Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland.
Department of Biology, Illinois Institute of Technology, Chicago, IL 60616, USA.
G3 (Bethesda). 2023 Sep 30;13(10). doi: 10.1093/g3journal/jkad185.
Microsporidia are intracellular parasitic fungi whose genomes rank among the smallest of all known eukaryotes. A number of outstanding questions remain concerning the evolution of their large-scale variation in genome architecture, responsible for genome size variation of more than an order of magnitude. This genome report presents the first near-chromosomal assembly of a large-genome microsporidium, Hamiltosporidium tvaerminnensis. Combined Oxford Nanopore, Pacific Biosciences (PacBio), and Illumina sequencing led to a genome assembly of 17 contigs, 11 of which represent complete chromosomes. Our assembly is 21.64 Mb in length, has an N50 of 1.44 Mb, and consists of 39.56% interspersed repeats. We introduce a novel approach in microsporidia, PacBio Iso-Seq, as part of a larger annotation pipeline for obtaining high-quality annotations of 3,573 protein-coding genes. Based on direct evidence from the full-length Iso-Seq transcripts, we present evidence for alternative polyadenylation and variation in splicing efficiency, which are potential regulation mechanisms for gene expression in microsporidia. The generated high-quality genome assembly is a necessary resource for comparative genomics that will help elucidate the evolution of genome architecture in response to intracellular parasitism.
微孢子虫是一种细胞内寄生的真菌，其基因组是所有已知真核生物中最小的之一。关于其大规模基因组结构变异的进化，还有许多悬而未决的问题，这些变异导致了基因组大小变化超过一个数量级。本基因组报告介绍了第一个大型基因组微孢子虫——Hamiltosporidium tvaerminnensis 的近染色体组装。结合牛津纳米孔、太平洋生物科学（PacBio）和 Illumina 测序，得到了一个由 17 个连续序列组成的基因组组装，其中 11 个代表完整的染色体。我们的组装长度为 21.64 Mb，N50 为 1.44 Mb，由 39.56%的分散重复序列组成。我们引入了一种新的微孢子虫方法，即 PacBio Iso-Seq，作为获得 3573 个蛋白质编码基因高质量注释的更大注释管道的一部分。基于全长 Iso-Seq 转录本的直接证据，我们提出了可变多聚腺苷酸化和剪接效率变化的证据，这是微孢子虫基因表达的潜在调控机制。生成的高质量基因组组装是比较基因组学的必要资源，它将有助于阐明基因组结构对细胞内寄生的进化。
