Pepino Ma Marivic Capitle, Manalili Sam Edward, Sekida Satoko, Mezaki Takuma, Okumura Tomoyo, Kubota Satoshi
Kuroshio Science Program, Graduate School of Integrated Arts and Sciences, Kochi University, Nankoku, Kochi, Japan.
Kuroshio Science Unit, Multidisciplinary Science Cluster, Kochi University, Nankoku, Kochi, Japan.
PeerJ. 2024 Apr 16;12:e17182. doi: 10.7717/peerj.17182. eCollection 2024.
, a prized resource in Japan, plays a vital role in traditional arts and fishing industries. Because of diminished stock due to overexploitation, ongoing efforts are focused on restoration through transplantation. This study aimed to enhance our understanding of the reproductive biology of these valuable corals and find more efficient methods for sex determination, which may significantly contribute to conservation initiatives.
We used 12 three-month aquarium reared colony fragments, conducted histological analysis for maturity and sex verification, and performed transcriptome analysis via assembly and mapping using the transcriptome to explore gene expression differences between female and male .
Our histological observations enabled sex identification in 33% of incompletely mature samples. However, the sex of the remaining 67% of samples, classified as immature, could not be identified. RNA-seq yielded approximately 21-31 million short reads from 12 samples. assembly yielded 404,439 highly expressed transcripts. Among them, 855 showed significant differential expression, with 786 differentially expressed transcripts between females and males. Heatmap analysis highlighted 283 female-specific and 525 male-specific upregulated transcripts. Transcriptome assembly mapped to yielded 28,092 contigs, leading to the identification of 190 highly differentially expressed genes, with 113 upregulated exclusively in females and 70 upregulated exclusively in males. Blastp analysis provided putative protein annotations for 83 female and 72 male transcripts. Annotation analysis revealed that female biological processes were related to oocyte proliferation and reproduction, whereas those in males were associated with cell adhesion.
Transcriptome analysis revealed sex-specific gene upregulation in incompletely mature and shared transcripts with , providing insight into its gene expression patterns. This study highlights the importance of using both and reference-based assembly methods. Functional enrichment analysis showed that females exhibited enrichment in cell proliferation and reproduction pathways, while males exhibited enrichment in cell adhesion pathways. To the best of our knowledge, this is the first report on the gene expressions of each sex during the spawning season. Our findings offer valuable insights into the physiological ecology of incompletely mature red Japanese precious corals and suggest a method for identifying sex using various genes expressed in female and male individuals. In the future, techniques such as transplantation, artificial fertilization, and larval rearing may involve sex determination methods based on differences in gene expression to help conserve precious coral resources and ecosystems.
是日本的珍贵资源，在传统艺术和渔业中发挥着至关重要的作用。由于过度开发导致种群数量减少，目前正在通过移植进行恢复工作。本研究旨在加深我们对这些珍贵珊瑚生殖生物学的理解，并找到更有效的性别鉴定方法，这可能对保护举措有重大贡献。
我们使用了12个在水族箱中饲养三个月的 群体碎片，进行组织学分析以确定成熟度和性别，并通过使用 转录组进行组装和映射来进行转录组分析，以探索雌性和雄性 之间的基因表达差异。
我们的组织学观察能够在33%未完全成熟的样本中鉴定出性别。然而，其余67%被归类为未成熟的样本的性别无法鉴定。RNA测序从12个样本中产生了约2100万至3100万条短读长。 组装产生了404,439个高表达转录本。其中，855个显示出显著差异表达，雌性和雄性之间有786个差异表达转录本。热图分析突出了283个雌性特异性和525个雄性特异性上调转录本。转录组组装映射到 产生了28,092个重叠群，从而鉴定出190个高度差异表达的基因，其中113个仅在雌性中上调，70个仅在雄性中上调。Blastp分析为83个雌性和72个雄性转录本提供了推定的蛋白质注释。注释分析表明，雌性的生物学过程与卵母细胞增殖和繁殖有关，而雄性的生物学过程与细胞粘附有关。
转录组分析揭示了未完全成熟的 中性别特异性基因上调，并与 共享转录本，从而深入了解其基因表达模式。本研究强调了同时使用 和基于参考的组装方法的重要性。功能富集分析表明，雌性在细胞增殖和繁殖途径中表现出富集，而雄性在细胞粘附途径中表现出富集。据我们所知，这是关于产卵季节各性别基因表达的第一份报告。我们的发现为未完全成熟的日本红珊瑚的生理生态学提供了有价值的见解，并提出了一种利用雌性和雄性个体中表达的各种基因来鉴定性别的方法。未来，移植、人工授精和幼体饲养等技术可能会涉及基于基因表达差异的性别鉴定方法，以帮助保护珍贵的珊瑚资源和生态系统。
