Scaffolding a <i>Caenorhabditis</i> nematode genome with RNA-seq

Mortazavi, A; Schwarz, Erich M.; Williams, Brian A.; Schaeffer, Lorian; Antoshechkin, Igor; Wold, B; Sternberg, Paul W.

doi:10.1101/gr.111021.110

Cited by 84 publications

(91 citation statements)

References 55 publications

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“…The preparation was obtained from starved mixed-stage hermaphrodites, mostly L3 and L4 stage larvae, with some young adults and L2-stage larvae, and a few L1-stage larvae and eggs; as before, we briefly describe it as ‘larval RNA’. This larval RNA had previously been quantitated and tested for quality with a Bioanalyzer, and successfully used for standard full-length RNA-seq (Mortazavi et al, 2010). The two RNA-seq read sets counted as technical rather than biological replicates, because their starting RNA aliquots derived from a single whole larval RNA stock.…”

Section: Methodsmentioning

confidence: 99%

Nematophagous fungus Arthrobotrys oligospora mimics olfactory cues of sex and food to lure its nematode prey

Hsueh

Gronquist

Schwarz

et al. 2017

eLife

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To study the molecular basis for predator-prey coevolution, we investigated how Caenorhabditis elegans responds to the predatory fungus Arthrobotrys oligospora. C. elegans and other nematodes were attracted to volatile compounds produced by A. oligospora. Gas-chromatographic mass-spectral analyses of A. oligospora-derived volatile metabolites identified several odors mimicking food cues attractive to nematodes. One compound, methyl 3-methyl-2-butenoate (MMB) additionally triggered strong sex- and stage-specific attraction in several Caenorhabditis species. Furthermore, when MMB is present, it interferes with nematode mating, suggesting that MMB might mimic sex pheromone in Caenorhabditis species. Forward genetic screening suggests that multiple receptors are involved in sensing MMB. Response to fungal odors involves the olfactory neuron AWCs. Single-cell RNA-seq revealed the GPCRs expressed in AWC. We propose that A. oligospora likely evolved the means to use olfactory mimicry to attract its nematode prey through the olfactory neurons in C. elegans and related species.DOI: http://dx.doi.org/10.7554/eLife.20023.001

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Section: Methodsmentioning

confidence: 99%

Nematophagous fungus Arthrobotrys oligospora mimics olfactory cues of sex and food to lure its nematode prey

Hsueh

Gronquist

Schwarz

et al. 2017

eLife

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“…Transcripts >200nt were identified as lncRNAs if they did not overlap with known genomic annotations from the Ensembl Database and no coding potential was assessed by PhyloCSF. Next, the reads per kilo base of model per million base pairs sequenced (RPKM) was used to quantify the gene or lncRNA expression levels (25). …”

Section: Methodsmentioning

confidence: 99%

Extensive ceRNA–ceRNA interaction networks mediated by miRNAs regulate development in multiple rhesus tissues

Han

et al. 2016

Nucleic Acids Res

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Crosstalk between RNAs mediated by shared microRNAs (miRNAs) represents a novel layer of gene regulation, which plays important roles in development. In this study, we analyzed time series expression data for coding genes and long non-coding RNAs (lncRNAs) to identify thousands of interactions among competitive endogenous RNAs (ceRNAs) in four rhesus tissues. The ceRNAs exhibited dynamic expression and regulatory patterns during each tissue development process, which suggests that ceRNAs might work synergistically during different developmental stages or tissues to control specific functions. In addition, lncRNAs exhibit higher specificity as ceRNAs than coding-genes and their functions were predicted based on their competitive coding-gene partners to discover their important developmental roles. In addition to the specificity of tissue development, functional analyses demonstrated that the combined effects of multiple ceRNAs can have major impacts on general developmental and metabolic processes in multiple tissues, especially transcription-related functions where competitive interactions. Moreover, ceRNA interactions could sequentially and/or synergistically mediate the crosstalk among different signaling pathways during brain development. Analyzing ceRNA interactions during the development of multiple tissues will provideinsights in the regulation of normal development and the dysregulation of key mechanisms during pathogenesis.

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“…The analysis of transcription of Hc-daf-2 was carried out as described previously (Mortazavi et al, 2010; Schwarz et al, 2013).…”

Section: Methodsmentioning

confidence: 99%

Hc-daf-2 encodes an insulin-like receptor kinase in the barber’s pole worm, Haemonchus contortus, and restores partial dauer regulation

Lok

Gasser

et al. 2014

International Journal for Parasitology

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Infective L3s (iL3s) of parasitic nematodes share common behavioural, morphological and developmental characteristics with the developmentally arrested (dauer) larvae of the free-living nematode Caenorhabditis elegans. It is proposed that similar molecular mechanisms regulate entry into or exit from the dauer stage in C. elegans, and the transition from free-living to parasitic forms of parasitic nematodes. In C elegans, one of the key factors regulating the dauer transition is the insulin-like receptor (designated Ce-DAF-2) encoded by the gene Ce-daf-2. However, nothing is known about DAF-2 homologues in most parasitic nematodes. Here, using a PCR-based approach, we identified and characterised a gene (Hc-daf-2) and its inferred product (Hc-DAF-2) in Haemonchus contortus (a socioeconomically important parasitic nematode of ruminants). The sequence of Hc-DAF-2 displays significant sequence homology to insulin receptors (IR) in both vertebrates and invertebrates, and contains conserved structural domains. A sequence encoding an important proteolytic motif (RKRR) identified in the predicted peptide sequence of Hc-DAF-2 is consistent with that of the human IR, suggesting that it is involved in the formation of the IR complex. The Hc-daf-2 gene was transcribed in all life stages of H. contortus, with a significant up-regulation in the iL3 compared with other stages. To compare patterns of expression between Hc-daf-2 and Ce-daf-2, reporter constructs fusing the Ce-daf-2 or Hc-daf-2 promoter to sequence encoding GFP were microinjected into the N2 strain of C. elegans, and transgenic lines were established and examined. Both genes showed similar patterns of expression in amphidial (head) neurons, which relate to sensation and signal transduction. Further study by heterologous genetic complementation in a daf-2-deficient strain of C. elegans (CB1370) showed partial rescue of function by Hc-daf-2. Taken together, these findings provide a first insight into the roles of Hc-daf-2/Hc-DAF-2 in the biology and development of H. contortus, particularly in the transition to parasitism.

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Scaffolding a Caenorhabditis nematode genome with RNA-seq

Cited by 84 publications

References 55 publications

Nematophagous fungus Arthrobotrys oligospora mimics olfactory cues of sex and food to lure its nematode prey

Nematophagous fungus Arthrobotrys oligospora mimics olfactory cues of sex and food to lure its nematode prey

Extensive ceRNA–ceRNA interaction networks mediated by miRNAs regulate development in multiple rhesus tissues

Hc-daf-2 encodes an insulin-like receptor kinase in the barber’s pole worm, Haemonchus contortus, and restores partial dauer regulation

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