On the extent and origins of genic novelty in the phylum Nematoda

PLoS Neglected Tropical Diseases
James WasmuthMark Blaxter

Abstract

The phylum Nematoda is biologically diverse, including parasites of plants and animals as well as free-living taxa. Underpinning this diversity will be commensurate diversity in expressed genes, including gene sets associated specifically with evolution of parasitism. Here we have analyzed the extensive expressed sequence tag data (available for 37 nematode species, most of which are parasites) and define over 120,000 distinct putative genes from which we have derived robust protein translations. Combined with the complete proteomes of Caenorhabditis elegans and Caenorhabditis briggsae, these proteins have been grouped into 65,000 protein families that in turn contain 40,000 distinct protein domains. We have mapped the occurrence of domains and families across the Nematoda and compared the nematode data to that available for other phyla. Gene loss is common, and in particular we identify nearly 5,000 genes that may have been lost from the lineage leading to the model nematode C. elegans. We find a preponderance of novelty, including 56,000 nematode-restricted protein families and 26,000 nematode-restricted domains. Mapping of the latest time-of-origin of these new families and domains across the nematode phylogeny revealed ongo...Continue Reading

References

Aug 1, 1993·Nature Genetics·M S BoguskiC M Tolstoshev
Mar 1, 1997·Molecular and Cellular Biology·S TweedieA Bird
Jul 1, 1997·Molecular and Biochemical Parasitology·W F GregoryR M Maizels
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Jan 7, 1998·Genomics·E L Sonnhammer, R Durbin
Jun 6, 1998·Proceedings of the National Academy of Sciences of the United States of America·G SmantJ Bakker
Dec 16, 1998·Science·UNKNOWN C. elegans Sequencing Consortium
Dec 16, 1998·Trends in Biochemical Sciences·S F Altschul, E V Koonin
Mar 25, 2000·Science·M D AdamsJ C Venter
May 29, 2000·Trends in Genetics : TIG·P RiceA Bleasby
Jul 14, 2000·Nature·H PopeijusG Smant
Oct 4, 2000·Proceedings of the National Academy of Sciences of the United States of America·L AravindE V Koonin
Oct 24, 2001·Bioinformatics·A G HatzigeorgiouM Reczko
Jan 10, 2002·Genome Research·Berend SnelMartijn A Huynen
Mar 28, 2002·Nucleic Acids Research·A J EnrightC A Ouzounis
Apr 3, 2002·Transactions of the Royal Society of Tropical Medicine and Hygiene·Mark BlaxterUNKNOWN Filarial Genome Project
Apr 5, 2002·Genome Research·W James Kent
Jul 4, 2002·FEBS Letters·Stéphanie JaubertMarie-Noëlle Rosso
Sep 17, 2002·Briefings in Bioinformatics·Florence ServantDaniel Kahn
Oct 5, 2002·Science·Robert A HoltStephen L Hoffman
Jan 9, 2003·Structure·Naomi Siew, Daniel Fischer
Jan 16, 2003·Current Biology : CB·A Aziz Aboobaker, Mark L Blaxter
Jan 23, 2003·Bioinformatics·Zemin Zhang, William I Wood
Feb 14, 2003·Bioinformatics·John Parkinson, Mark Blaxter
Apr 23, 2003·Journal of Molecular Biology·Andreas Heger, Liisa Holm
Jul 12, 2003·Trends in Parasitology·John ParkinsonJames P McCarter
Jul 31, 2003·Nucleic Acids Research·Anton J EnrightChristos A Ouzounis
Oct 1, 2003·Proteins·Naomi Siew, Daniel Fischer
Oct 10, 2003·Bioinformatics·C LottazP Bucher
Oct 14, 2003·Cladistics : the International Journal of the Willi Hennig Society·Gonzalo GiribetCourtney Babbitt
Nov 19, 2003·PLoS Biology·Lincoln D SteinRobert H Waterston
Dec 19, 2003·Nucleic Acids Research·Jan WuytsYves Van De Peer
Dec 19, 2003·Nucleic Acids Research·Rolf ApweilerLai-Su L Yeh
Dec 19, 2003·Nucleic Acids Research·Minoru KanehisaMasahiro Hattori
Dec 19, 2003·Nucleic Acids Research·Todd WylieJames P McCarter
Dec 19, 2003·Nucleic Acids Research·John ParkinsonMark Blaxter
Jan 24, 2004·Current Biology : CB·Marie Anne Félix

❮ Previous
Next ❯

Citations

Jul 2, 2014·Trends in Parasitology·James D Wasmuth
Jul 5, 2011·Annual Review of Genetics·Ralf J Sommer, Adrian Streit
Nov 14, 2008·Proceedings of the National Academy of Sciences of the United States of America·Mary E RumphoJames R Manhart
Mar 20, 2009·BMC Genomics·Yong YinMakedonka Mitreva
Apr 14, 2009·Genome Research·James WasmuthJohn Parkinson
Oct 27, 2009·PLoS Neglected Tropical Diseases·Paul J BrindleySara Lustigman
Jan 30, 2010·BMC Developmental Biology·Ja-On ParkHarald Hutter
Oct 29, 2010·BMC Evolutionary Biology·Ignacio Marín
Dec 24, 2010·The Journal of Experimental Biology·Mary E RumphoDebashish Bhattacharya
Feb 22, 2011·Nature Genetics·Makedonka MitrevaRichard K Wilson
Apr 29, 2011·PLoS Biology·Mark Blaxter
Jun 15, 2011·PLoS Neglected Tropical Diseases·Johnathan J DalzellAaron G Maule
May 5, 2011·Molecular Plant-microbe Interactions : MPMI·Annelies HaegemanEtienne G J Danchin
Apr 30, 2009·Annual Review of Phytopathology·M N RossoP Abad
Oct 8, 2011·Developmental and Comparative Immunology·D Ellen K Tarr
Nov 9, 2011·Gene·Annelies HaegemanGodelieve Gheysen
Nov 3, 2011·Parasite Immunology·M BlaxterB Elsworth
Jan 1, 2012·Worm·Sujai KumarMark Blaxter
May 3, 2013·PloS One·Juan A Subirana, Xavier Messeguer
Jun 23, 2009·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Ramiro Morales-Hojas
Apr 30, 2009·International Journal for Parasitology·Victoria GillanEileen Devaney
Mar 25, 2017·International Journal for Parasitology·Yesid Cuesta-AstrozGuilherme Oliveira
Jun 26, 2015·Nature Communications·Andrew R BurnsPeter J Roy
Mar 14, 2020·Medicinal Research Reviews·Daniel Sepúlveda-CrespoMaría Martínez-Valladares
Nov 23, 2019·Nature Communications·Deborah J WeinsteinJohn R Bracht
Aug 3, 2018·Scientific Reports·Satish Kumar RajasekharanJintae Lee
Aug 23, 2012·PloS One·Yan FuGuangyou Yang

❮ Previous
Next ❯

Methods Mentioned

BETA
EST sequencing
EST

Software Mentioned

MCL
Wormpep
annot8r
BLAST
mkdom2
CLOBB
SignalP
RPS
PostgreSQL
ProDom suite

Related Concepts

Related Feeds

Cancer Epigenetics & Metabolism (Keystone)

Epigenetic changes are present and dysregulated in many cancers, including DNA methylation, non-coding RNA segments and post-translational protein modifications. The epigenetic changes may or may not provide advantages for the cancer cells. This feed focuses on the relationship between cell metabolism, epigenetics and tumor differentiation.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
Charles H OppermanEric Windham
Nucleic Acids Research
John ParkinsonMark Blaxter
© 2021 Meta ULC. All rights reserved