PacBio full length transcript sequencing and Illumina transcriptome insight into immune defense mechanism of Litopenaeus vannamei under ammonia-N stress

Zhang, Xin; Pan, Luqing; Tong, Ruixue; Li, Yufen; Tian, Yimeng; Li, Dongyu; Si, Lingjun

doi:10.1016/j.aquaculture.2021.736457

Cited by 16 publications

(7 citation statements)

References 68 publications

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“…In the most recent study, Zhang et al 87 analysed the effects of gene expression due to ammonia stress on the immune response mechanisms of P. vannamei haemocytes, using PacBio and Illumina technologies. They found that the high concentration of ammonia in the water induced cell membrane receptors (HT7R, NACHR and TLR3) to signalling genes in the haemocytes to induce effector proteins, reducing the immune parameters, such as total haemocyte count, PO activity, haemocytic phagocytosis rate, antibacterial and bacteriolytic activities.…”

Section: Immune Responses Against Ammonia Exposurementioning

confidence: 99%

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Shrimp immune response: A transcriptomic perspective

Fajardo

Martı́nez-Rodrı́guez

Costas

et al. 2021

Reviews in Aquaculture

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During the last 15 years, a significant amount of data related to the crustacean immune system has been generated, mainly led by the advances made in the field of transcriptomic analysis through massive mRNA sequencing technology. In order to shed new light on the genes and metabolic pathways associated with the immune system in shrimp species, we have carried out a meta‐analysis using the current literature and the Sequence Read Archive (SRA) database of the National Center for Biotechnology Information (NCBI), which has 1195 published transcriptomic data sets until 31 December 2020, from different tissues and 14 Penaeus species. The transcriptomic analyses published so far have explored the effects of the challenge from viral and bacterial pathogens, as well as abiotic stressors, such as ammonia, temperature, salinity, oxygen deprivation and pH. They have also explored the effect of dietary factors and beneficial microbes (pre‐ and probiotics) in the immune response. In order to harness the vast amount of information available, multidisciplinary efforts have to generate better genomic tools to overcome the complexity of the genome and to implement the knowledge gained into commercial applications for the improvement of the culture conditions, adaptation of more sustainable feeds and producing strains showing more resilience/tolerance to diseases.

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Section: Immune Responses Against Ammonia Exposurementioning

confidence: 99%

Section: Molecular Signatures Linked To Abiotic Factorsmentioning

confidence: 99%

Shrimp immune response: A transcriptomic perspective

Fajardo

Martı́nez-Rodrı́guez

Costas

et al. 2021

Reviews in Aquaculture

View full text Add to dashboard Cite

show abstract

“…In recent years, high-throughput third-generation sequencing (TGS) technology such as single-molecule real-time (SMRT) sequencing has been successfully applied to functional genome research and widely used in aquatic animals [ 5 , 6 , 7 , 8 ]. Compared with second-generation sequencing (SGS), TGS provides longer read lengths, which makes it very suitable for unsolved problems in genomic, transcriptome and epigenetic research [ 8 ].…”

Section: Introductionmentioning

confidence: 99%

Full-length transcriptome and analysis of bmp-related genes in Platypharodon extremus

Wu¹,

Gong²,

Chen³

et al. 2022

Heliyon

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“…This technology is being increasingly applied to the study of aquatic animals. The full-length transcriptome has been used to investigate the molecular responses of Coilia nasus to salinity stress [ 27 ], of Exopalaemon carinicauda to thermal stress [ 28 ], of Litopenaeus vannamei to ammonia-N stress [ 29 ], and of M. mercenaria to air exposure [ 30 ]. However, to the best of our knowledge, the full-length transcriptome of C. fluminea has not been characterized or applied to explore the molecular mechanisms responding to environmental stresses.…”

Section: Introductionmentioning

confidence: 99%

PacBio Full-Length and Illumina Transcriptomes of the Gill Reveal the Molecular Response of Corbicula fluminea under Aerial Exposure

Zhang

Huang

et al. 2022

IJMS

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Air exposure is a common stress for Corbicula fluminea, an economically important freshwater shellfish consumed in China, during aquaculture and transportation. However, little is known about its molecular responses to air exposure. Therefore, this study used a combination of PacBio full-length and Illumina transcriptomes to investigate its molecular responses to air exposure. A total of 36,772 transcripts were obtained using PacBio sequencing. Structural analysis identified 32,069 coding sequences, 1906 transcription factors, 8873 simple sequence repeats, and 17,815 long non-coding RNAs. Subcellular localization analysis showed that most transcripts were located in the cytoplasm and nucleus. After 96-h of air exposure, 210 differentially expressed genes (DEGs) in the gill were obtained via Illumina sequencing. Among these DEGs, most of the genes related to glycolysis, tricarboxylic acid cycle, lipid metabolism, and amino acid metabolism were upregulated. Additionally, many DEGs associated with immunity, cytoskeleton reorganization, autophagy, and ferroptosis were identified. These findings indicated that metabolic strategy change, immune response, cytoskeleton reconstruction, autophagy, and ferroptosis might be the important mechanisms that C. fluminea use to cope with air exposure. This study will enrich the gene resources of C. fluminea and provide valuable data for studying the molecular mechanisms coping with air exposure in C. fluminea and other freshwater mollusks.

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PacBio full length transcript sequencing and Illumina transcriptome insight into immune defense mechanism of Litopenaeus vannamei under ammonia-N stress

Cited by 16 publications

References 68 publications

Shrimp immune response: A transcriptomic perspective

Shrimp immune response: A transcriptomic perspective

Full-length transcriptome and analysis of bmp-related genes in Platypharodon extremus

PacBio Full-Length and Illumina Transcriptomes of the Gill Reveal the Molecular Response of Corbicula fluminea under Aerial Exposure

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