Eye development and photoreceptor differentiation in the cephalopod Doryteuthis pealeii

Genome and transcriptome mechanisms driving cephalopod evolution

Cephalopods are known for their large nervous systems, complex behaviors and morphological innovations. To investigate the genomic underpinnings of these features, we assembled the chromosomes of the Boston market squid, Doryteuthis (Loligo) pealeii, and the California two-spot octopus, Octopus bimaculoides, and compared them with those of the Hawaiian bobtail squid, Euprymna scolopes. The genomes of the soft-bodied (coleoid) cephalopods are highly rearranged relative to other extant molluscs, indicating an intense, early burst of genome restructuring. The coleoid genomes feature multi-megabase, tandem arrays of genes associated with brain development and cephalopod-specific innovations. We find that a known coleoid hallmark, extensive A-to-I mRNA editing, displays two fundamentally distinct patterns: one exclusive to the nervous system and concentrated in genic sequences, the other widespread and directed toward repetitive elements. We conclude that coleoid novelty is mediated in part by substantial genome reorganization, gene family expansion, and tissue-dependent mRNA editing.

“Cephalopods are known for their large nervous systems, complex behaviors, and morphological innovations. Here, the authors find that soft-bodied cephalopod genomes are more rearranged than other extant molluscs and that mRNA editing patterns are associated with the nervous system and repetitive elements”.

Allometry for Eyes and Optic Lobes in Oval Squid (Sepioteuthis lessoniana) with Special Reference to Their Ontogenetic Asymmetry

Eyes develop in relation to body size and brain area for visual processing in some vertebrates. Meanwhile, it is well known that many animals exhibit left–right asymmetry in both morphology and behavior, namely, lateralization. However, it remains unclear whether the eyes and visual processing brain areas synchronously develop for their asymmetry. Oval squid (Sepioteuthis lessoniana) exhibits lateralization of optic lobe volume and left or right eye usage toward specific targets during their ontogeny. We address the question of how left–right asymmetry of the eyes and optic lobes exhibit an allometric pattern. To examine this question, we estimated the left and right volumes of eyes and optic lobes using microcomputed tomography. We found that, for the optic lobe volume, the right enlargement that appeared at ages 45 and 80 days then shifted to the left at age 120 days. In contrast, the volume of eyes did not show any left–right asymmetries from hatching to age 120 days. We also found that the volume of the eyes and optic lobes showed a slower increase than that of the whole-body size. Within these two visually related organs, the eyes grew faster than the optic lobes until age 120 days. These results are discussed in the context of the survival strategy of oval squid that form schools, two months post-hatching.

Co-option of the limb patterning program in cephalopod eye development

Background

Across the Metazoa, similar genetic programs are found in the development of analogous, independently evolved, morphological features. The functional significance of this reuse and the underlying mechanisms of co-option remain unclear. Cephalopods have evolved a highly acute visual system with a cup-shaped retina and a novel refractive lens in the anterior, important for a number of sophisticated behaviors including predation, mating, and camouflage. Almost nothing is known about the molecular-genetics of lens development in the cephalopod.

Results

Here we identify the co-option of the canonical bilaterian limb patterning program during cephalopod lens development, a functionally unrelated structure. We show radial expression of transcription factors SP6-9/sp1, Dlx/dll, Pbx/exd, Meis/hth, and a Prdl homolog in the squid Doryteuthis pealeii, similar to expression required in Drosophila limb development. We assess the role of Wnt signaling in the cephalopod lens, a positive regulator in the developing Drosophila limb, and find the regulatory relationship reversed, with ectopic Wnt signaling leading to lens loss.

Conclusion

This regulatory divergence suggests that duplication of SP6-9 in cephalopods may mediate the co-option of the limb patterning program. Thus, our study suggests that this program could perform a more universal developmental function in radial patterning and highlights how canonical genetic programs are repurposed in novel structures.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-021-01182-2.

Semper's cells in the insect compound eye: Insights into ocular form and function

The arthropod compound eye represents one of two major eye types in the animal kingdom and has served as an essential experimental paradigm for defining fundamental mechanisms underlying sensory organ formation, function, and maintenance. One of the most distinguishing features of the compound eye is the highly regular array of lens facets that define individual eye (ommatidial) units. These lens facets are produced by a deeply conserved quartet of cuticle-secreting cells, called Semper cells (SCs). Also widely known as cone cells, SCs were originally identified for their secretion of the dioptric system, i.e. the corneal lens and underlying crystalline cones. Additionally, SCs are now known to execute a diversity of patterning and glial functions in compound eye development and maintenance. Here, we present an integrated account of our current knowledge of SC multifunctionality in the Drosophila compound eye, highlighting emerging gene regulatory modules that may drive the diverse roles for these cells. Drawing comparisons with other deeply conserved retinal glia in the vertebrate single lens eye, this discussion speaks to glial cell origins and opens new avenues for understanding sensory system support programs.

