Comparison of C. elegans and C. briggsae Genome Sequences Reveals Extensive Conservation of Chromosome Organization and Synteny

Hillier, LaDeana W.; Miller, Raymond D.; Baird, Scott Everet; Chinwalla, Asif T.; Fulton, Lucinda A.; Koboldt, Daniel C.; Waterston, Robert H.

doi:10.1371/journal.pbio.0050167

Cited by 169 publications

(248 citation statements)

References 45 publications

(53 reference statements)

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“…Consistent with this, transcriptional profiling in C. elegans revealed a significant underrepresentation of meiosis and sperm-expressed genes on the X (Reinke et al 2000). It is likely that this underrepresentation of meiosis and spermatogenesis genes is also true of the Caenorhabditis group as a whole as there is a high degree of synteny between the X chromosomes in those species with good genomic assemblies (Hillier et al 2007;Fierst et al 2015) and expression analyses have uncovered a depletion of malebiased expressed genes on the X chromosome of C. briggsae, C. remanei, C. brenneri, as well as the more distantly related Pristionchus pacificus (Albritton et al 2014).…”

Section: Why Meiotic Silencing In Caenorhabditis?supporting

confidence: 54%

Plasticity in the Meiotic Epigenetic Landscape of Sex Chromosomes inCaenorhabditisSpecies

Larson

Van

Nakayama³

et al. 2016

Genetics

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During meiosis in the heterogametic sex in some species, sex chromosomes undergo meiotic sex chromosome inactivation (MSCI), which results in acquisition of repressive chromatin and transcriptional silencing. In Caenorhabditis elegans, MSCI is mediated by MET-2 methyltransferase deposition of histone H3 lysine 9 dimethylation. Here we examined the meiotic chromatin landscape in germ lines of four Caenorhabditis species; C. remanei and C. brenneri represent ancestral gonochorism, while C. briggsae and C. elegans are two lineages that independently evolved hermaphroditism. While MSCI is conserved across all four species, repressive chromatin modifications are distinct and do not correlate with reproductive mode. In contrast to C. elegans and C. remanei germ cells where X chromosomes are enriched for histone H3 lysine 9 dimethylation, X chromosomes in C. briggsae and C. brenneri germ cells are enriched for histone H3 lysine 9 trimethylation. Inactivation of C. briggsae MET-2 resulted in germ-line X chromosome transcription and checkpoint activation. Further, both histone H3 lysine 9 di-and trimethylation were reduced in Cbr-met-2 mutant germ lines, suggesting that in contrast to C. elegans, H3 lysine 9 di-and trimethylation are interdependent. C. briggsae H3 lysine 9 trimethylation was redistributed in the presence of asynapsed chromosomes in a sex-specific manner in the related process of meiotic silencing of unsynapsed chromatin. However, these repressive marks did not influence X chromosome replication timing. Examination of additional Caenorhabditis species revealed diverse H3 lysine 9 methylation patterns on the X, suggesting that the sex chromosome epigenome evolves rapidly.

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Section: Why Meiotic Silencing In Caenorhabditis?supporting

confidence: 54%

Plasticity in the Meiotic Epigenetic Landscape of Sex Chromosomes inCaenorhabditisSpecies

Larson

Van

Nakayama³

et al. 2016

Genetics

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“…We restricted our analysis to C. briggsae because C. remanei and C. brenneri DNA sequences have not yet been assembled into chromosomes. There is extensive conservation of chromosome organization and synteny between C. elegans and C. briggsae (Stein et al 2003;Hillier et al 2007). In C. briggsae, the syntenic regions of the two major C. elegans piRNA clusters on chromosome IV also produced high levels of piRNAs ( Fig.…”

Section: Evolution Of Small Rna Pathways In Nematodesmentioning

confidence: 99%

High-throughput sequencing reveals extraordinary fluidity of miRNA, piRNA, and siRNA pathways in nematodes

Shi

Montgomery

et al. 2013

Genome Res.

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The nematode Caenorhabditis elegans contains each of the broad classes of eukaryotic small RNAs, including microRNAs (miRNAs), endogenous small-interfering RNAs (endo-siRNAs), and piwi-interacting RNAs (piRNAs). To better understand the evolution of these regulatory RNAs, we deep-sequenced small RNAs from C. elegans and three closely related nematodes: C. briggsae, C. remanei, and C. brenneri. The results reveal a fluid landscape of small RNA pathways with essentially no conservation of individual sequences aside from a subset of miRNAs. We identified 54 miRNA families that are conserved in each of the four species, as well as numerous miRNAs that are species-specific or shared between only two or three species. Despite a lack of conservation of individual piRNAs and siRNAs, many of the features of each pathway are conserved between the different species. We show that the genomic distribution of 26G siRNAs and the tendency for piRNAs to cluster is conserved between C. briggsae and C. elegans. We also show that, in each species, 26G siRNAs trigger stage-specific secondary siRNA formation. piRNAs in each species also trigger secondary siRNA formation from targets containing up to three mismatches. Finally, we show that the production of male-and female-specific piRNAs is conserved in all four species, suggesting distinct roles for piRNAs in male and female germlines.

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“…Species-specific miRNAs have most likely emerged in the specific lineages rather than lost in all other lineages, which allows estimation of miRNA gene fixation rate. Given the estimated 80-110 Myr divergence time between C. elegans and C. briggsae (Hillier et al 2007) and de Wit et al…”

Section: Mirna Conservation Patternsmentioning

confidence: 99%

Repertoire and evolution of miRNA genes in four divergent nematode species

Wit

Linsen²,

Cuppen³

et al. 2009

Genome Res.

111

133

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miRNAs are ∼22-nt RNA molecules that play important roles in post-transcriptional regulation. We have performed small RNA sequencing in the nematodes Caenorhabditis elegans, C. briggsae, C. remanei, and Pristionchus pacificus, which have diverged up to 400 million years ago, to establish the repertoire and evolutionary dynamics of miRNAs in these species. In addition to previously known miRNA genes from C. elegans and C. briggsae we demonstrate expression of many of their homologs in C. remanei and P. pacificus, and identified in total more than 100 novel expressed miRNA genes, the majority of which belong to P. pacificus. Interestingly, more than half of all identified miRNA genes are conserved at the seed level in all four nematode species, whereas only a few miRNAs appear to be species specific. In our compendium of miRNAs we observed evidence for known mechanisms of miRNA evolution including antisense transcription and arm switching, as well as miRNA family expansion through gene duplication. In addition, we identified a novel mode of miRNA evolution, termed “hairpin shifting,” in which an alternative hairpin is formed with up- or downstream sequences, leading to shifting of the hairpin and creation of novel miRNA* species. Finally, we identified 21U-RNAs in all four nematodes, including P. pacificus, where the upstream 21U-RNA motif is more diverged. The identification and systematic analysis of small RNA repertoire in four nematode species described here provides a valuable resource for understanding the evolutionary dynamics of miRNA-mediated gene regulation.

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Comparison of C. elegans and C. briggsae Genome Sequences Reveals Extensive Conservation of Chromosome Organization and Synteny

Cited by 169 publications

References 45 publications

Plasticity in the Meiotic Epigenetic Landscape of Sex Chromosomes inCaenorhabditisSpecies

Plasticity in the Meiotic Epigenetic Landscape of Sex Chromosomes inCaenorhabditisSpecies

High-throughput sequencing reveals extraordinary fluidity of miRNA, piRNA, and siRNA pathways in nematodes

Repertoire and evolution of miRNA genes in four divergent nematode species

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