly, we identified four polyketide synthase genes that could potentially encode proteins producing UV- and oxidation-blocking compounds in slug cell membranes. The genome of E. crispata is a quality resource that provides potential targets for functional analyses and enables further investigation into the evolution and mechanisms of kleptoplasty in animals.

Prey species and abundance affect growth and photosynthetic performance of the polyphagous sea slug Elysia crispata

Some sacoglossan sea slugs steal functional macroalgal chloroplasts (kleptoplasts). In this study, we investigated the effects of algal prey species and abundance on the growth and photosynthetic capacity of the tropical polyphagous sea slug Elysia crispata. Recently hatched sea slugs fed and acquired chloroplasts from the macroalga Bryopsis plumosa, but not from Acetabularia acetabulum. However, adult sea slugs were able to switch diet to A. acetabulum, rapidly replacing the great majority of the original kleptoplasts. When fed with B. plumosa, higher feeding frequency resulted in significantly higher growth and kleptoplast photosynthetic yield, as well as a slower relative decrease in these parameters upon starvation. Longevity of A. acetabulum-derived chloroplasts in E. crispata was over twofold that of B. plumosa. Furthermore, significantly lower relative weight loss under starvation was observed in sea slugs previously fed on A. acetabulum than on B. plumosa. This study shows that functionality and longevity of kleptoplasts in photosynthetic sea slugs depend on the origin of the plastids. Furthermore, we have identified A. acetabulum as a donor of photosynthetically efficient chloroplasts common to highly specialized monophagous and polyphagous sea slugs capable of long-term retention, which opens new experimental routes to unravel the unsolved mysteries of kleptoplasty.

Phylogenomic resolution of the root of Panpulmonata, a hyperdiverse radiation of gastropods: new insight into the evolution of air breathing

Transitions to terrestriality have been associated with major animal radiations including land snails and slugs in Stylommatophora (>20 000 described species), the most successful lineage of 'pulmonates' (a non-monophyletic assemblage of air-breathing gastropods). However, phylogenomic studies have failed to robustly resolve relationships among traditional pulmonates and affiliated marine lineages that comprise clade Panpulmonata (Mollusca, Gastropoda), especially two key taxa: Sacoglossa, a group including photosynthetic sea slugs, and Siphonarioidea, intertidal limpet-like snails with a non-contractile pneumostome (narrow opening to a vascularized pallial cavity). To clarify the evolutionary history of the panpulmonate radiation, we performed phylogenomic analyses on datasets of up to 1160 nuclear protein-coding genes for 110 gastropods, including 40 new transcriptomes for Sacoglossa and Siphonarioidea. All 18 analyses recovered Sacoglossa as the sister group to a clade we named Pneumopulmonata, within which Siphonarioidea was sister to the remaining lineages in most analyses. Comparative modelling indicated shifts to marginal habitat (estuarine, mangrove and intertidal zones) preceded and accelerated the evolution of a pneumostome, present in the pneumopulmonate ancestor along with a one-sided plicate gill. These findings highlight key intermediate stages in the evolution of air-breathing snails, supporting the hypothesis that adaptation to marginal zones played an important role in major sea-to-land transitions.

A molecular phylogeny of Thuridilla Bergh, 1872 sea slugs (Gastropoda, Sacoglossa) reveals a case of flamboyant and cryptic radiation in the marine realm

