Whole genome survey and microsatellite motif identification ofArtemia franciscana

Abstract

Artemia is an industrially important genus used in aquaculture as a nutritious diet for fish and as an aquatic model organism for toxicity tests. However, despite the significance of Artemia, genomic research remains incomplete and knowledge on its genomic characteristics is insufficient. In particular, A. franciscana of North America has been widely used in fisheries of other continents, resulting in invasion to native species. Therefore, studies on population genetics and molecular marker development as well as morphological analyses are required to investigate its population structure and to discriminate closely related species. Here, we used the Illumina Hi-Seq platform to estimate the genomic characteristics of A. franciscana through genome survey sequencing. Further, simple sequence repeat (SSR) loci were identified for microsatellite marker development. The predicted genome size was ~867 Mb using K-mer analysis (K=17), and heterozygosity and duplication rates were 0.655% and 0.809%, respectively. A total of 421,467 SSRs were identified from the genome survey assembly, most of which were dinucleotide motifs with a frequency of 77.22%. This study will be a useful basis in genomic and genetic research for A. franciscana.

ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp

“…Two genome assemblies and a high density linkage map are currently available for the American A. franciscana (Jo et al . 2021a; Han et al .…”

“…However, their potential as models for ZW chromosome evolution and comparative genomics in general was until recently hampered by a lack of genomic resources. The publication of two genomes for the American A. franciscana has already shed new light on how these charismatic organisms survive in their extreme environments (Jo et al 2021a;De Vos et al 2021), but no information on sex linkage was provided, and the lack of a close outgroup sequence (other than the distant Daphnia) made comparative analyses difficult. A draft genome was recently described for A. sp.…”

“…Two genome assemblies and a high density linkage map are currently available for the American A. franciscana (Jo et al 2021a;Han et al 2021;De Vos et al 2021), but resources for the Eurasian clade are more limited, with only an A. sp. Kazakhstan draft genome assembly recently described in Boyer et al (2022).…”

“…4 for all chromosomes), showing that chromosome 1 is the Z chromosome. To check for homology with the A. franciscana differentiated region, we mapped the scaffolds from the A. franciscana genome of (Jo et al 2021a) to the new A. sinica assembly based on their shared gene content, and plotted the coverage values that we had previously estimated (Huylmans et al 2019) based on the A. sinica coordinates. Fig.…”

Sex-Biased Gene Expression and Isoform Profile of Brine Shrimp Artemia franciscana by Transcriptome Analysis

“…The genus Artemia is considered to be a model organism for studying ZW sex-determining systems due to its short life cycle; ease of raising; and the appearance of two reproductive strategies, sexual and asexual [ 33 , 35 , 36 ]. Moreover, Artemia has utility as an organism for toxicological testing and as a food source for aquaculture industries [ 49 , 50 , 51 , 52 ]. This study provides a basis for the sex-biased gene expression and isoform-level transcriptome study of Artemia and helps to understand sex determination and differentiation in crustacean species using the ZW sex determination system.…”