A New Reference Genome Assembly for the Microcrustacean Daphnia pulex

Abstract

Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact of effective population size on genome evolution. For this purpose, we present a high quality genome assembly of Daphnia pulex (PA42), and compare this with the first sequenced genome of this species (TCO), which was derived from an isolate from a population with .90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at the gene level, with an average amino acid sequence identity of 98.8 and .60% of orthologous proteins identical. Nonetheless, there is a highly elevated number of genes in the TCO genome annotation, with 7000 excess genes appearing to be false positives. This view is supported by the high GC content, lack of introns, and short length of these suspicious gene annotations. Consistent with the view that reduced effective population size can facilitate the accumulation of slightly deleterious genomic features, we observe more proliferation of transposable elements (TEs) and a higher frequency of gained introns in the TCO genome. KEYWORDSgenome annotation effective population size gene number intron mobile elementsThe ultimate goal of comparative genomics is to form a synthesis integrating the fundamental evolutionary forces explaining the variation of genomic architecture across a wide range of phylogenetic lineages. The reduced effective population size (N e ) of eukaryotic species relative to prokaryotic species is hypothesized to be centrally involved in the emergence and distribution of numerous genomic features unique to eukaryotes, and the associated principles should naturally extend to variation among lineages of closely related species (Lynch 2007). However, until recently, it has been difficult to study the impact of reduced N e on the evolution of genomic architecture because of the lack of genomic data from closely related species or populations with disparate population sizes. Moreover, a lack of parallel understanding of other fundamental microevolutionary parameters such as mutation and recombination rates complicates efforts to single out the role of N e (and the associated power of random genetic drift) on genome evolution.Here, we focus on the comparative genomics of two cyclically parthenogenetic Daphnia pulex clones (PA42 and TCO), which come from populations differing substantially in historical N e . The D. pulex species complex consists of a vast array of populations inhabiting hundreds of thousands of ponds and lakes, throughout the northern temperate zone, most of which (including PA42 and TCO) reproduce by repeated generations of clonal reproduction via unfertilized eggs, punctuated by a phase of sexual reproduction. PA42 was sampled from a woodland vernal pond within Portland Arch Nature Preserve, IN, whereas TCO was derived from a permanent pond in the Siuslaw National Forest, near the Pacific coast in OR. A complex geological history in western OR contributes to the presence of divergent lineages of multiple zooplan...

Quantitative Proteomics Reveals Remodeling of Protein Repertoire Across Life Phases of Daphnia pulex

“…We also observed that proteins identified as mutual best BLAST hits between the TCO protein reference used in this analysis and a more recent PA42 D. pulex protein reference are highly enriched among the proteins we were able to detect. Out of 11 697 such proteins, we detected 4312 (expected = 2004), while among the 18 063 proteins with ambiguous hits or no hits, we detected only 786 (expected = 3094; Fisher exact test p < 1 × 10 –248 ).…”

Quantitative proteomics reveals remodeling of protein repertoire across life phases ofDaphnia pulex

“…We also observed that proteins identified as mutual best BLAST hits between the TCO protein reference used in this analysis and a more recent PA42 D.pulex protein reference [24] are highly enriched among the proteins we were able to detect. Out of 11697 such proteins we detected 4312 (expected=2004), while among the 18063 proteins with ambiguous hits or no hits we detected only 786 (expected=3094; Fisher Exact Test P<1E-248).…”

“…Although Daphnia pulex genome is relatively well characterized [23,24], the exact number of protein coding genes in the genome is still subject of debate, as it varies significantly between closely related genomes and/or between gene model methodologies [24].…”

Daphnia magna microRNAs respond to nutritional stress and ageing but are not transgenerational

“…Identifying mRNA targets computationally with miRanda results in many false positives due to the redundancy of the 6–8 bp miRNA‐binding seed sequence (Agarwal, Bell, Nam, & Bartel, ; Peterson et al., ). Of the 116 miRNAs (5p and 3p) we quantified, 4256 potential mRNA targets were identified, an average of 37 per miRNA, a figure possibly further inflated by overaggressive annotation of the D. magna genome (Ye et al., ). Currently, there are 29,128 gene predictions, but this may drop significantly with future resources, as was the case for Daphnia pulex (Colbourne et al., ; Orsini et al., ; Ye et al., ).…”

“…Of the 116 miRNAs (5p and 3p) we quantified, 4256 potential mRNA targets were identified, an average of 37 per miRNA, a figure possibly further inflated by overaggressive annotation of the D. magna genome (Ye et al., ). Currently, there are 29,128 gene predictions, but this may drop significantly with future resources, as was the case for Daphnia pulex (Colbourne et al., ; Orsini et al., ; Ye et al., ). Functional characterization of the processes regulated by miRNAs of interest is therefore inaccurate at best.…”