The genus Thuridilla Bergh, 1872 comprises mostly tropical sap-sucking sea slugs species with flamboyantly coloured forms. However, the potential for cryptic or pseudocryptic species masked by convergent or polymorphic colour patterns has not been tested using molecular characters. In this study, we sampled 20 of the 23 recognized worldwide species and performed the most comprehensive molecular phylogenetic analysis of the genus to date using a multi-locus approach combining two mitochondrial (cytochrome c oxidase subunit I, 16S rRNA) and two nuclear (Histone H3, 28S rRNA) genes using maximum likelihood, maximum-parsimony and Bayesian criteria. Three molecular species delimitation methods (ABGD, GMYC, bPTP) and the morphology of radular teeth were additionally used to aid in species delimitation. Our analyses supported 35 species within Thuridilla, of which more than one-third (13) are part of a single radiation here named the Thuridilla gracilis (Risbec, 1928) species-complex. This complex includes T. gracilis, T. splendens (Baba, 1949), T. bayeri (Er. Marcus, 1965), and T. ratna (Er. Marcus, 1965), plus nine additional undescribed species. All 13 species are distinguishable by radular characters, external morphology and their DNA. The detection of this radiation led diversity of Thuridilla to be underestimated by about 25% and provides a new comparative system for studying the role of colour patterns in marine diversification.

Pigment and Fatty Acid Heterogeneity in the Sea Slug Elysia crispata Is Not Shaped by Habitat Depth

Simple Summary

Some species of sacoglossan sea slugs are able to steal chloroplasts from the algae they feed on and maintain them functional for several months, a process termed “kleptoplasty”. One of these photosynthetic slugs is Elysia crispata, found in coral reefs of the Gulf of Mexico. This sacoglossan inhabits different depths (0–25 m), being exposed to different food sources and contrasting light conditions. In this work, we characterized the pigment and fatty acid (FA) profiles, and quantified the total lipid, glycolipid and phospholipid contents of E. crispata from shallow (0–4 m) and deeper (8–12 m) waters, after a month of starvation to determine the longest and more stable retention of chloroplasts and its relation to habitat depth. Biochemical analyses allowed the identification of 12 photosynthetic pigments and 27 FAs. Heterogeneity in the composition of pigments confirmed the long-term retention of functional chloroplasts ingested from different algae. However, the differences found in pigment profile, total lipid content, and FA composition on individuals of E. crispata were not related to habitat depth. High amounts of glycolipids, exclusive chloroplast lipids, suggest a good condition of these photosynthetic organelles in animal cells. These results contribute baseline physiological data that may help explain evolutionary associations such as endosymbiosis.

Abstract

Long-term retention of functional chloroplasts in animal cells occurs only in sacoglossan sea slugs. Analysis of molecules related to the maintenance of these organelles can provide valuable information on this trait (kleptoplasty). The goal of our research was to characterize the pigment and fatty acid (FA) composition of the sea slug Elysia crispata and their associated chloroplasts that are kept functional for a long time, and to quantify total lipid, glycolipid and phospholipid contents, identifying differences between habitats: shallow (0–4 m) and deeper (8–12 m) waters. Specimens were sampled and analyzed after a month of food deprivation, through HPLC, GC-MS and colorimetric methods, to ensure an assessment of long-term kleptoplasty in relation to depth. Pigment signatures indicate that individuals retain chloroplasts from different macroalgal sources. FA classes, phospholipid and glycolipid contents displayed dissimilarities between depths. However, heterogeneities in pigment and FA profiles, as well as total lipid, glycolipid and phospholipid amounts in E. crispata were not related to habitat depth. The high content of chloroplast origin molecules, such as Chl a and glycolipids after a month of starvation, confirms that E. crispata retains chloroplasts in good biochemical condition. This characterization fills a knowledge gap of an animal model commonly employed to study kleptoplasty.

The Digestive Diverticula in the Carnivorous Nudibranch, Melibe leonina, Do Not Contain Photosynthetic Symbionts

