A molecular and karyological approach to the taxonomy of Nautilus

The gold-ringed octopus (Amphioctopus fangsiao) genome and cerebral single-nucleus transcriptomes provide insights into the evolution of karyotype and neural novelties

BACKGROUND

Coleoid cephalopods have distinctive neural and morphological characteristics compared to other invertebrates. Early studies reported massive genomic rearrangements occurred before the split of octopus and squid lineages (Proc Natl Acad Sci U S A 116:3030-5, 2019), which might be related to the neural innovations of their brain, yet the details remain elusive. Here we combine genomic and single-nucleus transcriptome analyses to investigate the octopod chromosome evolution and cerebral characteristics.

RESULTS

We present a chromosome-level genome assembly of a gold-ringed octopus, Amphioctopus fangsiao, and a single-nucleus transcriptome of its supra-esophageal brain. Chromosome-level synteny analyses estimate that the chromosomes of the ancestral octopods experienced multiple chromosome fission/fusion and loss/gain events by comparing with the nautilus genome as outgroup, and that a conserved genome organization was detected during the evolutionary process from the last common octopod ancestor to their descendants. Besides, protocadherin, GPCR, and C2H2 ZNF genes are thought to be highly related to the neural innovations in cephalopods (Nature 524:220-4, 2015), and the chromosome analyses pinpointed several collinear modes of these genes on the octopod chromosomes, such as the collinearity between PCDH and C2H2 ZNF, as well as between GPCR and C2H2 ZNF. Phylogenetic analyses show that the expansion of the octopod protocadherin genes is driven by a tandem-duplication mechanism on one single chromosome, including two separate expansions at 65 million years ago (Ma) and 8-14 Ma, respectively. Furthermore, we identify eight cell types (i.e., cholinergic and glutamatergic neurons) in the supra-esophageal brain of A. fangsiao, and the single-cell expression analyses reveal the co-expression of protocadherin and GPCR in specific neural cells, which may contribute to the neural development and signal transductions in the octopod brain.

CONCLUSIONS

The octopod genome analyses reveal the dynamic evolutionary history of octopod chromosomes and neural-related gene families. The single-nucleus transcriptomes of the supra-esophageal brain indicate their cellular heterogeneities and functional interactions with other tissues (i.e., gill), which provides a foundation for further octopod cerebral studies.

Significance of the suture line in cephalopod taxonomy revealed by 3D morphometrics in the modern nautilids Nautilus and Allonautilus

Assessing the taxonomic importance of the suture line in shelled cephalopods is a key to better understanding the diversity of this group in Earth history. Because fossils are subject to taphonomic artifacts, an in-depth knowledge of well-preserved modern organisms is needed as an important reference. Here, we examine the suture line morphology of all known species of the modern cephalopods Nautilus and Allonautilus. We applied computed tomography and geometric morphometrics to quantify the suture line morphology as well as the conch geometry and septal spacing. Results reveal that the suture line and conch geometry are useful in distinguishing species, while septal spacing is less useful. We also constructed cluster trees to illustrate the similarity among species. The tree based on conch geometry in middle ontogeny is nearly congruent with those previously reconstructed based on molecular data. In addition, different geographical populations of the same species of Nautilus separate out in this tree. This suggests that genetically distinct (i.e., geographically isolated) populations of Nautilus can also be distinguished using conch geometry. Our results are applicable to closely related fossil cephalopods (nautilids), but may not apply to more distantly related forms (ammonoids).

Genomic insights into the adaptation and evolution of the nautilus, an ancient but evolving "living fossil"

The nautilus, commonly known as a "living fossil," is endangered and may be at risk of extinction. The lack of genomic information hinders a thorough understanding of its biology and evolution, which can shed light on the conservation of this endangered species. Here, we report the first high-quality chromosome-level genome assembly of Nautilus pompilius. The assembled genome size comprised 785.15 Mb. Comparative genomic analyses indicated that transposable elements (TEs) and large-scale genome reorganizations may have driven lineage-specific evolution in the cephalopods. Remarkably, evolving conserved genes and recent TE insertion activities were identified in N. pompilius, and we speculate that these findings reflect the strong adaptability and long-term survival of the nautilus. We also identified gene families that are potentially responsible for specific adaptation and evolution events. Our study provides unprecedented insights into the specialized biology and evolution of N. pompilius, and the results serve as an important resource for future conservation genomics of the nautilus and closely related species.

