Genome sequencing and integrative gene annotation of Malassezia sympodialis

The skin commensal yeast Malassezia is associated with several skin disorders. To establish a reference resource, we sought to determine the complete genome sequence of Malassezia sympodialis strain ATCC 42132 and identify its protein-coding genes. Through long-read DNA sequencing on the PacBio RS II system, we obtained a gap free genome assembly, comprising eight nuclear and one mitochondrial chromosome. We additionally sequenced and independently assembled the genomes of four M. sympodialis clinical isolates (KS004, KS024, KS269 and KS327) using the same methodology. The sequence reads indicated the existence of multiple mitochondrial genome configurations and the ATCC 42132 mitochondrial sequence deposited here represents one of those. A novel genome annotation workflow combining RNA-seq, proteomics and manual curation was developed to determine gene structures with high accuracy across the M. sympodialis ATCC 42132 genome. The resulting annotation contains 4,494 protein-coding genes, all of which were supported by RNA-seq and 86% confirmed by proteomics data. The RNA-seq data have been deposited in the ArrayExpress repository (accession E-MTAB-4589) and the proteomics data in the PRIDE repository (accession PXD003773).

皮肤共生酵母马拉色菌（Malassezia）与多种皮肤疾病相关。为构建参考资源，本研究旨在测定合轴马拉色菌（Malassezia sympodialis）菌株ATCC 42132的完整基因组序列，并鉴定其蛋白质编码基因。通过PacBio RS II系统的长读长DNA测序，我们获得了无间隙的基因组组装结果，包含8条核染色体与1条线粒体染色体。此外，本研究采用相同方法对4株合轴马拉色菌临床分离株（KS004、KS024、KS269、KS327）进行了基因组测序与独立组装。测序读段数据显示存在多种线粒体基因组构型，本次提交的ATCC 42132线粒体序列即为其中之一。本研究开发了一套整合RNA测序（RNA-seq）、蛋白质组学与人工注释的新型基因组注释流程，以高精度解析合轴马拉色菌ATCC 42132全基因组的基因结构。最终得到的注释集包含4494个蛋白质编码基因，所有基因均有RNA-seq数据支持，其中86%得到了蛋白质组学数据的验证。RNA-seq数据已提交至ArrayExpress数据库（登录号E-MTAB-4589），蛋白质组学数据已提交至PRIDE数据库（登录号PXD003773）。