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For: Jhaveri N, van den Berg W, Hwang BJ, Muller HM, Sternberg PW, Gupta BP. Genome annotation of Caenorhabditis briggsae by TEC-RED identifies new exons, paralogs, and conserved and novel operons. G3 Genes|Genomes|Genetics 2022;12:6575897. [PMID: 35485953 PMCID: PMC9258526 DOI: 10.1093/g3journal/jkac101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/14/2022] [Indexed: 11/14/2022]

For:	Jhaveri N, van den Berg W, Hwang BJ, Muller HM, Sternberg PW, Gupta BP. Genome annotation of Caenorhabditis briggsae by TEC-RED identifies new exons, paralogs, and conserved and novel operons. G3 Genes\|Genomes\|Genetics 2022;12:6575897. [PMID: 35485953 PMCID: PMC9258526 DOI: 10.1093/g3journal/jkac101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/14/2022] [Indexed: 11/14/2022]

Number

Cited by Other Article(s)

Aleksander SA, Anagnostopoulos AV, Antonazzo G, Arnaboldi V, Attrill H, Becerra A, Bello SM, Blodgett O, Bradford YM, Bult CJ, Cain S, Calvi BR, Carbon S, Chan J, Chen WJ, Cherry JM, Cho J, Crosby MA, De Pons JL, D’Eustachio P, Diamantakis S, Dolan ME, dos Santos G, Dyer S, Ebert D, Engel SR, Fashena D, Fisher M, Foley S, Gibson AC, Gollapally VR, Gramates LS, Grove CA, Hale P, Harris T, Hayman GT, Hu Y, James-Zorn C, Karimi K, Karra K, Kishore R, Kwitek AE, Laulederkind SJF, Lee R, Longden I, Luypaert M, Markarian N, Marygold SJ, Matthews B, McAndrews MS, Millburn G, Miyasato S, Motenko H, Moxon S, Muller HM, Mungall CJ, Muruganujan A, Mushayahama T, Nash RS, Nuin P, Paddock H, Pells T, Perrimon N, Pich C, Quinton-Tulloch M, Raciti D, Ramachandran S, Richardson JE, Gelbart SR, Ruzicka L, Schindelman G, Shaw DR, Sherlock G, Shrivatsav A, Singer A, Smith CM, Smith CL, Smith JR, Stein L, Sternberg PW, Tabone CJ, Thomas PD, Thorat K, Thota J, Tomczuk M, Trovisco V, Tutaj MA, Urbano JM, Van Auken K, Van Slyke CE, Vize PD, Wang Q, Weng S, Westerfield M, Wilming LG, Wong ED, Wright A, Yook K, Zhou P, Zorn A, Zytkovicz M. Updates to the Alliance of Genome Resources central infrastructure. Genetics 2024;227:iyae049. [PMID: 38552170 PMCID: PMC11075569 DOI: 10.1093/genetics/iyae049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 04/09/2024] Open

Affiliation(s)