The evo-devo of molluscs: Insights from a genomic perspective

Molluscs represent one of ancient and evolutionarily most successful groups of marine invertebrates, with a tremendous diversity of morphology, behavior, and lifestyle. Molluscs are excellent subjects for evo-devo studies; however, understanding of the evo-devo of molluscs has been largely hampered by incomplete fossil records and limited molecular data. Recent advancement of genomics and other technologies has greatly fueled the molluscan "evo-devo" field, and decoding of several molluscan genomes provides unprecedented insights into molluscan biology and evolution. Here, we review the recent progress of molluscan genome sequencing as well as novel insights gained from their genomes, by emphasizing how molluscan genomics enhances our understanding of the evo-devo of molluscs.

Postmortem transport in fossil and modern shelled cephalopods

The chambered shells of cephalopod mollusks, such as modern Nautilus and fossil ammonoids, have the potential to float after death, which could result in significant postmortem transport of shells away from living habitats. Such transport would call into question these clades' documented biogeographic distributions and therefore the many (paleo)biological interpretations based on them. It is therefore imperative to better constrain the likelihood and extent of postmortem transport in modern and fossil cephalopods. Here, I combine the results of classic experiments on postmortem buoyancy with datasets on cephalopod shell form to determine that only those shells with relatively high inflation are likely to float for a significant interval after death and therefore potentially experience postmortem transport. Most ammonoid cephalopods have shell forms making postmortem transport unlikely. Data on shell forms and geographic ranges of early Late Cretaceous cephalopod genera demonstrate that even genera with shell forms conducive to postmortem buoyancy do not, in fact, show artificially inflated biogeographic ranges relative to genera with non-buoyant morphologies. Finally, georeferenced locality data for living nautilid specimens and dead drift shells indicate that most species have relatively small geographic ranges and experience limited drift. Nautilus pompilius is the exception, with a broad Indo-Pacific range and drift shells found far from known living populations. Given the similarity of N. pompilius to other nautilids in its morphology and ecology, it seems unlikely that this species would have a significantly different postmortem fate than its close relatives. Rather, it is suggested that drift shells along the east African coast may indicate the existence of modern (or recently extirpated) living populations of nautilus in the western Indian Ocean, which has implications for the conservation of these cephalopods.

Cytogenetic studies in three octopods, Octopusminor, Amphioctopusfangsiao, and Cistopuschinensis from the coast of China

To provide markers to identify chromosomes in the genome of octopods, chromosomes of three octopus species were subjected to NOR/C-banding. In addition, we examined their genome size (C value) to submit it to the Animal Genome Size Database. Silver staining revealed that the number of Ag-nucleoli was 2 (Octopusminor (Sasaki, 1920)), 2 (Amphioctopusfangsiao (d'Orbigny, 1839)) and 1 (Cistopuschinensis Zheng et al., 2012), respectively, and the number of Ag-nucleoli visible was the same as that of Ag-NORs on metaphase plates in the same species. In all analyzed metaphases, Ag-NORs were mainly located terminally on the long arms of chromosomes 3 (3^rd) of O.minor and on the short arms of chromosomes 4 (4^th) of A.fangsiao, whereas only one of the chromosomes 23 (23^rd) was found Ag-NORs of C.chinensis. C-bands were localized predominantly in the centromeric regions of chromosomes in the three species, while other conspicuous stable C-bands were observed in terminal regions, including the Ag-NORs. That means these three chromosome pairs (3^rd, 4^th and 23^rd) could be considered species-specific cytogenetic markers. The mean C values of O.minor, A.fangsiao and C.chinensis were 7.81±0.39 pg (0.070 pg per unit length), 8.31±0.18 pg (0.068 pg per unit length) and 5.29±0.10 pg (0.038 pg per unit length), respectively, and results showed that C values of the three species were not proportional to the relative length of the chromosomes. These cytogenetic characteristics will provide more theoretical foundation for further researches on chromosome evolution in octopods.

