Reconstructing the genomes of bilaterian ancestors is central to our understanding of animal evolution, where knowledge from ancient and/or slow-evolving bilaterian lineages is critical. Here we report a high-quality, chromosome-anchored reference genome for the scallop Patinopecten yessoensis, a bivalve mollusc that has a slow-evolving genome with many ancestral features. Chromosome-based macrosynteny analysis reveals a striking correspondence between the 19 scallop chromosomes and the 17 presumed ancestral bilaterian linkage groups at a level of conservation previously unseen, suggesting that the scallop may have a karyotype close to that of the bilaterian ancestor. Scallop Hox gene expression follows a new mode of subcluster temporal co-linearity that is possibly ancestral and may provide great potential in supporting diverse bilaterian body plans. Transcriptome analysis of scallop mantle eyes finds unexpected diversity in phototransduction cascades and a potentially ancient Pax2/5/8-dependent pathway for noncephalic eyes. The outstanding preservation of ancestral karyotype and developmental control makes the scallop genome a valuable resource for understanding early bilaterian evolution and biology.

Bivalve molluscs are descendants of an early-Cambrian lineage superbly adapted to benthic filter feeding. Adaptations in form and behavior are well recognized, but the underlying molecular mechanisms are largely unknown. Here, we investigate the genome, various transcriptomes, and proteomes of the scallop Chlamys farreri, a semi-sessile bivalve with well-developed adductor muscle, sophisticated eyes, and remarkable neurotoxin resistance. The scallop’s large striated muscle is energy-dynamic but not fully differentiated from smooth muscle. Its eyes are supported by highly diverse, intronless opsins expanded by retroposition for broadened spectral sensitivity. Rapid byssal secretion is enabled by a specialized foot and multiple proteins including expanded tyrosinases. The scallop uses hepatopancreas to accumulate neurotoxins and kidney to transform to high-toxicity forms through expanded sulfotransferases, probably as deterrence against predation, while it achieves neurotoxin resistance through point mutations in sodium channels. These findings suggest that expansion and mutation of those genes may have profound effects on scallop’s phenotype and adaptation.

Almost all written languages currently used in the world are alphabetic or phonologically-based scripts (e.g., English) whose word recognition involves discrimination of one-dimensional linear combinations of several dozens of letters or phonological units, except written Chinese whose vocabulary consists of a large number of block characters, the analysis of which relies on the extraction of 2-dimensional form information at multiple levels including radical, character, and multiple-character word. Whether the dramatic contrast between the 2 types of orthography leads to distinctive mental processes is a fundamental question in psycholinguistic research unanswered in the past three decades. Using event-related potentials and visual lexical decision tasks, we asked native Chinese speakers to discriminate between real Chinese words and pseudo-or non-words and observed a widespread negative deflection with centro-parietal focus elicited 200 ms post-stimulus onset. This N200 response showed a clear and large amplitude enhancement upon word repetition and seems to be specific to Chinese as no similar effects had been reported in word recognition studies involving alphabetic scripts under similar experimental conditions. Further evidence showed that this N200 could not be attributed to non-linguistic sensori-perceptual processes, nor phonological or semantic processes, but likely reflects very early identification of the orthography of individual words involving extensive and higher-level visual analysis. Recently the first author proposed a meaning-spelling theory of written Chinese vocabulary proposing that the Chinese and alphabetic scripts are the only 2 possible logical types of mature human writing systems, and that the former is more thoroughly a visual language compared with the latter and thus shall emphasize more of visual processing. Reinforcing each other, the meaning-spelling theory and the discovery of the centro-parietal N200 reveal the uniqueness of Chinese both theoretically and empirically, and provide strong arguments for the intrinsic distinction between written Chinese and alphabetic scripts.

Echinoderms exhibit several fascinating evolutionary innovations that are rarely seen in the animal kingdom, but how these animals attained such features is not well understood. Here we report the sequencing and analysis of the genome and extensive transcriptomes of the sea cucumber Apostichopus japonicus, a species from a special echinoderm group with extraordinary potential for saponin synthesis, aestivation and organ regeneration. The sea cucumber does not possess a reorganized Hox cluster as previously assumed for all echinoderms, and the spatial expression of Hox7 and Hox11/13b potentially guides the embryo-to-larva axial transformation. Contrary to the typical production of lanosterol in animal cholesterol synthesis, the oxidosqualene cyclase of sea cucumber produces parkeol for saponin synthesis and has “plant-like” motifs suggestive of convergent evolution. The transcriptional factors Klf2 and Egr1 are identified as key regulators of aestivation, probably exerting their effects through a clock gene-controlled process. Intestinal hypometabolism during aestivation is driven by the DNA hypermethylation of various metabolic gene pathways, whereas the transcriptional network of intestine regeneration involves diverse signaling pathways, including Wnt, Hippo and FGF. Decoding the sea cucumber genome provides a new avenue for an in-depth understanding of the extraordinary features of sea cucumbers and other echinoderms.

No abstract