Faculty of Biology and Environmental Protection, Department of Biodiversity Studies and Bioeducation, University of Lodz, Banacha 1/3, 90-237 Lodz, Poland.
Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland.
Genome Biol Evol. 2024 Oct 9;16(10). doi: 10.1093/gbe/evae211.
The multigene family of the major histocompatibility complex (MHC) codes for the key antigen-presenting molecules of the vertebrate immune system. In birds, duplicated MHC class II (MHC-II) genes are highly homogenized by concerted evolution, and thus, identification of their orthologous relationships across long evolutionary timescales remains challenging. Relatively low evolutionary rate of avian MHC class IIA genes has been expected to provide a promising avenue to allow such inferences, but availability of MHC-IIA sequences in nonmodel bird species has been limited until recently. Here, taking advantage from accumulating genomic resources, we identified and analyzed MHC-IIA sequences from the most basal lineage of extant birds (Palaeognathae). Conserved region of the MHC-IIA membrane-proximal domain was used to search for orthologous relationships between palaeognath birds and nonavian reptiles. First, analyses of palaeognath sequences revealed the presence of a separate MHC-IIA gene lineage (DAA3) in kiwis, which did not cluster with previously described avian MHC-IIA lineages (DAA1 and DAA2). Next, phylogenetic reconstruction showed that kiwi DAA3 sequences form a single well-supported cluster with turtle MHC-IIA. High similarity of these sequences most likely reflects their remarkable evolutionary conservation and retention of ancient orthologous relationships, which can be traced back to basal archosauromorphs ca. 250 million years ago. Our analyses offer novel insights into macroevolutionary history of the MHC and reinforce the view that rapid accumulation of high-quality genome assemblies across divergent nonmodel species can substantially advance our understanding of gene evolution.
主要组织相容性复合体 (MHC) 的多基因家族编码脊椎动物免疫系统的关键抗原呈递分子。在鸟类中，重复的 MHC 类 II（MHC-II）基因通过协同进化高度同质化，因此，在长进化时间尺度上识别它们的同源关系仍然具有挑战性。相对较低的鸟类 MHC 类 IIA 基因进化率预计将为提供这样的推断提供有希望的途径，但直到最近，非模式鸟类物种的 MHC-IIA 序列可用性仍然有限。在这里，我们利用积累的基因组资源，从现存鸟类（古颌类）的最基础谱系中鉴定和分析了 MHC-IIA 序列。MHC-IIA 膜近端结构域的保守区域用于搜索古颌鸟类与非鸟类爬行动物之间的同源关系。首先，古颌序列的分析表明，几维鸟中存在一个单独的 MHC-IIA 基因谱系（DAA3），它与先前描述的鸟类 MHC-IIA 谱系（DAA1 和 DAA2）没有聚类。接下来，系统发育重建表明，几维鸟 DAA3 序列与海龟 MHC-IIA 形成一个单一的支持良好的聚类。这些序列的高度相似性很可能反映了它们显著的进化保守性和古老同源关系的保留，这些关系可以追溯到大约 2.5 亿年前的基干槽齿目动物。我们的分析提供了 MHC 宏观进化历史的新见解，并强化了这样的观点，即跨越不同非模式物种快速积累高质量基因组组装可以大大提高我们对基因进化的理解。