Comparison of the genetic relationship between nine Cephalopod species based on cluster analysis of karyotype evolutionary distance

Karyotype analysis was carried out on gill cells of three species of octopods using a conventional air-drying method. The karyotype results showed that all the three species have the same diploid chromosome number, 2n=60, but with different karyograms as 2n=38M+6SM+8ST+8T, FN (fundamental number)=104 (Cistopus chinensis Zheng et al., 2012), 2n=42M+6SM+4ST+8T, FN=108 (Octopus minor (Sasaki, 1920)) and 2n=32M+16SM+12T, FN=108 (Amphioctopus fangsiao (d'Orbigny, 1839-1841)). These findings were combined with data from earlier studies to infer the genetic relationships between nine species via cluster analysis using the karyotype evolutionary distance (D_e ) and resemblance-near coefficient (λ). The resulting tree revealed a clear distinction between different families and orders which was substantially consistent with molecular phylogenies. The smallest intraspecific evolutionary distance (D_e =0.2013, 0.2399) and largest resemblance-near coefficient (λ=0.8184, 0.7871) appeared between O. minor and C. chinensis, and Sepia esculenta Hoyle, 1885 and S. lycidas Gray, 1849, respectively, indicating that these species have the closest relationship. The largest evolutionary gap appeared between species with complicated karyotypes and species with simple karyotypes. Cluster analysis of D_e and λ provides information to supplement traditional taxonomy and molecular systematics, and it would serve as an important auxiliary for routine phylogenetic study.

The octopus genome and the evolution of cephalopod neural and morphological novelties

Coleoid cephalopods (octopus, squid, and cuttlefish) are active, resourceful predators with a rich behavioral repertoire¹. They have the largest nervous systems among the invertebrates² and present other striking morphological innovations including camera-like eyes, prehensile arms, a highly derived early embryogenesis, and the most sophisticated adaptive coloration system among all animals^1,3. To investigate the molecular bases of cephalopod brain and body innovations we sequenced the genome and multiple transcriptomes of the California two-spot octopus, Octopus bimaculoides. We found no evidence for hypothesized whole genome duplications in the octopus lineage^4–6. The core developmental and neuronal gene repertoire of the octopus is broadly similar to that found across invertebrate bilaterians, except for massive expansions in two gene families formerly thought to be uniquely enlarged in vertebrates: the protocadherins, which regulate neuronal development, and the C2H2 superfamily of zinc finger transcription factors. Extensive mRNA editing generates transcript and protein diversity in genes involved in neural excitability, as previously described⁷, as well as in genes participating in a broad range of other cellular functions. We identified hundreds of cephalopod-specific genes, many of which showed elevated expression levels in such specialized structures as the skin, the suckers, and the nervous system. Finally, we found evidence for large-scale genomic rearrangements that are closely associated with transposable element expansions. Our analysis suggests that substantial expansion of a handful of gene families, along with extensive remodeling of genome linkage and repetitive content, played a critical role in the evolution of cephalopod morphological innovations, including their large and complex nervous systems.

DNA barcoding in Nautilus pompilius (Mollusca : Cephalopoda): evolutionary divergence of an ancient species in modern times

DNA barcoding studies to elucidate the evolutionary and dispersal history of the current populations of Nautilus pompilius allow us to develop a greater understanding of their biology, their movement and the systematic relationships between different groups. Phylogenetic analyses were conducted on Australian N. pompilius, and COI sequences were generated for 98 discrete accessions. Sequences from samples collected across the distribution were sourced from GenBank and included in the analyses. Maximum likelihood revealed three distinct clades for N. pompilius: (1) populations sourced from west Australia, Indonesia and the Philippines; (2) populations collected from east Australia and Papua New Guinea; (3) western Pacific accessions from Vanuatu, American Samoa and Fiji, supporting previous findings on the evolutionary divergence of N. pompilius. A minimum spanning tree revealed 49 discrete haplotypes for the 128 accessions, from a total of 16 discrete sampling locations. Population similarity reflects oceanic topographic features, with divergence between populations across the N. pompilius range mirroring geographical separation. This illustrates the success of DNA barcoding as a tool to identify geographic origin, and looks to the future role of such technology in population genetics and evolutionary biology.