A number of nudibranchs, including Melibe engeli and Melibe pilosa, harbor symbiotic photosynthetic zooxanthellae. Melibe leonina spends most of its adult life on seagrass or kelp, capturing planktonic organisms in the water column with a large, tentacle-lined oral hood that brings food to its mouth. M. leonina also has an extensive network of digestive diverticula, located just beneath its translucent integument, that are typically filled with pigmented material likely derived from ingested food. Therefore, the focus of this project was to test the hypothesis that M. leonina accumulates symbiotic photosynthetic dinoflagellates in these diverticula. First, we conducted experiments to determine if M. leonina exhibits a preference for light, which would allow chloroplasts that it might be harboring to carry out photosynthesis. We found that most M. leonina preferred shaded areas and spent less time in direct sunlight. Second, we examined the small green circular structures in cells lining the digestive diverticula. Like chlorophyll, they exhibited autofluorescence when illuminated at 480 nm, and they were also about the same size as chloroplasts and symbiotic zooxanthellae. However, subsequent electron microscopy found no evidence of chloroplasts in the digestive diverticula of M. leonina; the structures exhibiting autofluorescence at 480 nm were most likely heterolysosomes, consistent with normal molluscan digestion. Third, we did not find evidence of altered oxygen consumption or production in M. leonina housed in different light conditions, suggesting the lack of any significant photosynthetic activity in sunlight. Fourth, we examined the contents of the diverticula, using HPLC, thin layer chromatography, and spectroscopy. The results of these studies indicate that the diverticula did not contain any chlorophyll, but rather harbored other pigments, such as astaxanthin, which likely came from crustaceans in their diet. Together, all of these data suggest that M. leonina does sequester pigments from its diet, but not for the purpose of symbiosis with photosynthetic zooxanthellae. Considering the translucent skin of M. leonina, the pigmented diverticula may instead provide camouflage.

Evolution of life cycle dimorphism: An example of sacoglossan sea slugs

Many sea slugs of Sacoglossa (Mollusca: Heterobranchia) are sometimes called "solar-powered sea slugs" because they keep chloroplasts obtained from their food algae and receive photosynthetic products (termed kleptoplasty). Some species show life cycle dimorphism, in which a single species has some individuals with a complex life cycle (the mother produces planktotrophic larvae, which later settle in the adult habitat) and others with a simple life cycle (mothers produce benthic offspring by direct development or short-term nonfeeding larvae in which feeding planktonic stages are skipped). Life cycle dimorphism is not common among marine species. In this paper, we ask whether some aspects of the ecology of solar-powered sea slugs have promoted the evolution of life cycle dimorphism in them. We study the population dynamics of the two life-cycle types that differ in summer (one with planktonic life and the other with benthic life), but both have benthic life in other seasons. We obtain the conditions in which two types with different life cycles coexist stably or a single type generating offspring with different life cycles evolves. We conclude that the stable coexistence of two life cycles can evolve if benthic individuals in summer experience strongly density-dependent processes or if the between-year fluctuation of biomass growth in summer is very large. We discuss whether these results match the life cycles of solar-powered sea slugs with life cycle dimorphism.

Identification of scavenger receptors and thrombospondin-type-1 repeat proteins potentially relevant for plastid recognition in Sacoglossa

Functional kleptoplasty is a photosymbiotic relationship, in which photosynthetically active chloroplasts serve as an intracellular symbiont for a heterotrophic host. Among Metazoa, functional kleptoplasty is only found in marine sea slugs belonging to the Sacoglossa and recently described in Rhabdocoela worms. Although functional kleptoplasty has been intensively studied in Sacoglossa, the fundamentals of the specific recognition of the chloroplasts and their subsequent incorporation are unknown. The key to ensure the initiation of any symbiosis is the ability to specifically recognize the symbiont and to differentiate a symbiont from a pathogen. For instance, in photosymbiotic cnidarians, several studies have shown that the host innate immune system, in particular scavenger receptors (SRs) and thrombospondin-type-1 repeat (TSR) protein superfamily, is playing a major role in the process of recognizing and differentiating symbionts from pathogens. In the present study, SRs and TSRs of three Sacoglossa sea slugs, Elysia cornigera, Elysia timida, and Elysia chlorotica, were identified by translating available transcriptomes into potential proteins and searching for receptor specific protein and/or transmembrane domains. Both receptors classes are highly diverse in the slugs, and many new domain arrangements for each receptor class were found. The analyses of the gene expression of these three species provided a set of species-specific candidate genes, that is, SR-Bs, SR-Es, C-type lectins, and TSRs, that are potentially relevant for the recognition of kleptoplasts. The results set the base for future experimental studies to understand if and how these candidate receptors are indeed involved in chloroplast recognition.

