测序宝
图片来源：www.phys.org
2016年5月8日 讯 /生物谷BIOON/ –近日，发表在国际杂志Molecular Biology and Evolution上的一项研究论文中，来自美国能源部联合基因组研究所等机构的研究人员通过对10株白腐真菌和褐腐真菌进行全基因组测序阐明了真菌中和木质纤维素分解相关的酶类起源的时间轴。
真菌是植物体的天然降解帮手，其包含有特殊的酶类可以帮助科学家从事很多应用性研究。对白腐真菌和褐腐真菌进行全基因组测序研究其酶类家族填补了研究者们长期以来在真菌进化领域研究的空白，同时也提供了更加精确的时间轴来揭示可以在不同时间段对植物体进行降解的关键真菌。
生物能源的研究人员一直以来都非常感兴趣从事朽木菌的研究，因为朽木菌所产生的酶类可以降解多种植物原材料，比如纤维素、半纤维素和木质素等，褐腐真菌被认为仅可以降解纤维素和半纤维素，而白腐真菌则可以降解所有的植物体组分，比如纤维素等。对真菌基因组的大范围测序或许就可以帮助研究者们制定更为深入的真菌降解朽木的策略；文章中研究人员构建了一种比较基因组学的分析技术来帮助进行10株真菌的测序，组装以及信息注解，这样一来就可以更好地追溯真菌木质素降解关键酶类的起源了。
早在2012年研究人员就在Science杂志上刊文表示，3亿年前白腐真菌的进化正好与成煤石炭纪的结束同时进行，而这就影响到了地球的碳循环；该研究中研究者并没有对早期分化的真菌进行全基因组的测序研究。而本文研究中研究人员进行了大量的测序研究揭示了真菌关键降解酶类的起源问题，为后期生物能源学家们有效利用真菌的降解特性来从事更多深入的研究，同时鉴别新型的降解酶类提供了新的线索。（生物谷Bioon.com）
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doi:10.1126/science.1221748
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The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes
Dimitrios Floudas1, Manfred Binder1, Robert Riley2, Kerrie Barry2, Robert A. Blanchette3, Bernard Henrissat4, Angel T. Martínez5, Robert Otillar2, Joseph W. Spatafora6, Jagjit S. Yadav7, Andrea Aerts2, Isabelle Benoit8,9, Alex Boyd6, Alexis Carlson1, Alex Copeland2, Pedro M. Coutinho4, Ronald P. de Vries8,9, Patricia Ferreira10, Keisha Findley11, Brian Foster2, Jill Gaskell12, Dylan Glotzer1, Paweł Górecki13, Joseph Heitman11, Cedar Hesse6, Chiaki Hori14, Kiyohiko Igarashi14, Joel A. Jurgens3, Nathan Kallen1, Phil Kersten12, Annegret Kohler15, Ursula Kües16, T. K. Arun Kumar17, Alan Kuo2, Kurt LaButti2, Luis F. Larrondo18, Erika Lindquist2, Albee Ling1, Vincent Lombard4, Susan Lucas2, Taina Lundell19, Rachael Martin1, David J. McLaughlin17, Ingo Morgenstern20, Emanuelle Morin15, Claude Murat15, Laszlo G. Nagy1, Matt Nolan2, Robin A. Ohm2, Aleksandrina Patyshakuliyeva9, Antonis Rokas21, Francisco J. Ruiz-Dueñas5, Grzegorz Sabat22, Asaf Salamov2, Masahiro Samejima14, Jeremy Schmutz23, Jason C. Slot21, Franz St. John12, Jan Stenlid24, Hui Sun2, Sheng Sun11, Khajamohiddin Syed7, Adrian Tsang20, Ad Wiebenga9, Darcy Young1, Antonio Pisabarro25, Daniel C. Eastwood26, Francis Martin15, Dan Cullen12, Igor V. Grigoriev2,*, David S. Hibbett1,*
Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non–lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.
doi:10.1093/molbev/msv337
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Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities
László G. Nagy*,1, Robert Riley2, Andrew Tritt2, Catherine Adam2, Chris Daum2, Dimitrios Floudas3, Hui Sun2, Jagjit S. Yadav4, Jasmyn Pangilinan2, Karl-Henrik Larsson5, Kenji Matsuura6, Kerrie Barry2, Kurt Labutti2, Rita Kuo2, Robin A. Ohm2,7, Sukanta S. Bhattacharya4, Takashi Shirouzu8, Yuko Yoshinaga2, Francis M. Martin9, Igor V. Grigoriev2 and David S. Hibbett*,10
Evolution of lignocellulose decomposition was one of the most ecologically important innovations in fungi. White-rot fungi in the Agaricomycetes (mushrooms and relatives) are the most effective microorganisms in degrading both cellulose and lignin components of woody plant cell walls (PCW). However, the precise evolutionary origins of lignocellulose decomposition are poorly understood, largely because certain early-diverging clades of Agaricomycetes and its sister group, the Dacrymycetes, have yet to be sampled, or have been undersampled, in comparative genomic studies. Here, we present new genome sequences of ten saprotrophic fungi, including members of the Dacrymycetes and early-diverging clades of Agaricomycetes (Cantharellales, Sebacinales, Auriculariales, and Trechisporales), which we use to refine the origins and evolutionary history of the enzymatic toolkit of lignocellulose decomposition. We reconstructed the origin of ligninolytic enzymes, focusing on class II peroxidases (AA2), as well as enzymes that attack crystalline cellulose. Despite previous reports of white rot appearing as early as the Dacrymycetes, our results suggest that white-rot fungi evolved later in the Agaricomycetes, with the first class II peroxidases reconstructed in the ancestor of the Auriculariales and residual Agaricomycetes. The exemplars of the most ancient clades of Agaricomycetes that we sampled all lack class II peroxidases, and are thus concluded to use a combination of plesiomorphic and derived PCW degrading enzymes that predate the evolution of white rot.
