Paper: Intron Evolution - Testing Hypotheses of Intron Evolution Using the Phylogenomics of Tetraspanins

Intron Evolution: Testing Hypotheses of Intron Evolution Using the
Phylogenomics of Tetraspanins
Antonio Garcia-España 1,2, Roso Mares 1, Tung-Tien Sun 3,4,5,6, Rob DeSalle
7

1 Unitat de Recerca, Hospital Joan XXIII, Institut de Investigacio Sanitaria
Rovira I Virgili (IISPV), Universitat Rovira i Virgili, Tarragona, Spain,
2 CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM),
Universitat Rovira i Virgili, Tarragona, Spain,
3 Department of Cell Biology, New York University School of Medicine, New
York, New York, United States of America,
4 Department of Dermatology, New York University School of Medicine, New
York, New York, United States of America,
5 Department of Pharmacology, New York University School of Medicine, New
York, New York, United States of America,
6 Department of Urology, New York University School of Medicine, New York,
New York, United States of America,
7 Sackler Institute for Comparative Genomics, American Museum of Natural
History, New York, New York, United States of America

Abstract
Background
Although large scale informatics studies on introns can be useful in making
broad inferences concerning patterns of intron gain and loss, more specific
questions about intron evolution at a finer scale can be addressed using a
gene family where structure and function are well known. Genome wide surveys
of tetraspanins from a broad array of organisms with fully sequenced genomes
are an excellent means to understand specifics of intron evolution. Our
approach incorporated several new fully sequenced genomes that cover the
major lineages of the animal kingdom as well as plants, protists and fungi.
The analysis of exon/intron gene structure in such an evolutionary broad set
of genomes allowed us to identify ancestral intron structure in tetraspanins
throughout the eukaryotic tree of life.

Methodology/Principal Findings
We performed a phylogenomic analysis of the intron/exon structure of the
tetraspanin protein family. In addition, to the already characterized
tetraspanin introns numbered 1 through 6 found in animals, three additional
ancient, phase 0 introns we call 4a, 4b and 4c were found. These three novel
introns in combination with the ancestral introns 1 to 6, define three basic
tetraspanin gene structures which have been conserved throughout the animal
kingdom. Our phylogenomic approach also allows the estimation of the time at
which the introns of the 33 human tetraspanin paralogs appeared, which in
many cases coincides with the concomitant acquisition of new introns. On the
other hand, we observed that new introns (introns other than 1-6, 4a, b and
c) were not randomly inserted into the tetraspanin gene structure. The
region of tetraspanin genes corresponding to the small extracellular loop
(SEL) accounts for only 10.5% of the total sequence length but had 46% of
the new animal intron insertions.

Conclusions/Significance
Our results indicate that tests of intron evolution are strengthened by the
phylogenomic approach with specific gene families like tetraspanins. These
tests add to our understanding of genomic innovation coupled to major
evolutionary divergence events, functional constraints and the timing of the
appearance of evolutionary novelty.

Source: PLoS One [Open Access]
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004680

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