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

A chromosome-level reference genome for the common octopus, Octopus vulgaris (Cuvier, 1797)

Cephalopods are emerging animal models and include iconic species for studying the link between genomic innovations and physiological and behavioral complexities. Coleoid cephalopods possess the largest nervous system among invertebrates, both for cell counts and brain-to-body ratio. Octopus vulgaris has been at the center of a long-standing tradition of research into diverse aspects of cephalopod biology, including behavioral and neural plasticity, learning and memory recall, regeneration, and sophisticated cognition. However, no chromosome-scale genome assembly was available for O. vulgaris to aid in functional studies. To fill this gap, we sequenced and assembled a chromosome-scale genome of the common octopus, O. vulgaris. The final assembly spans 2.8 billion basepairs, 99.34% of which are in 30 chromosome-scale scaffolds. Hi-C heatmaps support a karyotype of 1n = 30 chromosomes. Comparisons with other octopus species' genomes show a conserved octopus karyotype and a pattern of local genome rearrangements between species. This new chromosome-scale genome of O. vulgaris will further facilitate research in all aspects of cephalopod biology, including various forms of plasticity and the neural machinery underlying sophisticated cognition, as well as an understanding of cephalopod evolution.

Transcriptomic analysis of oxidative stress mechanisms induced by acute nanoplastic exposure in Sepia esculenta larvae

Nanoplastics (NPs), as a new type of pollutant with a size small than 1 μm, are ubiquitous and harmful to organisms. There has been an increasing amount of research concerning the effects of NPs on organisms over recent years, especially on aquatic animals. However, there is a limited study on the impact of NPs on mollusk cephalopods. In this research, Sepia esculenta, belonging to Cephalopoda, Coleoidea, Sepioidea, was selected to explore the effects caused by NPs exposure. The S. esculenta larvae were exposed to polystyrene NPs (PS-NPs) with diameter 50 nm (100 mg/L) for 4 h. The detection of oxidative stress biomarkers displayed an obvious increase in SOD (superoxide dismutase) activity and MDA (malondialdehyde) level. Then, RNA-Seq was performed to explore the oxidative stress response at mRNA level. The transcriptome analysis demonstrated that the expression of 2,570 genes was affected by PS-NPs. Besides, the signaling pathways of ribosome, ribosome biogenesis in eukaryotes, proteasome, and MAPK were enriched. This study not only provides novel references for understanding the mechanisms of oxidative stress response induced by NPs, but also reminds us to follow with interest the influence of acute exposure to NPs.

Acute effects of polystyrene nanoplastics on the immune response in Sepia esculenta larvae

With extensive use of plastic products, microplastics (MPs, < 5 mm) and nanoplastics (NPs, < 1 μm) have become major pollutants in ecosystem, especially in marine environment. In recent years, researches on the impact of NPs on organisms have gradually increased. However, studies on the influence of NPs on cephalopods are still limited. Golden cuttlefish (Sepia esculenta), an important economic cephalopod, is a shallow marine benthic organism. In this study, the effect of acute exposure (4 h) to 50-nm polystyrene nanoplastics (PS-NPs, 100 μg/L) on the immune response of S. esculenta larvae was analyzed via transcriptome data. A total of 1260 DEGs were obtained in the gene expression analysis. The analyses of GO, KEGG signaling pathway enrichment, and protein-protein interaction (PPI) network were then performed to explore the potential molecular mechanisms of the immune response. Finally, 16 key immune-related DEGs were obtained according to the number of KEGG signaling pathways involved and the PPI number. This study not only confirmed that NPs had an impact on cephalopod immune response, but also provided novel insights for further unmasking the toxicological mechanisms of NPs.

