Typification and genome analyses of early described fungal species: a case study of Lysurus mokusin, the first new fungal species described in China

LIANG Junmin, WANG Ke, DU Zhuo, ZHAO Mingjun, CAI Lei, DAI Yucheng

Mycosystema ›› 2025, Vol. 44 ›› Issue (4) : 240296.

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Mycosystema ›› 2025, Vol. 44 ›› Issue (4) : 240296. DOI: 10.13346/j.mycosystema.240296
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Typification and genome analyses of early described fungal species: a case study of Lysurus mokusin, the first new fungal species described in China

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epitype / DNA barcoding / HiFi sequencing / two-speed genome / biosynthetic gene cluster

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LIANG Junmin, WANG Ke, DU Zhuo, ZHAO Mingjun, CAI Lei, DAI Yucheng. Typification and genome analyses of early described fungal species: a case study of Lysurus mokusin, the first new fungal species described in China[J]. Mycosystema, 2025, 44(4): 240296 https://doi.org/10.13346/j.mycosystema.240296
海南是中国灵芝属真菌资源非常丰富的地区(李碧英等 2013；吴芳等2020；马海霞等2022；崔宝凯等 2023)。在海南当地的贸易市场，常常有野生的灵芝出售(钟金霞等 1998)，人们将这些灵芝子实体用来泡酒或煮汤，以达到养生和保健的目的(吴兴亮 2019；曾念开和蒋帅 2020)。其中有一类灵芝当地人称为“竹灵芝”，其形态特点是菌盖小，菌柄长。竹灵芝因在治疗各类亚健康疾病上具有良好的效果，所以在海南民间非常受欢迎。最近的研究表明，竹灵芝的基原物种之一是亚弯柄灵芝Ganoderma subflexipes B.K. Cui, J.H. Xing & Y.F. Sun (Sun et al. 2022)。
长期以来，市场对亚弯柄灵芝的需求仅依靠采摘的野生子实体。由于野生资源的逐年减少，遵循着“物以稀为贵”的市场规律，该灵芝的价格逐年攀升。随着价格的提高，野生子实体则遭受更为“疯狂”的采集；尤为严重的是，在实际采摘过程中，子实体尚未成熟就被采摘下来，由此导致亚弯柄灵芝无孢子可传播，不能进行有性繁殖，年复一年，使该灵芝面临濒危境地(曾念开和蒋帅 2020)。
目前灵芝属真菌已经成功实现商业化栽培，在我国福建、浙江、山东、吉林等地更是分布着大规模的灵芝栽培产区(王恬恬等 2024)，但成功实现规模化栽培的灵芝属真菌仅几个种，如灵芝G. lingzhi Sheng H. Wu, Y. Cao & Y.C. Dai、紫芝G. sinense J.D. Zhao, L.W. Hsu & X.Q. Zhang、白肉灵芝G. leucocontextum T.H. Li, W.Q. Deng, Sheng H. Wu, Dong M. Wang & H.P. Hu。对其他灵芝属真菌的人工栽培有待进一步深入研究。因此，开展亚弯柄灵芝的生物学特性研究和人工栽培，不仅有益于该灵芝野生资源的保护，而且能满足市场的需求。为此，本研究在野外考察、野生菌种分离的基础上，通过单因素试验和正交试验，探讨了不同培养条件和不同营养条件对亚弯柄灵芝菌丝生长的影响，同时对其子实体进行驯化栽培。

1 材料与方法

1.1 供试材料

1.1.1 野外考察、标本采集和鉴定

野外考察和标本采集根据Xue et al. (2023)的方法，研究的标本保存于海南医学院真菌标本馆(FHMU)和中国科学院昆明植物研究所隐花植物标本馆(KUN-HKAS)。采用形态解剖与基于ITS分子序列相结合的方法，对所采标本进行鉴定(Sun et al. 2022)。

1.1.2 供试菌株

编号为FHMU2299的供试菌株分离自海南热带雨林国家公园。凭证标本的ITS序列已上传至GenBank (PP415779)。

1.1.3 供试培养基

PDA培养基；碳源基础培养基(酵母浸粉0.2%，KH2PO4 0.1%，MgSO4 0.05%，琼脂粉2%)；氮源基础培养基(葡萄糖2%，KH2PO4 0.1%，MgSO4 0.05%，琼脂粉2%)；无机盐基础培养基(葡萄糖2%，酵母浸粉0.2%，琼脂粉2%)；生长因子基础培养基(葡萄糖2%，酵母浸粉0.2%，KH2PO4 0.1%，MgSO4 0.05%，琼脂粉2%)；马铃薯葡萄糖液体培养基(马铃薯浸粉0.5%、葡萄糖2%、氯霉素0.01%)。