Identification of neural progenitor cells and their progeny reveals long distance migration in the developing octopus brain

Cephalopods have evolved nervous systems that parallel the complexity of mammalian brains in terms of neuronal numbers and richness in behavioral output. How the cephalopod brain develops has only been described at the morphological level, and it remains unclear where the progenitor cells are located and what molecular factors drive neurogenesis. Using histological techniques, we located dividing cells, neural progenitors and postmitotic neurons in Octopus vulgaris embryos. Our results indicate that an important pool of progenitors, expressing the conserved bHLH transcription factors achaete-scute or neurogenin, is located outside the central brain cords in the lateral lips adjacent to the eyes, suggesting that newly formed neurons migrate into the cords. Lineage-tracing experiments then showed that progenitors, depending on their location in the lateral lips, generate neurons for the different lobes, similar to the squid Doryteuthis pealeii. The finding that octopus newborn neurons migrate over long distances is reminiscent of vertebrate neurogenesis and suggests it might be a fundamental strategy for large brain development.

Embryonic development of the camouflaging dwarf cuttlefish, Sepia bandensis

BACKGROUND

The dwarf cuttlefish Sepia bandensis, a camouflaging cephalopod from the Indo-Pacific, is a promising new model organism for neuroscience, developmental biology, and evolutionary studies. Cuttlefish dynamically camouflage to their surroundings by altering the color, pattern, and texture of their skin. The skin's "pixels" (chromatophores) are controlled by motor neurons projecting from the brain. Thus, camouflage is a visible representation of neural activity. In addition to camouflage, the dwarf cuttlefish uses dynamic skin patterns for social communication. Despite more than 500 million years of evolutionary separation, cuttlefish and vertebrates converged to form limbs, camera-type eyes and a closed circulatory system. Moreover, cuttlefish have a striking ability to regenerate their limbs. Interrogation of these unique biological features will benefit from the development of a new set of tools. Dwarf cuttlefish reach sexual maturity in 4 months, they lay dozens of eggs over their 9-month lifespan, and the embryos develop to hatching in 1 month.

RESULTS

Here, we describe methods to culture dwarf cuttlefish embryos in vitro and define 25 stages of cuttlefish development.

CONCLUSION

This staging series serves as a foundation for future technologies that can be used to address a myriad of developmental, neurobiological, and evolutionary questions.

Krüppel-like factor/specificity protein evolution in the Spiralia and the implications for cephalopod visual system novelties

The cephalopod visual system is an exquisite example of convergence in biological complexity. However, we have little understanding of the genetic and molecular mechanisms underpinning its elaboration. The generation of new genetic material is considered a significant contributor to the evolution of biological novelty. We sought to understand if this mechanism may be contributing to cephalopod-specific visual system novelties. Specifically, we identified duplications in the Krüppel-like factor/specificity protein (KLF/SP) sub-family of C2H2 zinc-finger transcription factors in the squid Doryteuthis pealeii. We cloned and analysed gene expression of the KLF/SP family, including two paralogs of the DpSP6-9 gene. These duplicates showed overlapping expression domains but one paralog showed unique expression in the developing squid lens, suggesting a neofunctionalization of DpSP6-9a. To better understand this neofunctionalization, we performed a thorough phylogenetic analysis of SP6-9 orthologues in the Spiralia. We find multiple duplications and losses of the SP6-9 gene throughout spiralian lineages and at least one cephalopod-specific duplication. This work supports the hypothesis that gene duplication and neofunctionalization contribute to novel traits like the cephalopod image-forming eye and to the diversity found within Spiralia.

Evolution and development of complex eyes: a celebration of diversity

For centuries, the eye has fascinated scientists and philosophers alike, and as a result the visual system has always been at the forefront of integrating cutting-edge technology in research. We are again at a turning point at which technical advances have expanded the range of organisms we can study developmentally and deepened what we can learn. In this new era, we are finally able to understand eye development in animals across the phylogenetic tree. In this Review, we highlight six areas in comparative visual system development that address questions that are important for understanding the developmental basis of evolutionary change. We focus on the opportunities now available to biologists to study the developmental genetics, cell biology and morphogenesis that underlie the incredible variation of visual organs found across the Metazoa. Although decades of important work focused on gene expression has suggested homologies and potential evolutionary relationships between the eyes of diverse animals, it is time for developmental biologists to move away from this reductive approach. We now have the opportunity to celebrate the differences and diversity in visual organs found across animal development, and to learn what it can teach us about the fundamental principles of biological systems and how they are built.

