Asymmetric Fitness of Second-Generation Interspecific Hybrids Between Ciona robusta and Ciona intestinalis

A simple inland culture system provides insights into ascidian post-embryonic developmental physiology

Maintenance and breeding of experimental organisms are fundamental to life sciences, but both initial and running costs, and hands-on zootechnical demands can be challenging for many laboratories. Here, we first aimed to further develop a simple protocol for reliable inland culture of tunicate model species of the Ciona genus. We cultured both Ciona robusta and Ciona intestinalis in controlled experimental conditions, with a focus on dietary variables, and quantified growth and maturation parameters. From statistical analysis of these standardized datasets, we gained insights into the post-embryonic developmental physiology of Ciona and inferred an improved diet and culturing conditions for sexual maturation. We showed that body length is a critical determinant of both somatic and sexual maturation, which suggests the existence of systemic control mechanisms of resource allocation towards somatic growth or maturation and supports applying size selection as a predictor of reproductive fitness in our inland culture to keep the healthiest animals at low density in the system. In the end, we successfully established a new protocol, including size selection, to promote both sperm and egg production. Our protocol using small tanks will empower researchers to initiate inland Ciona cultures with low costs and reduced space constraints.

The CsPPR gene with RNA-editing function involved in leaf color asymmetry of the reciprocal hybrids derived from Cucumis sativus and C. hystrix

MAIN CONCLUSION

The leaf color asymmetry found in the reciprocal hybrids C. hystrix × C. sativus (HC) and C. sativus × C. hystrix (CH) could be influenced by the CsPPR gene (CsaV3_1G038250.1). Most angiosperm organelles are maternally inherited; thus, the reciprocal hybrids usually exhibit asymmetric phenotypes that are associated with the maternal parent. However, there are two sets of organelle genomes in the plant cytoplasm, and the mechanism of reciprocal differences are more complex and largely unknown, because the chloroplast genes are involved besides mitochondrial genes. Cucumis spp. contains the species, i.e., cucumber and melon, which chloroplasts and mitochondria are maternally inherited and paternally inherited, respectively, serving as good materials for the study of reciprocal differences. In this study, leaf color asymmetry was observed in the reciprocal hybrids (HC and CH) derived from C. sativus (2n = 14, CC) and C. hystrix (2n = 24, HH), where the leaves of HC were found to have reduced chlorophyll content, abnormal chloroplast structure and lower photosynthetic capacity. Transcriptomic analysis revealed that the chloroplast development-related genes were differentially expressed in leaf color asymmetry. Genetic analysis showed that leaf color asymmetry was caused by the maternal chloroplast genome. Comparative analysis of chloroplast genomes revealed that there was no mutation in the chloroplast genome during interspecific hybridization. Moreover, a PPR gene (CsaV3_1G038250.1) with RNA-editing function was found to be involved in the regulation of leaf color asymmetry. These findings provide new insights into the regulatory mechanisms of asymmetric phenotypes in plant reciprocal crosses.

Cellular remodeling and JAK inhibition promote zygotic gene expression in the Ciona germline

Transcription control is a major determinant of cell fate decisions in somatic tissues. By contrast, early germline fate specification in numerous vertebrate and invertebrate species relies extensively on RNA-level regulation, exerted on asymmetrically inherited maternal supplies, with little-to-no zygotic transcription. However delayed, a maternal-to-zygotic transition is nevertheless poised to complete the deployment of pre-gametic programs in the germline. Here, we focus on early germline specification in the tunicate Ciona to study zygotic genome activation. We first demonstrate that a peculiar cellular remodeling event excludes localized postplasmic Pem-1 mRNA, which encodes the general inhibitor of transcription. Subsequently, zygotic transcription begins in Pem-1-negative primordial germ cells (PGCs), as revealed by histochemical detection of elongating RNA Polymerase II, and nascent Mef2 transcripts. In addition, we uncover a provisional antagonism between JAK and MEK/BMPRI/GSK3 signaling, which controls the onset of zygotic gene expression, following cellular remodeling of PGCs. We propose a 2-step model for the onset of zygotic transcription in the Ciona germline and discuss the significance of germ plasm dislocation and remodeling in the context of developmental fate specification.

