Phylogenomic analysis of vertebrate thrombospondins reveals fish-specific paralogues, ancestral gene relationships and a tetrapod innovation.

BMC Evolutionary Biology
Patrick McKenzieJ C Adams

Abstract

Thrombospondins (TSPs) are evolutionarily-conserved, extracellular, calcium-binding glycoproteins with important roles in cell-extracellular matrix interactions, angiogenesis, synaptogenesis and connective tissue organisation. Five TSPs, designated TSP-1 through TSP-5, are encoded in the human genome. All but one have known roles in acquired or inherited human diseases. To further understand the roles of TSPs in human physiology and pathology, it would be advantageous to extend the repertoire of relevant vertebrate models. In general the zebrafish is proving an excellent model organism for vertebrate biology, therefore we set out to evaluate the status of TSPs in zebrafish and two species of pufferfish. We identified by bioinformatics that three fish species encode larger numbers of TSPs than vertebrates, yet all these sequences group as homologues of TSP-1 to -4. By phylogenomic analysis of neighboring genes, we uncovered that, in fish, a TSP-4-like sequence is encoded from the gene corresponding to the tetrapod TSP-5 gene. Thus, all TSP genes show conservation of synteny between fish and tetrapods. In the human genome, the TSP-1, TSP-3, TSP-4 and TSP-5 genes lie within paralogous regions that provide insight into the ancestra...Continue Reading

References

Sep 15, 1991·Proceedings of the National Academy of Sciences of the United States of America·B E HuberT A Krenitsky
May 24, 1991·Science·A LupasJ Stock
Jul 2, 1991·Biochemistry·J SottileD F Mosher
Aug 1, 1995·Developmental Dynamics : an Official Publication of the American Association of Anatomists·R P TuckerJ Lawler
Jun 1, 1993·Journal of Molecular Evolution·J LawlerT F Smith
Mar 1, 1997·Developmental Dynamics : an Official Publication of the American Association of Anatomists·R P TuckerJ Lawler
Apr 16, 1998·The Journal of Clinical Investigation·J LawlerR O Hynes
May 5, 1998·Developmental Dynamics : an Official Publication of the American Association of Anatomists·L A UrryD W DeSimone
May 30, 1998·Proceedings of the National Academy of Sciences of the United States of America·J SchultzC P Ponting
Apr 13, 1999·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·A Wagner
Sep 29, 1999·Mammalian Genome : Official Journal of the International Mammalian Genome Society·G NewtonJ Lawler
Aug 31, 2000·Journal of Molecular Biology·C NotredameJ Heringa
Sep 9, 2000·Current Opinion in Cell Biology·J Lawler
Dec 5, 2000·Matrix Biology : Journal of the International Society for Matrix Biology·P BornsteinZ Yang
Jan 9, 2001·Arteriosclerosis, Thrombosis, and Vascular Biology·R RiessenJ Lawler
Mar 10, 2001·Nature·J D McPhersonUNKNOWN International Human Genome Mapping Consortium
Mar 10, 2001·Nature·C A TilfordD C Page
Jul 13, 2001·Current Opinion in Genetics & Development·A F Schier
Nov 1, 2001·Annual Review of Cell and Developmental Biology·J C Adams
Mar 28, 2002·DNA Sequence : the Journal of DNA Sequencing and Mapping·K W Adolph
Apr 23, 2002·Nature Genetics·Laurent Abi-RachedHidetoshi Inoko
May 25, 2002·Molecular and Cellular Biology·Liz SvenssonAke Oldberg
May 29, 2002·Nature Genetics·Aoife McLysaghtKenneth H Wolfe
Jul 27, 2002·Science·Samuel AparicioSydney Brenner
Aug 16, 2002·Nature·Simon G GregoryDavid R Bentley
Aug 31, 2002·Genesis : the Journal of Genetics and Development·Yutaka SatouNori Satoh
Nov 28, 2002·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Steven L KleinPaul Richardson
Feb 21, 2003·DNA Sequence : the Journal of DNA Sequencing and Mapping·Kenneth W Adolph
Apr 10, 2003·Trends in Genetics : TIG·S Blair Hedges, Sudhir Kumar
Apr 15, 2003·Journal of Molecular Biology·Josephine C AdamsJuergen Engel
Oct 8, 2003·Systematic Biology·Stéphane Guindon, Olivier Gascuel
Oct 14, 2003·Proceedings of the National Academy of Sciences of the United States of America·Yu-Wen ZhangGeorge F Vande Woude
Oct 28, 2003·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Trista E North, Leonard I Zon
Dec 25, 2003·Molecular Biology and Evolution·Marc Robinson-RechaviVincent Laudet

❮ Previous
Next ❯

Citations

May 24, 2008·The Journal of Biological Chemistry·C Britt CarlsonDeane F Mosher
Dec 17, 2010·Molecular Biology of the Cell·Suat OzbekJosephine C Adams
Apr 30, 2010·Molecular Biology and Evolution·Amber A Bentley, Josephine C Adams
Aug 31, 2011·Cold Spring Harbor Perspectives in Biology·Josephine C Adams, Jack Lawler
Jan 12, 2008·Arteriosclerosis, Thrombosis, and Vascular Biology·Jeff S IsenbergWilliam A Frazier
Oct 24, 2007·Life Sciences·Subir Kumar Das, D M Vasudevan
Jul 18, 2017·International Journal of Molecular Sciences·Dimitry A ChistiakovAlexander N Orekhov
Mar 14, 2019·Molecular Biology and Evolution·Deborah K ShoemarkJosephine C Adams
Oct 24, 2006·Matrix Biology : Journal of the International Society for Matrix Biology·Julie Huxley-JonesRaymond P Boot-Handford
Feb 27, 2007·Experimental Eye Research·Erin Tolhurst DunkleDennis O Clegg
Sep 9, 2021·American Journal of Physiology. Cell Physiology·Tessa ForbesJosephine C Adams
Jan 24, 2012·Matrix Biology : Journal of the International Society for Matrix Biology·Deane F Mosher, Josephine C Adams

❮ Previous
Next ❯

Datasets Mentioned

BETA
CV067510

Methods Mentioned

BETA
gene knockouts
Genome sequencing

Software Mentioned

COILS
BLAT
BLASTX
BLAST Genomes
Phylip
Genoscope
Boxshade
CLUSTALW
HUGO
Phylip DRAWTREE

Related Concepts

Related Feeds

Cancer Genomics (Keystone)

Cancer genomics approaches employ high-throughput technologies to identify the complete catalog of somatic alterations that characterize the genome, transcriptome and epigenome of cohorts of tumor samples. Discover the latest research using such technologies in this feed.

Brain developing: Influences & Outcomes

This feed focuses on influences that affect the developing brain including genetics, fetal development, prenatal care, and gene-environment interactions. Here is the latest research in this field.