TrBase: A genome and transcriptome database of Temnopleurus reevesii

Sea urchins have a long history as model organisms in biology, but their use in genetics is limited because of their long breeding cycle. In sea urchin genetics, genome editing technology was first established in Hemicentrotus pulcherrimus, whose genome has already been published. However, because this species also has a long breeding cycle, new model sea urchins that are more suitable for genetics have been sought. Here, we report a draft genome of another Western Pacific species, Temnopleurus reevesii, which we established as a new model sea urchin recently since this species has a comparable developmental process to other model sea urchins but a short breeding cycle of approximately half a year. The genome of T. reevesii was assembled into 28,742 scaffold sequences with an N50 length of 67.6 kb and an estimated genome size of 905.9 Mb. In the assembled genome, 27,064 genes were identified, 23,624 of which were expressed in at least one of the seven developmental stages. To provide genetic information, we constructed the genome database TrBase (https://cell-innovation.nig.ac.jp/Tree/). We also constructed the Western Pacific Sea Urchin Genome Database (WestPac-SUGDB) (https://cell-innovation.nig.ac.jp/WPAC/) with the aim of establishing a portal site for genetic information on sea urchins in the West Pacific. This site contains genomic information on two species, T. reevesii and H. pulcherrimus, and is equipped with homology search programs for comparing the two datasets. Therefore, TrBase and WestPac-SUGDB are expected to contribute not only to genetic research using sea urchins but also to comparative genomics and evolutionary research.

Temnopleurus reevesii as a new sea urchin model in genetics

Echinoderms, including sea urchins and starfish, have played important roles in cell, developmental and evolutionary biology research for more than a century. However, since most of them take a long time to mature sexually and their breeding seasons are limited, it has been difficult to obtain subsequent generations in the laboratory, resulting in them not being recognized as model organisms in recent genetics research. To overcome this issue, we maintained and obtained gametes from several nonmodel sea urchins in Japan and finally identified Temnopleurus reevesii as a suitable model for sea urchin genetics. Genomic and transcriptomic information was obtained for this model, and the DNA database TrBase was made publicly available. In this review, we describe how we found this species useful for biological research and show an example of CRISPR/Cas9 based knockout sea urchin.

Establishment of homozygous knock-out sea urchins

Yaguchi et al. establish a homozygous knock-out sea urchin line by applying the CRISPR-Cas9 system to a new model species, Temnopleurus reevesii, whose breeding cycle takes about half a year.

Temnopleurus as an emerging echinoderm model

Sea urchins have played important roles in cell and developmental biology. They have the potential to be even more useful as models if the ability to create transgenic animals and maintain genetic lines are developed. Here, I describe the methods to produce next-generation lines using a newly introduced sea urchin model, Temnopleurus reevesii, in the laboratory. The embryos of T. reevesii have wide range of temperature tolerance between 15°C to 30°C and have high transparency, which can be a strong point in live-imaging and fluorescent immunohistochemistry. I describe how to grow and culture the embryos/larvae/juveniles/adults of T. reevesii to address the challenge of establishing inbred strains followed by introducing genetics into this species in the future.

Transforming growth factor-β signal regulates gut bending in the sea urchin embryo

During gastrulation, one of the most important morphogenetic events in sea urchin embryogenesis, the gut bends toward the ventral side to form an open mouth. Although the involvement of transforming growth factor-β (TGF-β) signals in the cell-fate specification of the ectoderm and endoderm along the dorsal-ventral axis has been well reported, it remains unclear what controls the morphogenetic behavior of gut bending. Here, using two sea urchin species, Hemicentrotus pulcherrimus and Temnopleurus reevesii, we show that TGF-β signals are required for gut bending toward the ventral side. To search for the common morphogenetic cue in these two species, we initially confirmed the expression patterns of the dorsal-ventral regulatory TGF-β members, nodal, lefty, bmp2/4, and chordin, in T. reevesii because these factors are appropriate candidates to investigate the cue that starts gut bending, although genetic information about the body axes is entirely lacking in this species. Based on their expression patterns and a functional analysis of Nodal, the dorsal-ventral axis formation of T. reevesii is likely regulated by these TGF-β members, as in other sea urchins. When the Alk4/5/7 signal was inhibited by its specific inhibitor, SB431542, before the late gastrula stage of T. reevesii, the gut was extended straight toward the anterior tip region, although the ectodermal dorsal-ventral polarity was normal. By contrast, H. pulcherrimus gut bending was sensitive to SB431542 until the prism stage. These data clearly indicate that gut bending is commonly dependent on a TGF-β signal in sea urchins, but the timing of the response varies in different species.

Troponin-I is present as an essential component of muscles in echinoderm larvae

The troponin complex, composed of Troponin-I, Troponin-T and Troponin-C, is an essential mediator of the contraction of striated muscle downstream of calcium signaling in almost all bilaterians. However, in echinoderms and hemichordates, collectively termed Ambulacraria, the components of the troponin complex have never been isolated, thus suggesting that these organisms lost the troponin system during evolution. Here, by analyzing genomic information from sea urchins, we identify the troponin-I gene and isolate its complete mRNA sequence. Using this information, we reveal that the larval muscles express this gene and its translated product and that the protein is definitely a functional molecule expressed in sea urchin larvae by showing that Troponin-I morphants are unable to swallow algae. We conclude that muscular contraction in all bilaterians universally depends on a regulatory system mediated by Troponin-I, which emerged in the common ancestor of bilaterians.

Morphological diversity of blastula formation and gastrulation in temnopleurid sea urchins

Embryos of temnopleurid sea urchins exhibit species-specific morphologies. While Temnopleurus toreumaticus has a wrinkled blastula and then invaginates continuously at gastrulation, others have a smooth blastula and their invagination is stepwise. We studied blastula and gastrula formation in four temnopleurids using light and scanning electron microscopy to clarify the mechanisms producing these differences. Unlike T. toreumaticus, blastomeres of mid-blastulae in T. reevesii, T. hardwickii and Mespilia globulus formed pseudopods. Before primary mesenchyme cells ingressed, embryos developed an area of orbicular cells in the vegetal plate. The cells surrounding the orbicular cells extended pseudopods toward the orbicular cell area in three Temnopleurus species. In T. toreumaticus, the extracellular matrix was well-developed and developed a hole-like structure that was not formed in others. Gastrulation of T. reevesii, T. hardwickii and M. globulus was stepwise, suggesting that differences of gastrulation are caused by all or some of the following factors: change of cell shape, rearrangement, pushing up and towing of cells. We conclude that (1) many aspects of early morphogenesis differ even among very closely related sea urchins with indirect development and (2) many of these differences may be caused by the cell shape and structure of blastomeres or by differences in extracellular matrix composition.