Transcriptome profiling of claw muscle of the mud crab (Scylla paramamosain) at different fattening stages

Jiang, Qingling; Bao, Chenchang; Yang, Yanan; Liu, An; Liu, Fang; Huang, Huiyang; Ye, Haihui

doi:10.1371/journal.pone.0188067

Cited by 9 publications

(6 citation statements)

References 57 publications

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“…The third-generation sequencing technology is the most advanced technology, which could obtain full-length transcripts on a large scale. In this study, a total of 79005 high-quality unique transcripts is obtained, among which 50% transcripts is full-length, which is more efficient than RACE and the second-generation sequencing technology 30,32,33,48 . These full-length transcripts identified in this study will facilitate further study of S .…”

Section: Discussionmentioning

confidence: 99%

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The Single-molecule long-read sequencing of Scylla paramamosain

Wan

Jia

Zou

et al. 2019

Sci Rep

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Scylla paramamosain is an important aquaculture crab, which has great economical and nutritional value. To the best of our knowledge, few full-length crab transcriptomes are available. In this study, a library composed of 12 different tissues including gill, hepatopancreas, muscle, cerebral ganglion, eyestalk, thoracic ganglia, intestine, heart, testis, ovary, sperm reservoir, and hemocyte was constructed and sequenced using Pacific Biosciences single-molecule real-time (SMRT) long-read sequencing technology. A total of 284803 full-length non-chimeric reads were obtained, from which 79005 high-quality unique transcripts were obtained after error correction and sequence clustering and redundant. Additionally, a total of 52544 transcripts were annotated against protein database (NCBI nonredundant, Swiss-Prot, KOG, and KEGG database). A total of 23644 long non-coding RNAs (lncRNAs) and 131561 simple sequence repeats (SSRs) were identified. Meanwhile, the isoforms of many genes were also identified in this study. Our study provides a rich set of full-length cDNA sequences for S . paramamosain , which will greatly facilitate S . paramamosain research.

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Section: Discussionmentioning

confidence: 99%

“…In crab and shrimp, the high-throughput sequencing technology has been applied in Eriocheir sinensis 1–21 , Portunus trituberculatus 22–29 , S . paramamosain 30–33 , S . olivacea 34 , Carcinus maenas 35,36 , Gecarcinus lateralis 37–41 , P .…”

Section: Introductionmentioning

confidence: 99%

The Single-molecule long-read sequencing of Scylla paramamosain

Wan

Jia

Zou

et al. 2019

Sci Rep

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“…They were reared in tanks (temperature: 26 ± 0.5 °C), fed with shrimp meat, and the water was changed every day. Mud crabs at three molt stages were sampled according to the previous study 16 . Post-molt stage: the mud crab just molted for 1–2 days, it was very thin, only dorsal carapace edge hard,Inter-molt stage: the dominant phase of the inter-molt period, the mud crab was full of meat, the exoskeleton was consolidated and hardened,Pre-molt stage: the fourth phase of the pre-molt period, namely double shell crab, pleural suture cracks between the carapace and the abdomen.…”

Section: Methodsmentioning

confidence: 99%

“…Mud crabs ( Scylla species) are found throughout tropical and warm temperate zones in the Indo-Pacific, and S. paramamosain is a commercially important marine fishery species in the Southeast coast of China 15 . Transcriptomics is an emerging discipline, which can now be used to examine patterns of gene transcription relative to crustacean immunity, growth and molting 12 , 14 , 16 . In this study, we used RNA-Seq to investigate the immune responses in the hepatopancreas at three molt stages in the mud crab, S. paramamosain to understand the mechanism of immune defense during the crustacean molt cycle.…”

Section: Introductionmentioning

confidence: 99%

Hepatopancreas immune response during molt cycle in the mud crab, Scylla paramamosain

Liu

et al. 2020

Sci Rep

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Molt is a critical developmental process in crustaceans. Recent studies have shown that the hepatopancreas is an important source of innate immune molecules, yet hepatopancreatic patterns of gene expression during the molt cycle which may underlie changes in immune mechanism are unknown. In this study, we performed Illumina sequencing for the hepatopancreas of the mud crab, Scylla paramamosain during molt cycle (pre-molt stage, post-molt stage, and inter-molt stage). A total of 44.55 Gb high-quality reads were obtained from the normalized cDNA of hepatopancreas. A total of 70,591 transcripts were assembled; 55,167 unigenes were identified. Transcriptomic comparison revealed 948 differentially expressed genes (DEGs) in the hepatopancreas from the three molt stages. We found that genes associated with immune response patterns changed in expression during the molt cycle. Antimicrobial peptide genes, inflammatory response genes, Toll signaling pathway factors, the phenoloxidase system, antioxidant enzymes, metal-binding proteins and other immune related genes are significantly up-regulated at the post-molt stage and inter-molt stage compared with the pre-molt stage, respectively. These genes are either not expressed or are expressed at low levels at the pre-molt stage. To our knowledge, this is the first systematic transcriptome analysis of genes capable of mobilizing a hepatopancreas immune response during the molt cycle in crustaceans, and this study will contribute to a better understanding of the hepatopancreas immune system and mud crab prophylactic immune mechanisms at the post-molt stage.

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“…The rising demands of live mud crab provide economic opportunities for many regions (Jahan & Islam, ; Paterson & Mann, ; Poole et al, ), and the knowledge about mud crab farming continues to grow (Jiang et al, ; Rumisha, Huyghe, Rapanoel, Mascaux, & Kochzius, ; Waiho et al, ). Here, we described a novel technique for detecting crab ECG through implanting an electrode close to the crab heart.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of suitable temperature range for post‐harvest processing of mud crabs through cardiac performance

2019

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Measurements of either heartbeats or heart rate variability provide important information on metabolic changes and stress responses. In this study, we aimed to determine the suitable temperature conditions for maintaining product quality for post‐harvest processing of mud crab (Scylla serrata) through measuring cardiac performance. A bundle of implanted electrodes was used to record the electrocardiogram, from which the heart rate (HR) and heart rate variability (HRV) were derived to evaluate the physiological performances of the crabs under tying at different seawater temperatures. The lowest standard deviation of HR was detected at the seawater temperature of 18°C for the group of ascending temperatures and at 10°C for the group of descending temperatures. Lower HRV was detected at the range from 10 to 14°C. The results suggest that the temperature range of 14–18°C is suitable to reduce variability in heart rate and may decrease physiological stress. These conditions might help maintain the quality of live crabs during post‐harvest processing and transportation.

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Transcriptome profiling of claw muscle of the mud crab (Scylla paramamosain) at different fattening stages

Cited by 9 publications

References 57 publications

The Single-molecule long-read sequencing of Scylla paramamosain

The Single-molecule long-read sequencing of Scylla paramamosain

Hepatopancreas immune response during molt cycle in the mud crab, Scylla paramamosain

Evaluation of suitable temperature range for post‐harvest processing of mud crabs through cardiac performance

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