RNA-seq analysis to identify genes related to resting egg production of panarctic Daphnia pulex.

BACKGROUND: The genus Daphnia switches its reproductive mode from subitaneous egg production to resting egg production in response to environmental stimuli. Although this life history trait is essential for surviving unsuitable environments, the molecular mechanism of resting egg production is little understood. In this study, we examined genes related to induction of resting egg production using two genotypes of panarctic Daphnia pulex, the JPN1 and JPN2 lineages, which differ genetically in the frequency of resting egg production. We reared these genotypes under high and low food levels. At the high food level, individuals of both genotypes continually produced subitaneous eggs, whereas at the low food level, only the JPN2 genotype produced resting eggs. Then, we performed RNA-seq analysis on specimens of three instars, including before and after egg production. RESULTS: These results showed that expressed genes differed significantly between individuals grown under high and low food levels and among individuals of different instars and genotypes. Among these differentially expressed genes (DEGs), we found 16 that changed expression level before resting egg production. Some of these genes showed high-level expression only before resting egg production and one gene was an ortholog of bubblegum (bgm), which is reportedly up-regulated before diapause in bumblebees. According to gene ontology (GO) enrichment analysis, one GO term annotated as long-chain fatty acid biosynthetic process was enriched among these 16 genes. In addition, GO terms related to glycometabolism were enriched among down-regulated genes of individuals holding resting eggs, compared to those before resting egg production. CONCLUSIONS: We found candidate genes highly expressed only before resting egg production. Although functions of candidate genes found in this study have not been reported previously in Daphnia, catabolism of long-chain fatty acids and metabolism of glycerates are related to diapause in other organisms. Thus, it is highly probable that candidate genes identified in this study are related to the molecular mechanism regulating resting egg production in Daphnia.

Rediscovery after Almost 120 Years: Morphological and Genetic Evidence Supporting the Validity of Daphnia mitsukuri (Crustacea: Cladocera).

We examined the morphology of Daphnia individuals maintained in our laboratory for several years, originally collected in Lake Inbanuma, Chiba, Japan. We determined partial sequences of the mitochondrial cytochrome c oxidase subunit I and 12S rRNA genes from specimens in the cultured material. These animals are morphologically similar to D. obtusa Kurz, 1874 , but genetically distinct from this species. Our detailed observation shows that the morphological characteristics in the female and male individuals of our material are highly congruent with those of D. mitsukuri Ishikawa, 1896 , which has not been identified positively for more than 120 years since its original description, with its taxonomic identity having been questioned for almost 90 years. Based on our morphological and genetic data, we conclude that D. mitsukuri should be regarded as a taxonomically valid species. A search among public DNA sequence databases suggests D. mitsukuri is also distributed in China, although these Chinese sequences have been labeled as 'Daphnia pulex', representing misidentification.