The serine repeat antigen (SERA) gene family phylogeny in Plasmodium: the impact of GC content and reconciliation of gene and species trees.
Details
Serval ID
serval:BIB_32014
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
The serine repeat antigen (SERA) gene family phylogeny in Plasmodium: the impact of GC content and reconciliation of gene and species trees.
Journal
Molecular Biology and Evolution
ISSN
0737-4038 (Print)
ISSN-L
0737-4038
Publication state
Published
Issued date
2004
Volume
21
Number
11
Pages
2161-2171
Language
english
Abstract
Plasmodium falciparum is the parasite responsible for the most acute form of malaria in humans. Recently, the serine repeat antigen (SERA) in P. falciparum has attracted attention as a potential vaccine and drug target, and it has been shown to be a member of a large gene family. To clarify the relationships among the numerous P. falciparum SERAs and to identify orthologs to SERA5 and SERA6 in Plasmodium species affecting rodents, gene trees were inferred from nucleotide and amino acid sequence data for 33 putative SERA homologs in seven different species. (A distance method for nucleotide sequences that is specifically designed to accommodate differing GC content yielded results that were largely compatible with the amino acid tree. Standard-distance and maximum-likelihood methods for nucleotide sequences, on the other hand, yielded gene trees that differed in important respects.) To infer the pattern of duplication, speciation, and gene loss events in the SERA gene family history, the resulting gene trees were then "reconciled" with two competing Plasmodium species tree topologies that have been identified by previous phylogenetic studies. Parsimony of reconciliation was used as a criterion for selecting a gene tree/species tree pair and provided (1) support for one of the two species trees and for the core topology of the amino acid-derived gene tree, (2) a basis for critiquing fine detail in a poorly resolved region of the gene tree, (3) a set of predicted "missing genes" in some species, (4) clarification of the relationship among the P. falciparum SERA, and (5) some information about SERA5 and SERA6 orthologs in the rodent malaria parasites. Parsimony of reconciliation and a second criterion--implied mutational pattern at two key active sites in the SERA proteins-were also seen to be useful supplements to standard "bootstrap" analysis for inferred topologies.
Keywords
Algorithms, Animals, Base Composition, Base Sequence, Cytidine/genetics, Databases, Genetic, Guanosine/genetics, Likelihood Functions, Models, Genetic, Models, Theoretical, Phylogeny, Plasmodium/genetics, Plasmodium falciparum/genetics, Serine/chemistry, Species Specificity
OAI-PMH
Pubmed
Web of science
Open Access
Yes
Create date
19/11/2007 11:01
Last modification date
20/08/2019 14:17