The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion.
The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion.
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DOI：
10.1371/journal.pgen.1000618
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发表时间：
2009-08
期刊：
影响因子：
4.5
通讯作者：
Vanetten HD
中科院分区：
文献类型：
--
作者：
Coleman JJ;Rounsley SD;Rodriguez-Carres M;Kuo A;Wasmann CC;Grimwood J;Schmutz J;Taga M;White GJ;Zhou S;Schwartz DC;Freitag M;Ma LJ;Danchin EG;Henrissat B;Coutinho PM;Nelson DR;Straney D;Napoli CA;Barker BM;Gribskov M;Rep M;Kroken S;Molnár I;Rensing C;Kennell JC;Zamora J;Farman ML;Selker EU;Salamov A;Shapiro H;Pangilinan J;Lindquist E;Lamers C;Grigoriev IV;Geiser DM;Covert SF;Temporini E;Vanetten HD
子囊真菌血镰刀菌（镰刀菌）是一种名为“镰刀菌群”的50种真菌中的一员。该复合体的成员具有多种生物学特性，包括在100个属的植物上引起疾病和在人类中引起机会性感染的能力。目前的研究分析了该复合体中研究最广泛的成员，即血球菌交配种群VI （MPVI）。控制这个物种的个别分离株在特定栖息地定居的能力的几个基因位于多余的染色体上。光学图谱显示，测序的分离物有17条染色体，长度从530 kb到6.52 Mb不等，基因组的物理大小为54.43 Mb，预测的基因数量为15,707，是子囊菌中报道的最多的。两类基因对基因扩增有贡献：在其他真菌中没有发现的特定基因，包括与其序列最接近的近亲镰刀菌；以及在其他真菌中通常以单拷贝形式出现的基因，但在嗜血奈索菌MPVI中以多拷贝形式存在。其中一些额外的基因似乎是由基因复制事件造成的，而另一些可能是通过水平基因转移获得的。在一些分离株的脉冲场凝胶电泳实验中，通过证明这些分离株缺乏在这些染色体末端发现的染色体特异性序列，证实了14,15和17三条染色体的多余性质。这些多余染色体含有更多的重复序列，富含独特和重复的基因，与其他染色体相比，G+C含量较低。虽然这些额外基因和额外染色体的起源尚不清楚，但基因的扩展及其庞大的基因组大小与该物种的多样化栖息地范围相一致。此外，多余染色体上独特基因的存在可能解释了个体分离物具有不同环境生态位的原因。血红Nectria haematococca MPVI是一种腐生植物，存在于不同的栖息地，也是一种植物和动物病原体。它也是第一个被发现含有额外染色体的真菌，这些染色体具有独特的栖息地定义基因。目前的研究表明，它具有最大的真菌基因组之一（15,707个基因），这可能与它的栖息地多样性有关，并描述了两条额外的染色体。研究人员发现了两类有助于基因扩增的基因：1)在其他真菌中没有发现的特定基因；2)在红链球菌中以多个拷贝形式存在，但在其他真菌中通常以单个拷贝形式存在的基因。其中一些基因的特性表明它们是通过水平基因转移获得的。我们发现这三条多余染色体不同于正常染色体；它们含有更多的重复序列，特别富含独特和重复的基因，并且具有较低的G+C含量。此外，这些染色体上的基因的生化功能表明它们可能参与了生态位适应。这些染色体的可有可无的性质和拥有的生境决定基因使它们在生物学上等同于细菌的质粒。我们认为它们有助于微生物多样性，但在真菌进化模型中被忽视了。
The ascomycetous fungus Nectria haematococca, (asexual name Fusarium solani), is a member of a group of >50 species known as the “Fusarium solani species complex”. Members of this complex have diverse biological properties including the ability to cause disease on >100 genera of plants and opportunistic infections in humans. The current research analyzed the most extensively studied member of this complex, N. haematococca mating population VI (MPVI). Several genes controlling the ability of individual isolates of this species to colonize specific habitats are located on supernumerary chromosomes. Optical mapping revealed that the sequenced isolate has 17 chromosomes ranging from 530 kb to 6.52 Mb and that the physical size of the genome, 54.43 Mb, and the number of predicted genes, 15,707, are among the largest reported for ascomycetes. Two classes of genes have contributed to gene expansion: specific genes that are not found in other fungi including its closest sequenced relative, Fusarium graminearum; and genes that commonly occur as single copies in other fungi but are present as multiple copies in N. haematococca MPVI. Some of these additional genes appear to have resulted from gene duplication events, while others may have been acquired through horizontal gene transfer. The supernumerary nature of three chromosomes, 14, 15, and 17, was confirmed by their absence in pulsed field gel electrophoresis experiments of some isolates and by demonstrating that these isolates lacked chromosome-specific sequences found on the ends of these chromosomes. These supernumerary chromosomes contain more repeat sequences, are enriched in unique and duplicated genes, and have a lower G+C content in comparison to the other chromosomes. Although the origin(s) of the extra genes and the supernumerary chromosomes is not known, the gene expansion and its large genome size are consistent with this species' diverse range of habitats. Furthermore, the presence of unique genes on supernumerary chromosomes might account for individual isolates having different environmental niches. Nectria haematococca MPVI occurs as a saprophyte in diverse habitats and as a plant and animal pathogen. It also was the first fungus shown to contain supernumerary chromosomes with unique habitat-defining genes. The current study reveals that it has one of the largest fungal genomes (15,707 genes), which may be related to its habitat diversity, and describes two additional supernumerary chromosomes. Two classes of genes were identified that have contributed to gene expansion: 1) specific genes that are not found in other fungi, and 2) genes that are present as multiple copies in N. haematococca but commonly occur as a single copy in other fungi. Some of these genes have properties suggesting their acquisition by horizontal gene transfer. We show that the three supernumerary chromosomes are different from the normal chromosomes; they contain more repeat sequences, are particularly enriched in unique and duplicated genes, and have a lower G+C content. Additionally, the biochemical functions of genes on these chromosomes suggest they may be involved in niche adaptation. The dispensable nature and possession of habitat-determining genes by these chromosomes make them the biological equivalent of bacterial plasmids. We believe they contribute to microbial diversity and have been overlooked in models of fungal evolution.
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