1.2 生物学特性研究

1.2.1 菌株活化

将保藏于4 ℃冰箱的亚弯柄灵芝菌株移至PDA培养基，于32 ℃下暗培养。待菌丝覆盖整个培养基表面时，便可用于后续的单因素和多因素试验(张晓宇等 2019)。

1.2.2 不同培养条件对菌丝生长的影响

温度对菌丝生长的影响：采用PDA培养基，分别置于20、22、24、26、28、30、32、34、36及38 ℃共10个温度下暗培养，pH自然，每个温度处理重复6次。使用直径为8.5 mm的打孔器，将一活化菌种块转移至培养皿上，分别于设置的温度下暗培养。当其中一个温度处理的菌丝覆盖整个培养基表面时，停止培养，用十字交叉法测量菌落直径，同时观察菌丝生长势(张晓宇等 2019)。
初始pH对菌丝生长的影响：采用PDA培养基，分别用0.1 mol/L的HCl和NaOH溶液调pH为4、5、6、7、8、9制成平板，每个pH处理重复6次。使用直径为8.5 mm的打孔器，将一活化菌种块转移至培养皿上，于32 ℃下暗培养。当其中一个pH处理的菌丝覆盖整个培养基表面时，停止培养，用十字交叉法测量菌落直径，同时观察菌丝生长势(蒋帅等 2021)。
光照时间对菌丝生长的影响：采用PDA培养基，设置连续光照(1 500 lx)、12 h光暗交替 (1 500 lx)和连续黑暗3种条件，pH自然，每个处理重复6次。使用直径为8.5 mm的打孔器，将一活化菌种块转移至培养皿上，于32 ℃下培养。当其中一个光照处理的菌丝覆盖整个培养基表面时，停止培养，使用十字交叉法测量菌落直径，同时观察菌丝生长势(康晟菀等 2023)。
光质对菌丝生长的影响：采用PDA培养基，设置红光(625-635 nm)、蓝光(455-460 nm)、绿光(500-560 nm)、白光(400-830 nm)、黄光(570-590 nm)、紫光(390-400 nm) 6种不同光质条件，每个处理重复6次。使用直径为8.5 mm的打孔器，将一活化菌种块转移至培养皿上，于32 ℃下培养。当其中一个光质处理的菌丝覆盖整个培养基表面时，停止培养，使用十字交叉法测量菌落的直径，同时观察菌丝生长势(王立华等 2011)。

1.2.3 不同营养源对菌丝生长的影响

碳源对菌丝生长的影响：以碳源空白培养基为对照组，分别将葡萄糖、果糖、木糖、蔗糖、甘露醇、红糖、乳糖、糊精、蜂蜜、麦芽糖、核糖，以及可溶性淀粉加入碳源基础培养基，每个处理重复6次。使用直径为8.5 mm的打孔器，将一活化菌种块转移至培养皿上，于1.2.2优化后的条件下培养。当其中一个碳源处理的菌丝覆盖整个培养基表面时停止培养，使用十字交叉法测量菌落的直径，同时观察菌丝生长势(张晓宇等 2019)。
氮源对菌丝生长的影响：以氮源空白培养基为对照组，分别将牛肉蛋白胨、胰蛋白胨、NH4H2PO4、(NH4)2HPO4、(NH4)2CO3、柠檬酸铵、尿素、酵母浸膏、麦芽浸粉、6-苄氨基嘌呤、酒石酸铵、酵母浸粉、牛肉浸膏、蛋白胨、KNO3、(NH4)2SO4以及NH4Cl加入氮源基础培养基，每个处理重复6次。使用直径为8.5 mm的打孔器，将一活化菌种块转移至培养皿上，于1.2.2优化后的条件下培养。当其中一个氮源处理的菌丝覆盖整个培养基表面时停止培养，使用十字交叉法测量菌落的直径，同时观察菌丝生长势(张晓宇等 2019)。
无机盐对菌丝生长的影响：以无机盐空白培养基为对照组，分别将MgSO4、ZnSO4、CaSO4、MnSO4、FeSO4、KCl、KH2PO4以及K2HPO4加入无机盐基础培养基，每个处理重复6次。使用直径为8.5 mm的打孔器，将一活化菌种块转移至培养皿上，于1.2.2优化后的条件下培养。当其中一个无机盐处理的菌丝覆盖整个培养基表面时停止培养，使用十字交叉法测量菌落的直径，同时观察菌丝生长势(张晓宇等 2019)。
生长因子对菌丝生长的影响：以生长因子空白培养基为对照组，分别将VC、椰子汁、平菇汁、VE、VB1、VB12、VB2、复合VB、VB3、烟酰胺、VB6、叶酸以及L-谷氨酸加入生长因子基础培养基，每个处理重复6次。使用直径为8.5 mm的打孔器，将一活化菌种块转移至培养皿上，于1.2.2优化后的条件下培养。当其中一个生长因子处理的菌丝覆盖整个培养基表面时，停止培养，使用十字交叉法测量菌落的直径，同时观察菌丝生长势(张晓宇等 2019)。