Cephalopod Biology: At the Intersection Between Genomic and Organismal Novelties

Cephalopods are resourceful marine predators that have fascinated generations of researchers as well as the public owing to their advanced behavior, complex nervous system, and significance in evolutionary studies. Recent advances in genomics have accelerated the pace of cephalopod research. Many traditional areas focusing on evolution, development, behavior, and neurobiology, primarily on the morphological level, are now transitioning to molecular approaches. This review addresses the recent progress and impact of genomic and other molecular resources on research in cephalopods. We outline several key directions in which significant progress in cephalopod research is expected and discuss its impact on our understanding of the genetic background behind cephalopod biology and beyond.

Coupled Genomic Evolutionary Histories as Signatures of Organismal Innovations in Cephalopods: Co-evolutionary Signatures Across Levels of Genome Organization May Shed Light on Functional Linkage and Origin of Cephalopod Novelties

How genomic innovation translates into organismal organization remains largely unanswered. Possessing the largest invertebrate nervous system, in conjunction with many species-specific organs, coleoid cephalopods (octopuses, squids, cuttlefishes) provide exciting model systems to investigate how organismal novelties evolve. However, dissecting these processes requires novel approaches that enable deeper interrogation of genome evolution. Here, the existence of specific sets of genomic co-evolutionary signatures between expanded gene families, genome reorganization, and novel genes is posited. It is reasoned that their co-evolution has contributed to the complex organization of cephalopod nervous systems and the emergence of ecologically unique organs. In the course of reviewing this field, how the first cephalopod genomic studies have begun to shed light on the molecular underpinnings of morphological novelty is illustrated and their impact on directing future research is described. It is argued that the application and evolutionary profiling of evolutionary signatures from these studies will help identify and dissect the organismal principles of cephalopod innovations. By providing specific examples, the implications of this approach both within and beyond cephalopod biology are discussed.

Octopus insularis as a new marine model for evolutionary developmental biology

Octopuses are intriguing organisms that, together with squids and cuttlefishes, form the extant coleoid cephalopods. This group includes many species that can potentially be used as models in the fields of biomedicine, developmental biology, evolution, neuroscience and even for robotics research. The purpose of this work is to first present a simple method for maintaining Octopus insularis embryos under a laboratory setup. Second, we show that these embryos are suitable for detailed analyses of specific traits that appear during developmental stages, including the eyes, hearts, arms, suckers, chromatophores and Kölliker's organs. Similar complex traits between cephalopods and vertebrates such as the visual, cardiovascular, neural and pigmentation systems are generally considered to be a result of parallel evolution. We propose that O. insularis embryos could be used as a model for evolutionary developmental biology (or EvoDevo) research, where comparisons of the morphogenetic steps in the building of equivalent organs between cephalopods and known vertebrate model systems could shed light on evolutionary convergences and deep homologies.

Cephalopod Brains: An Overview of Current Knowledge to Facilitate Comparison With Vertebrates

Cephalopod and vertebrate neural-systems are often highlighted as a traditional example of convergent evolution. Their large brains, relative to body size, and complexity of sensory-motor systems and behavioral repertoires offer opportunities for comparative analysis. Despite various attempts, questions on how cephalopod 'brains' evolved and to what extent it is possible to identify a vertebrate-equivalence, assuming it exists, remain unanswered. Here, we summarize recent molecular, anatomical and developmental data to explore certain features in the neural organization of cephalopods and vertebrates to investigate to what extent an evolutionary convergence is likely. Furthermore, and based on whole body and brain axes as defined in early-stage embryos using the expression patterns of homeodomain-containing transcription factors and axonal tractography, we describe a critical analysis of cephalopod neural systems showing similarities to the cerebral cortex, thalamus, basal ganglia, midbrain, cerebellum, hypothalamus, brain stem, and spinal cord of vertebrates. Our overall aim is to promote and facilitate further, hypothesis-driven, studies of cephalopod neural systems evolution.

Conserved characteristics of ocular refractive development - Did the eye evolve once?