The Chordate Origins of Heart Regeneration

The human heart is infamous for not healing after infarction in adults, prompting biomedical interest in species that can regenerate damaged hearts. In such animals as zebrafish and neonatal mice, cardiac repair relies on remaining heart tissue supporting cardiomyocyte proliferation. Natural de novo cardiogenesis in post-embryonic stages thus remains elusive. Here we show that the tunicate Ciona, an ascidian among the closest living relatives to the vertebrates, can survive complete chemogenetic ablation of the heart and loss of cardiac function, and recover both cardiac tissue and contractility. As in vertebrates, Ciona heart regeneration relies on Bone Morphogenetic Protein (BMP) signaling-dependent proliferation of cardiomyocytes, providing insights into the evolutionary origins of regenerative cardiogenesis in chordates. Remarkably, prospective lineage tracing by photoconversion of the fluorescent protein Kaede suggested that new cardiomyocytes can emerge from endodermal lineages in post-metamorphic animals, providing an unprecedented case of regenerative de novo cardiogenesis. Finally, while embryos cannot compensate for early losses of the cardiogenic lineage, forming heartless juveniles, developing animals gain their regenerative ability during metamorphosis, uncovering a fundamental transition between deterministic embryogenesis and regulative post-embryonic development.

Co-expression network analysis of environmental canalization in the ascidian Ciona

BACKGROUND

Canalization, or buffering, is defined as developmental stability in the face of genetic and/or environmental perturbations. Understanding how canalization works is important in predicting how species survive environmental change, as well as deciphering how development can be altered in the evolutionary process. However, how developmental gene expression is linked to buffering remains unclear. We addressed this by co-expression network analysis, comparing gene expression changes caused by heat stress during development at a whole-embryonic scale in reciprocal hybrid crosses of sibling species of the ascidian Ciona that are adapted to different thermal environments.

RESULTS

Since our previous work showed that developmental buffering in this group is maternally inherited, we first identified maternal developmental buffering genes (MDBGs) in which the expression level in embryos is both correlated to the level of environmental canalization and also differentially expressed depending on the species' gender roles in hybrid crosses. We found only 15 MDBGs, all of which showed high correlation coefficient values for expression with a large number of other genes, and 14 of these belonged to a single co-expression module. We then calculated correlation coefficients of expression between MDBGs and transcription factors in the central nervous system (CNS) developmental gene network that had previously been identified experimentally. We found that, compared to the correlation coefficients between MDBGs, which had an average of 0.96, the MDBGs are loosely linked to the CNS developmental genes (average correlation coefficient 0.45). Further, we investigated the correlation of each developmental to MDBGs, showing that only four out of 62 CNS developmental genes showed correlation coefficient > 0.9, comparable to the values between MDBGs, and three of these four genes were signaling molecules: BMP2/4, Wnt7, and Delta-like.

CONCLUSIONS

We show that the developmental pathway is not centrally located within the buffering network. We found that out of 62 genes in the developmental gene network, only four genes showed correlation coefficients as high as between MDBGs. We propose that loose links to MDBGs stabilize spatiotemporally dynamic development.

Chromosomal Inversion Polymorphisms in Two Sympatric Ascidian Lineages

Chromosomal rearrangements can reduce fitness of heterozygotes and can thereby prevent gene flow. Therefore, such rearrangements can play a role in local adaptation and speciation. In particular, inversions are considered to be a major potential cause for chromosomal speciation. There are two closely related, partially sympatric lineages of ascidians in the genus Ciona, which we call type-A and type-B animals in the present study. Although these invertebrate chordates are largely isolated reproductively, hybrids can be found in wild populations, suggesting incomplete prezygotic barriers. Although the genome of type-A animals has been decoded and widely used, the genome for type-B animals has not been decoded at the chromosomal level. In the present study, we sequenced the genomes of two type-B individuals from different sides of the English Channel (in the zone of sympatry with type-A individuals) and compared them at the chromosomal level with the type-A genome. Although the overall structures were well conserved between type A and type B, chromosomal alignments revealed many inversions differentiating these two types of Ciona; it is probable that the frequent inversions have contributed to separation between these two lineages. In addition, comparisons of the genomes between the two type-B individuals revealed that type B had high rates of inversion polymorphisms and nucleotide polymorphisms, and thus type B might be in the process of differentiation into multiple new types or species. Our results suggest an important role of inversions in chromosomal speciation of these broadcasting spawners.