Yacoub Mark N, Stajich Jason E
Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA 92521, USA.
Graduate Program in Microbiology, University of California Riverside, Riverside, CA 92521, USA.
Genome Biol Evol. 2025 May 30;17(6). doi: 10.1093/gbe/evaf114.
The Global Panzootic Lineage (GPL) of Batrachochytrium dendrobatidis (Bd) has been described as a main driver of amphibian extinctions. Pathogen studies have benefited from three Bd-GPL strain genomes, but identifying the genetic and molecular features that distinguish the B. dendrobatidis lineages requires additional high-quality genomes from diverse lineages. We sequenced and assembled genomes with Oxford Nanopore Technologies to produce assemblies of three Bd-BRAZIL isolates and one nonpathogen outgroup species Polyrhizophydium stewartii. The Bd-BRAZIL assembly sizes ranged between 22.0 and 26.1 Mb with 8,495 to 8,620 predicted protein-coding genes. We sought to categorize the pangenome of the species by identifying homologous genes across the sampled genomes as either being core and present in all strains, or accessory and shared among strains in a lineage, an analysis that has not yet been conducted on B. dendrobatidis and its lineages. We identified a core genome consisting of 6,278 gene families, and an accessory genome of 202 Bd-BRAZIL and 172 Bd-GPL specific gene families. We discovered copy number differences in pathogenicity gene families: M36 Peptidases, Crinkler Necrosis genes, Aspartyl Peptidases, Carbohydrate-Binding Module-18 genes, and S41 Proteases, between Bd-BRAZIL and Bd-GPL strains. Comparison of B. dendrobatidis and two closely related saprophytic species identified differences in protein sequence and domain counts for M36 and CBM18 families respectively. Our pangenome analysis of lineage-specific gene content led us to explore how the selection of the reference genome affects recovery of RNAseq transcripts when comparing different strains. We tested the hypothesis that genomic variation among Bd-GPL and Bd-BRAZIL lineages can impact transcript count data by comparing results with our new Bd-BRAZIL genomes as the reference genomes. Our analysis examines the genomic variation between strains in Bd-BRAZIL and Bd-GPL and offers insights into the application of these high-quality reference genomes resources for future studies.
蛙壶菌（Batrachochytrium dendrobatidis，Bd）的全球泛动物疫情谱系（GPL）被认为是两栖动物灭绝的主要驱动因素。病原体研究受益于三个Bd - GPL菌株基因组，但要确定区分蛙壶菌谱系的遗传和分子特征，还需要来自不同谱系的更多高质量基因组。我们使用牛津纳米孔技术对基因组进行测序和组装，以产生三个Bd - BRAZIL分离株和一个非病原体外群物种斯图尔特多聚根肿菌（Polyrhizophydium stewartii）的组装体。Bd - BRAZIL组装体大小在22.0至26.1 Mb之间，预测有8495至8620个蛋白质编码基因。我们试图通过将采样基因组中的同源基因分类为核心基因（存在于所有菌株中）或辅助基因（在一个谱系的菌株中共享）来对该物种的泛基因组进行分类，这种分析尚未在蛙壶菌及其谱系上进行过。我们确定了一个由6278个基因家族组成的核心基因组，以及202个Bd - BRAZIL和172个Bd - GPL特异性基因家族的辅助基因组。我们发现致病性基因家族存在拷贝数差异：M36肽酶、卷曲坏死基因、天冬氨酰肽酶、碳水化合物结合模块 - 18基因和S41蛋白酶，在Bd - BRAZIL和Bd - GPL菌株之间存在差异。对蛙壶菌和两个密切相关的腐生物种的比较分别确定了M36和CBM18家族在蛋白质序列和结构域数量上的差异。我们对谱系特异性基因内容的泛基因组分析使我们探索在比较不同菌株时参考基因组的选择如何影响RNAseq转录本的回收率。我们通过将结果与我们新的Bd - BRAZIL基因组作为参考基因组进行比较，检验了Bd - GPL和Bd - BRAZIL谱系之间的基因组变异会影响转录本计数数据的假设。我们的分析研究了Bd - BRAZIL和Bd - GPL菌株之间的基因组变异，并为这些高质量参考基因组资源在未来研究中的应用提供了见解。
