Each day, as the amount of genomic data and bioinformatics resources grows, researchers are increasingly challenged with selecting the most appropriate approach to analyze their data. In addition, the opportunity to undertake comparative genomic analyses is growing rapidly. This is especially true for fungi due to their small genome sizes (i.e., mean 1C = 44.2 Mb). Given these opportunities and aiming to gain novel insights into the evolution of mutualisms, we focus on comparing the quality of whole genome assemblies for fungus-growing ants cultivars (Hymenoptera: Formicidae: Attini) and a free-living relative. Our analyses reveal that currently available methodologies and pipelines for analyzing whole-genome sequence data need refining. By using different genome assemblers, we show that the genome assembly size depends on what software is used. This, in turn, impacts gene number predictions, with higher gene numbers correlating positively with genome assembly size. Furthermore, the majority of fungal genome size data currently available are based on estimates derived from whole-genome assemblies generated from short-read genome data, rather than from the more accurate technique of flow cytometry. Here, we estimated the haploid genome sizes of three ant fungal symbionts by flow cytometry using the fungus Pleurotus ostreatus (Jacq.) P. Kumm. (1871) as a calibration standard. We found that published genome sizes based on genome assemblies are 2.5- to 3-fold larger than our estimates based on flow cytometry. We, therefore, recommend that flow cytometry is used to precalibrate genome assembly pipelines, to avoid incorrect estimates of genome sizes and ensure robust assemblies.

中文翻译：

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基因组大小与基因组组合：多倍体真菌共生体中的基因组是否真正扩展？

每天，随着基因组数据和生物信息学资源量的增长，研究人员在选择最合适的方法来分析他们的数据方面面临越来越大的挑战。此外，进行比较基因组分析的机会正在迅速增加。这对于真菌来说尤其如此，因为它们的基因组很小（即，平均 1C = 44.2 Mb）。鉴于这些机会并旨在获得对共生关系进化的新见解，我们专注于比较真菌生长的蚂蚁品种（膜翅目：蚁科：Attini）和自由生活亲戚的全基因组组装质量。我们的分析表明，目前用于分析全基因组序列数据的可用方法和管道需要改进。通过使用不同的基因组组装器，我们表明基因组组装的大小取决于使用的软件。这反过来又会影响基因数量的预测，更高的基因数量与基因组组装大小呈正相关。此外，目前可用的大多数真菌基因组大小数据是基于从短读基因组数据生成的全基因组组装中得出的估计值，而不是更准确的流式细胞术技术。在这里，我们使用真菌通过流式细胞术估计了三种蚂蚁真菌共生体的单倍体基因组大小Pleurotus ostreatus (Jacq.) P. Kumm。(1871) 作为校准标准。我们发现基于基因组组装的已发表基因组大小比我们基于流式细胞术的估计大 2.5 到 3 倍。因此，我们建议使用流式细胞术来预校准基因组组装管道，以避免对基因组大小的错误估计并确保可靠的组装。