The Alliance of Genome Resources Consortium
Suzanne A Aleksander Department of Genetics, Stanford University , Stanford, CA 94305
Anna V Anagnostopoulos The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Giulia Antonazzo Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
Valerio Arnaboldi Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Helen Attrill Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
Andrés Becerra European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
Susan M Bello The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Olin Blodgett The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Yvonne M Bradford Institute of Neuroscience, University of Oregon , Eugene, OR 97403
Carol J Bult The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Scott Cain Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
Brian R Calvi Department of Biology, Indiana University , Bloomington, IN 47408 , USA
Seth Carbon Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA
Juancarlos Chan Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Wen J Chen Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
J Michael Cherry Department of Genetics, Stanford University , Stanford, CA 94305
Jaehyoung Cho Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Madeline A Crosby The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
Jeffrey L De Pons Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
Peter D’Eustachio NYU Grossman School of Medicine, New York , NY 10016
Stavros Diamantakis European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
Mary E Dolan The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Gilberto dos Santos The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
Sarah Dyer European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
Dustin Ebert Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
Stacia R Engel Department of Genetics, Stanford University , Stanford, CA 94305
David Fashena Institute of Neuroscience, University of Oregon , Eugene, OR 97403
Malcolm Fisher Division of Developmental Biology, Cincinnati Children's Hospital Medical Center , 3333 Burnet Ave, Cincinnati, OH 45229 , USA
Saoirse Foley Department of Biological Sciences, Carnegie Mellon University , 5000 Forbes Ave, Pittsburgh, PA 15203
Adam C Gibson Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
Varun R Gollapally Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
L Sian Gramates The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
Christian A Grove Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Paul Hale The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Todd Harris Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
G Thomas Hayman Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
Yanhui Hu Department of Genetics, Howard Hughes Medical Institute , Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115 , USA
Christina James-Zorn Division of Developmental Biology, Cincinnati Children's Hospital Medical Center , 3333 Burnet Ave, Cincinnati, OH 45229 , USA
Kamran Karimi Department of Biological Sciences, University of Calgary , 507 Campus Dr NW, Calgary, AB T2N 4V8 , Canada
Kalpana Karra Department of Genetics, Stanford University , Stanford, CA 94305
Ranjana Kishore Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Anne E Kwitek Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
Stanley J F Laulederkind Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
Raymond Lee Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Ian Longden The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
Manuel Luypaert European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
Nicholas Markarian Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Steven J Marygold Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
Beverley Matthews The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
Monica S McAndrews The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Gillian Millburn Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
Stuart Miyasato Department of Genetics, Stanford University , Stanford, CA 94305
Howie Motenko The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Sierra Moxon Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA
Hans-Michael Muller Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Christopher J Mungall Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA
Anushya Muruganujan Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
Tremayne Mushayahama Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
Robert S Nash Department of Genetics, Stanford University , Stanford, CA 94305
Paulo Nuin Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
Holly Paddock Institute of Neuroscience, University of Oregon , Eugene, OR 97403
Troy Pells Department of Biological Sciences, University of Calgary , 507 Campus Dr NW, Calgary, AB T2N 4V8 , Canada
Norbert Perrimon Department of Genetics, Howard Hughes Medical Institute , Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115 , USA
Christian Pich Institute of Neuroscience, University of Oregon , Eugene, OR 97403
Mark Quinton-Tulloch European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
Daniela Raciti Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Sridhar Ramachandran Institute of Neuroscience, University of Oregon , Eugene, OR 97403
Joel E Richardson Institute of Neuroscience, University of Oregon , Eugene, OR 97403
Susan Russo Gelbart The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
Leyla Ruzicka Institute of Neuroscience, University of Oregon , Eugene, OR 97403
Gary Schindelman Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
David R Shaw The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Gavin Sherlock Department of Genetics, Stanford University , Stanford, CA 94305
Ajay Shrivatsav Department of Genetics, Stanford University , Stanford, CA 94305
Amy Singer Institute of Neuroscience, University of Oregon , Eugene, OR 97403
Constance M Smith The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Cynthia L Smith The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Jennifer R Smith Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
Lincoln Stein Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
Paul W Sternberg Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Christopher J Tabone The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
Paul D Thomas Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
Ketaki Thorat Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
Jyothi Thota Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
Monika Tomczuk The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Vitor Trovisco Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
Marek A Tutaj Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
Jose-Maria Urbano Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
Kimberly Van Auken Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Ceri E Van Slyke Institute of Neuroscience, University of Oregon , Eugene, OR 97403
Peter D Vize Department of Biological Sciences, University of Calgary , 507 Campus Dr NW, Calgary, AB T2N 4V8 , Canada
Qinghua Wang Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Shuai Weng Department of Genetics, Stanford University , Stanford, CA 94305
Monte Westerfield Institute of Neuroscience, University of Oregon , Eugene, OR 97403
Laurens G Wilming The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Edith D Wong Department of Genetics, Stanford University , Stanford, CA 94305
Adam Wright Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
Karen Yook Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Pinglei Zhou The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
Aaron Zorn Division of Developmental Biology, Cincinnati Children's Hospital Medical Center , 3333 Burnet Ave, Cincinnati, OH 45229 , USA
Mark Zytkovicz The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA

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Aleksander SA, Anagnostopoulos AV, Antonazzo G, Arnaboldi V, Attrill H, Becerra A, Bello SM, Blodgett O, Bradford YM, Bult CJ, Cain S, Calvi BR, Carbon S, Chan J, Chen WJ, Michael Cherry J, Cho J, Crosby MA, De Pons JL, D’Eustachio P, Diamantakis S, Dolan ME, Santos GD, Dyer S, Ebert D, Engel SR, Fashena D, Fisher M, Foley S, Gibson AC, Gollapally VR, Sian Gramates L, Grove CA, Hale P, Harris T, Thomas Hayman G, Hu Y, James-Zorn C, Karimi K, Karra K, Kishore R, Kwitek AE, Laulederkind SJF, Lee R, Longden I, Luypaert M, Markarian N, Marygold SJ, Matthews B, McAndrews MS, Millburn G, Miyasato S, Motenko H, Moxon S, Muller HM, Mungall CJ, Muruganujan A, Mushayahama T, Nash RS, Nuin P, Paddock H, Pells T, Perrimon N, Pich C, Quinton-Tulloch M, Raciti D, Ramachandran S, Richardson JE, Gelbart SR, Ruzicka L, Schindelman G, Shaw DR, Sherlock G, Shrivatsav A, Singer A, Smith CM, Smith CL, Smith JR, Stein L, Sternberg PW, Tabone CJ, Thomas PD, Thorat K, Thota J, Tomczuk M, Trovisco V, Tutaj MA, Urbano JM, Auken KV, Van Slyke CE, Vize PD, Wang Q, Weng S, Westerfield M, Wilming LG, Wong ED, Wright A, Yook K, Zhou P, Zorn A, Zytkovicz M. Updates to the Alliance of Genome Resources Central Infrastructure Alliance of Genome Resources Consortium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567935. [PMID: 38045425 PMCID: PMC10690154 DOI: 10.1101/2023.11.20.567935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]