1.2.4 培养基优化实验

培养基优化试验设计基于正交表(表1)，其中包括了针对碳源、氮源、无机盐和生长因子这4个因素的3个水平的选择。根据该正交表，制定相应的氮源、碳源、无机盐和生长因子，每个处理重复6次(胡日瓦和图力古尔 2019)。分别在这9组的组合培养基上接种，于1.2.2优化后的条件下培养。当其中一组的菌丝覆盖整个培养基表面时，停止培养，使用十字交叉法测量菌落的直径，同时观察菌丝生长势(张晓宇等 2019)。
Table 1 L9 (34) Design form of orthogonal experiment

表1 L9 (34)正交试验设计因素水平表

水平
Levels		 因素
Factors
A 碳源
Carbon source		 B 氮源
Nitrogen source		 C 无机盐
Inorganic salt		 D 生长因子
Growth factor
1 葡萄糖 Glucose 麦芽浸粉 Malt extract powder CaSO4 VB12
2 蔗糖 Sucrose 酵母浸粉 Yeast extract powder K2HPO4 烟酰胺 Nicotinamide
3 麦芽糖 Maltose 牛肉蛋白胨 Beef peptone KH2PO4 L-谷氨酸 L-glutamate

1.3 驯化栽培

用直径8.5 mm的打孔器从培养好的亚弯柄灵芝菌丝平板中取5块菌种块接种于马铃薯葡萄糖液体培养基中。该液体培养基在250 mL的三角瓶中装量100 mL，在32 ℃、130 r/min下黑暗培养6 d；将培养好的液体种子100 mL接种到以栓皮栎Quercus variabilis Blume的茎为菌材的菌棒中，于32 °C、黑暗条件下发菌；至菌丝长满培养袋后，采用覆土栽培的方法，于室温下进行子实体的诱导。

1.4 数据处理

采用SPSS 17.0和GraphPad prism 8.0.2软件进行数据处理、差异显著性分析和方差分析，菌丝生长速度用平均值±标准差(x¯±SD)来表示。

2 结果与分析

2.1 亚弯柄灵芝的时空分布信息

亚弯柄灵芝最早描述于我国广东省，同时江西省也有分布报道(Sun et al. 2022)。本研究发现该灵芝在海南省和福建省也有分布(图1，表2)。从其分布地点可以看出，亚弯柄灵芝是一种分布于我国亚热带、热带的种类，且其子实体在我国的6月份到8月份均能发生(表2)。
Fig. 1 Wild basidiomata of Ganoderma subflexipes

(A from FHMU5725; B from FHMU2320).

图1 亚弯柄灵芝的野生子实体

(A来自FHMU5725；B来自FHMU2320)

Full size|PPT slide

Table 2 Temporal and spatial distributions of basidiomata of Ganoderma subflexipes