Finding the Sweet Spot: Sub-Ambient Light Increases Fitness and Kleptoplast Survival in the Sea Slug Plakobranchus cf. ianthobaptus Gould, 1852

Sacoglossans, or "sap-sucking" sea slugs, are primarily algivorous, with many taxa exhibiting kleptoplasty, the feeding and retaining of photosynthetically active chloroplasts from algae. The Plakobranchus species complex exhibits some of the longest kleptoplast retention and survival times under starvation conditions, but the contributions of these kleptoplasts to their survival and overall fitness have been widely debated. In this study we assessed the effects of starvation and light on the fitness of Plakobranchus cf. ianthobaptus and its kleptoplasts by placing starved individuals in eight daily average light treatments, ranging from near dark (2 µmol photon m^-2 s^-1) to ambient light (470 µmol photon m^-2 s^-1). Slug weight was used as a metric of fitness, and kleptoplast photosynthetic activity was determined via maximum quantum yield (F_v/F_m) by pulse-amplitude modulated fluorometry as a proxy for kleptoplast health. Plakobranchus individuals in near-dark and high light treatments (>160 µmol photon m^-2 s^-1) experienced significantly greater weight loss than those in low light (65 µmol photon m^-2 s^-1) and moderate light treatments (95-135 µmol photon m^-2 s^-1). Additionally, individuals in high light treatments experienced a rapid decline in kleptoplast photosynthetic activity, while all other treatments experienced minimal decline. This relationship between kleptoplast degradation and weight loss suggests an important link between fitness and kleptoplasty. Given the significant negative effects of ambient conditions, regular refreshment and replenishment of kleptoplasts or physiological or behavioral adjustments are likely employed for the benefits of kleptoplasty to be maintained.

A new case of kleptoplasty in animals: Marine flatworms steal functional plastids from diatoms

To date, sea slugs have been considered the only animals known to sequester functional algal plastids into their own cells, via a process called "kleptoplasty." We report here, however, that endosymbionts in the marine flatworms Baicalellia solaris and Pogaina paranygulgus are isolated plastids stolen from diatoms. Ultrastructural data show that kleptoplasts are located within flatworm cells, while algal nuclei and other organelles are absent. Transcriptomic analysis and rbcL amplicons confirm the absence of algal nuclear mRNA and reveal that the plastids originate from different species of diatoms. Laboratory experiments demonstrated photosynthetic activity and short-term retention of kleptoplasts in starved worms. This lineage of flatworms represents the first known case of functional kleptoplasty involving diatoms and only the second known case of kleptoplasty across the entire tree of animals.

Polymorphic adaptations in metazoans to establish and maintain photosymbioses

Mutualistic symbioses are common throughout the animal kingdom. Rather unusual is a form of symbiosis, photosymbiosis, where animals are symbiotic with photoautotrophic organisms. Photosymbiosis is found among sponges, cnidarians, flatworms, molluscs, ascidians and even some amphibians. Generally the animal host harbours a phototrophic partner, usually a cyanobacteria or a unicellular alga. An exception to this rule is found in some sea slugs, which only retain the chloroplasts of the algal food source and maintain them photosynthetically active in their own cytosol - a phenomenon called 'functional kleptoplasty'. Research has focused largely on the biodiversity of photosymbiotic species across a range of taxa. However, many questions with regard to the evolution of the ability to establish and maintain a photosymbiosis are still unanswered. To date, attempts to understand genome adaptations which could potentially lead to the evolution of photosymbioses have only been performed in cnidarians. This knowledge gap for other systems is mainly due to a lack of genetic information, both for non-symbiotic and symbiotic species. Considering non-photosymbiotic species is, however, important to understand the factors that make symbiotic species so unique. Herein we provide an overview of the diversity of photosymbioses across the animal kingdom and discuss potential scenarios for the evolution of this association in different lineages. We stress that the evolution of photosymbiosis is probably based on genome adaptations, which (i) lead to recognition of the symbiont to establish the symbiosis, and (ii) are needed to maintain the symbiosis. We hope to stimulate research involving sequencing the genomes of various key taxa to increase the genomic resources needed to understand the most fundamental question: how have animals evolved the ability to establish and maintain a photosymbiosis?

