@article{f181a8efa521476f8e3cb40f0cafec8b,
title = "Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales",
abstract = "We aimed to identify genomic traits of transitions to ectomycorrhizal ecology within the Boletales by comparing the genomes of 21 symbiotrophic species with their saprotrophic brown-rot relatives. Gene duplication rate is constant along the backbone of Boletales phylogeny with large loss events in several lineages, while gene family expansion sharply increased in the late Miocene, mostly in the Boletaceae. Ectomycorrhizal Boletales have a reduced set of plant cell-wall-degrading enzymes (PCWDEs) compared with their brown-rot relatives. However, the various lineages retain distinct sets of PCWDEs, suggesting that, over their evolutionary history, symbiotic Boletales have become functionally diverse. A smaller PCWDE repertoire was found in Sclerodermatineae. The gene repertoire of several lignocellulose oxidoreductases (e.g. laccases) is similar in brown-rot and ectomycorrhizal species, suggesting that symbiotic Boletales are capable of mild lignocellulose decomposition. Transposable element (TE) proliferation contributed to the higher evolutionary rate of genes encoding effector-like small secreted proteins, proteases, and lipases. On the other hand, we showed that the loss of secreted CAZymes was not related to TE activity but to DNA decay. This study provides novel insights on our understanding of the mechanisms influencing the evolutionary diversification of symbiotic boletes.",
author = "Gang Wu and Shingo Miyauchi and Emmanuelle Morin and Alan Kuo and Elodie Drula and Torda Varga and Annegret Kohler and Bang Feng and Yang Cao and Anna Lipzen and Christopher Daum and Hope Hundley and Jasmyn Pangilinan and Jenifer Johnson and Kerrie Barry and Kurt LaButti and Vivian Ng and Steven Ahrendt and Byoungnam Min and Choi, {In Geol} and Hongjae Park and Plett, {Jonathan M.} and Jon Magnuson and Spatafora, {Joseph W.} and Nagy, {L{\'a}szl{\'o} G.} and Bernard Henrissat and Grigoriev, {Igor V.} and Yang, {Zhu Liang} and Jianping Xu and Martin, {Francis M.}",
note = "Funding Information: This work was supported by the Strategic Priority Research Program of Chinese Academy of Sciences (grant no. XDB31000000 to ZLY), the Laboratory of Excellence ARBRE (grant no. ANR‐11‐LABX‐0002‐01), the Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, the Region Lorraine, and the European Regional Development Fund (to FMM). We also acknowledge grants from the International Partnership Program of Chinese Academy of Sciences (grant no. 151853KYSB20170026 to ZLY), the National Natural Science Foundation of China (grant no. 31970015 to GW), the Yunnan Ten Thousand Talents Program Plan Young & Elite Talents project (to GW), the Youth Innovation Promotion Association of the Chinese Academy of Sciences (grant no. 2017436 to GW), the Yunling Scholars Funds of the Ten‐Thousand‐Talents Program of Yunnan Provincial Government (to ZLY), the Momentum Program of the Hungarian Academy of Sciences (grant no. LP2019/13‐2019 to LGN), the National Research, Development and Innovation Office (contract no. GINOP‐2.3.2‐15‐2016‐00052 to LGN), and the Natural Science Foundation of Yunnan Province (grant no. 2017FB025 to YC). This work was also funded by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, and supported by the Office of Science of the US Department of Energy under contract no. DE‐AC02‐05CH11231 within the framework of the Mycorrhizal Genomics Initiative (CSP no. 305), Metatranscriptomics of Forest Soil Ecosystems project (CSP no. 570), and the 1000 Fungal Genome project (CSP no. 1974). GW would like to thank the China Scholarship Council for supporting his research stay at INRAE and thank Dr Hong Luo for his advice in performing genomic DNA isolation. Funding Information: This work was supported by the Strategic Priority Research Program of Chinese Academy of Sciences (grant no. XDB31000000 to ZLY), the Laboratory of Excellence ARBRE (grant no. ANR-11-LABX-0002-01), the Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, the Region Lorraine, and the European Regional Development Fund (to FMM). We also acknowledge grants from the International Partnership Program of Chinese Academy of Sciences (grant no. 151853KYSB20170026 to ZLY), the National Natural Science Foundation of China (grant no. 31970015 to GW), the Yunnan Ten Thousand Talents Program Plan Young & Elite Talents project (to GW), the Youth Innovation Promotion Association of the Chinese Academy of Sciences (grant no. 2017436 to GW), the Yunling Scholars Funds of the Ten-Thousand-Talents Program of Yunnan Provincial Government (to ZLY), the Momentum Program of the Hungarian Academy of Sciences (grant no. LP2019/13-2019 to LGN), the National Research, Development and Innovation Office (contract no. GINOP-2.3.2-15-2016-00052 to LGN), and the Natural Science Foundation of Yunnan Province (grant no. 2017FB025 to YC). This work was also funded by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, and supported by the Office of Science of the US Department of Energy under contract no. DE-AC02-05CH11231 within the framework of the Mycorrhizal Genomics Initiative (CSP no. 305), Metatranscriptomics of Forest Soil Ecosystems project (CSP no. 570), and the 1000 Fungal Genome project (CSP no. 1974). GW would like to thank the China Scholarship Council for supporting his research stay at INRAE and thank Dr Hong Luo for his advice in performing genomic DNA isolation. Publisher Copyright: {\textcopyright} 2021 The Authors. New Phytologist {\textcopyright} 2021 New Phytologist Foundation",
year = "2021",
doi = "10.1111/nph.17858",
language = "English",
volume = "233",
pages = "1383--1400",
journal = "New Phytologist",
issn = "0028-646X",
publisher = "Wiley-Blackwell",
number = "3",
}