The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.
The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.
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DOI：
10.1371/journal.pgen.1003820
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发表时间：
2013
期刊：
影响因子：
4.5
通讯作者：
Nowrousian M
中科院分区：
文献类型：
--
作者：
Traeger S;Altegoer F;Freitag M;Gabaldon T;Kempken F;Kumar A;Marcet-Houben M;Pöggeler S;Stajich JE;Nowrousian M
真菌是几乎所有生态系统中发现的一大类真核生物。超过 250 个真菌基因组已被测序，极大地提高了我们对真菌进化、生理学和发育的理解。然而，对于盘菌纲（丝状子囊菌的一种早期分化谱系）来说，迄今为止只有一个可用的基因组，即黑松露的基因组，即黑松块菌的基因组，这是一种具有不寻常的地下子实体的菌根物种。为了帮助缩小基础丝状子囊菌之间的序列差距，并得出有关真菌发育进化的结论，我们对 Pyronema conluens 发育过程中的基因组进行了测序并分析了转录组，这是一种腐生的盘菌，具有典型的子囊菌作为子实体。该基因组大小为 50 Mb，包含约 13,400 个蛋白质编码基因，与大型、重复丰富的松露基因组相比，更具有高等丝状子囊菌的特征；然而，P. confluens 谱系中的一些典型特征有所不同，例如交配型基因的基因组环境在高等丝状子囊菌中保守，但在 P. confluens 中仅部分保守。另一方面，P. confluens 具有完整的真菌光感受器，表达研究表明光感知可能与远缘子囊菌相似，因此代表了丝状子囊菌的基本特征。对剪接 RNA-seq 序列读数的分析允许检测 281 个基因的天然反义转录本。 P. confluens 基因组包含异常大量的预测孤儿基因，其中许多在性发育过程中被上调，这与性别相关基因快速进化的想法一致。比较转录组学鉴定了转录因子基因 pro44，该基因在 P. confluens 和 Sordariomycete Sordaria macrospora 的发育过程中上调。 P. confluens pro44 基因 (PCON_06721) 用于补充 S. macrospora pro44 缺失突变体，显示了该发育调节因子的功能保守性。真菌是形态和生理上多样化的生物体，对几乎所有生态系统都有巨大影响。近年来，许多真菌物种的基因组已被测序，极大地提高了我们对真菌生物学的理解。子囊菌是最大的真菌类群，其基因组测序数量最多；然而，对于 Pezizales（丝状子囊菌的一种早期分化谱系）来说，迄今为止只有一个基因组被测序，即黑松露的基因组。虽然松露是最有价值的食用真菌之一，但它们作为植物共生体具有特殊的生活方式，可产生地下子实体。因此，仅从一种松露基因组中很难得出有关基础子囊菌的结论。因此，我们对基础子囊菌 Pyronema conluens 的基因组和几个转录组进行了测序，它具有许多子囊菌典型的腐生生活方式。与其他真菌基因组比较表明，P. confluens具有两个保守的交配型基因，但交配型基因的基因组环境与高等子囊菌不同。我们还发现大量孤儿基因，即在其他真菌中没有同源物的基因，在性发育过程中被上调。这与性别相关基因的快速进化是一致的。
Fungi are a large group of eukaryotes found in nearly all ecosystems. More than 250 fungal genomes have already been sequenced, greatly improving our understanding of fungal evolution, physiology, and development. However, for the Pezizomycetes, an early-diverging lineage of filamentous ascomycetes, there is so far only one genome available, namely that of the black truffle, Tuber melanosporum, a mycorrhizal species with unusual subterranean fruiting bodies. To help close the sequence gap among basal filamentous ascomycetes, and to allow conclusions about the evolution of fungal development, we sequenced the genome and assayed transcriptomes during development of Pyronema confluens, a saprobic Pezizomycete with a typical apothecium as fruiting body. With a size of 50 Mb and ∼13,400 protein-coding genes, the genome is more characteristic of higher filamentous ascomycetes than the large, repeat-rich truffle genome; however, some typical features are different in the P. confluens lineage, e.g. the genomic environment of the mating type genes that is conserved in higher filamentous ascomycetes, but only partly conserved in P. confluens. On the other hand, P. confluens has a full complement of fungal photoreceptors, and expression studies indicate that light perception might be similar to distantly related ascomycetes and, thus, represent a basic feature of filamentous ascomycetes. Analysis of spliced RNA-seq sequence reads allowed the detection of natural antisense transcripts for 281 genes. The P. confluens genome contains an unusually high number of predicted orphan genes, many of which are upregulated during sexual development, consistent with the idea of rapid evolution of sex-associated genes. Comparative transcriptomics identified the transcription factor gene pro44 that is upregulated during development in P. confluens and the Sordariomycete Sordaria macrospora. The P. confluens pro44 gene (PCON_06721) was used to complement the S. macrospora pro44 deletion mutant, showing functional conservation of this developmental regulator. Fungi are a morphologically and physiologically diverse group of organisms with huge impacts on nearly all ecosystems. In recent years, genomes of many fungal species have been sequenced and have greatly improved our understanding of fungal biology. Ascomycetes are the largest fungal group with the highest number of sequenced genomes; however, for the Pezizales, an early-diverging lineage of filamentous ascomycetes, only one genome has been sequence to date, namely that of the black truffle. While truffles are among the most valuable edible fungi, they have a specialized life style as plant symbionts producing belowground fruiting bodies; thus it is difficult to draw conclusions about basal ascomycetes from one truffle genome alone. Therefore, we have sequenced the genome and several transcriptomes of the basal ascomycete Pyronema confluens, which has a saprobic life style typical of many ascomycetes. Comparisons with other fungal genomes showed that P. confluens has two conserved mating type genes, but that the genomic environment of the mating type genes is different from that of higher ascomycetes. We also found that a high number of orphan genes, i.e. genes without homologs in other fungi, are upregulated during sexual development. This is consistent with rapid evolution of sex-associated genes.
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DOI：
10.1073/pnas.0304170101
发表时间：
2004-02-10
影响因子：
11.1
作者：
Butler, G;Kenny, C;Wolfe, KH
通讯作者：
Wolfe, KH
影响因子：
14.8
作者：
Bok, Jin Woo;Chiang, Yi-Ming;Szewczyk, Edyta;Reyes-Domingez, Yazmid;Davidson, Ashley D.;Sanchez, James F.;Lo, Hsien-Chun;Watanabe, Kenji;Strauss, Joseph;Oakley, Berl R.;Wang, Clay C. C.;Keller, Nancy P.
通讯作者：
Keller, Nancy P.
影响因子：
3.4
作者：
Bushley KE;Ripoll DR;Turgeon BG
通讯作者：
Turgeon BG
DOI：
10.1093/bioinformatics/btp348
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capella-Gutiérrez S;Silla-Martínez JM;Gabaldón T
通讯作者：
Gabaldón T
影响因子：
11.4
作者：
Ballario, P;Vittorioso, P;Macino, G
通讯作者：
Macino, G