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Genome annotation of Caenorhabditis briggsae by TEC-RED identifies new exons, paralogs, and conserved and novel operons

Jhaveri, Nikita and van den Berg, Wouter and Hwang, Byung Joon and Müller, Hans-Michael and Sternberg, Paul W. and Gupta, Bhagwati P. (2022) Genome annotation of Caenorhabditis briggsae by TEC-RED identifies new exons, paralogs, and conserved and novel operons. G3: Genes, Genomes, Genetics . ISSN 2160-1836. doi:10.1093/g3journal/jkac101. (In Press) https://resolver.caltech.edu/CaltechAUTHORS:20210929-161511442

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Abstract

The nematode Caenorhabditis briggsae is routinely used in comparative and evolutionary studies involving its well-known cousin C. elegans. The C. briggsae genome sequence has accelerated research by facilitating the generation of new resources, tools, and functional studies of genes. While substantial progress has been made in predicting genes and start sites, experimental evidence is still lacking in many cases. Here, we report an improved annotation of the C. briggsae genome using the Trans-spliced Exon Coupled RNA End Determination (TEC-RED) technique. In addition to identifying the 5' ends of expressed genes, we have discovered operons and paralogs. In summary, our analysis yielded 10,243 unique 5' end sequence tags with matches in the C. briggsae genome. Of these, 6,395 were found to represent 4,252 unique genes along with 362 paralogs and 52 previously unknown exons. These genes included 14 that are exclusively trans-spliced in C. briggsae when compared with C. elegans orthologs. A major contribution of this study is the identification of 493 operons, of which two-thirds are fully supported by tags. In addition, two SL1-type operons were discovered. Interestingly, comparisons with C. elegans showed that only 40% of operons are conserved. Of the remaining operons, 73 are novel, including 12 that entirely lack orthologs in C. elegans. Further analysis revealed that four of the 12 novel operons are conserved in C. nigoni. Altogether, the work described here has significantly advanced our understanding of the C. briggsae system and serves as a rich resource to aid biological studies involving this species.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1093/g3journal/jkac101DOIArticle
https://doi.org/10.1101/2021.09.24.461604DOIDiscussion Paper
https://jbrowse.org/jb2/Related ItemJbrowse 2
ORCID:
AuthorORCID
van den Berg, Wouter0000-0001-6824-5993
Hwang, Byung Joon0000-0003-2449-0684
Sternberg, Paul W.0000-0002-7699-0173
Gupta, Bhagwati P.0000-0001-8572-7054
Alternate Title:Gene identification and genome annotation in Caenorhabditis briggsae by high throughput 5’ RNA end determination
Additional Information:© The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Received: 30 January 2022; Accepted: 14 April 2022; Published: 29 April 2022. We thank WormBase for assistance with some aspects of data analysis, Mary Ann Allen and Tom Blumenthal for discussions on C. elegans operons, and members of the Gupta lab for feedback on the manuscript. We are especially grateful to Paulo Nuin and Scott Cain (WormBase) for allowing us to use the demo version of Jbrowse 2 (https://jbrowse.org/jb2/) for some of the figures. This work was supported by grants to BPG (NSERC Discovery) and PWS (U24-HG002223). PWS was an Investigator with the HHMI, which partially supported this work.
Group:Tianqiao and Chrissy Chen Institute for Neuroscience
Funders:
Funding AgencyGrant Number
Natural Sciences and Engineering Research Council of Canada (NSERC)UNSPECIFIED
NIHU24-HG002223
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Subject Keywords:Nematode, C. briggsae, Trans-splicing, Spliced leader, Operons, Paralog, Genome annotation
DOI:10.1093/g3journal/jkac101
Record Number:CaltechAUTHORS:20210929-161511442
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20210929-161511442
Official Citation:Nikita Jhaveri, Wouter van den Berg, Byung Joon Hwang, Hans-Michael Muller, Paul W Sternberg, Bhagwati P Gupta, Genome annotation of Caenorhabditis briggsae by TEC-RED identifies new exons, paralogs, and conserved and novel operons, G3 Genes,Genomes,Genetics, 2022, jkac101, https://doi.org/10.1093/g3journal/jkac101
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:111088
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:29 Sep 2021 17:31
Last Modified:04 May 2022 21:04

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