Litopenaeus vannamei Transcriptome Profile of Populations Evaluated for Growth Performance and Exposed to White Spot Syndrome Virus (WSSV)

Santos, Camilla A.; Andrade, Sónia C. S.; Teixeira, Ana Karina; Farias, Flávio; Kurkjian, Karin; Guerrelhas, Ana C.; Rocha, J. L.; Galetti, Pedro M.; Freitas, Patrícia D.

doi:10.3389/fgene.2018.00120

Cited by 23 publications

(23 citation statements)

References 37 publications

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“…Domesticated shrimps could not mature well with declining growth rates over generations (Jackson & Wang, 1998). Albeit its importance, the knowledge on genes controlling shrimp’s growth remained limited partly due to the lack of the genome, thus up-to-now most growth-related genes identified in P. monodon were from L. vannamei (Gao et al, 2017; Gao et al, 2015; Santos et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes

Uengwetwanit

Pootakham

Nookaew

et al. 2020

Preprint

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The black tiger shrimp (Penaeus monodon) is one of the most prominent farmed crustacean species with an average annual global production of 0.5 million tons in the last decade. To ensure sustainable and profitable production through genetic selective breeding programs, several research groups have attempted to generate a reference genome using short-read sequencing technology. However, the currently available assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA in this species. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of novel genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several gene groups involved in nutrient metabolism pathways and revealed 67 newly identified growth-associated genes. Our high-quality genome assembly provides an invaluable resource for accelerating the development of improved shrimp strain in breeding programs and future studies on gene regulations and comparative genomics.

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Section: Discussionmentioning

confidence: 99%

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes

Uengwetwanit

Pootakham

Nookaew

et al. 2020

Preprint

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“…To support this idea, we used the data set from a robust L. vannamei transcriptome (Santos et al . ), which reported more than 20 thousand unigenes with known gene products. Using the data information from the supplementary material of Santos et al .…”

Section: Microrna Biogenesis In Penaeid Shrimpmentioning

confidence: 99%

“…Using the data information from the supplementary material of Santos et al . , available online, which include all the blastX hits found for 20 865 transcripts in the SwissProt database obtained for L. vannamei , we performed a search and found hits related to DGCR8, Exportin 5, DDX5 and DDX17. This observation indicates that these proteins are expressed in shrimp, probably having a role on microRNAs biogenesis pathway.…”

Section: Microrna Biogenesis In Penaeid Shrimpmentioning

confidence: 99%

“…The expression of key components of microRNAs biogenesis pathway in shrimp, suggests that other components maybe also expressed. To support this idea, we used the data set from a robust L. vannamei transcriptome (Santos et al 2018), which reported more than 20 thousand unigenes with known gene products. Using the data information from the supplementary material of Santos et al 2018, available online, which include all the blastX hits found for 20 865 transcripts in the SwissProt database obtained for L. vannamei, we performed a search and found hits related to DGCR8, Exportin 5, DDX5 and DDX17.…”

Section: Microrna Biogenesis In Penaeid Shrimpmentioning

confidence: 99%

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The role of shrimp microRNAs in immune response and beyond

González-Duarte¹,

García‐Carreño²

2018

Reviews in Aquaculture

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MicroRNAs are a class of small non‐coding RNAs that regulate gene expression at post‐transcriptional level. Regulatory RNAs were discovered in the nematode Caenorhabditis elegans, since then, their biological functions have been studied on different animals, including marine organisms. Several species of penaeid shrimp are important in ecology and fishing, including aquaculture. Overcrowding in aquaculture calls for infectious diseases, which threaten the development of shrimp aquaculture worldwide. Given that microRNAs play crucial regulatory roles in a wide variety of biological processes, there is a scientific interest to understand their contribution on shrimp physiology and pathology, specifically during immune and stress response. Increasing evidence has shown that the expression of microRNAs is affected during virus or bacterial infection and upon stress in shrimp. This information provides valuable insights for a better understanding of shrimp biology by means of microRNA regulation to bacterial and viral diseases.

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“…Litopenaeus vannamei ( L. vannamei ) is the most profitable species in shrimp farming, and it has become a commercially important species widely distributed in the world. However, the production and economic benefit of shrimp farming declined dramatically due to the outbreak of disease caused by various pathogens, such as bacteria, virus and mycotoxin (Lee et al, ; Santos et al, ; Zeng et al, ).…”

Section: Introductionmentioning

confidence: 99%

A global view of hepatopancreas and intestinal reveals the potential influencing mechanism of aflatoxin B1 on nutrition and metabolism inLitopenaeus vannamei

et al. 2019

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The present study was to determine the time‐dependent alterations in growth performance, histomorphology, digestive enzymes activities and the genes expression related to target of rapamycin (TOR) signalling pathway involved in hepatopancreas and intestine of Litopenaeus vannamei at 3, 6, 12, 18, 24 and 30 days after Aflatoxin B1 (AFB1) challenge. The results manifested that AFB1 could induce a significant decrease in growth performance and visible variations of the hepatopancreas and intestine structures in shrimp. Meanwhile, the digestive enzymes activities and genes expression level were significantly lower in the experimental group than in the control group and showed a time‐dependent decrease (p < 0.05). The expression levels of tor and s6k were significantly higher in the experimental group than in the control group from days 6 to 24 and showed a tendency to increase first and then decrease as a whole (p < 0.05). Meanwhile, we analysed candidate pathways involved in hepatopancreas and intestine of shrimp in metabolic response to AFB1. The mainly disturbed pathways related to metabolism in hepatopancreas were involved in pyrimidine, glycosylphosphatidylinositol, glycosaminoglycan, vitamin and amino acid biosynthesis and metabolism, while the mainly disturbed metabolic pathways in intestine were glycosaminoglycan, vitamin and amino acid biosynthesis and metabolism.

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Litopenaeus vannamei Transcriptome Profile of Populations Evaluated for Growth Performance and Exposed to White Spot Syndrome Virus (WSSV)

Cited by 23 publications

References 37 publications

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes

The role of shrimp microRNAs in immune response and beyond

A global view of hepatopancreas and intestinal reveals the potential influencing mechanism of aflatoxin B1 on nutrition and metabolism inLitopenaeus vannamei

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