How does temperature affect functional kleptoplasty? Comparing populations of the solar-powered sister-species Elysia timida Risso, 1818 and Elysia cornigera Nuttall, 1989 (Gastropoda: Sacoglossa)

Background

Despite widespread interest in solar-powered sea slugs (Sacoglossa: Gastropoda), relatively little is know about how they actually perform functional kleptoplasty. Sister-taxa Elysia timida and E. cornigera provide an ideal model system for investigating this phenomenon, since they feed on the same algal genus and only E. timida is capable of long-term kleptoplasty. Recent research has explored factors regarding functional kleptoplasty in E. timida, including their starvation longevity, digestive activity, autophagal response and photosynthetic efficiency under two different temperature conditions (18 °C and 21 °C). These studies revealed the trends E. timida displays regarding each factor during starvation as well as influences temperature has on some aspects of functional kleptoplasty. This study examines E. cornigera regarding each of these factors in an attempt to elucidate differences between each species that could explain their differing kleptoplastic abilities. Since both species naturally occur in 25 °C seawater (E. timida peak summer temperature, E. cornigera low winter temperature), each species was acclimatized to 25 °C to facilitate comparison and determine if these species exhibit physiological differences to starvation when under the same environmental conditions.

Results

When comparing the different E. timida temperature treatments, it becomes clear that increased temperatures compromise E. timida’s kleptoplastic abilities. Specimens acclimatized to 25 °C revealed shorter starvation longevities surviving an average 42.4 days compared to the 95.9 day average observed in specimens exposed to 18 °C. Each temperature treatment displayed a significantly different decrease throughout the starvation period in both, the rate of photosynthetic efficiency and in the decreasing functional kleptoplast abundance. Lysosomal abundances are assessed here as indicators of different aspects of metabolic activity, which could be correlated to temperature. E. cornigera, also acclimatized to 25 °C did not display significantly similar patterns as any of the E. timida temperature treatments, having fewer incorporated kleptoplasts, a higher lysosomal response to starvation, a faster decrease in photosynthetic efficiency and a lower starvation longevity.

Conclusions

These results confirm that each species has different physiological reactions to starvation and kleptoplast retention, even under the same conditions. While temperature affects aspects of functional kleptoplasty, it is likely not responsible for the differences in kleptoplastic abilities seen in these species.

Electronic supplementary material

The online version of this article (10.1186/s12983-018-0264-y) contains supplementary material, which is available to authorized users.

Chloroplast digestion and the development of functional kleptoplasty in juvenile Elysia timida (Risso, 1818) as compared to short-term and non-chloroplast-retaining sacoglossan slugs

Sacoglossan sea slugs are the only metazoans known to perform functional kleptoplasty, the sequestration and retention of functional chloroplasts within their digestive gland cells. Remarkably, a few species with this ability can survive starvation periods of 3–12 months likely due to their stolen chloroplasts. There are no reports of kleptoplast transfer from mother slug to either eggs or juveniles, demonstrating that each animal must independently acquire its kleptoplasts and develop the ability to maintain them within its digestive gland. We present here an investigation into the development of functional kleptoplasty in a long-term kleptoplast retaining species, Elysia timida. Laboratory-reared juvenile slugs of different post-metamorphic ages were placed in starvation and compared to 5 known short-term retaining slug species and 5 non-retaining slug species. The subsequent results indicate that functional kleptoplasty is not performed by E. timida until after 15 days post-metamorphosis and that by 25 days, these animals outlive many of the short-term retention species. Digestive activity was also monitored using lysosomal abundance as an indicator, revealing different patterns in starving juveniles versus adults. Starved juveniles were reintroduced to food to determine any differences in digestive activity when starvation ends, resulting in an increase in the number of kleptoplasts, but no overall change in lysosomal activity. By revealing some of the changes that occur during early development in these animals, which begin as non-kleptoplast-retaining and grow into long-term retaining slugs, this investigation provides a basis for future inquiries into the origin and development of this remarkable ability.

