The serine repeat antigen (SERA) gene family phylogeny in Plasmodium:: The impact of GC content and reconciliation of gene and species trees
The serine repeat antigen (SERA) gene family phylogeny in Plasmodium:: The impact of GC content and reconciliation of gene and species trees
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DOI：
10.1093/molbev/msh228
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发表时间：
2004-11-01
影响因子：
10.7
通讯作者：
Speed, TP
中科院分区：
文献类型：
--
作者：
Bourgon, R;Delorenzi, M;Speed, TP
恶性疟原虫是引起人类最严重疟疾的寄生虫。近年来，恶性疟原虫的丝氨酸重复抗原（serine repeat antigen，SERA）作为一个潜在的疫苗和药物靶点引起了人们的关注，并已被证明是一个大基因家族的成员。为了阐明许多恶性疟原虫SERA之间的关系，并确定影响啮齿动物的疟原虫物种中SERA 5和SERA 6的直系同源物，从7个不同物种中33个推定的SERA同源物的核苷酸和氨基酸序列数据推断基因树。（专门设计用于适应不同GC含量的核苷酸序列的距离方法产生的结果在很大程度上与氨基酸树相容。另一方面，核苷酸序列的标准距离法和最大似然法产生的基因树在重要方面有所不同。）为了推断SERA基因家族史中的重复、物种形成和基因丢失事件的模式，将所得基因树与先前系统发育研究确定的两种竞争疟原虫物种树拓扑结构进行“调和”。调和的简约性被用作选择基因树/物种树对的标准，并提供（1）对两个物种树之一和氨基酸衍生的基因树的核心拓扑结构的支持，（2）对基因树的分辨率差的区域中的精细细节进行批评的基础，（3）一些物种中的一组预测的“缺失基因”，（4）阐明恶性疟原虫SERA之间的关系;（5）啮齿类疟原虫SERA 5和SERA 6同源基因的一些信息。简约的和解和第二个标准暗示的突变模式在两个关键的活性位点的SERA蛋白质也被认为是有用的补充，标准的“引导”分析推断的拓扑结构。
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.