Moya ND, Stevens L, Miller IR, Sokol CE, Galindo JL, Bardas AD, Koh ESH, Rozenich J, Yeo C, Xu M, Andersen EC. Novel and improved Caenorhabditis briggsae gene models generated by community curation. BMC Genomics 2023;24:486. [PMID: 37626289 PMCID: PMC10463891 DOI: 10.1186/s12864-023-09582-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open

Abstract

BACKGROUND

The nematode Caenorhabditis briggsae has been used as a model in comparative genomics studies with Caenorhabditis elegans because of their striking morphological and behavioral similarities. However, the potential of C. briggsae for comparative studies is limited by the quality of its genome resources. The genome resources for the C. briggsae laboratory strain AF16 have not been developed to the same extent as C. elegans. The recent publication of a new chromosome-level reference genome for QX1410, a C. briggsae wild strain closely related to AF16, has provided the first step to bridge the gap between C. elegans and C. briggsae genome resources. Currently, the QX1410 gene models consist of software-derived gene predictions that contain numerous errors in their structure and coding sequences. In this study, a team of researchers manually inspected over 21,000 gene models and underlying transcriptomic data to repair software-derived errors.

RESULTS

We designed a detailed workflow to train a team of nine students to manually curate gene models using RNA read alignments. We manually inspected the gene models, proposed corrections to the coding sequences of over 8,000 genes, and modeled thousands of putative isoforms and untranslated regions. We exploited the conservation of protein sequence length between C. briggsae and C. elegans to quantify the improvement in protein-coding gene model quality and showed that manual curation led to substantial improvements in the protein sequence length accuracy of QX1410 genes. Additionally, collinear alignment analysis between the QX1410 and AF16 genomes revealed over 1,800 genes affected by spurious duplications and inversions in the AF16 genome that are now resolved in the QX1410 genome.

CONCLUSIONS

Community-based, manual curation using transcriptome data is an effective approach to improve the quality of software-derived protein-coding genes. The detailed protocols provided in this work can be useful for future large-scale manual curation projects in other species. Our manual curation efforts have brought the QX1410 gene models to a comparable level of quality as the extensively curated AF16 gene models. The improved genome resources for C. briggsae provide reliable tools for the study of Caenorhabditis biology and other related nematodes.

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Moya ND, Stevens L, Miller IR, Sokol CE, Galindo JL, Bardas AD, Koh ESH, Rozenich J, Yeo C, Xu M, Andersen EC. Novel and improved Caenorhabditis briggsae gene models generated by community curation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541014. [PMID: 37292880 PMCID: PMC10245686 DOI: 10.1101/2023.05.16.541014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]

Abstract

Background

The nematode Caenorhabditis briggsae has been used as a model for genomics studies compared to Caenorhabditis elegans because of its striking morphological and behavioral similarities. These studies yielded numerous findings that have expanded our understanding of nematode development and evolution. However, the potential of C. briggsae to study nematode biology is limited by the quality of its genome resources. The reference genome and gene models for the C. briggsae laboratory strain AF16 have not been developed to the same extent as C. elegans . The recent publication of a new chromosome-level reference genome for QX1410, a C. briggsae wild strain closely related to AF16, has provided the first step to bridge the gap between C. elegans and C. briggsae genome resources. Currently, the QX1410 gene models consist of protein-coding gene predictions generated from short- and long-read transcriptomic data. Because of the limitations of gene prediction software, the existing gene models for QX1410 contain numerous errors in their structure and coding sequences. In this study, a team of researchers manually inspected over 21,000 software-derived gene models and underlying transcriptomic data to improve the protein-coding gene models of the C. briggsae QX1410 genome.

Results

We designed a detailed workflow to train a team of nine students to manually curate genes using RNA read alignments and predicted gene models. We manually inspected the gene models using the genome annotation editor, Apollo, and proposed corrections to the coding sequences of over 8,000 genes. Additionally, we modeled thousands of putative isoforms and untranslated regions. We exploited the conservation of protein sequence length between C. briggsae and C. elegans to quantify the improvement in protein-coding gene model quality before and after curation. Manual curation led to a substantial improvement in the protein sequence length accuracy of QX1410 genes. We also compared the curated QX1410 gene models against the existing AF16 gene models. The manual curation efforts yielded QX1410 gene models that are similar in quality to the extensively curated AF16 gene models in terms of protein-length accuracy and biological completeness scores. Collinear alignment analysis between the QX1410 and AF16 genomes revealed over 1,800 genes affected by spurious duplications and inversions in the AF16 genome that are now resolved in the QX1410 genome.

Conclusions

Community-based, manual curation using transcriptome data is an effective approach to improve the quality of software-derived protein-coding genes. Comparative genomic analysis using a related species with high-quality reference genome(s) and gene models can be used to quantify improvements in gene model quality in a newly sequenced genome. The detailed protocols provided in this work can be useful for future large-scale manual curation projects in other species. The chromosome-level reference genome for the C. briggsae strain QX1410 far surpasses the quality of the genome of the laboratory strain AF16, and our manual curation efforts have brought the QX1410 gene models to a comparable level of quality to the previous reference, AF16. The improved genome resources for C. briggsae provide reliable tools for the study of Caenorhabditis biology and other related nematodes.

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