An improved genome assembly and annotation of the Antarctic copepod Tigriopus kingsejongensis and comparison of fatty acid metabolism between T. kingsejongensis and the temperate copepod T. japonicus

Functional characterization reveals a diverse array of metazoan fatty acid biosynthesis genes

Long-chain (≥C₂₀ ) polyunsaturated fatty acids (LC-PUFAs) are physiologically important fatty acids for most animals, including humans. Although most LC-PUFA production occurs in aquatic primary producers such as microalgae, recent research indicates the ability of certain groups of (mainly marine) invertebrates for endogenous LC-PUFA biosynthesis and/or bioconversion from dietary precursors. The genetic pathways for and mechanisms behind LC-PUFA biosynthesis remain unknown in many invertebrates to date, especially in non-model species. However, the numerous genomic and transcriptomic resources currently available can contribute to our knowledge of the LC-PUFA biosynthetic capabilities of metazoans. Within our previously generated transcriptome of the benthic harpacticoid copepod Platychelipus littoralis, we detected expression of one methyl-end desaturase, one front-end desaturase, and seven elongases, key enzymes responsible for LC-PUFA biosynthesis. To demonstrate their functionality, we characterized eight of them using heterologous expression in yeast. The P. littoralis methyl-end desaturase has Δ15/17/19 desaturation activity, enabling biosynthesis of α-linolenic acid, eicosapentaenoic acid and docosahexaenoic acid (DHA) from 18:2 n-6, 20:4 n-6 and 22:5 n-6, respectively. Its front-end desaturase has Δ4 desaturation activity from 22:5 n-3 to DHA, implying that P. littoralis has multiple pathways to produce this physiologically important fatty acid. All studied P. littoralis elongases possess varying degrees of elongation activity for saturated and unsaturated fatty acids, producing aliphatic hydrocarbon chains with lengths of up to 30 carbons. Our investigation revealed a functionally diverse range of fatty acid biosynthesis genes in copepods, which highlights the need to scrutinize the role that primary consumers could perform in providing essential nutrients to upper trophic levels.

Identification and characterization of homeobox gene clusters in harpacticoid and calanoid copepods

In this study, we have identified the entire complement of typical homeobox (Hox) genes (Lab, Pb, Dfd, Scr, Antp, Ubx, Abd-A, and Abd-B) in harpacticoid and calanoid copepods and compared them with the cyclopoid copepod Paracyclopina nana. The harpacticoid copepods Tigriopus japonicus and Tigriopus kingsejongensis have seven Hox genes (Lab, Dfd, Scr, Antp, Ubx, Abd-A, and Abd-B) and the Pb and Ftz genes are also present in the cyclopoid copepod P. nana. In the Hox gene cluster of the calanoid copepod Eurytemora affinis, all the Hox genes were present linearly in the genome but the Antp gene was duplicated. Of the three representative copepods, the P. nana Hox gene cluster was the most compact due to its small genome size. The Hox gene expression profile patterns in the three representative copepods were stage-specific. The Lab, Dfd, Scr, Pb, Ftz, and Hox3 genes showed a high expression in early developmental stages but Antp, Ubx, Abd-A, and Abd-B genes were mostly expressed in later developmental stages, implying that these Hox genes may be closely associated with the development of segment identity during early development.

Influence of Microalgae Diets on the Biological and Growth Parameters of Oithona nana (Copepoda: Cyclopoida)

Simple Summary

The success of marine fish farming is primarily determined by diet in early life. While both artemia and rotifers are commonly used as live feed in aquaculture laboratories in Peru, there has been little work studying the use of native food species. Here, we report our research on the use of a native copepod (Oithona nana) for its potential use in Peruvian marine aquaculture. We collected specimens of the native copepod O. nana and performed culturing experiments with two microalgae that have been widely used in aquaculture. Results show that this species adapted positively to our culture conditions, achieving high densities. We also report on the copepod’s reproduction and growth characteristics. Because of these promising results, we recommend that O. nana be studied further and propose it as a species with potential use as a live feed.

