The genomic region (~4 Mb) of the human major histocompatibility complex (MHC) on chromosome 6p21 is a prime model for the study and understanding of conserved polymorphic sequences (CPSs) and structural diversity of ancestral haplotypes (AHs)/conserved extended haplotypes (CEHs). The aim of this study was to use a set of 95 MHC genomic sequences downloaded from a publicly available BioProject database at NCBI to identify and characterise polymorphic human leukocyte antigen (HLA) class I genes and pseudogenes, MICA and MICB, and retroelement indels as haplotypic lineage markers, and single-nucleotide polymorphism (SNP) crossover loci in DNA sequence alignments of different haplotypes across the Olfactory Receptor (OR) gene region (~1.2 Mb) and the MHC class I region (~1.8 Mb) from the GPX5 to the MICB gene. Our comparative sequence analyses confirmed the identity of 12 haplotypic retroelement markers and revealed that they partitioned the HLA-A/B/C haplotypes into distinct evolutionary lineages. Crossovers between SNP-poor and SNP-rich regions defined the sequence range of haplotype blocks, and many of these crossover junctions occurred within particular transposable elements, lncRNA, OR12D2, MUC21, MUC22, PSORS1A3, HLA-C, HLA-B, and MICA. In a comparison of more than 250 paired sequence alignments, at least 38 SNP-density crossover sites were mapped across various regions from GPX5 to MICB. In a homology comparison of 16 different haplotypes, seven CEH/AH (7.1, 8.1, 18.2, 51.x, 57.1, 62.x, and 62.1) had no detectable SNP-density crossover junctions and were SNP poor across the entire ~2.8 Mb of sequence alignments. Of the analyses between different recombinant haplotypes, more than half of them had SNP crossovers within 10 kb of LTR16B/ERV3-16A3_I, MLT1, Charlie, and/or THE1 sequences and were in close vicinity to structurally polymorphic Alu and SVA insertion sites. These studies demonstrate that (1) SNP-density crossovers are associated with putative ancestral recombination sites that are widely spread across the MHC class I genomic region from at least the telomeric OR12D2 gene to the centromeric MICB gene and (2) the genomic sequences of MHC homozygous cell lines are useful for analysing haplotype blocks, ancestral haplotypic landscapes and markers, CPSs, and SNP-density crossover junctions.

染色体 6p21 上人类主要组织相容性复合体 (MHC) 的基因组区域 (~4 Mb) 是研究和理解保守多态序列 (CPS) 和祖先单倍型 (AH)/保守扩展单倍型结构多样性的主要模型。 CEH）。本研究的目的是使用从 NCBI 公开的 BioProject 数据库下载的一组 95 个 MHC 基因组序列来识别和表征多态性人类白细胞抗原 (HLA) I 类基因和假基因，云母和微生物学CB和逆转录元件插入缺失作为单倍型谱系标记，以及不同单倍型 DNA 序列比对中的单核苷酸多态性 (SNP) 交叉位点嗅觉感受器（或者) 基因区域 (~1.2 Mb) 和 MHC I 类区域 (~1.8 Mb)GPX5到微生物学CB基因。我们的比较序列分析证实了 12 个单倍型逆转录元件标记的身份，并揭示它们将HLA-A/B/C单倍型分为不同的进化谱系。SNP 缺乏和 SNP 丰富区域之间的交叉定义了单倍型块的序列范围，并且许多这些交叉连接发生在特定的转座元件、lncRNA、OR12D2、MUC21、MUC22、PSORS1A3、HLA-C、HLA-B， 和云母。在对 250 多个配对序列比对的比较中，至少 38 个 SNP 密度交叉位点被映射到各个区域GPX5到微生物学CB。在16个不同单倍型的同源性比较中，7个CEH/AH（7.1、8.1、18.2、51.x、57.1、62.x， 和62.1）没有可检测到的 SNP 密度交叉连接，并且在整个约 2.8 Mb 的序列比对中 SNP 较差。在不同重组单倍型之间的分析中，超过一半的单倍型在 10 kb 范围内有 SNP 交叉。LTR16B/ERV3-16A3_I，MLT1，查理，和/或THE1序列并且与结构多态性非常接近铝和广电总局插入位点。这些研究表明 (1) SNP 密度交叉与假定的祖先重组位点相关，这些位点至少从端粒广泛分布在 MHC I 类基因组区域。或12D2基因到着丝粒微生物学CB基因和 (2) MHC 纯合细胞系的基因组序列可用于分析单倍型块、祖先单倍型景观和标记、CPS 和 SNP 密度交叉连接。