Giant genome of the vampire squid reveals the derived state of modern octopod karyotypes

Abstract

Ancient evolutionary transitions in animal chromosomal complements and their phenotypic impacts remain understudied. Few systems exist where these events can be dissected into individual steps. In coleoid cephalopods (octopus, squid, cuttlefish), an ancient coleoid chromosomal rearrangement event (ACCRE) resulted in a substantial increase in the chromosome number. However, the discrepancies between extant octopodiform (octopus, ∼30 chromosomes) and decapodiform (squid and cuttlefish, ∼46 chromosomes) karyotypes and the direction of this transition remain unexplained. Through sequencing of the basally branching octopodiform, the vampire squid Vampyroteuthis sp., we reveal its partial retention of the decapodiform karyotype. Together with the chromosome-level assembly of the pelagic octopod Argonauta hians, we show that modern octopod genomes were extensively shaped by chromosomal fusion-with-mixing followed by inter-chromosomal translocations. These irreversible processes have resulted in a more entangled genomic configuration in octopods. Our results offer broader insights into general patterns of chromosomal evolution following large-scale rearrangement in animal genomes.

Keywords: Evolutionary mechanisms; Genetics; Genomic analysis; Marine organism; Phylogenetics.

Graphical abstract

Figure 1

Early origins of coleoid cephalopods and conflicting chromosome evolution scenarios (A) Phylogenetic time tree of mitochondrial genomes with the major coleoid cephalopod clades and their closest outgroups. Node branches are labeled according to the major cephalopod evolutionary transitions. Node bars show the confidence intervals of the divergence times. (B) Two conflicting scenarios how coleoid karyotypes evolved, reduction and expansion (via fission) scenarios. Fusion-with-mixing (FWM) provides a powerful synapomorphic character to profile irreversible changes. (C) Vampyroteuthis specimen used for sequencing. Scale bar represents 1 cm. ACCRE: ancient coleoid chromosomal rearrangement event.

Figure 2

Vampyroteuthis genome suggests ancestral coleoid karyotype was decapodiform-like, followed by karyotype reduction in Octopodiformes Synteny dotplots showing Octopodiformes and Argonauta-Octopus shared FWM characters, relative to the Doryteuthis pealeii chromosomes. Doryteuthis chromosomes are ordered in the same way across the three species comparisons. The color codings indicate representative examples of the ancestral coleoid chromosome (green), ancestral Octopodiformes mixed chromosome (pink), and fused-and-mixed chromosomes in octopods (blue), respectively (corresponding to the phylogenetic nodes highlighted in Figure 1).

Figure 3

Chromosomal evolutionary pattern suggests additional ancestral translocations in octopods (A) Dotplot representation for the three cases highlighted in Figure 1, with the y axis indicating the chromosomes of Doryteuthis. Green indicates conserved coleoid chromosomes, as suggested by the conservation of genes in the chromosomes of all compared coleoids, despite translocation of the genes’ location within the chromosomes (intrachromosomal rearrangements; “mixing in a chromosome”). Meanwhile, ancestral Octopodiformes (pink) indicate fusions of different Doryteuthis chromosomes, which happened in ancestral Octopodiformes. The third example (blue) shows the formation of complex patterns of fusion-with-mixing, where orthologous genes undergoing intrachromosomal translocations in specific regions of the chromosomes of Doryteuthis are present in multiple chromosomes in compared species. (B) Two main scenarios for the observed complex chromosomal evolutionary patterns. The first one involves a fusion-with-mixing of intact (in red) and partial (in blue) chromosomes following inter-chromosomal translocations (blue) that occurred in Octopodiformes after divergence from the decapodiform karyotypes. A second possible scenario suggests that following the split of Octopodiformes and Decapodiformes, each lineage experienced distinct fusion-with-mixing events involving multiple ancestral chromosomes. In Octopodiformes, two specific chromosomes fused and mixed (red and blue), while in Decapodiformes, a different pair of chromosomes (blue and yellow) underwent a similar FWM process.

Figure 4

Conserved non-coding element complement in coleoid genomes (A) Vampyroteuthis-centered whole genome alignments show the total content (in alignment numbers) of coding and non-coding alignments. (B) Ribbon diagram showing location of homologous alignments of coding (red, CDS) and non-coding (orange) regions between Doryteuthis chromosomes (top) to Vampyroteuthis (middle) and Octopus vulgaris (bottom) for the complex FWM shown in Figures 2 and 3 (pink and blue colors). Zoom-in on a middle portion of O. vulgaris chromosome 2 (Ovu2) is highlighted below (NCBI genome browser) with gene track of annotation and conservation of both coding and non-coding elements derived from one homologous Vampyroteuthis contig and its pre-octopodiform unmixed state on two chromosomes Dpe29 and Dpe23 (pink color). Two Vampyroteuthis contigs homologous to Dpe09 and Dpe08, on the other hand, remain unmixed and their homologs undergo FWM only in octopods (blue color).