Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia

Abstract

Ecological genomics aims to understand the functional association between environmental gradients and the genes underlying adaptive traits. Many genes that are identified by genome-wide screening in ecologically relevant species lack functional annotations. Although gene functions can be inferred from sequence homology, such approaches have limited power. Here, we introduce ecological regulatory genomics by presenting an ontology-free gene prioritization method. Specifically, our method combines transcriptome profiling with high-throughput cis-regulatory sequence analysis in the water fleas Daphnia pulex and Daphnia magna. It screens coexpressed genes for overrepresented DNA motifs that serve as transcription factor binding sites, thereby providing insight into conserved transcription factors and gene regulatory networks shaping the expression profile. We first validated our method, called Daphnia-cisTarget, on a D. pulex heat shock data set, which revealed a network driven by the heat shock factor. Next, we performed RNA-Seq in D. magna exposed to the cyanobacterium Microcystis aeruginosa. Daphnia-cisTarget identified coregulated gene networks that associate with the moulting cycle and potentially regulate life history changes in growth rate and age at maturity. These networks are predicted to be regulated by evolutionary conserved transcription factors such as the homologues of Drosophila Shavenbaby and Grainyhead, nuclear receptors, and a GATA family member. In conclusion, our approach allows prioritising candidate genes in Daphnia without bias towards prior knowledge about functional gene annotation and represents an important step towards exploring the molecular mechanisms of ecological responses in organisms with poorly annotated genomes.

Targeted gene disruption by use of CRISPR/Cas9 ribonucleoprotein complexes in the water flea Daphnia pulex

“…The complete genome of D. pulex sequenced in 2011 (Colbourne et al, 2011) opened a door to challenging research in these fields, and recent omics analyses have profiled a large number of putative factors involved in several characteristics of its unique life history (cf. Dircksen et al, 2011;Spanier et al, 2017). The recent establishment of two gene manipulation techniques in this species, RNA interference (RNAi) (Hiruta et al, 2013) and transcription activator-like effector nuclease (TALEN) (Hiruta et al, 2014), enables researchers to use gene silencing and disruption to characterize the function of genes in D. pulex.…”

Identification of General Patterns of Sex-Biased Expression in Daphnia, a Genus with Environmental Sex Determination

“…Since the publication of the D. pulex genome ( Colbourne et al 2011 ), the amount of genomic and transcriptomic resources for the genus has markedly increased ( Routtu et al 2014 ; Xu et al 2015 ; Dukić et al 2016 ; Orsini et al 2016 ; Huylmans et al 2016 ; Giraudo et al 2017 ; Lynch et al 2017; Spanier et al 2017 ; Toyota et al 2017 ; Ye et al 2017 ; Herrmann et al 2018 ). Previous studies have investigated sex-biased gene expression in two Daphnia species ( Colbourne et al 2011 ; Eads et al 2007 ; Huylmans et al 2016 ).…”

Reduced stress defence responses contribute to the higher toxicity of a pesticide under warming

“…Disentangling the direct effects of stressor treatments versus indirect effects of stressor treatments operating through changes in development can be challenging in transcriptomic studies (e.g., Spanier et al, 2017, Genome Biology and Evolution). The transcriptomic differences between stressor treatments are, however, unlikely to be caused by developmental differences as there was only a subtle 5% difference in development between the two temperatures, and more importantly larvae at the two temperatures were still relatively far from pupation when assayed (>80% of the L4 larval stage still ahead, see Supplementary ).…”