It has been speculated that the unitary eyes of vertebrates and molluscs, and the compound eyes of insects and crustaceans, evolved separately. On the other hand, the common use of rhodopsin as a photoreceptor molecule, and the conservation of Pax6 as a master control gene for eye development, suggest instead that the eye evolved once. Yet, recently the molecular genetics that had seemed to suggest a definitive answer to this evolutionary point has once again become cloudy. Here we propose an alternative approach to addressing the question of eye evolution through comparative analyses of physiological optics. Serendipitous discoveries involving form deprivation and defocusing with young monkeys and chicks demonstrated the conserved importance of visual experience on eye development. Similar results have been demonstrated in teleosts, although differences exist in eye anatomy, physiology and optics. In particular, since fish grow throughout life, these effects can also be demonstrated in adults. In comparison, the cephalopod eye is an often-cited example of convergent evolution with the vertebrate eye, although considerable developmental differences exist. Nevertheless, squid eyes from animals raised under alternative lighting exhibit anatomical and refractive changes that agree with those found in vertebrates. Together, these observations provide functional and structural support for the view that the eye evolved once. Because of their very compressed lifespans (only one to two years) cephalopods may be ideal animal models for the study of ocular refractive development.

Hierarchical role for transcription factors and chromatin structure in genome organization along adipogenesis

The three dimensional folding of mammalian genomes is cell type specific and difficult to alter suggesting that it is an important component of gene regulation. However, given the multitude of chromatin-associating factors, the mechanisms driving the colocalization of active chromosomal domains and the role of this organization in regulating the transcription program in adipocytes are not clear. Analysis of genome-wide chromosomal associations revealed cell type-specific spatial clustering of adipogenic genes in 3T3-L1 cells. Time course analysis demonstrated that the adipogenic 'hub', sampled by PPARγ and Lpin1, undergoes orchestrated reorganization during adipogenesis. Coupling the dynamics of genome architecture with multiple chromatin datasets indicated that among all the transcription factors (TFs) tested, RXR is central to genome reorganization at the beginning of adipogenesis. Interestingly, at the end of differentiation, the adipogenic hub was shifted to an H3K27me3-repressive environment in conjunction with attenuation of gene transcription. We propose a stage-specific hierarchy for the activity of TFs contributing to the establishment of an adipogenic genome architecture that brings together the adipogenic genetic program. In addition, the repositioning of this network in a H3K27me3-rich environment at the end of differentiation may contribute to the stabilization of gene transcription levels and reduce the developmental plasticity of these specialized cells.

DATABASE

All sequence data reported in this paper have been deposited at GEO (http://www.ncbi.nlm.nih.gov/geo/) (GSE92475).

Eye Development in Sepia officinalis Embryo: What the Uncommon Gene Expression Profiles Tell Us about Eye Evolution

In metazoans, there is a remarkable diversity of photosensitive structures; their shapes, physiology, optical properties, and development are different. To approach the evolution of photosensitive structures and visual function, cephalopods are particularly interesting organisms due to their most highly centralized nervous system and their camerular eyes which constitute a convergence with those of vertebrates. The eye morphogenesis in numerous metazoans is controlled mainly by a conserved Retinal Determination Gene Network (RDGN) including pax, six, eya, and dac playing also key developmental roles in non-retinal structures and tissues of vertebrates and Drosophila. Here we have identified and explored the role of Sof-dac, Sof-six1/2, Sof-eya in eye morphogenesis, and nervous structures controlling the visual function in Sepia officinalis. We compare that with the already shown expressions in eye development of Sof-otx and Sof-pax genes. Rhodopsin is the pigment responsible for light sensitivity in metazoan, which correlate to correlate visual function and eye development. We studied Sof-rhodopsin expression during retina differentiation. By in situ hybridization, we show that (1) all of the RDGN genes, including Sof-pax6, are expressed in the eye area during the early developmental stages but they are not expressed in the retina, unlike Sof-otx, which could have a role in retina differentiation; (2) Sof-rhodopsin is expressed in the retina just before vision gets functional, from stage 23 to hatching. Our results evidence a role of Sof-six1/2, Sof-eya, and Sof-dac in eye development. However, the gene network involved in the retinal photoreceptor differentiation remains to be determined. Moreover, for the first time, Sof-rhodopsin expression is shown in the embryonic retina of cuttlefish suggesting the evolutionary conservation of the role of rhodopsin in visual phototransduction within metazoans. These findings are correlated with the physiological and behavioral observations suggesting that S. officinalis is able to react to light stimuli from stage 25 of organogenesis on, as soon as the first retinal pigments appear.