Genome structure analysis of molluscs revealed whole genome duplication and lineage specific repeat variation

Comparative genome structure analysis allows us to identify novel genes, repetitive sequences and gene duplications. To explore lineage-specific genomic changes of the molluscs that is good model for development of nervous system in invertebrate, we conducted comparative genome structure analyses of three molluscs, pygmy squid, nautilus and scallops using partial genome shotgun sequencing. Most effective elements on the genome structural changes are repetitive elements (REs) causing expansion of genome size and whole genome duplication producing large amount of novel functional genes. Therefore, we investigated variation and proportion of REs and whole genome duplication. We, first, identified variations of REs in the three molluscan genomes by homology-based and de novo RE detection. Proportion of REs were 9.2%, 4.0%, and 3.8% in the pygmy squid, nautilus and scallop, respectively. We, then, estimated genome size of the species as 2.1, 4.2 and 1.8 Gb, respectively, with 2× coverage frequency and DNA sequencing theory. We also performed a gene duplication assay based on coding genes, and found that large-scale duplication events occurred after divergence from the limpet Lottia, an out-group of the three molluscan species. Comparison of all the results suggested that RE expansion did not relate to the increase in genome size of nautilus. Despite close relationships to nautilus, the squid has the largest portion of REs and smaller genome size than nautilus. We also identified lineage-specific RE and gene-family expansions, possibly relate to acquisition of the most complicated eye and brain systems in the three species.

Evolution of nacre: biochemistry and proteomics of the shell organic matrix of the cephalopod Nautilus macromphalus

In mollusks, one of the most widely studied shell textures is nacre, the lustrous aragonitic layer that constitutes the internal components of the shells of several bivalves, a few gastropods,and one cephalopod: the nautilus. Nacre contains a minor organic fraction, which displays a wide range of functions in relation to the biomineralization process. Here, we have biochemically characterized the nacre matrix of the cephalopod Nautilus macromphalus. The acid-soluble matrix contains a mixture of polydisperse and discrete proteins and glycoproteins, which interact with the formation of calcite crystals. In addition, a few bind calcium ions. Furthermore, we have used a proteomic approach,which was applied to the acetic acid-soluble and -insoluble shell matrices, as well as to spots obtained after 2D gel electrophoresis. Our data demonstrate that the insoluble and soluble matrices, although different in their bulk monosaccharide and amino acid compositions, contain numerous shared peptides. Strikingly, most of the obtained partial sequences are entirely new. A few only partly match with bivalvian nacre proteins.Our findings have implications for knowledge of the long-term evolution of molluskan nacre matrices.

The Hemocyanin from a Living Fossil, the Cephalopod Nautilus pompilius: Protein Structure, Gene Organization, and Evolution

By electron microscopic and immunobiochemical analyses we have confirmed earlier evidence that Nautilus pompilius hemocyanin (NpH) is a ring-like decamer (M(r) = approximately 3.5 million), assembled from 10 identical copies of an approximately 350-kDa polypeptide. This subunit in turn is substructured into seven sequential covalently linked functional units of approximately 50 kDa each (FUs a-g). We have cloned and sequenced the cDNA encoding the complete polypeptide; it comprises 9198 bp and is subdivided into a 5' UTR of 58 bp, a 3' UTR of 365 bp, and an open reading frame for a signal peptide of 21 amino acids plus a polypeptide of 2903 amino acids (M(r) = 335,881). According to sequence alignments, the seven FUs of Nautilus hemocyanin directly correspond to the seven FU types of the previously sequenced hemocyanin "OdH" from the cephalopod Octopus dofleini. Thirteen potential N-glycosylation sites are distributed among the seven Nautilus hemocyanin FUs; the structural consequences of putatively attached glycans are discussed on the basis of the published X-ray structure for an Octopus dofleini and a Rapana thomasiana FU. Moreover, the complete gene structure of Nautilus hemocyanin was analyzed; it resembles that of Octopus hemocyanin with respect to linker introns but shows two internal introns that differ in position from the three internal introns of the Octopus hemocyanin gene. Multiple sequence alignments allowed calculation of a rather robust phylogenetic tree and a statistically firm molecular clock. This reveals that the last common ancestor of Nautilus and Octopus lived 415 +/- 24 million years ago, in close agreement with fossil records from the early Devonian.