Full-length transcriptome and long non-coding RNA profiling of whiteleg shrimp Penaeus vannamei hemocytes in response to Spiroplasma eriocheiris infection

Ren, Yaoqing; Li, Jingyu; Guo, Liang; Liu, Jian Ning; Wan, Hui; Meng, Qingguo; Wang, Hui; Lv, Lishuang; Dong, Xiaohui; Zhao, Wei; Zeng, Qifan; Ou, Jiangtao

doi:10.1016/j.fsi.2020.06.057

Cited by 24 publications

(9 citation statements)

References 46 publications

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“…Fortunately, full-length transcriptome sequencing has been employed as an effective approach to obtain high-quality transcript sequences in the absence of reference genomes. Single-molecule real-time (SMRT) sequencing developed by Pacific Biosciences (PacBio) can obtain full-length sequences without post-sequencing assembly (Holmes et al, 2021), which has been used for wholetranscriptome profiling in many crustaceans (Cao et al, 2020;Ren et al, 2020;Zheng et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Full-Length Transcriptome Sequencing and Comparative Transcriptomic Analysis Provide Insights Into the Ovarian Maturation of Exopalaemon carinicauda

Wang

Li²,

Ge³

et al. 2022

Front. Mar. Sci.

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The ridgetail white shrimp Exopalaemon carinicauda has the potential to be used as a useful experimental organism in the field of crustacean research due to its transparent body, large egg, and short reproductive cycle. However, little is known about the regulatory mechanisms of ovarian maturation in E. carinicauda. In this study, we applied PacBio single-molecule long-read sequencing technology to unveil the whole transcriptome landscape of Exopalaemon carinicauda to better understand the molecular mechanisms of ovarian development. A total of 49.05 G polymerase read bases were generated, finally, 15, 151 unigenes were successfully identified with a mean length of 4, 257 bp and an N50 of 4, 884 bp from ovary tissues (five different ovarian developmental stages). A total of 14, 007 unigenes were successfully annotated in at least one public database. In addition, 8, 861 coding sequences, 4, 594 lncRNAs and 895 transcription factors were identified. Furthermore, we performed RNA-Seq analysis combined with Iso-Seq results to investigate ovarian maturation regulation mechanism and validated the results by quantitative real-time PCR. We annotated five vitellogenin isoforms in the full-length transcriptome, meanwhile these five genes and vitellogenin receptor suggested an important role during previtellogenesis of E. carinicauda. Genes were involved in PI3K-Akt signaling pathway, retinol metabolism, cell cycle and hedgehog signaling pathway, which showed obvious associations with ovarian maturation of E. carinicauda. We identified 40 DEGs, such as forkhead box protein L2, which may be related to ovarian development in the comparisons. The expression profiles of genes such as ecdysone receptor, ecdysone-induced protein 74EF, ecdysone inducible gene E75 and post-molt protein suggest that they were significantly associated with reproductive molting in the ovarian mature stage. In conclusion, the present study identified important genes and pathways involved in ovarian maturation, which might be useful for studying the reproductive regulation and mechanisms of ovarian maturation in E. carinicauda.

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Section: Introductionmentioning

confidence: 99%

Full-Length Transcriptome Sequencing and Comparative Transcriptomic Analysis Provide Insights Into the Ovarian Maturation of Exopalaemon carinicauda

Wang

Li²,

Ge³

et al. 2022

Front. Mar. Sci.

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“…Superoxide dismutase (SOD), catalase (CAT), lysozyme (LYZ), and phenoloxidase (PO) are four important immune enzymes, which have the function of anti-oxidant and anti-pathogen (Holmblad and Söderhäll, 1999;Cerenius and Söderhäll, 2004;Kaizu et al, 2011). The activity of these immune enzymes is usually used to reflect the impact of shrimp immunity after a pathogen infection (such as WSSV, IHHNV, Vibrio parahaemolyticus, and Spiroplasma eriocheiris) (Arockiaraj et al, 2012;Ren et al, 2020;Zhu et al, 2020;Jiao et al, 2021), harmful substance invasion (such as microcystin and tributyltin) (Wu et al, 2014;Chen et al, 2015), or dietary improvement (such as polypeptides and dietary hydrolyzable tannins) (Liao et al, 2019;Zhu et al, 2021). With the rapid development of high-throughput RNA sequencing technologies, including RNA sequencing (RNA-seq), more and more studies use RNA-seq to expose the immune molecular mechanism of shrimp against viral infections, bacterial infections, and environmental stress (Kurita and Nakajima, 2012;Wang et al, 2014;Zeng et al, 2014;Qin et al, 2018;Jin and Zhu, 2019;Nian et al, 2019;Duan et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

The Molecular Mechanism of Hemocyte Immune Response in Marsupenaeus japonicus Infected With Decapod Iridescent Virus 1

Zhao

Chen

et al. 2021

Front. Microbiol.

