College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
Center for Genomics, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
Genome Biol. 2023 Dec 5;24(1):280. doi: 10.1186/s13059-023-03093-7.
The dikaryotic stage dominates most of the life cycle in basidiomycetes, and each cell carries two different haploid nuclei. Accurate phasing of these two nuclear genomes and their interactions have long been of interest.
We combine PacBio HiFi reads, Nanopore ultra-long reads, and Hi-C data to generate a complete, high-quality asymmetric dikaryotic genome of Tremella fuciformis Tr01, including Haplotypes A and B genomes. We assemble a meiotic haploid DBZ04 genome and detect three recombination events in these two haplotypes. We identify several chromosomal rearrangements that lead to differences in chromosome number, length, content, and sequence arrangement between these two haplotypes. Each nucleus contains a two-speed genome, harboring three accessory chromosomes and two accessory compartments that affect horizontal chromatin transfer between nuclei. We find few basidiospores are ejected from fruiting bodies of Tr01. Most monospore isolates sequenced belong to Tr01-Haplotype A genome architecture. More than one-third of monospore isolates carry one or two extra chromosomes including Chr12B and two new chromosomes ChrN1 and ChrN2. We hypothesize that homologous regions of seven sister chromatids pair into a large complex during meiosis, followed by inter-chromosomal recombination at physical contact sites and formation of new chromosomes.
We assemble two haplotype genomes of T. fuciformis Tr01 and provide the first overview of basidiomycetous genomes with discrete genomic architecture. Meiotic activities of asymmetric dikaryotic genomes result in formation of new chromosomes, aneuploidy of some daughter cells, and inviability of most other daughter cells. We propose a new approach for breeding of sporeless mushroom.
双核阶段在担子菌的大部分生命周期中占主导地位，每个细胞携带两个不同的单倍体核。准确相位这些两个核基因组及其相互作用一直是人们关注的焦点。
我们结合 PacBio HiFi reads、Nanopore 超长 reads 和 Hi-C 数据，生成了完整的、高质量的银耳 Tr01 不对称双核基因组，包括 Haplotypes A 和 B 基因组。我们组装了一个减数分裂单倍体 DBZ04 基因组，并在这两个单倍体中检测到三个重组事件。我们鉴定了几个染色体重排，导致这两个单倍体之间的染色体数目、长度、内容和序列排列存在差异。每个核都包含一个双速基因组，包含三个附加染色体和两个附加隔室，影响核间水平染色质转移。我们发现很少有担孢子从 Tr01 的子实体中释放出来。大多数测序的单核分离物属于 Tr01-Haplotype A 基因组结构。超过三分之一的单核分离物携带一个或两个额外的染色体，包括 Chr12B 和两个新的染色体 ChrN1 和 ChrN2。我们假设七个姐妹染色单体的同源区域在减数分裂期间配对成一个大复合物，然后在物理接触位点进行染色体间重组，并形成新的染色体。
我们组装了银耳 Tr01 的两个单倍型基因组，并提供了第一个具有离散基因组结构的担子菌基因组概述。不对称双核基因组的减数分裂活动导致新染色体的形成、一些子细胞的非整倍性和大多数其他子细胞的不可育性。我们提出了一种新的无孢子蘑菇育种方法。
