A phylogenomic approach for studying plastid endosymbiosis

Moustafa, Ahmed, Chan, Cheong Xin, Danforth, Megan, Zear, David, Ahmed, Hiba, Jadhav, Nagnath, Savage, Trevor and Bhattacharya, Debashish (2008). A phylogenomic approach for studying plastid endosymbiosis. In: Jonathan Arthur and See-Kiong Ng, Genome Informatics 2008: Proceedings of the 19th International Conference. 19th International Conference on Genome Informatics (GIW 2008), Gold Coast , Qld., Australia, (165-176). 1 - 3 December 2008.

Author Moustafa, Ahmed
Chan, Cheong Xin
Danforth, Megan
Zear, David
Ahmed, Hiba
Jadhav, Nagnath
Savage, Trevor
Bhattacharya, Debashish
Title of paper A phylogenomic approach for studying plastid endosymbiosis
Conference name 19th International Conference on Genome Informatics (GIW 2008)
Conference location Gold Coast , Qld., Australia
Conference dates 1 - 3 December 2008
Proceedings title Genome Informatics 2008: Proceedings of the 19th International Conference   Check publisher's open access policy
Journal name Genome Informatics Workshop. Proceedings   Check publisher's open access policy
Place of Publication London, United Kingdom
Publisher Imperial College Press
Publication Year 2008
Sub-type Fully published paper
ISBN 9781848163317
ISSN 0919-9454
Editor Jonathan Arthur
See-Kiong Ng
Volume 21
Start page 165
End page 176
Total pages 12
Language eng
Formatted Abstract/Summary
Gene transfer is a major contributing factor to functional innovation in genomes. Endosymbiotic
gene transfer (EGT) is a specific instance of lateral gene transfer (LGT) in
which genetic materials are acquired by the host genome from an endosymbiont that has
been engulfed and retained in the cytoplasm. Here we present a comprehensive approach
for detecting gene transfer within a phylogenetic framework. We applied the approach
to examine EGT of red algal genes into Thalassiosira pseudonana, a free-living diatom
for which a complete genome sequence has recently been determined. Out of 11,390 predicted
protein-coding sequences from the genome of T. pseudonana, 124 (1.1%, clustered
into 80 gene families) are inferred to be of red algal origin (bootstrap support:::: 75%).
Of these 80 gene families, 22 (27.5%) encode novel, unknown functions. We found 21.3%
of the gene families to putatively encode non-plastid-targeted proteins. Our results suggest
that EGT of red algal genes provides a relatively minor contribution to the nuclear
genome of the diatom, but the transferred genes have functions that extend beyond photosynthesis.
This assertion awaits experimental validation. Whereas the current study is
focused within the context of secondary endosymbiosis, our approach can be applied to
large-scale detection of gene transfer in any system.
Keyword Phylogenomics
Endosymbiotic gene transfer
Lateral gene transfer
Q-Index Code E1
Q-Index Status Provisional Code
Institutional Status Non-UQ

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Created: Thu, 10 Nov 2011, 14:54:53 EST by Susan Allen on behalf of Institute for Molecular Bioscience