Otalora Katherin, Gómez-Garrido Jessica, Baldo Laura
Department of Evolutionary Biology, Ecology and Environmental Sciences, Biology Faculty, University of Barcelona (UB), Av. Diagonal 643, Barcelona, 08028, Spain.
Fundación FUNMAJO, RAIEC, Biodiversity Branch, EBA, Cucaita, Boyacá, Colombia.
BMC Genomics. 2025 Jul 21;26(1):677. doi: 10.1186/s12864-025-11797-2.
Reptiles exhibit remarkable resistance to infections, making them a critical model for studying the molecular basis of innate immunity. Key components of their innate immune response are the antimicrobial peptides (AMPs), small, rapidly evolving molecules with a broad spectrum of antimicrobial activity. Despite their importance, AMPs in reptiles remain largely understudied, with no current studies available on one of the most successful reptilian lineages, lizards from the Lacertidae family. In this study, we performed an extensive mining of published Lacertidae genomes and present the first comprehensive characterization of their major AMP families -beta-defensins (BDs), ovo-defensins (OVODs), and cathelicidins (CATHs) - with the aim of understanding their genomic diversity and evolution.
We first identified a nearly complete catalogue of antimicrobial proteins from Podarcis lilfordi, an endemic lizard of the Balearic Islands (Spain): this included 63 BDs, eight OVODs, three of which are proline-rich proteins (OVOD-PrAMPs), and four CATHs. These AMPs are arranged in chromosome clusters of mostly contiguous peptides, flanked by highly conserved marker proteins. Using this fine-scale annotation, we mined corresponding orthologues and closed paralogues from P. muralis, P. raffonei and Zootoca vivipara, identifying a total of 58 AMPs. All AMPs consistently locate on chromosome 3 (BDs and OVODs) and chromosome 12 (CATHs), supporting a monophyletic origin for the reptilian antimicrobial defense. All Lacertidae AMPs show a multiple exon structure (two to four exons) and a characteristic cysteine motif (six cysteines in BDs, eight in OVODs, and four in CATHs), consistently with previous findings for vertebrates. Comparative sequence analyses indicate pervasive duplication events in tandem of both BDs and OVODs, with clear evidence of recent gene expansion. In contrast, OVOD-PrAMPs and CATHs mostly present a one-to-one ortholog across species. Despite this high level of intra-genomic diversity, we also identified multiple instances in which different species from distantly related Squamata families (Lacertidae, Varanidae and Dactyloidae) share identical or nearly identical peptides, suggesting convergent evolution.
Overall, our findings support a remarkable diversity of AMPs in lizards, driven by an ongoing process of gene expansion, primarily via duplication in tandem, and rapid diversification. The observed instances of peptide identity or similarity, along with the putative maintenance of specific polymorphisms across species, provide a basis for investigating the potential functional equivalence of these peptides among lizards and underscore the need for population-level studies of allele intraspecific diversity.
爬行动物对感染表现出显著的抵抗力，使其成为研究先天免疫分子基础的关键模型。其先天免疫反应的关键组成部分是抗菌肽（AMPs），这是一类小分子、快速进化且具有广泛抗菌活性的分子。尽管抗菌肽很重要，但爬行动物中的抗菌肽在很大程度上仍未得到充分研究，目前对于最成功的爬行动物谱系之一——蜥蜴科蜥蜴，尚无相关研究。在本研究中，我们对已发表的蜥蜴科基因组进行了广泛挖掘，并首次全面表征了其主要的抗菌肽家族——β-防御素（BDs）、卵防御素（OVODs）和cathelicidins（CATHs），旨在了解它们的基因组多样性和进化情况。
我们首先确定了来自西班牙巴利阿里群岛的特有蜥蜴丽纹攀蜥（Podarcis lilfordi）的几乎完整的抗菌蛋白目录：其中包括63种BDs、8种OVODs，其中3种是富含脯氨酸的蛋白（OVOD-PrAMPs），以及4种CATHs。这些抗菌肽排列在染色体簇中，大多为连续的肽段，两侧是高度保守的标记蛋白。利用这种精细注释，我们从意大利壁蜥（P. muralis）、拉氏攀蜥（P. raffonei）和胎生蜥蜴（Zootoca vivipara）中挖掘出相应的直系同源物和封闭的旁系同源物，共鉴定出58种抗菌肽。所有抗菌肽始终定位于3号染色体（BDs和OVODs）和12号染色体（CATHs）上，支持爬行动物抗菌防御的单系起源。所有蜥蜴科抗菌肽都显示出多个外显子结构（2至4个外显子）和特征性的半胱氨酸基序（BDs中有6个半胱氨酸，OVODs中有8个，CATHs中有4个），这与之前对脊椎动物的研究结果一致。比较序列分析表明，BDs和OVODs都存在广泛的串联重复事件，有明显的近期基因扩张证据。相比之下，OVOD-PrAMPs和CATHs在物种间大多呈现一对一的直系同源关系。尽管基因组内存在高度多样性，但我们也发现了多个实例，即来自远缘有鳞目家族（蜥蜴科、巨蜥科和安乐蜥科）的不同物种共享相同或几乎相同的肽段，这表明存在趋同进化。
总体而言，我们的研究结果支持蜥蜴中抗菌肽具有显著的多样性，这是由持续的基因扩张过程驱动的，主要通过串联重复和快速多样化实现。观察到的肽段同一性或相似性实例，以及跨物种特定多态性的假定维持，为研究这些肽段在蜥蜴中的潜在功能等效性提供了基础，并强调了对等位基因种内多样性进行群体水平研究的必要性。
