Quanchao Wang

Transforming growth factor β (TGF-β) superfamily genes can regulate many aspects of physiological embryogenesis and adult tissue homeostasis. To understand the evolution and divergence patterns of the TGF-β gene family in sea urchins, genome-wide data from Heliocidaris erythrogramma, Heliocidaris tuberculate, Hemicentrotus pulcherrimus, Lytechinus variegatus, Strongylocentrotus purpuratus, and Temnopleurus reevesii were systematically analyzed based on bioinformatics methods. A total of 87 TGF-β genes were identified in 6 sea urchins. The phylogenetic tree supported that these genes were divided into 15 clusters. The structural features of these genes showed large variations in sequence length among different species, although the lengths and the numbers of exons exhibited high degrees of similarity. Furthermore, the spatiotemporal expression of TGF-β genes from S. purpuratus provided some new insights into their potential functions. These results provide a theoretical basis for further studies of the molecular evolutionary patterns and function of the TGF-β gene family.

The sea urchin Mesocentrotus nudus holds significant economic importance, making a comprehensive understanding of its sex differentiation and development mechanisms crucial for facilitating genetic enhancement. In this study, a high-quality chromosome-level assembly of the M. nudus genome was accomplished, spanning 707 Mb and encompassing 21 chromosomes, which together represented 97.6% of the assembly. Analysis of the locations of sex-linked markers indicated that sex determination in M. nudus may be predominantly governed by a confined region on chromosome 7. Within this specific area, an initial screening identified 37 protein-coding genes, encompassing 64 transcripts. Subsequent comparative transcriptome analysis revealed notable differences in the expression patterns of 11 genes (comprising 12 transcripts) between the testes and ovaries of M. nudus. In conclusion, this genome assembly serves as an invaluable resource for future investigations into the population genetics, evolutionary history, and genetic mechanism analysis of M. nudus. Moreover, the identification of the genomic location of the sex-linked region in M. nudus, coupled with the identification of candidate sex-determining genes, lends further credence to the notion of rapid evolution in sex-determining mechanisms among sea urchins.

Hemicentrotus pulcherrimus is an important commercial aquatic species. However, wild stocks have dramatically decreased in recent decades, and the gonads of H. pulcherrimus of different sexes showed significant differences in gonad index, gonad color, and flavour. Understanding the population genetic structure and sex-differentiation/determination mechanism can provide vital information for genetic conservation and improvement. In the present study, the SuperGBS method was used to identify genome-wide SNPs from a collection of 80 individuals consisting of four geographical populations covering the natural habitats of H. pulcherrimus in China seas. A total of 5785 high-quality SNPs were detected by using SuperGBS technology. The genetic diversity index showed that all populations had similar patterns with high F_is and low N_e, suggesting that it is necessary to carry out the conservation of H. pulcherrimus in China. Low genetic differentiation among the four geographical populations was detected by pairwise F_st, PCA, and admixture analysis. In addition, three sex-related SNPs located on three scaffolds were identified, suggesting a ZW-ZZ sex determination system in H. pulcherrimus. However, no sex-specific marker was identified in this study. Therefore, larger sample sizes and marker numbers need to be implemented to investigate the sex-associated markers and genes of H. pulcherrimus. In general, this study provides a molecular basis for population genetic structure and sex-differentiation/determination mechanism of H. pulcherrimus.

The Sox gene family, a collection of transcription factors widely distributed throughout the animal kingdom, plays a crucial role in numerous developmental processes. Echinoderms occupy a pivotal position in many research fields, such as neuroscience, sex determination and differentiation, and embryonic development. However, to date, no comprehensive study has been conducted to characterize and analyze Sox genes in echinoderms. In the present study, the evolution and expression of Sox family genes across 11 echinoderms were analyzed using bioinformatics methods. The results revealed a total of 70 Sox genes, with counts ranging from 5 to 8 across different echinoderms. Phylogenetic analysis revealed that the identified Sox genes could be categorized into seven distinct classes: the SoxB1 class, SoxB2 class, SoxC class, SoxD class, SoxE class, SoxF class and SoxH class. Notably, the SoxB1, SoxB2, and SoxF genes were ubiquitously present in all the echinoderms studied, which suggests that these genes may be conserved in echinoderms. The spatiotemporal expression patterns observed for Sox genes in the three echinoderms indicated that various Sox members perform distinct functional roles. Notably, SoxB1 is likely involved in echinoderm ovary development, while SoxH may play a crucial role in testis development in starfish and sea cucumber. In general, the present investigation provides a molecular foundation for exploring the Sox gene in echinoderms, providing a valuable resource for future phylogenetic and genomic studies.

The doublesex-mab3-related transcription factor (Dmrt) gene family is a class of crucial transcription factors characterized by one or several DM domains. Dmrt family genes play important roles in sex determination/differentiation. Polychaete annelids are critically important in most marine ecosystems. However, to date, the genome-wide characterization and analysis of Dmrt genes in polychaetes have not been investigated. In this study, the identification and analysis of Dmrt genes were performed in three representative polychaetes, including Capitella teleta, Dimorphilus gyrociliatus, and Owenia fusiformis. A total of 12 Dmrt genes have been found, and the number of Dmrt genes in different polychaetes ranges from 3 to 5. The phylogenetic tree showed that all identified Dmrt genes were classified into 4 classes: Dmrt2/11E, Dmrt3/93B, Dmrt4/5/99B, and DSX. Furthermore, the selection pressure analysis suggested that all the Dmrt genes underwent strong purifying selection pressure. The spatiotemporal expression profile in O. fusiformis suggested that Dmrt genes have diverse functions, and the Dmrt2/11E-like gene may play an important role in the sex determination/differentiation of polychaetes. In general, this study provides a molecular basis for polychaete Dmrt genes and may serve as a reference for in-depth phylogenomics.