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As a new type of shrimp lethal virus, decapod iridescent virus 1 (DIV1) has caused huge economic losses to shrimp farmers in China. Up to now, DIV1 has been detected in a variety of shrimps, but there is no report in Marsupenaeus japonicus. In the current study, we calculated the LC50 to evaluate the toxicity of DIV1 to M. japonicus and determined through nested PCR that M. japonicus can be the host of DIV1. Through enzyme activity study, it was found that DIV1 can inhibit the activities of superoxide dismutase, catalase, lysozyme, and phenoloxidase, which could be a way for DIV1 to achieve immune evasion. In a comprehensive study on the transcriptomic changes of M. japonicus in response to DIV1 infection, a total of 52,287 unigenes were de novo assembled, and 20,342 SSR markers associated with these unigenes were obtained. Through a comparative transcriptomic analysis, 6,900 differentially expressed genes were identified, including 3,882 upregulated genes and 3,018 downregulated genes. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that some GO terms related to virus invasion, replication, and host antiviral infection were promoted under DIV1 infection, such as carbohydrate binding, chitin binding, chitin metabolic process, and DNA replication initiation, and some KEGG pathways related to immune response were significantly influenced by DIV1 infection, including Toll and IMD signaling pathway, JAK-STAT signaling pathway, IL-17 signaling pathway, C-type lectin receptor signaling pathway, complement and coagulation cascades, antigen processing and presentation, necroptosis, apoptosis, NOD-like receptor signaling pathway, apoptosis—multiple species, and TNF signaling pathway. Further analysis showed that STAT, Dorsal, Relish, heat shock protein 70 (HSP70), C-type lectins, and caspase play an important role in DIV1 infection. This is the first detailed study of DIV1 infection in M. japonicus, which initially reveals the molecular mechanism of DIV1 infection in M. japonicus by using the transcriptome analysis of hemocytes combined with enzyme activity study.

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“…ncRNA, especially lncRNA, has been shown to inhibit viral infection or stimulate the host antiviral immune response (Wang, 2019). Multiple lncRNAs were co-expressed with immunerelated genes to regulate the immune defense of blood cells during Spiroplasma Eriocheiris infections in L. vannamei (Ren et al, 2020). Liu et al (2019) identified 163 immune-related lncRNAs by transcriptome assembly involved in the immune response to large yellow croaker (Larimichthys crocea) infection with Vibrio parahaemolyticus.…”

Section: Discussionmentioning

confidence: 99%

Host-microbiota interactions and responses of Metapenaeus ensis infected with decapod iridescent virus 1

Liao

Liao²,

Long³

et al. 2023

Front. Microbiol.

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IntroductionDecapod iridescent virus 1 (DIV1) has caused severe economic losses in shrimp aquaculture. So far, Researchs on DIV1-infected shrimp have mainly focused on the hemocytes immune response, while studies on the host-intestine microbiota interactions during DIV1 infection have been scarce.MethodsThis study determined the lethal concentration 50 (LC50) of DIV1 to Metapenaeus ensis, preliminarily determining that M. ensis could serve as a susceptible object for DIV1. The interactions and responses between the immune and intestine microbiota of shrimp under DIV1 infection were also investigated.Results and DiscussionDIV1 infection decreases intestine bacterial diversity and alters the composition of intestine microbiota. Specifically, DIV1 infection decreases the abundance of potentially beneficial bacteria (Bacteroidetes, Firmicutes, and Actinobacteria), and significantly increases the abundance of pathogenic bacteria such as Vibrio and Photobacterium, thereby increasing the risk of secondary bacterial infections. The results of PICRUSt functional prediction showed that altered intestine microbiota induces host metabolism disorders, which could be attributed to the bioenergetic and biosynthetic requirements for DIV1 replication in shrimp. The comparative transcriptomic analysis showed that some metabolic pathways related to host immunity were significantly activated following DIV1 infection, including ncRNA processing and metabolic process, Ascorbate and aldarate metabolism, and Arachidonic acid metabolism. M. ensis may against DIV1 infection by enhancing the expression of some immune-related genes, such as Wnt16, heat shock protein 90 (Hsp90) and C-type lectin 3 (Ctl3). Notably, correlation analysis of intestinal microbial variation with host immunity showed that expansion of pathogenic bacteria (Vibrio and Photobacterium) in DIV1 infection could increased the expression of NF-κB inhibitors cactus-like and Toll interacting protein (Tollip), which may limit the TLR-mediated immune response and ultimately lead to further DIV1 infection.Significance and Impact of the StudyThis study enhances our understanding of the interactions between shrimp immunity and intestinal microbiota. The ultimate goal is to develop novel immune enhancers for shrimp and formulate a safe and effective DIV1 defense strategy.

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Full-length transcriptome and long non-coding RNA profiling of whiteleg shrimp Penaeus vannamei hemocytes in response to Spiroplasma eriocheiris infection

Cited by 24 publications

References 46 publications

Full-Length Transcriptome Sequencing and Comparative Transcriptomic Analysis Provide Insights Into the Ovarian Maturation of Exopalaemon carinicauda

Full-Length Transcriptome Sequencing and Comparative Transcriptomic Analysis Provide Insights Into the Ovarian Maturation of Exopalaemon carinicauda

The Molecular Mechanism of Hemocyte Immune Response in Marsupenaeus japonicus Infected With Decapod Iridescent Virus 1

Host-microbiota interactions and responses of Metapenaeus ensis infected with decapod iridescent virus 1

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