Differential gene transcription across the life cycle in Daphnia magna using a new all genome custom-made microarray

Abstract

BackgroundUnravelling the link between genes and environment across the life cycle is a challenging goal that requires model organisms with well-characterized life-cycles, ecological interactions in nature, tractability in the laboratory, and available genomic tools. Very few well-studied invertebrate model species meet these requirements, being the waterflea Daphnia magna one of them. Here we report a full genome transcription profiling of D. magna during its life-cycle. The study was performed using a new microarray platform designed from the complete set of gene models representing the whole transcribed genome of D. magna.ResultsUp to 93% of the existing 41,317 D. magna gene models showed differential transcription patterns across the developmental stages of D. magna, 59% of which were functionally annotated. Embryos showed the highest number of unique transcribed genes, mainly related to DNA, RNA, and ribosome biogenesis, likely related to cellular proliferation and morphogenesis of the several body organs. Adult females showed an enrichment of transcripts for genes involved in reproductive processes. These female-specific transcripts were essentially absent in males, whose transcriptome was enriched in specific genes of male sexual differentiation genes, like doublesex.ConclusionOur results define major characteristics of transcriptional programs involved in the life-cycle, differentiate males and females, and show that large scale gene-transcription data collected in whole animals can be used to identify genes involved in specific biological and biochemical processes.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4725-7) contains supplementary material, which is available to authorized users.

Does differential iron supply to algae affect Daphnia life history? An ionome-wide study

“…On the other hand, Cu and Si occupied opposite sides of the balance in algae and Daphnia, potentially indicating strong regulation of these elements in daphniids because they are known to be toxic (e.g., de Schamphelaere & Janssen 2002;Karimi et al 2019). Such ionomic data should be useful in understanding the mechanisms by which Fe impacts expression of life history traits in ecologically important taxa, and in deciphering vast transcriptomic differences among life stages (Campos et al 2018). Finally, note that the contents of C, N, P, and Al in Daphnia were not part of any nutrient balances constructed, indicating that they are relatively homeostatic.…”

Transcriptomic analysis of the black tiger shrimp (Penaeus monodon) reveals insights into immune development in their early life stages

“…Their morphology, physiology and ecology are drastically transformed during the early life stages. To understand biological and physiological processes at larval stages, differential gene expression analysis was carried out in various crustaceans such as Pacific white shrimp ( P. vannamei ) 19 , 20 , water flea ( Daphnia magna ) 21 , barnacle ( Amphibalanus amphitrite ) 22 and crab ( Portunus pelagicus ) 23 . Molting- and exoskeleton developmentally-related genes are mostly found associated in early developmental stages of Pacific white shrimp 24 and crab 23 during their metamorphosis.…”

Ex vivo Comprehensive Multiphase NMR of whole organisms: A complementary tool to in vivo NMR

“…The neonates are considered to be juvenile after they have undergone two molting periods (1-week-old). Following two more molting periods, the juvenile Daphnia become sexually mature [ 42 ]. Daphnia have an average lifespan of 40–56 days (in laboratory settings) [ 23 ] and can reproduce until death.…”

“…The fact that the mothers deplete their solid lipid stores during pregnancy (see above) supports the Daphnids’ ability to transfer lipids from a stored solid form into a more readily accessible mobile form. 2) The lipids appear prominent in comparison to other solid components (mainly chitin in exoskeleton [ 33 , 34 , 42 ] (protein/carbohydrate complex)) as the exoskeleton in the juveniles is still developing, making the lipids stand out on a relative basis.…”

“…There has been very little study of the purine salvage pathway outside of animals [ 56 ], plants [ 57 , 58 ], and bacteria [ 54 , 56 ], however this pathway is thought to exist in Daphnia pulex [ 59 ] (according to the KEGG: Kyoto Encyclopedia of Genes and Genomes Pathway Database), a close relative of Daphnia magna, implying its likely occurrence in D. magna. Pregnant Daphnia transfer RNA, amongst other nutrients, to the eggs such that the offspring have a higher chance of survival and development [ 42 ]. It seems likely that the mothers are concentrating xanthosine within the eggs, which later the juveniles will convert into the required nucleosides.…”