The interspecific hybrid scallops generated from the hermaphroditic bay scallops (Argopecten irradians) and Peruvian scallops (Argopecten purpuratus) showed significant heterosis in growth. However, its sterility limits large-scale hybridization and hinders the development of the scallop breeding industry. Hybrid sterility is regulated by plenty of genes and involves a range of biochemical and physiological transformations. In this study, whole-genome re-sequencing and transcriptomic analysis were performed in sterile and fertile hybrid scallops. The potential genetic variations and abnormally expressed genes were detected to explore the mechanism underlying hybrid sterility in hermaphroditic Argopecten scallops. Compared with fertile hybrids, 24 differentially expressed genes (DEGs) with 246 variations were identified to be related to fertility regulation, which were mainly enriched in germarium-derived egg chamber formation, spermatogenesis, spermatid development, mismatch repair, mitotic and meiotic cell cycles, Wnt signaling pathway, MAPK signaling pathway, calcium modulating pathway, and notch signaling pathway. Specifically, variation and abnormal expression of these genes might inhibit the progress of mitosis and meiosis, promote cell apoptosis, and impede the genesis and maturation of gametes in sterile hybrid scallops. Eleven DEGs (XIAP, KAZN, CDC42, MEIS1, SETD1B, NOTCH2, TRPV5, M- EXO1, GGT1, SBDS, and TBCEL) were confirmed by qRT-PCR validation. Our findings may enrich the determination mechanism of hybrid sterility and provide new insights into the use of interspecific hybrids for extensive breeding.

DNA methylation is an important epigenetic modification factor in regulating fertility. Corresponding process remains poorly investigated in hermaphroditic scallops. The interspecific F₁ hybrids between the hermaphroditic bay scallops (Argopecten irradians) and Peruvian scallops (Argopecten purpuratus) exhibited significant heterosis in yield, but sterility in hybrids obstructs the utilization of the genetic resources. However, the determination mechanism of hybrid sterility in the hermaphroditic Argopecten scallops is still unclear. In this study, the effect of DNA methylation in the hybrid sterility of hermaphroditic Argopecten scallops was explored. The results showed that the mean methylation level was higher in sterile hybrids than fertile hybrids, especially on chromosome 11 of the paternal parent. A total of 61,062 differentially methylated regions (DMRs) were identified, containing 3619 differentially methylated genes (DMGs) and 1165 differentially methylated promoters that are located in the DMRs of CG sequence context. The hyper-methylated genes were enriched into five KEGG pathways, including ubiquitin-mediated proteolysis, ECM-receptor interaction, non-homologous end-joining, notch signaling, and the mismatch repair pathways. The DMGs might induce hybrid sterility by inhibition of oogenesis and egg maturation, induction of apoptosis, increased ROS, and insufficient ATP supply. Our results would enrich the determination mechanism of hybrid sterility and provide new insights into the utilization of the genetic resources of the interspecific hybrids.

Due to the great advantages in selection accuracy and efficiency, genomic selection (GS) has been widely studied in livestock, crop and aquatic animals. Our previous study based on one full-sib family of Litopenaeus vannamei (L. vannamei) showed that GS was feasible in penaeid shrimp. However, the applicability of GS might be influenced by many factors including heritability, marker density and population structure etc. Therefore it is necessary to evaluate the major factors affecting the prediction ability of GS in shrimp. The aim of this study was to evaluate the factors influencing the GS accuracy for growth traits in L. vannamei. Genotype and phenotype data of 200 individuals from 13 full-sib families were used for this analysis. In the present study, the heritability of growth traits in L. vannamei was estimated firstly based on the full set of markers (23 K). It was 0.321 for body weight and 0.452 for body length. The estimated heritability increased rapidly with the increase of the marker density from 0.05 K to 3.2 K, and then it tended to be stable for both traits. For genomic prediction on the growth traits in L. vannamei, three statistic models (RR-BLUP, BayesA and Bayesian LASSO) showed similar performance for the prediction accuracy of genomic estimated breeding value (GEBV). The prediction accuracy was improved with the increasing of marker density. However, the marker density would bring a weak effect on the prediction accuracy after the marker number reached 3.2 K. In addition, the genetic relationship between reference and validation population could influence the GS accuracy significantly. A distant genetic relationship between reference and validation population resulted in a poor performance of genomic prediction for growth traits in L. vannamei. For the growth traits with moderate or high heritability, such as body weight and body length, the number of about 3.2 K SNPs distributed evenly along the genome was able to satisfy the need for accurate GS prediction in the investigated L.vannamei population. The genetic relationship between the reference population and the validation population showed significant effects on the accuracy for genomic prediction. Therefore it is very important to optimize the design of the reference population when applying GS to shrimp breeding.