Full-length transcriptome analysis provides new insights into the innate immune system of Marsupenaeus japonicus

Zheng, Jinbin; Wang, Panpan; Mao, Yong; Su, Yongquan; Wang, Jun

doi:10.1016/j.fsi.2020.07.018

Cited by 19 publications

(12 citation statements)

References 38 publications

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Section: Discussionmentioning

confidence: 99%

“…PacBio RNA-seq has fast sequencing speed, high accuracy, and long readings. Because of the advantages of PacBio RNA-seq, it has been widely used in various species research ( Ma et al, 2019 ; Xue et al, 2019 ; Luo et al, 2020 ; Zheng et al, 2020 ; Chen et al, 2021 ). Because C. antiquata is an important economic shellfish with high medicinal potential, there are many studies now.…”

Section: Discussionmentioning

confidence: 99%

“…Total RNA was separately extracted from these tissue samples ( Jia et al, 2020 ; Zheng et al, 2020 ). The purity, concentration, and absorption peak of the extracted RNA were measured using a NanoDrop 2,000 spectrophotometer (Thermo Fisher Scientific Inc., United States).…”

Section: Methodsmentioning

confidence: 99%

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SMRT Sequencing of the Full-Length Transcriptome of the Coelomactra antiquata

Deng

Yao

et al. 2021

Front. Genet.

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Coelomactra antiquata is an important aquatic economic shellfish with high medicinal value. However, because C. antiquata has no reference genome, a lot of molecular biology research cannot be carried out, so the analysis of its transcripts is an important step to study the regulatory genes of various substances in C. antiquata. In the present study, we conducted the first full-length transcriptome analysis of C. antiquata by using PacBio single-molecule real-time (SMRT) sequencing technology. The results identified a total of 39,209 unigenes with an average length of 2,732 bp, 23,338 CDSs, 251 AS events, 9,881 lncRNAs, 20,106 SSRs, and 2,316 TFs. Subsequently, 59.22% (23,220) of the unigenes were successfully annotated, of which 23,164, 18,711, 15,840, 13,534, and 13,474 unigenes could be annotated using NR, Swiss-prot, KOG, GO, and KEGG databases, respectively. This study lays the foundation for the follow-up research of molecular biology and provides a reference for studying the more medicinal value of C. antiquata.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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SMRT Sequencing of the Full-Length Transcriptome of the Coelomactra antiquata

Deng

Yao

et al. 2021

Front. Genet.

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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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“…[194][195][196] Noteworthy progress has been achieved in the characterization of diverse immune mechanisms and pathways. 195,[197][198][199] However, knowledge gaps in numerous immune mechanisms, including cellular and molecular basis, of aquatic animals persist, and the available information differs according to species. The complete development of immunology as a scientific discipline remains equitably incorporated in both fundamental and clinical research.…”

Section: Immunity In Fish and Aquatic Invertebratesmentioning

confidence: 99%

Carotenoids modulate stress tolerance and immune responses in aquatic animals

Lim

Yusoff

Karim

et al. 2022

Reviews in Aquaculture

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Aquaculture continues to expand swiftly and remains the fastest-growing food industry worldwide amidst ever-present threats from chronic stressors and emerging diseases. Nutrition plays a pivotal role in the profitability and viability of the aquaculture industry that steered a paradigm shift to therapeutic nutrition. Carotenoids, also termed tetraterpenoids, have garnered considerable attention owing to their therapeutic attributes and immeasurable health benefits, which incited a surge in global demand. These biological pigments are recognized to promote immune systems and antioxidant defence mechanisms in both aquatic vertebrates and invertebrates. This review brings forth existing scientific evidence and underscores the notable roles of carotenoids as biologically active constituents with anti-stress and immunostimulatory potentials in farmed aquatic animals whilst explicating possible mechanisms of action. Empirical data unequivocally established the modulatory functions of carotenoids on endogenous antioxidant enzymes, innate and adaptive arms of the immune response, as well as the expression of multiple antioxidant and immune-related genes. The comprehensive information presented is beneficial to deepen our understanding of the utilization of carotenoids as potent stress alleviators and immunostimulants in cultured aquatic animals, which is translated into improved health.Advancements in aquatic animal health and welfare could principally contribute to reconstructing a more sustainable aquaculture industry. This article may be useful for subsequent investigations towards further advances in research and innovation to a greener blue revolution in solving the challenge of global food security.

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Full-length transcriptome analysis provides new insights into the innate immune system of Marsupenaeus japonicus

Cited by 19 publications

References 38 publications

SMRT Sequencing of the Full-Length Transcriptome of the Coelomactra antiquata

SMRT Sequencing of the Full-Length Transcriptome of the Coelomactra antiquata

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

Carotenoids modulate stress tolerance and immune responses in aquatic animals

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