一个染色体规模的最小的腔菌基因组组装揭示了丝状真菌中一种独特的基因组压缩机制。

A chromosome-scale assembly of the smallest Dothideomycete genome reveals a unique genome compaction mechanism in filamentous fungi.

机构信息

State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi Province, China.

MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China.

出版信息

BMC Genomics. 2020 Apr 23;21(1):321. doi: 10.1186/s12864-020-6732-8.

DOI:10.1186/s12864-020-6732-8

PMID:32326892

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7181583/

Abstract

BACKGROUND

The wide variation in the size of fungal genomes is well known, but the reasons for this size variation are less certain. Here, we present a chromosome-scale assembly of ectophytic Peltaster fructicola, a surface-dwelling extremophile, based on long-read DNA sequencing technology, to assess possible mechanisms associated with genome compaction.

RESULTS

At 18.99 million bases (Mb), P. fructicola possesses one of the smallest known genomes sequence among filamentous fungi. The genome is highly compact relative to other fungi, with substantial reductions in repeat content, ribosomal DNA copies, tRNA gene quantity, and intron sizes, as well as intergenic lengths and the size of gene families. Transposons take up just 0.05% of the entire genome, and no full-length transposon was found. We concluded that reduced genome sizes in filamentous fungi such as P. fructicola, Taphrina deformans and Pneumocystis jirovecii occurred through reduction in ribosomal DNA copy number and reduced intron sizes. These dual mechanisms contrast with genome reduction in the yeast fungus Saccharomyces cerevisiae, whose small and compact genome is associated solely with intron loss.

CONCLUSIONS

Our results reveal a unique genomic compaction architecture of filamentous fungi inhabiting plant surfaces, and broaden the understanding of the mechanisms associated with compaction of fungal genomes.

摘要

背景

真菌基因组的大小差异很大，这是众所周知的，但导致这种大小差异的原因还不太确定。在这里，我们基于长读 DNA 测序技术，呈现了外生 Peltaster fructicola 的染色体规模组装，这是一种生活在表面的极端微生物，以评估与基因组紧缩相关的可能机制。

结果

P. fructicola 的基因组大小为 1899 万碱基对（Mb），在丝状真菌中拥有已知最小的基因组序列之一。与其他真菌相比，该基因组高度紧凑，重复含量、核糖体 DNA 拷贝数、tRNA 基因数量、内含子大小以及基因家族的大小都显著减少，基因间长度和内含子大小也显著减少。转座子仅占整个基因组的 0.05%，且未发现全长转座子。我们得出结论，P. fructicola、Taphrina deformans 和 Pneumocystis jirovecii 等丝状真菌的基因组缩小是通过核糖体 DNA 拷贝数的减少和内含子大小的减少而实现的。这两种机制与酵母真菌 Saccharomyces cerevisiae 的基因组缩小形成对比，后者的小而紧凑的基因组仅与内含子缺失有关。