Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma.
Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma.
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DOI：
10.1186/s12864-016-3244-7
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发表时间：
2016-11-09
期刊：
影响因子：
4.4
通讯作者：
Libkind D
中科院分区：
文献类型：
--
作者：
Bellora N;Moliné M;David-Palma M;Coelho MA;Hittinger CT;Sampaio JP;Gonçalves P;Libkind D
银耳菌纲（Agaricomycotina）包括超过380种真菌。虽然有一些可食用的银耳，目前生物技术上唯一使用的物种是产生虾青素的酵母Pastafiarhodozyma（Cystofilobasidiales）。除了具有强大抗氧化活性和对水产养殖和制药工业具有巨大价值的类胡萝卜素色素虾青素之外，P. rhodozyma还具有许多具有基础和应用价值的特殊特性。本研究的目的是获得并分析来自北方（CBS 7918 T，模式菌株）和南半球（CRUB 1149）的两个新的代表菌株的基因组序列，并将它们与先前公布的基因组序列（菌株CBS 6938）进行比较。分析了光保护和抗氧化相关基因以及有性生殖相关基因。两个基因组都有ca。19 Mb和6000个蛋白质编码基因，与CBS 6938相似。与其他真菌基因组相比，P. rhodozyma菌株和其他Cystofilobasidiales具有最高数量的含内含子的基因和最高数量的每个基因的内含子。巴塔哥尼亚菌株显示4.4%的核苷酸序列差异，而欧洲菌株之间的差异仅为0.073%。对所有已知的与虾青素合成相关的基因进行了注释。在新测序的红酵母菌株中发现了一个迄今未知的可能负责光保护的基因簇（菌孢菌素），但在非产菌孢菌素菌株CBS 6938中不存在。广泛的电池的酶，作为清除剂的自由基氧物种进行了检测，包括过氧化氢酶和超氧化物歧化酶（SOD）。此外，还发现并注释了与有性生殖有关的基因。红酵母模式菌株的基因组序列草图现已公布，与巴塔哥尼亚种群的基因组序列比较表明，后者应该被分配到一个不同的变种。揭示了一个意想不到的遗传性状，即在P. rhodozyma和其他Cystofilobasidiales中内含子的高出现率。还提供了对真菌同宗配合的新的基因组见解。几个额外的光保护和抗氧化策略的遗传基础进行了描述，表明P. rhodozyma是最好的装备，以科普环境氧化应激，一个因素，可能有助于塑造其基因组的真菌之一。本文的在线版本（doi：10.1186/s12864-016-3244-7）包含补充材料，可供授权用户使用。
The class Tremellomycete (Agaricomycotina) encompasses more than 380 fungi. Although there are a few edible Tremella spp., the only species with current biotechnological use is the astaxanthin-producing yeast Phaffia rhodozyma (Cystofilobasidiales). Besides astaxanthin, a carotenoid pigment with potent antioxidant activity and great value for aquaculture and pharmaceutical industries, P. rhodozyma possesses multiple exceptional traits of fundamental and applied interest. The aim of this study was to obtain, and analyze two new genome sequences of representative strains from the northern (CBS 7918T, the type strain) and southern hemispheres (CRUB 1149) and compre them to a previously published genome sequence (strain CBS 6938). Photoprotection and antioxidant related genes, as well as genes involved in sexual reproduction were analyzed. Both genomes had ca. 19 Mb and 6000 protein coding genes, similar to CBS 6938. Compared to other fungal genomes P. rhodozyma strains and other Cystofilobasidiales have the highest number of intron-containing genes and highest number of introns per gene. The Patagonian strain showed 4.4 % of nucleotide sequence divergence compared to the European strains which differed from each other by only 0.073 %. All known genes related to the synthesis of astaxanthin were annotated. A hitherto unknown gene cluster potentially responsible for photoprotection (mycosporines) was found in the newly sequenced P. rhodozyma strains but was absent in the non-mycosporinogenic strain CBS 6938. A broad battery of enzymes that act as scavengers of free radical oxygen species were detected, including catalases and superoxide dismutases (SODs). Additionally, genes involved in sexual reproduction were found and annotated. A draft genome sequence of the type strain of P. rhodozyma is now available, and comparison with that of the Patagonian population suggests the latter deserves to be assigned to a distinct variety. An unexpected genetic trait regarding high occurrence of introns in P. rhodozyma and other Cystofilobasidiales was revealed. New genomic insights into fungal homothallism were also provided. The genetic basis of several additional photoprotective and antioxidant strategies were described, indicating that P. rhodozyma is one of the fungi most well-equipped to cope with environmental oxidative stress, a factor that has probably contributed to shaping its genome. The online version of this article (doi:10.1186/s12864-016-3244-7) contains supplementary material, which is available to authorized users.
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影响因子：
2.6
作者：
GOLUBEV, WI
通讯作者：
GOLUBEV, WI
影响因子：
10.5
作者：
ERREDE, B;AMMERER, G
通讯作者：
AMMERER, G
影响因子：
4.5
作者：
David-Palma, Marcia;Sampaio, Jose Paulo;Goncalves, Paula
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影响因子：
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作者：
Fréalle, E;Noël, C;Delhaes, L
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全球对100个完整基因组的调查推断出富含内含子的真核祖先的详细历史。
影响因子：
4.3
作者：
Csuros M;Rogozin IB;Koonin EV
通讯作者：
Koonin EV