De novo assembly and annotation of the transcriptome of Astyanax lacustris liver unveil candidate genes to monitor response to environmental stress

Gnocchi, Karla Giavarini; Boldrini-França, Johara; Gomes, Levy Carvalho; Chippari-Gomes, Adriana Regina

doi:10.1016/j.margen.2020.100784

Cited by 5 publications

(6 citation statements)

References 18 publications

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“…The functional content of the liver transcriptome in South African sardines is consistent with the essential role that hepatic cells play in energy production, energy storage, digestion, secretory, physiological or immune responses to stressors, and the detoxification of harmful chemical compounds [11,16,17].…”

Section: Resultssupporting

confidence: 63%

“…Recent advances in DNA sequencing technologies and computational resources have made it possible to study the functional content of the genome in a way that was previously impossible. Massively parallel sequencing of the transcriptome from different tissue types has been used to address the biological questions of species from diverse terrestrial and marine environments [ 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 ].…”

Section: Introductionmentioning

confidence: 99%

“…The functional content of the liver transcriptome in marine vertebrates is particularly informative. Not only do hepatic cells play an essential role in the detoxification of harmful metabolites and anthropogenic pollutants that are accumulating in marine ecosystems at an unprecedented rate, but they are also involved in energy production, energy storage, and in the initiation of various physiological or immune responses necessary to fight pathogens [ 11 , 16 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

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Transcriptomic Diversity in the Livers of South African Sardines Participating in the Annual Sardine Run

Emami‐Khoyi

Roux

Adair

et al. 2021

Genes

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During austral winter, the southern and eastern coastlines of South Africa witness one of the largest animal migrations on the planet, the KwaZulu-Natal sardine run. Hundreds of millions of temperate sardines, Sardinops sagax, form large shoals that migrate north-east towards the subtropical Indian Ocean. Recent studies have highlighted the role that genetic and environmental factors play in sardine run formation. In the present study, we used massively parallel sequencing to assemble and annotate the first reference transcriptome from the liver cells of South African sardines, and to investigate the functional content and transcriptomic diversity. A total of 1,310,530 transcripts with an N50 of 1578 bp were assembled de novo. Several genes and core biochemical pathways that modulate energy production, energy storage, digestion, secretory processes, immune responses, signaling, regulatory processes, and detoxification were identified. The functional content of the liver transcriptome from six individuals that participated in the 2019 sardine run demonstrated heterogeneous levels of variation. Data presented in the current study provide new insights into the complex function of the liver transcriptome in South African sardines.

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Section: Resultssupporting

confidence: 63%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Transcriptomic Diversity in the Livers of South African Sardines Participating in the Annual Sardine Run

Emami‐Khoyi

Roux

Adair

et al. 2021

Genes

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“…In the present study, de novo transcriptome assembly of the Indian mackerel R. kanagurta was performed using Trinity. Trans Decoder was used to identify coding regions, and CD-HIT-EST was then used to remove redundant sequences (Gnocchi et al 2020). All metrics have shown that the overall quality of the transcriptome produced in this study is relatively high.…”

