Recent advances in crustacean genomics and their potential application in aquaculture

Abstract

Genomic resources are increasingly being used to improve the production efficiency and profitability of aquaculture. Crustaceans are a large group of invertebrates that encompasses some of the most important farmed species in the aquaculture industry. However, very few crustacean genomes have been published although an aquaculture genome project was proposed as early as 1997. Breakthroughs in next‐generation and third‐generation sequencing technologies and the development of high‐complexity sequence assembly strategies have promoted the publication of an increasing number of crustacean genomes, thus paving a broad way for biological and genetic studies and applications in aquaculture. In this review, we summarize recent advances in crustacean genomic research as of June 2022, including genome sequencing and assembly, genomic characteristics, and the genetic mechanisms underlying various biological phenotypes, such as environmental adaptation, lifestyle, development, and sex determination. This review also discusses the application of crustacean genomes in aquaculture, including genetic dissection of economic traits and genome‐based selective breeding via genome‐wide association studies and genomic selection. High‐quality genomes are important not only for understanding the genetic basis of biologically and economically important traits but also for the genetic improvement of aquaculture species. However, the utilization of crustacean genomics still lags far behind those in other animals. Therefore, additional multi‐omics studies and technological development are needed to accelerate the application of genomics in aquaculture.

Penaeid Shrimp Chromosome Studies Entering the Post-Genomic Era

“…Currently, genome-wide association studies (GWAS) have been conducted based on chromosome-level genome reference mapping to identify genes associated with economically relevant traits such as growth, sex, disease resistance, and environmental adaptation. Resequencing and selection characterization have also confirmed that genes linked to growth and disease resistance are indeed selected for in artificial breeding [71].…”

“…Of the 4683 scaffolds, 3275 were anchored to 44 pseudochromosomes, representing 87.34% of the genome assembly size. The L. vannamei genome was the first high-quality reference genome for penaeid shrimp, and since then, the strategy has been used to sequence most crustacean genomes, including various shrimp, crayfish, crabs, krill, isopods, and amphipods [10,71,79,82].…”

Spatio-temporal patterns of ovarian development and VgR gene silencing reduced fecundity in parthenogenetic Artemia

“…Exploring the reproductive patterns and mechanisms of A. parthenogenetica may contribute to understanding the evolutionary route of animal reproduction from the sea to land, and how Artemia adapt to environmental changes and maintain population stability. With the publication of the genome of Artemia franciscana [66,67] and the completion of whole-genome sequencing of A. parthenogenetica (data not shown, ARARC sequenced), it is possible to find more accurate and detailed molecular evidence to interpret the role of Artemia in the evolution of species at the omics level.…”

Genome architecture of an exceptionally invasive copepod crossing salinity boundaries

“…Investigating the genome architecture of this exceptionally invasive copepod species complex would provide fundamental insights into the genomic and evolutionary mechanisms facilitating their rapid habitat invasions [38,39]. However, high-quality genome resources have long been absent for most copepod groups [40,41]. Only four chromosome-level genome assemblies are available for copepods in the NCBI Genome database [42], namely for two parasitic copepods (Siphonostomatoida) and two species of the intertidal copepod Tigriopus (Harpacticoida).…”