Description of Caenorhabditis sinica sp. n. (Nematoda: Rhabditidae), a Nematode Species Used in Comparative Biology for C. elegans

Huang, Ren E.; Ren, Xiaoliang; Qiu, Yifei; Zhao, Zhongying

doi:10.1371/journal.pone.0110957

Cited by 28 publications

(29 citation statements)

References 25 publications

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“…The complex shape of the hook as first described for C. sinica as a specific character (Huang et al. ) now constitutes a clear apomorphy (derived character), with no pattern of convergent evolution (Fig. C).…”

Section: Resultsmentioning

confidence: 65%

Comparative genomics of 10 newCaenorhabditisspecies

et al. 2019

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The nematode Caenorhabditis elegans has been central to the understanding of metazoan biology. However, C. elegans is but one species among millions and the significance of this important model organism will only be fully revealed if it is placed in a rich evolutionary context. Global sampling efforts have led to the discovery of over 50 putative species from the genus Caenorhabditis , many of which await formal species description. Here, we present species descriptions for 10 new Caenorhabditis species. We also present draft genome sequences for nine of these new species, along with a transcriptome assembly for one. We exploit these whole‐genome data to reconstruct the Caenorhabditis phylogeny and use this phylogenetic tree to dissect the evolution of morphology in the genus. We reveal extensive variation in genome size and investigate the molecular processes that underlie this variation. We show unexpected complexity in the evolutionary history of key developmental pathway genes. These new species and the associated genomic resources will be essential in our attempts to understand the evolutionary origins of the C. elegans model.

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Section: Resultsmentioning

confidence: 65%

Comparative genomics of 10 newCaenorhabditisspecies

et al. 2019

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“…Based on the fact that all the known embryonic activators of elt-2 are GATA transcription factors, we can narrow down the candidate cis -regulatory sequences considerably. The ∼2 kb region upstream of the elt-2 start codon in C. elegans contains eighteen of the consensus GATA factor binding motif HGATAR, with thirteen conserved in sequence and relative spacing throughout the Elegans supergroup (sequence data from C. elegans , C. tropicalis, C. brenneri , C. remanei , C. sinica, C. briggsae, and C. japonica ) (Félix, Braendle, & Cutter, 2014; Huang, Ren, Qiu, & Zhao, 2014) (Fig. 1C).…”

Section: Introductionmentioning

confidence: 99%

Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis- regulatory elements

Tracy

Rifkin

2016

Developmental Biology

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Cis-regulatory elements (CREs) are crucial links in developmental gene regulatory networks, but in many cases, it can be difficult to discern whether similar CREs are functionally equivalent. We found that despite similar conservation and binding capability to upstream activators, different GATA cis-regulatory motifs within the promoter of the C. elegans endoderm regulator elt-2 play distinctive roles in activating and modulating gene expression throughout development. We fused wild-type and mutant versions of the elt-2 promoter to a gfp reporter and inserted these constructs as single copies into the C. elegans genome. We then counted early embryonic gfp transcripts using single-molecule RNA FISH (smFISH) and quantified gut GFP fluorescence. We determined that a single primary dominant GATA motif located -527 bp upstream of the elt-2 start codon was necessary for both embryonic activation and later maintenance of transcription, while nearby secondary GATA motifs played largely subtle roles in modulating postembryonic levels of elt-2. Mutation of the primary activating site increased low-level spatiotemporally ectopic stochastic transcription, indicating that this site acts repressively in non-endoderm cells. Our results reveal that CREs with similar GATA factor binding affinities in close proximity can play very divergent context-dependent roles in regulating the expression of a developmentally critical gene in vivo.

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“…11), and C. sinica (formerly C. sp. 5) (Felix et al 2014;Huang et al 2014). We also obtained the genomic sequence of C. nigoni (formerly C. sp.…”

Section: Materials and Methods Mirna Data Setsmentioning

confidence: 99%

Comparative genomic analysis of upstream miRNA regulatory motifs in Caenorhabditis

Jovelin¹,

Krizus²,

Taghizada³

et al. 2016

RNA

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MicroRNAs (miRNAs) comprise a class of short noncoding RNA molecules that play diverse developmental and physiological roles by controlling mRNA abundance and protein output of the vast majority of transcripts. Despite the importance of miRNAs in regulating gene function, we still lack a complete understanding of how miRNAs themselves are transcriptionally regulated. To fill this gap, we predicted regulatory sequences by searching for abundant short motifs located upstream of miRNAs in eight species of Caenorhabditis nematodes. We identified three conserved motifs across the Caenorhabditis phylogeny that show clear signatures of purifying selection from comparative genomics, patterns of nucleotide changes in motifs of orthologous miRNAs, and correlation between motif incidence and miRNA expression. We then validated our predictions with transgenic green fluorescent protein reporters and site-directed mutagenesis for a subset of motifs located in an enhancer region upstream of let-7. We demonstrate that a CT-dinucleotide motif is sufficient for proper expression of GFP in the seam cells of adult C. elegans, and that two other motifs play incremental roles in combination with the CT-rich motif. Thus, functional tests of sequence motifs identified through analysis of molecular evolutionary signatures provide a powerful path for efficiently characterizing the transcriptional regulation of miRNA genes.

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Description of Caenorhabditis sinica sp. n. (Nematoda: Rhabditidae), a Nematode Species Used in Comparative Biology for C. elegans

Cited by 28 publications

References 25 publications

Comparative genomics of 10 newCaenorhabditisspecies

Comparative genomics of 10 newCaenorhabditisspecies

Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis- regulatory elements

Comparative genomic analysis of upstream miRNA regulatory motifs in Caenorhabditis

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