Abstract

Several species of the planktonic free-living genus Oithona have been successfully used in the larviculture of marine fish and shrimp. However, few studies have been published that allow us to estimate the potential of Oithona nana culture under controlled conditions. This work evaluated the effect of the microalgae Isochrysis galbana and Chaetoceros calcitrans as single (200,000 cells/mL) and mixed diets (100,000 + 100,000 cells/mL) on population and individual growth, ingestion rate, number of spawnings, fertility, development time by stage, and sex ratio of O. nana. We cultured this copepod at 28 ± 0.5 °C, 35 PSU salinity, 125 lux, and 12:12 photoperiod. Results showed that diet had no effect on the final population level (6273–7966 ind/L) or on individual growth, nor on sex ratio, with less males than females. With C. calcitrans, O. nana had a higher filtration rate (57 ng C/ind/day). On the other hand, a mixed diet induced a higher number of spawns (0.4 events/day) and nauplii per spawn (23 ind). Similarly, a single or mixed diet, containing I. galbana, accelerated the development rate by 6.33–7.00 days. We concluded that O. nana can be cultured with both microalgae, indicating its potential use in an intensive system for production. However, more research is required to improve the productivity of O. nana rearing.

The salmon louse genome: Copepod features and parasitic adaptations

Copepods encompass numerous ecological roles including parasites, detrivores and phytoplankton grazers. Nonetheless, copepod genome assemblies remain scarce. Lepeophtheirus salmonis is an economically and ecologically important ectoparasitic copepod found on salmonid fish. We present the 695.4 Mbp L. salmonis genome assembly containing ≈60% repetitive regions and 13,081 annotated protein-coding genes. The genome comprises 14 autosomes and a ZZ-ZW sex chromosome system. Assembly assessment identified 92.4% of the expected arthropod genes. Transcriptomics supported annotation and indicated a marked shift in gene expression after host attachment, including apparent downregulation of genes related to circadian rhythm coinciding with abandoning diurnal migration. The genome shows evolutionary signatures including loss of genes needed for peroxisome biogenesis, presence of numerous FNII domains, and an incomplete heme homeostasis pathway suggesting heme proteins to be obtained from the host. Despite repeated development of resistance against chemical treatments L. salmonis exhibits low numbers of many genes involved in detoxification.

A complete enzymatic capacity for biosynthesis of docosahexaenoic acid (DHA, 22 : 6n-3) exists in the marine Harpacticoida copepod Tigriopus californicus

The long-standing paradigm establishing that global production of Omega-3 (n–3) long-chain polyunsaturated fatty acids (LC-PUFA) derived almost exclusively from marine single-cell organisms, was recently challenged by the discovery that multiple invertebrates possess methyl-end (or ωx) desaturases, critical enzymes enabling the biosynthesis of n–3 LC-PUFA. However, the question of whether animals with ωx desaturases have complete n–3 LC-PUFA biosynthetic pathways and hence can contribute to the production of these compounds in marine ecosystems remained unanswered. In the present study, we investigated the complete enzymatic complement involved in the n–3 LC-PUFA biosynthesis in Tigriopus californicus, an intertidal harpacticoid copepod. A total of two ωx desaturases, five front-end desaturases and six fatty acyl elongases were successfully isolated and functionally characterized. The T. californicus ωx desaturases enable the de novo biosynthesis of C₁₈ PUFA such as linoleic and α-linolenic acids, as well as several n–3 LC-PUFA from n–6 substrates. Functions demonstrated in front-end desaturases and fatty acyl elongases unveiled various routes through which T. californicus can biosynthesize the physiologically important arachidonic and eicosapentaenoic acids. Moreover, T. californicus possess a Δ4 desaturase, enabling the biosynthesis of docosahexaenoic acid via the ‘Δ4 pathway’. In conclusion, harpacticoid copepods such as T. californicus have complete n–3 LC-PUFA biosynthetic pathways and such capacity illustrates major roles of these invertebrates in the provision of essential fatty acids to upper trophic levels.