Long-read PacBio genome sequencing of four environmental saprophytic Sporothrix species spanning the pathogenic clade.
Long-read PacBio genome sequencing of four environmental saprophytic Sporothrix species spanning the pathogenic clade.
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跨越致病支系的四种环境腐生孢子丝菌的长阅读PacBio基因组测序。
DOI：
10.1186/s12864-022-08736-w
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发表时间：
2022-07-12
期刊：
影响因子：
4.4
通讯作者：
中科院分区：
文献类型：
--
作者：
孢子丝菌属属于Ophiostomatales目，主要含有腐土和植物真菌，尽管也存在能够引起人类感染的病原物种。致病物种的全基因组已经测序和注释，但没有全面的环境孢子丝菌属物种的基因组资源，从而限制了我们对毒力相关基因和致病性的进化起源的理解。4种环境孢子丝菌的基因组拼接结果表明，孢子丝菌的基因组大小约为30.9Mbp，孢子丝菌的基因组大小约为35 Mbp，孢子丝菌的基因组大小约为35 Mbp，孢子丝菌的基因组大小约为35 Mbp。弯孢霉S. Protearum中约39 Mbp; variecibatus，基因含量变异较大，从8142（S. phasma）至9502（S. variecibatus）。对移动的遗传元件的分析表明，测序基因组内转座元件的含量存在显着差异，其中S.与研究的其他孢子丝菌属基因组相比，孢子丝菌属缺乏几个I类和II类转座子。此外，临床和环境孢子丝菌基因组共享的正交群基因的比较分析显示，所有物种共享的3622个正交群的存在，而超过4200个基因是物种特异性的单拷贝基因产物。碳水化合物活性酶分析显示，总共有2608个蛋白质编码基因含有单个和/或多个CAZy结构域，导致致病性和环境物种之间没有统计学显著差异。尽管如此，有些科在临床物种中并未发现。此外，对于每个测序的孢子丝菌属物种，线粒体基因组组装在单个环状DNA分子中，范围从25，765 bp（S. varicibatus）到58，395 bp（S. phasma）。在这项研究中，我们提出了四个注释的基因组组装产生的PacBio SMRT测序数据从四个环境物种：S。curviconia、S. phasma，S. Protearum和S. variecibatus的目的是提供一个起点，为未来的比较基因组进化研究解决物种多样性，生态/宿主适应性和起源的病原谱系内属孢子丝菌。在线版本包含补充材料，可通过10.1186/s12864-022-08736-w获得。
The genus Sporothrix belongs to the order Ophiostomatales and contains mainly saprobic soil and plant fungi, although pathogenic species capable of causing human infections are also present. The whole-genomes of disease-causing species have already been sequenced and annotated but no comprehensive genomic resources for environmental Sporothrix species are available, thus limiting our understanding of the evolutionary origin of virulence-related genes and pathogenicity. The genome assembly of four environmental Sporothrix species resulted in genome size of ~ 30.9 Mbp in Sporothrix phasma, ~ 35 Mbp in S. curviconia, ~ 38.7 Mbp in S. protearum, and ~ 39 Mbp in S. variecibatus, with a variable gene content, ranging from 8142 (S. phasma) to 9502 (S. variecibatus). The analysis of mobile genetic elements showed significant differences in the content of transposable elements within the sequenced genomes, with the genome of S. phasma lacking several class I and class II transposons, compared to the other Sporothrix genomes investigated. Moreover, the comparative analysis of orthologous genes shared by clinical and environmental Sporothrix genomes revealed the presence of 3622 orthogroups shared by all species, whereas over 4200 genes were species-specific single-copy gene products. Carbohydrate-active enzyme analysis revealed a total of 2608 protein-coding genes containing single and/or multiple CAZy domains, resulting in no statistically significant differences among pathogenic and environmental species. Nevertheless, some families were not found in clinical species. Furthermore, for each sequenced Sporothrix species, the mitochondrial genomes was assembled in a single circular DNA molecule, ranging from 25,765 bp (S. variecibatus) to 58,395 bp (S. phasma). In this study, we present four annotated genome assemblies generated using PacBio SMRT sequencing data from four environmental species: S. curviconia, S. phasma, S. protearum and S. variecibatus with the aim to provide a starting point for future comparative genome evolution studies addressing species diversification, ecological/host adaptation and origin of pathogenic lineages within the genus Sporothrix. The online version contains supplementary material available at 10.1186/s12864-022-08736-w.
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影响因子：
4.3
作者：
Mallick H;Rahnavard A;McIver LJ;Ma S;Zhang Y;Nguyen LH;Tickle TL;Weingart G;Ren B;Schwager EH;Chatterjee S;Thompson KN;Wilkinson JE;Subramanian A;Lu Y;Waldron L;Paulson JN;Franzosa EA;Bravo HC;Huttenhower C
通讯作者：
Huttenhower C
DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
影响因子：
14.9
作者：
Chakraborty, Mahul;Baldwin-Brown, James G.;Emerson, J. J.
通讯作者：
Emerson, J. J.
影响因子：
3.9
作者：
Giosa D;Felice MR;Giuffrè L;Aiese Cigliano R;Paytuví-Gallart A;Lo Passo C;Barresi C;D'Alessandro E;Huang H;Criseo G;Mora-Montes HM;de Hoog S;Romeo O
通讯作者：
Romeo O
影响因子：
10.7
作者：
Katoh K;Standley DM
通讯作者：
Standley DM