Adil Guldiyar, Liu Shenglei, Bao Xiaoyan, Mamut Reyim
College of Life Sciences and Technology, Xinjiang University, Urumchi, Xinjiang, China.
Front Genet. 2025 Jul 23;16:1602048. doi: 10.3389/fgene.2025.1602048. eCollection 2025.
Lichens are globally distributed symbiotic organisms comprising fungi (mycobionts) and photosynthetic partners (photobionts), with exceptional adaptability to extreme environments. Despite growing interest in lichen symbiosis, chloroplast genome data for photobionts remain scarce, hindering insights into symbiotic coevolution and genomic architecture.
To address this gap, we characterized the chloroplast genome of Chloroidium sp. W5, a photobiont of the lichen Peltigera elisabethae, using next-generation sequencing. The circular genome (190,579 bp) was assembled and annotated using a combination of bioinformatics tools, including GetOrganelle for genome assembly and GeSeq for annotation. We conducted a comprehensive analysis of the genome's structure, gene content, and repetitive elements. Codon usage patterns were assessed using MEGA 11, and phylogenetic relationships were inferred using maximum likelihood analysis with IQ-tree.
The circular genome (190,579 bp) lacks the canonical quadripartite structure (LSC/IR/SSC) and exhibits a strong AT bias (56.1%). Annotation identified 110 functional genes, including 79 protein-coding genes, 28 tRNAs, and 3 rRNAs. Repetitive sequence analysis revealed 5,000 dispersed repeats (2.62% of the genome), predominantly forward and palindromic types, with SSR loci showing a significant A/T preference. Codon usage analysis demonstrated a pronounced bias toward A/U-ending codons (RSCU > 1), suggesting translational adaptation to symbiotic nutrient constraints. Phylogenetic reconstruction robustly placed Chloroidium sp. W5 within the Watanabeales clade (ML = 100), while synteny analysis revealed extensive genomic rearrangements compared to close relatives.
These findings enrich the chloroplast genome database for lichen photobionts, shedding light on symbiosis-driven genomic plasticity and providing a foundation for studying host-photobiont coevolution and lichen ecological adaptation.
地衣是一种全球分布的共生生物，由真菌（菌共生体）和光合伙伴（光共生体）组成，对极端环境具有非凡的适应能力。尽管人们对地衣共生的兴趣日益浓厚，但光共生体的叶绿体基因组数据仍然稀缺，这阻碍了我们对共生协同进化和基因组结构的深入了解。
为了填补这一空白，我们利用下一代测序技术对地衣伊丽莎白肺衣的光共生体绿球藻属W5的叶绿体基因组进行了特征分析。使用包括用于基因组组装的GetOrganelle和用于注释的GeSeq等生物信息学工具的组合，对环状基因组（190,579 bp）进行了组装和注释。我们对基因组的结构、基因内容和重复元件进行了全面分析。使用MEGA 11评估密码子使用模式，并使用IQ-tree通过最大似然分析推断系统发育关系。
环状基因组（190,579 bp）缺乏典型的四分体结构（LSC/IR/SSC），并表现出强烈的AT偏向（56.1%）。注释鉴定出110个功能基因，包括79个蛋白质编码基因、28个tRNA和3个rRNA。重复序列分析揭示了5000个分散重复序列（占基因组的2.62%），主要是正向和回文类型，SSR位点显示出对A/T的显著偏好。密码子使用分析表明对以A/U结尾的密码子有明显偏向（RSCU > 1），表明在翻译上适应共生营养限制。系统发育重建有力地将绿球藻属W5置于渡边藻科分支内（ML = 100），而共线性分析显示与近亲相比存在广泛的基因组重排。
这些发现丰富了地衣光共生体的叶绿体基因组数据库，揭示了共生驱动的基因组可塑性，并为研究宿主 - 光共生体协同进化和地衣生态适应提供了基础。
