The fatty acid elongation genes elovl4a and elovl4b are present and functional in the genome of tambaqui (Colossoma macropomum)

Ferraz, Renato; Machado, André M.; Navarro, Juan Carlos; Cunha, Isabel; Ozório, R.O.A.; Salaro, Ana Lúcia; Castro, L. Filipe C.; Monroig, Óscar

doi:10.1016/j.cbpb.2020.110447

Cited by 10 publications

(8 citation statements)

References 64 publications

(107 reference statements)

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“…Transcriptomic characterization of tambaqui exposed to (i) distinct climate change scenarios and (ii) during gonadal differentiation have provided a helpful resource for the understanding of the molecular mechanisms underlying both the adaptation to a future new climate and the process of sex determination [7,8,9]. Other molecular mechanisms related to enzymatic capacity for long-chain polyunsaturated fatty acid biosynthesis have also been confirmed by a functional characterization of core genes in these processes [10,11]. Moreover, the first steps for deciphering the structure and functional dynamics of the tambaqui genome have already been taken, with large-scale SNP discovery allowing the building of a high-density genetic linkage map of the species [12], along with preliminary microRNA identification and characterization [13].…”

Section: Introductionmentioning

confidence: 95%

Genome assembly and annotation of the tambaqui (Colossoma macropomum): an emblematic fish of the Amazon River basin

Hilsdorf

Uliano-Silva

Coutinho

et al. 2021

Preprint

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Colossoma macropomum known as tambaqui is the largest Characiformes fish in the Amazon River Basin and a leading species in Brazilian aquaculture and fisheries. Good quality meat and great adaptability to culture systems are some of its remarkable farming features. To support studies into the genetics and genomics of the tambaqui, we have produced the first high-quality genome for the species. We combined Illumina and PacBio sequencing technologies to generate a reference genome, assembled with 39X coverage of long reads and polished to a QV=36 with 130X coverage of short reads. The genome was assembled into 1,269 scaffolds to a total of 1,221,847,006 bases, with a scaffold N50 size of 40 Mb where 93% of all assembled bases were placed in the largest 54 scaffolds that corresponds to the diploid karyotype of the tambaqui. Furthermore, the NCBI Annotation Pipeline annotated genes, pseudogenes, and non-coding transcripts using the RefSeq database as evidence, guaranteeing a high-quality annotation. A Genome Data Viewer for the tambaqui was produced which benefits any groups interested in exploring unique genomic features of the species. The availability of a highly accurate genome assembly for tambaqui provides the foundation for novel insights about ecological and evolutionary facets and is a helpful resource for aquaculture purposes.

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Section: Introductionmentioning

confidence: 95%

Genome assembly and annotation of the tambaqui (Colossoma macropomum): an emblematic fish of the Amazon River basin

Hilsdorf

Uliano-Silva

Coutinho

et al. 2021

Preprint

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“…While freshwater sh species such as cyprinids could potentially utilize Elovl4 for C22 PUFA elongation, Elovl4 is postulated to compensate for the loss of Elovl2 in marine species (Betancor et al 2020; Luo et al 2021).Between the two isoforms, the P. micromegethes Elovl4a displayed higher elongation activities towards C18 PUFA while the Elovl4b showed higher activities towards the C20 substrates. Majority of the studied teleost species also reported higher rate of C20 and C22 PUFA elongation with Elovl4b(Ferraz et al 2020;Monroig et al 2010a;Morais et al 2020). In contrast, the African cat sh Elovl4a showed higher activities among the two paralogs(Oboh et al 2017b).…”

mentioning

confidence: 82%

A Complete Inventory of Long-Chain Polyunsaturated Fatty Acids Biosynthesis Pathway Enzymes in the Miniaturized Cyprinid Paedocypris Micromegethes

Sam

Lau

Kuah

et al. 2022

Preprint

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The capacity for long-chain polyunsaturated fatty acid (LC-PUFA) biosynthesis activity in a species depends on the enzymatic activities of fatty acyl desaturase (Fads) and elongation of very long-chain fatty acid (Elovl). The miniaturized fish Paedocypris micromegethes is a developmentally truncated cyprinid living in highly acidic water conditions in tropical peat swamps. The capacity for LC-PUFA biosynthesis in this species, which has a reduced genome size, is unknown. A high-quality de novo transcriptome assembly enabled the identification of a putative Fads2 and four Elovl. The Fads2 was verified as a P. micromegethes Fads2 ortholog with in vitro Δ5 and Δ6 activities. The Elovl sequences were established as an Elovl5, Elovl2, and two Elovl4 paralogs, namely Elovl4a and Elovl4b. These Elovl enzymes, mainly Elovl5 and Elovl2, fulfill the necessary C18, C20, and C22 PUFA elongation steps for LC-PUFA biosynthesis. Collectively, these results validate the presence of a complete repertoire of LC-PUFA biosynthesis enzymes in a tropical miniatured freshwater fish.

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“…The authors reported and annotated a total of 43,098 transcripts, which will address issues concerning different facets of tambaqui farming. Ferraz et al 228 presented a draft genome assembly for tambaqui and demonstrated its utility for studies of nutritional physiology. The authors focused on metabolism of long‐chain (C20–24) polyunsaturated fatty acids (LC‐PUFA) that are physiologically important nutrients for vertebrates.…”

Section: Genetics Genomics and Selective Breedingmentioning

confidence: 99%

“…Results of a recent molecular study demonstrated that tambaqui express all desaturase and elongase activities (ie fads2, elol5 and elovl2) required to convert LA and ALA to ARA, EPA and DHA. 228,285 Thus, the NRC 255 recommendations of supplying 5-20 g LNA kg −1 diet (based on total lipid content) and the importance of n-6 fatty acids in the nutrition and feeding of Neotropical fish species such as tambaqui are supported.…”

Section: N Utriti On and Feed Ingmentioning

confidence: 99%

The farming and husbandry ofColossoma macropomum: From Amazonian waters to sustainable production

Hilsdorf

Hallerman

Valladão

et al. 2021

Reviews in Aquaculture

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Within the rich diversity of South American freshwater fish, Colossoma macropomum (Characiformes: Serrasalmidae), known as tambaqui, cachama or blackfin pacu, can reach 30 kg, is a traditional product in regional fish markets and has drawn the attention of fish farmers since the 1930s. Considerable progress achieved in different fields of aquaculture science has contributed to the growth of tambaqui production.

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The fatty acid elongation genes elovl4a and elovl4b are present and functional in the genome of tambaqui (Colossoma macropomum)

Cited by 10 publications

References 64 publications

Genome assembly and annotation of the tambaqui (Colossoma macropomum): an emblematic fish of the Amazon River basin

Genome assembly and annotation of the tambaqui (Colossoma macropomum): an emblematic fish of the Amazon River basin

A Complete Inventory of Long-Chain Polyunsaturated Fatty Acids Biosynthesis Pathway Enzymes in the Miniaturized Cyprinid Paedocypris Micromegethes

The farming and husbandry ofColossoma macropomum: From Amazonian waters to sustainable production

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