Section: Resultsmentioning

confidence: 99%

IESFAC Proceedings 2023

2023

IJE

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The Indian Ecological Society, Punjab Agricultural University (PAU) is organizing 3 days conference on "Fisheries and Aquaculture: An Ecological Perspective" (IESFAC-2023) from 22 nd to 24 th February, 2023 in collaboration with Guru Angad Dev Veterinary and Animal Sciences University (GADVASU) at Ludhiana, Punjab; which is first of its kind in the State to deliberate on strategic innovations and key issues related to eco-sustainability, economic viability and resilience of aqua food production resources. Socio-economic contribution of fisheries sector is evident from its contributions towards food security, malnutrition, livelihood sustenance, employment generation and economic growth at community, regional, national and global levels; in special reference to rural development in developing countries like India. In view of prospective role of the fisheries sector in fulfilling united nations sustainable development goals (SDGs) to attain "Zero Hunger" and "Good Health and Well Being", it is vital to develop the sector in an eco-responsible manner. Further, conservation and sustainable use of aquatic resources advocated under the SDG-14 "Life below Water" also relates to economic value of fisheries sector in many ways.Veteran experts, scientists, young fisheries professionals, farmers and industry representatives will be sharing the conference platform to present latest innovative technologies, requirements, issues and strategies for sustainable development of the sector; under different theme areas covering aquaculture production systems; sustainable aquafeeds and feed technologies; genetics, breeding and biotechnology, aquaculture environment/health management and one health; responsible aquaculture and climate resilience in fisheries; aquatic ecosystem assessment, management and conservation; processing, value addition, quality assurance and marketing; and capacity building and socio-economic empowerment. National and international experts have contributed their research findings and experiences for wider sharing and debate for fruitful linkages and applications. Keynote and lead speakers from esteemed national and international institutes will interact with the participants on important issues related to human resource requirements; sustainable economic utilization of aquatic resources; species and production system diversifications; organic recycling based integrated aquafarming technologies; quality assurance; economic and smart feed technologies; AMR and responsible aquaculture; processing towards circular bioeconomy; marketing and export; and doubling farmers income through food and ornamental fish/shellfish culture in freshwater, brackish water and marine water resources.An effective forward and backward feedback system is required to address need based regional requirements of the stakeholders to remove weak links within the supply chain and in this context an "Academia-Farmer-Industry" interface during the conference will help in spotlighting required actions to reinforce the sector in interest of stak...

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“…Yellowtail Lambari are small fish (10-15 cm in length) that inhabit small lakes, streams, and rivers and have an omnivorous feeding habit (Bennemann et al 2005;Viana et al 2013). This species is an important natural resource and a good model in environmental studies, since changes in environmental quality affect its metabolic conditions (Stevanato and Ostrensky 2018;Gnocchi et al 2020;Macêdo et al 2020;Warren and Burr 2020;Zafra-Lemos et al 2021).…”

Section: Impact Statementmentioning

confidence: 99%

Metabolic responses in the gills of Yellowtail Lambari Astyanax lacustris under low‐ and high‐temperature thermal stress

Schleger,

Pereira,

Resende

et al. 2024

J Aqua Anim Hlth

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ObjectiveEctothermic fish are directly affected by temperature changes in the environment. The aim of this study was to evaluate the metabolic responses in the gills of Yellowtail Lambari Astyanax lacustris under thermal stress.MethodsTo this end, we used spectrophotometry to evaluate the biomarkers of carbohydrate and protein metabolism, antioxidant defense, and oxidative damage in fish subjected to low (15°C) and high (31°C) temperatures, with control groups held at 23°C, for 2, 6, 12, 24, 48, and 96 h.ResultThe results showed that cold thermal stress did not change the energy demand, and the antioxidant defense was reduced; therefore, the gills were vulnerable to the action of reactive oxygen species (ROS), presenting increased protein carbonylation at 12 h. With heat thermal stress, a higher energy demand was observed, which was verified by an increase in aerobic metabolism by glycolysis and the citric acid cycle. High‐temperature stress also increased the antioxidant defenses, as verified by the increased activities of glutathione peroxidase, glutathione reductase, and glutathione S‐transferase. However, the antioxidant defense system could not protect tissues from the action of ROS, as protein carbonylation increased at 6 and 24 h, indicating oxidative stress.ConclusionThe results showed that (1) temperature variations caused metabolic adjustments in the gills of Yellowtail Lambari, (2) the adaptive responses were different for winter and summer temperatures, and (3) Yellowtail Lambari recovered homeostasis when subjected to thermal stress, even with the occurrence of oxidative stress.

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De novo assembly and annotation of the transcriptome of Astyanax lacustris liver unveil candidate genes to monitor response to environmental stress

Cited by 5 publications

References 18 publications

Transcriptomic Diversity in the Livers of South African Sardines Participating in the Annual Sardine Run

Transcriptomic Diversity in the Livers of South African Sardines Participating in the Annual Sardine Run

IESFAC Proceedings 2023

Metabolic responses in the gills of Yellowtail Lambari Astyanax lacustris under low‐ and high‐temperature thermal stress

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