Table_2_The Marine Mammal Class II Major Histocompatibility Complex Organization.XLSX

Sirenians share with cetaceans and pinnipeds several convergent traits selected for the aquatic lifestyle. Living in water poses new challenges not only for locomotion and feeding but also for combating new pathogens, which may render the immune system one of the best tools aquatic mammals have for dealing with aquatic microbial threats. So far, only cetaceans have had their class II Major Histocompatibility Complex (MHC) organization characterized, despite the importance of MHC genes for adaptive immune responses. This study aims to characterize the organization of the marine mammal class II MHC using publicly available genomes. We located class II sequences in the genomes of one sirenian, four pinnipeds and eight cetaceans using NCBI-BLAST and reannotated the sequences using local BLAST search with exon and intron libraries. Scaffolds containing class II sequences were compared using dotplot analysis and introns were used for phylogenetic analysis. The manatee class II region shares overall synteny with other mammals, however most DR loci were translocated from the canonical location, past the extended class II region. Detailed analysis of the genomes of closely related taxa revealed that this presumed translocation is shared with all other living afrotherians. Other presumptive chromosome rearrangements in Afrotheria are the deletion of DQ loci in Afrosoricida and deletion of DP in E. telfairi. Pinnipeds share the main features of dog MHC: lack of a functional pair of DPA/DPB genes and inverted DRB locus between DQ and DO subregions. All cetaceans share the Cetartiodactyla inversion separating class II genes into two subregions: class IIa, with DR and DQ genes, and class IIb, with non-classic genes and a DRB pseudogene. These results point to three distinct and unheralded class II MHC structures in marine mammals: one canonical organization but lacking DP genes in pinnipeds; one bearing an inversion separating IIa and IIb subregions lacking DP genes found in cetaceans; and one with a translocation separating the most diverse class II gene from the MHC found in afrotherians and presumptive functional DR, DQ, and DP genes. Future functional research will reveal how these aquatic mammals cope with pathogen pressures with these divergent MHC organizations.

海牛目（Sirenia）动物与鲸目（Cetacea）、鳍足类共享多项为适应水生生活演化出的趋同性状。水生生活不仅为运动与摄食带来全新挑战，同时也使宿主需对抗新型病原体，因此免疫系统堪称水生哺乳动物应对水生微生物威胁的核心防御手段之一。截至目前，仅有鲸目动物的II类主要组织相容性复合体（Major Histocompatibility Complex, MHC）基因组结构得到解析，尽管MHC基因在适应性免疫应答中发挥着至关重要的作用。本研究旨在利用公开可用的基因组数据，解析海洋哺乳动物II类MHC的基因组组织形式。我们通过NCBI-BLAST在1种海牛目动物、4种鳍足类以及8种鲸目动物的基因组中定位II类MHC序列，并利用基于外显子与内含子文库的本地BLAST搜索对上述序列进行重新注释。通过点图分析对包含II类MHC序列的基因组支架（scaffolds）进行比较，并利用内含子序列开展系统发育分析。海牛的II类MHC区域整体与其他哺乳动物呈现共线性特征，但绝大多数DR基因座已从经典位置发生易位，跨越了延伸型II类MHC区域。对近缘类群基因组的详细分析显示，这一推测的易位事件在所有现存非洲兽总目（Afrotheria）类群中均存在。非洲兽总目其他推测的染色体重排事件包括：非洲鼩目（Afrosoricida）的DQ基因座缺失，以及E. telfairi的DP基因座缺失。鳍足类的MHC具备犬科MHC的主要特征：缺乏功能型DPA/DPB基因对，且DRB基因座在DQ与DO亚区域之间发生倒位。所有鲸目动物均共享鲸偶蹄目（Cetartiodactyla）的倒位事件，该倒位将II类基因划分为两个亚区域：包含DR与DQ基因的IIa亚区域，以及包含非经典基因与DRB假基因的IIb亚区域。本研究结果揭示了海洋哺乳动物中三种此前未被报道的II类MHC基因组结构：其一为鳍足类所具备的经典组织形式，但缺失DP基因；其二为鲸目动物拥有的倒位型结构，该结构将IIa与IIb亚区域分隔开，同样缺失DP基因；其三为非洲兽总目类群的易位型结构，该结构将多样性最高的II类基因与MHC区域分离，且保留了功能型DR、DQ与DP基因。后续功能研究将进一步阐明这些水生哺乳动物如何通过这些分化的MHC基因组结构应对病原体压力。