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The Draft Genome and Transcriptome of Panagrellus redivivus Are Shaped by the Harsh Demands of a Free-Living Lifestyle

Srinivasan, Jagan and Dillman, Adler R. and Macchietto, Marissa G. and Heikkinen, Liisa and Lakso, Merja and Fracchia, Kelley M. and Antoshechkin, Igor and Mortazavi, Ali and Wong, Garry and Sternberg, Paul W. (2013) The Draft Genome and Transcriptome of Panagrellus redivivus Are Shaped by the Harsh Demands of a Free-Living Lifestyle. Genetics, 193 (4). pp. 1279-1295. ISSN 0016-6731. PMCID PMC3606103. doi:10.1534/genetics.112.148809. https://resolver.caltech.edu/CaltechAUTHORS:20130507-103412407

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Abstract

Nematodes compose an abundant and diverse invertebrate phylum with members inhabiting nearly every ecological niche. Panagrellus redivivus (the “microworm”) is a free-living nematode frequently used to understand the evolution of developmental and behavioral processes given its phylogenetic distance to Caenorhabditis elegans. Here we report the de novo sequencing of the genome, transcriptome, and small RNAs of P. redivivus. Using a combination of automated gene finders and RNA-seq data, we predict 24,249 genes and 32,676 transcripts. Small RNA analysis revealed 248 microRNA (miRNA) hairpins, of which 63 had orthologs in other species. Fourteen miRNA clusters containing 42 miRNA precursors were found. The RNA interference, dauer development, and programmed cell death pathways are largely conserved. Analysis of protein family domain abundance revealed that P. redivivus has experienced a striking expansion of BTB domain-containing proteins and an unprecedented expansion of the cullin scaffold family of proteins involved in multi-subunit ubiquitin ligases, suggesting proteolytic plasticity and/or tighter regulation of protein turnover. The eukaryotic release factor protein family has also been dramatically expanded and suggests an ongoing evolutionary arms race with viruses and transposons. The P. redivivus genome provides a resource to advance our understanding of nematode evolution and biology and to further elucidate the genomic architecture leading to free-living lineages, taking advantage of the many fascinating features of this worm revealed by comparative studies.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1534/genetics.112.148809 DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3606103/PubMed CentralArticle
ORCID:
AuthorORCID
Srinivasan, Jagan0000-0001-5449-7938
Dillman, Adler R.0000-0001-7171-4332
Antoshechkin, Igor0000-0002-9934-3040
Mortazavi, Ali0000-0002-4259-6362
Sternberg, Paul W.0000-0002-7699-0173
Additional Information:© 2013 Genetics Society of America. Available freely online through the author-supported open access option. Manuscript received December 15, 2012; accepted for publication January 8, 2013. We thank Hillel Schwartz, Margaret C. Ho, Alexei Aravin, Claire C. de la Cova, Iva Greenwald, Kay Hofmann, and Raymond Deshaies for discussions. We thank Alicia Rogers and Zane Goodwin for their patience and help with some of the computations. This work was supported by a National Institutes of Health U.S. Public Health Service Training Grant (T32GM07616) to A.R.D. and by the Howard Hughes Medical Institute (with which P.W.S. is an Investigator). Sequencing was carried out at the Millard and Muriel Jacobs Genome Facility at the California Institute of Technology.
Funders:
Funding AgencyGrant Number
NIH Predoctoral FellowshipT32GM07616
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Subject Keywords:Panagrellus redivivus; microRNA; BTB domain; F-box; eRF1; cullin
Issue or Number:4
PubMed Central ID:PMC3606103
DOI:10.1534/genetics.112.148809
Record Number:CaltechAUTHORS:20130507-103412407
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20130507-103412407
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:38318
Collection:CaltechAUTHORS
Deposited By: Jason Perez
Deposited On:07 May 2013 20:32
Last Modified:09 Nov 2021 23:36

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