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Title: A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis

Abstract

Genome-wide resources, such as collections of cDNA clones encoding for complete proteins (full-ORF clones), are crucial tools for studying the evolution of gene function and genetic interactions. Non-model organisms, in particular marine organisms, provide a rich source of functional diversity. Marine organism genomes are, however, frequently highly polymorphic and encode proteins that diverge significantly from those of well-annotated model genomes. The construction of full-ORF clone collections from non-model organisms is hindered by the difficulty of predicting accurately the N-terminal ends of proteins, and distinguishing recent paralogs from highly polymorphic alleles. We also report a computational strategy that overcomes these difficulties, and allows for accurate gene level clustering of transcript data followed by the automated identification of full-ORFs with correct 5'- and 3'-ends. It is robust to polymorphism, includes paralog calling and does not require evolutionary proximity to well annotated model organisms. Here, we developed this pipeline for the ascidian Ciona intestinalis, a highly polymorphic member of the divergent sister group of the vertebrates, emerging as a powerful model organism to study chordate gene function, Gene Regulatory Networks and molecular mechanisms underlying human pathologies. Furthermore, using this pipeline we have generated the first full-ORF collection for a highly polymorphic marine invertebrate.more » It contains 19,163 full-ORF cDNA clones covering 60% of Ciona coding genes, and full-ORF orthologs for approximately half of curated human disease-associated genes.« less

Authors:
; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Univ. of the Mediterranean Aix-Marseille II, Marseille (France)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1556199
Alternate Identifier(s):
OSTI ID: 1344888
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Published Article
Journal Name:
Developmental Biology
Additional Journal Information:
Journal Name: Developmental Biology Journal Volume: 404 Journal Issue: 2; Journal ID: ISSN 0012-1606
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Full-ORF; Functional genomics; Prediction pipeline; Ascidians; Transcriptomics; Human disease

Citation Formats

Gilchrist, Michael J., Sobral, Daniel, Khoueiry, Pierre, Daian, Fabrice, Laporte, Batiste, Patrushev, Ilya, Matsumoto, Jun, Dewar, Ken, Hastings, Kenneth E. M., Satou, Yutaka, Lemaire, Patrick, and Rothbächer, Ute. A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis. United States: N. p., 2015. Web. doi:10.1016/j.ydbio.2015.05.014.
Gilchrist, Michael J., Sobral, Daniel, Khoueiry, Pierre, Daian, Fabrice, Laporte, Batiste, Patrushev, Ilya, Matsumoto, Jun, Dewar, Ken, Hastings, Kenneth E. M., Satou, Yutaka, Lemaire, Patrick, & Rothbächer, Ute. A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis. United States. https://doi.org/10.1016/j.ydbio.2015.05.014
Gilchrist, Michael J., Sobral, Daniel, Khoueiry, Pierre, Daian, Fabrice, Laporte, Batiste, Patrushev, Ilya, Matsumoto, Jun, Dewar, Ken, Hastings, Kenneth E. M., Satou, Yutaka, Lemaire, Patrick, and Rothbächer, Ute. 2015. "A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis". United States. https://doi.org/10.1016/j.ydbio.2015.05.014.
@article{osti_1556199,
title = {A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis},
author = {Gilchrist, Michael J. and Sobral, Daniel and Khoueiry, Pierre and Daian, Fabrice and Laporte, Batiste and Patrushev, Ilya and Matsumoto, Jun and Dewar, Ken and Hastings, Kenneth E. M. and Satou, Yutaka and Lemaire, Patrick and Rothbächer, Ute},
abstractNote = {Genome-wide resources, such as collections of cDNA clones encoding for complete proteins (full-ORF clones), are crucial tools for studying the evolution of gene function and genetic interactions. Non-model organisms, in particular marine organisms, provide a rich source of functional diversity. Marine organism genomes are, however, frequently highly polymorphic and encode proteins that diverge significantly from those of well-annotated model genomes. The construction of full-ORF clone collections from non-model organisms is hindered by the difficulty of predicting accurately the N-terminal ends of proteins, and distinguishing recent paralogs from highly polymorphic alleles. We also report a computational strategy that overcomes these difficulties, and allows for accurate gene level clustering of transcript data followed by the automated identification of full-ORFs with correct 5'- and 3'-ends. It is robust to polymorphism, includes paralog calling and does not require evolutionary proximity to well annotated model organisms. Here, we developed this pipeline for the ascidian Ciona intestinalis, a highly polymorphic member of the divergent sister group of the vertebrates, emerging as a powerful model organism to study chordate gene function, Gene Regulatory Networks and molecular mechanisms underlying human pathologies. Furthermore, using this pipeline we have generated the first full-ORF collection for a highly polymorphic marine invertebrate. It contains 19,163 full-ORF cDNA clones covering 60% of Ciona coding genes, and full-ORF orthologs for approximately half of curated human disease-associated genes.},
doi = {10.1016/j.ydbio.2015.05.014},
url = {https://www.osti.gov/biblio/1556199}, journal = {Developmental Biology},
issn = {0012-1606},
number = 2,
volume = 404,
place = {United States},
year = {2015},
month = {8}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at https://doi.org/10.1016/j.ydbio.2015.05.014

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Cited by: 8 works
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