Rhesus macaque class I duplicon structures, organization, and evolution within the alpha block of the major histocompatibility complex
Rhesus macaque class I duplicon structures, organization, and evolution within the alpha block of the major histocompatibility complex
复制标题
DOI：
10.1093/molbev/msh216
复制
发表时间：
2004-11-01
影响因子：
10.7
通讯作者：
Inoko, H
中科院分区：
文献类型：
--
作者：
Kulski, JK;Anzai, T;Inoko, H
人类和黑猩猩的主要组织相容性复合体（MHC）I类基因组区域的α块含有10至11个重复的MHC I类基因，包括HLA/Patr-A、-G和-F基因。相比之下，恒河猴（Macaca mulatta，Mamu）的α区在该邻位区域内具有额外的20个MHC I类基因。本研究描述了识别和分析的重复的节段性基因组结构（duplicons）和基因组标记内的α块的恒河猴和它们的使用，以重建该区域内的基因的复制历史。使用多种MHC I类基因、假基因、转座子和反转录转座子，如Alu和ERV 16，将28个重复子分为四种不同的结构类别。通过使用相邻连接（NJ）方法检查重复子内的MHC I类基因、Alu和LTR 16 B序列的系统发育关系。两个单重复子串联重复，两个polyduplicon串联重复，每个重复伴随一个反转产物，8个polyduplicon串联重复步骤，12个缺失，和至少两个重组被重建，以解释高度复杂的组织和进化的28个重复子（9个反转）内的Mamu α块。根据系统发育证据和重建的串联重复历史的28个duplicons，Mamu/Patr/HLA-F直系同源物是第一个MHC I类基因已被固定没有。在灵长类动物的阿尔法区中进一步复制。假设恒河猴和黑猩猩/人类谱系在大约2400万年至3100万年前的分歧时开始具有相同数量的MHC I类重复子，那么恒河猴中α区块内的基因数量以大约三倍于人类或黑猩猩的速度复制。
The alpha block of the human and chimpanzee major histocompatibility complex (MHC) class I genomic region contains 10 to 11 duplicated MHC class I genes, including the HLA/Patr-A, -G, and -F genes. In comparison, the alpha block of the rhesus macaque (Macaca mulatta, Mamu) has an additional 20 MHC class I genes within this orthologous region. The present study describes the identification and analysis of the duplicated segmental genomic structures (duplicons) and genomic markers within the alpha block of the rhesus macaque and their use to reconstruct the duplication history of the genes within this region. A variety of MHC class I genes, pseudogenes, transposons, and retrotransposons, such as Alu and ERV16, were used to categorize the 28 duplicons into four distinct structural categories. The phylogenetic relationship of MHC class I genes, Alu, and LTR16B sequences within the duplicons was examined by use of the Neighbor-Joining (NJ) method. Two single-duplicon tandem duplications, two polyduplicon tandem duplications with an accompanying inversion product per duplication, eight polyduplicon tandem duplications steps, 12 deletions, and at least two recombinations were reconstructed to explain the highly complex organization and evolution of the 28 duplicons (nine inversions) within the Mamu alpha block. On the basis of the phylogenetic evidence and the reconstructed tandem duplication history of the 28 duplicons, the Mamu/Patr/HLA-F ortholog was the first MHC class I gene to have been fixed without. further duplication within the alpha block of primates. Assuming that the rhesus macaque and the chimpanzee/human lineages had started with the same number of MHC class I duplicons at the time of their divergence approximately 24 to 31 MYA, then the number of genes within the alpha block have been duplicated at an approximately three times greater rate in the rhesus macaque than in either the human or chimpanzee.