Time-dependent immune injury induced by short-term exposure to nanoplastics in the Sepia esculenta larvae

Marine organisms are threatened by various environmental contaminants, and nanoplastics (NPs) is one of the most concerned. Studied have shown that NPs has a certain impact on marine organisms, but the specific molecular mechanism is still unclear. At present, researches on the effect of NPs on marine life mostly focus on crustaceans, gastropods, and bivalves. In this study, cephalopod Sepia esculenta larvae were first used to investigate the potential immune response molecular mechanisms caused by PS-NPs (50 nm, 50 mg/L) short-term exposure (4 and 24 h). Through S. esculenta larvae transcriptome profile of gene expression analysis, 548 and 1990 genes showed differential expression at 4 and 24 h after NPs exposure, respectively. GO and KEGG enrichment analysis were performed to find immune related DEGs. Then, the interaction relationship between the immune related DEGs after NPs exposure was known through the constructed protein-protein interaction network. 20 hub genes were found on the base of KEGG pathway numbers involved and protein-protein interaction numbers. This research supply valuable genes for the study of cephalopod immune response caused by NPs, which can help us further uncover the molecular mechanisms of organism against NPs.

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.

High-Density Genetic Linkage Map of the Southern Blue-ringed Octopus (Octopodidae: Hapalochlaena maculosa)

Genetic linkage maps provide a useful resource for non-model genomes and can aid in genome reassembly to form more contiguous pseudo-chromosomes. We present the first linkage map of any cephalopod, H. maculosa, composed of 47 linkage groups (LG). A total of 2166 single nucleotide polymorphisms and 2455 presence–absence variant loci were utilised by Lep-Map3 in linkage map construction. The map length spans 2016.62 cM with an average marker distance of 0.85 cM. Integration of the recent H. maculosa genome allowed 1151 scaffolds comprising 34% of the total genomic sequence to be orientated and/or placed using 1278 markers across all 47 LG. The linkage map generated provides a new perspective on HOX gene distribution in octopods. In the H. maculosa linkage map three (SCR, LOX4 and POST1) of six identified HOX genes (HOX1/LAB, SCR, LOX2, LOX4, LOX5, POST1) were located within the same LG (LG 9). The generation of a linkage map for H. maculosa has provided a valuable resource for understanding the evolution of cephalopod genomes and will provide a base for future work.

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.

Deeply conserved synteny and the evolution of metazoan chromosomes

Animal genomes show networks of deeply conserved gene linkages whose phylogenetic scope and chromosomal context remain unclear. Here, we report chromosome-scale conservation of synteny among bilaterians, cnidarians, and sponges and use comparative analysis to reconstruct ancestral chromosomes across major animal groups. Comparisons among diverse metazoans reveal the processes of chromosome evolution that produced contemporary karyotypes from their Precambrian progenitors. On the basis of these findings, we introduce a simple algebraic representation of chromosomal change and use it to establish a unified systematic framework for metazoan chromosome evolution. We find that fusion-with-mixing, a previously unappreciated mode of chromosome change, has played a central role. We find that relicts of several metazoan chromosomal units are preserved in unicellular eukaryotes. These conserved pre-metazoan linkages include the chromosomal unit that encodes the most diverse set of metazoan homeobox genes, suggesting a candidate genomic context for the early diversification of this key gene family.

Genetic structure of Octopus minor around Chinese waters as indicated by nuclear DNA variations (Mollusca, Cephalopoda)

Octopus minor is an economically important resource commonly found in Chinese coastal waters. The nuclear gene (RD and ODH) approach of investigation has not reported in this species. Rhodopsin (RD) and octopine dehydrogenase (ODH) genes were used to elaborate the genetic structure collected from eight localities ranging from the northern to the southern coast of China. In total, 118 individuals for the RD gene and 108 for the ODH were sequenced. Overall (RD and ODH) genes resulted in high (0.741±0.032; 0.805±0.038) haplotype and low nucleotide (0.01261±0.00165; 0.00747±0.00086) diversity. Molecular variance displayed higher values among the populations and lower values within the population where the fixation index FST denoted 0.880 and 0.584 in RD and ODH genes respectively. The Dongshan population clustered separately in a phylogenetic tree as in the haplotype networking assessment. The current data suggests that the Dongshan population needs separate management.

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.