On Being the Right Size as an Animal with Plastids

Plastids typically reside in plant or algal cells-with one notable exception. There is one group of multicellular animals, sea slugs in the order Sacoglossa, members of which feed on siphonaceous algae. The slugs sequester the ingested plastids in the cytosol of cells in their digestive gland, giving the animals the color of leaves. In a few species of slugs, including members of the genus Elysia, the stolen plastids (kleptoplasts) can remain morphologically intact for weeks and months, surrounded by the animal cytosol, which is separated from the plastid stroma by only the inner and outer plastid membranes. The kleptoplasts of the Sacoglossa are the only case described so far in nature where plastids interface directly with the metazoan cytosol. That makes them interesting in their own right, but it has also led to the idea that it might someday be possible to engineer photosynthetic animals. Is that really possible? And if so, how big would the photosynthetic organs of such animals need to be? Here we provide two sets of calculations: one based on a best case scenario assuming that animals with kleptoplasts can be, on a per cm2 basis, as efficient at CO2 fixation as maize leaves, and one based on 14CO2 fixation rates measured in plastid-bearing sea slugs. We also tabulate an overview of the literature going back to 1970 reporting direct measurements or indirect estimates of the CO2 fixing capabilities of Sacoglossan slugs with plastids.

Mitochondrial Genome Assemblies of Elysia timida and Elysia cornigera and the Response of Mitochondrion-Associated Metabolism during Starvation

Some sacoglossan sea slugs sequester functional plastids (kleptoplasts) from their food, which continue to fix CO2 in a light dependent manner inside the animals. In plants and algae, plastid and mitochondrial metabolism are linked in ways that reach beyond the provision of energy-rich carbon compounds through photosynthesis, but how slug mitochondria respond to starvation or alterations in plastid biochemistry has not been explored. We assembled the mitochondrial genomes of the plastid-sequestering sea slugs Elysia timida and Elysia cornigera from RNA-Seq data that was complemented with standard sequencing of mitochondrial DNA through primer walking. Our data confirm the sister species relationship of the two Sacoglossa and from the analysis of changes in mitochondrial-associated metabolism during starvation we speculate that kleptoplasts might aid in the rerouting or recycling of reducing power independent of, yet maybe improved by, photosynthesis.

Why It Is Time to Look Beyond Algal Genes in Photosynthetic Slugs

Eukaryotic organelles depend on nuclear genes to perpetuate their biochemical integrity. This is true for mitochondria in all eukaryotes and plastids in plants and algae. Then how do kleptoplasts, plastids that are sequestered by some sacoglossan sea slugs, survive in the animals’ digestive gland cells in the absence of the algal nucleus encoding the vast majority of organellar proteins? For almost two decades, lateral gene transfer (LGT) from algae to slugs appeared to offer a solution, but RNA-seq analysis, later supported by genome sequencing of slug DNA, failed to find any evidence for such LGT events. Yet, isolated reports continue to be published and are readily discussed by the popular press and social media, making the data on LGT and its support for kleptoplast longevity appear controversial. However, when we take a sober look at the methods used, we realize that caution is warranted in how the results are interpreted. There is no evidence that the evolution of kleptoplasty in sea slugs involves LGT events. Based on what we know about photosystem maintenance in embryophyte plastids, we assume kleptoplasts depend on nuclear genes. However, studies have shown that some isolated algal plastids are, by nature, more robust than those of land plants. The evolution of kleptoplasty in green sea slugs involves many promising and unexplored phenomena, but there is no evidence that any of these require the expression of slug genes of algal origin.