Univ Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, 75205, Paris Cedex 13, France.
Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
Mol Genet Genomics. 2019 Feb;294(1):177-190. doi: 10.1007/s00438-018-1497-3. Epub 2018 Oct 4.
Mechanisms involved in fine adaptation of fungi to their environment include differential gene regulation associated with single nucleotide polymorphisms and indels (including transposons), horizontal gene transfer, gene copy amplification, as well as pseudogenization and gene loss. The two Podospora genome sequences examined here emphasize the role of pseudogenization and gene loss, which have rarely been documented in fungi. Podospora comata is a species closely related to Podospora anserina, a fungus used as model in several laboratories. Comparison of the genome of P. comata with that of P. anserina, whose genome is available for over 10 years, should yield interesting data related to the modalities of genome evolution between these two closely related fungal species that thrive in the same types of biotopes, i.e., herbivore dung. Here, we present the genome sequence of the mat + isolate of the P. comata reference strain T. Comparison with the genome of the mat + isolate of P. anserina strain S confirms that P. anserina and P. comata are likely two different species that rarely interbreed in nature. Despite having a 94-99% of nucleotide identity in the syntenic regions of their genomes, the two species differ by nearly 10% of their gene contents. Comparison of the species-specific gene sets uncovered genes that could be responsible for the known physiological differences between the two species. Finally, we identified 428 and 811 pseudogenes (3.8 and 7.2% of the genes) in P. anserina and P. comata, respectively. Presence of high numbers of pseudogenes supports the notion that difference in gene contents is due to gene loss rather than horizontal gene transfers. We propose that the high frequency of pseudogenization leading to gene loss in P. anserina and P. comata accompanies specialization of these two fungi. Gene loss may be more prevalent during the evolution of other fungi than usually thought.
真菌适应其环境的机制包括与单核苷酸多态性和插入缺失（包括转座子）相关的差异基因调控、水平基因转移、基因拷贝扩增，以及假基因化和基因丢失。本文研究的两个 Podospora 基因组序列强调了假基因化和基因丢失的作用，这些作用在真菌中很少被记录。Podospora comata 是一种与 Podospora anserina 密切相关的物种，后者是多个实验室使用的模型真菌。比较 P. comata 的基因组与 P. anserina 的基因组，后者的基因组已经存在了 10 多年，应该会产生与这两个在同一生物群落中茁壮成长的密切相关的真菌物种之间的基因组进化模式相关的有趣数据，即食草动物粪便。在这里，我们展示了 P. comata 参考菌株 T 的 mat+ 分离物的基因组序列。与 P. anserina 菌株 S 的 mat+ 分离物的基因组比较证实，P. anserina 和 P. comata 可能是两个很少在自然界中杂交的不同物种。尽管它们的基因组在同源区域的核苷酸同一性为 94-99%，但这两个物种的基因含量差异近 10%。比较物种特异性基因集揭示了可能导致这两个物种之间已知生理差异的基因。最后，我们在 P. anserina 和 P. comata 中分别鉴定出 428 个和 811 个假基因（分别占基因的 3.8%和 7.2%）。大量假基因的存在支持了这样一种观点，即基因含量的差异是由于基因丢失而不是水平基因转移造成的。我们提出，P. anserina 和 P. comata 中假基因化导致基因丢失的高频发生伴随着这两种真菌的特化。基因丢失在其他真菌的进化过程中可能比通常认为的更为普遍。