表2 亚弯柄灵芝子实体的时空分布信息

标本号
Voucher		 GenBank序列号(ITS)
GenBank accesion
No. (ITS)		 采集点
Collecting locality		 采集时间
Collecting
time		 参考文献
Reference
N.K. Zeng242
(FHMU2299)		 PP415779 海南热带雨林国家公园
Hainan Tropical Rainforest National Park,
Hainan Province, China		 2009.6.4 本研究
This study
KUN-HKAS79603 PP465550 广东省封开县黑石顶自然保护区
Heishiding Nature Reserve, Fengkai
County, Guangdong Province, China		 2013.7.2 本研究
This study
KUN-HKAS81926-1 PP465549 福建省三明市格氏栲国家森林公园
Geshikao National Forest Park, Sanming
City, Fujian Province, China		 2013.7.8 本研究
This study
KUN-HKAS81926-3 PP465553 福建省三明市格氏栲国家森林公园
Geshikao National Forest Park, Sanming
City, Fujian Province, China		 2013.7.8 本研究
This study
N.K. Zeng1455
(FHMU2320)		 PP465552 福建省漳平市新桥镇城口村
Chengkou Village, Xinqiao Town
Zhangping City, Fujian Province, China		 2013.8.20 本研究
This study
N.K. Zeng4114
(FHMU5725)		 PP465551 广东省韶关市丹霞山国家级自然保护区
Danxia National Nature Reserve,
Shaoguan City, Guangdong Province, China		 2019.6.5 本研究
This study
Cui17247
(BJFC034105)		 MZ354921 广东省韶关市丹霞山国家级自然保护区
Danxia National Nature Reserve,
Shaoguan City, Guangdong Province, China		 2019.6.4 Sun et al.
2022
Cui17257
(BJFC034115)		 MZ354922 广东省韶关市丹霞山国家级自然保护区
Danxia National Nature Reserve,
Shaoguan City, Guangdong Province, China		 2019.6.4 Sun et al.
2022
Cui17258
(BJFC034116)		 — 广东省韶关市丹霞山国家级自然保护区
Danxia National Nature Reserve,
Shaoguan City, Guangdong Province, China		 2019.6.4 Sun et al.
2022
Dai23665
(BJFC038237)		 — 江西省上饶市大茅山公园
Damaoshan Park, Shangrao City,
Jiangxi Province, China		 2021.8.30 Sun et al.
2022

2.2 不同培养条件对菌丝生长的影响

2.2.1 温度对菌丝生长的影响

亚弯柄灵芝菌丝在温度介于20-38 ℃之间均可生长，然而，不同温度对其生长产生的影响呈现显著差异(表3)。从生长速度角度观察，随着温度的升高，菌丝的生长速度逐渐增加，达到最高值的温度为32 ℃；随后，随着温度的进一步上升，菌丝的生长速度逐渐减缓。从生长势的角度来看，30 ℃和32 ℃为最适宜的温度。显著性分析结果显示，30 ℃和32 ℃对菌丝生长速度的影响没有显著差异，然而，它们与其他温度处理组之间存在显著的差异。综合考虑，亚弯柄灵芝菌丝的适宜生长温度范围为30-32 ℃。
Table 3 Impact of varied temperatures on the mycelial growth of Ganoderma subflexipes (x¯±SD, n=6)

表3 不同温度条件对亚弯柄灵芝菌丝生长的影响

温度
Temperature (℃)		 生长速度
Mycelial growth (mm/d)		 差异显著性
Significance levels		 菌丝生长势
Mycelial growth vigor
0.05 0.01
20 6.95±0.84 f F +
22 11.50±0.22 d D +
24 10.21±0.42 e E +
26 13.25±1.00 c E +
28 19.00±1.85 b B ++
30 20.50±1.12 a A +++
32 21.31±0.13 a A +++
34 18.20±1.24 b B ++
36 14.00±0.79 c C +
38 5.12±0.26 g G +
+++表示菌丝密、长势壮；++表示菌丝生长较密；+表示菌丝稀疏、较弱. 同一列中不同大、小写字母表示P<0.01、P<0.05水平存在显著性差异. 下同
+++ Indicate strong mycelial growth; ++ indicate moderate mycelial growth; + indicate feeble mycelial growth. Different lowercase (P<0.05) or capital (P<0.01) letters indicate significant differences. The same below.

2.2.2 培养基初始pH对菌丝生长的影响

亚弯柄灵芝菌丝在pH 4-9的范围内都能生长，但是不同的pH值对菌丝生长的影响不同(表4)。从生长速度来看，从大到小依次是pH 6、8、5、7、9、4；从菌丝生长势来看，当pH 4和pH 9时，菌落菌丝稀疏，生长势不佳，而pH 5、6、7、8时，菌落菌丝浓密、生长势旺盛。显著性测试结果表明，各处理的pH，其菌丝生长速度没有显著差异。可见亚弯柄灵芝的菌丝在酸碱环境下都能生长，但综合菌丝生长速度和生长势来看，pH 5-8时，更有益于该菌的生长。
Table 4 Effects of different pH values on mycelial growth of Ganoderma subflexipes (x¯±SD, n=6)

表4 不同pH条件对亚弯柄灵芝菌丝生长的影响

pH 生长速度
Mycelial growth (mm/d)		 差异显著性
Significance levels		 菌丝生长势
Mycelial growth vigor
0.05 0.01
4 13.87±1.69 b A ++
5 15.75±0.89 ab A +++
6 16.50±1.79 a A +++
7 15.54±1.21 ab A +++
8 15.79±1.63 ab A +++
9 14.71±2.33 ab A ++

2.2.3 光照对菌丝生长的影响

亚弯柄灵芝菌丝在3种光照处理中均能生长，但不同的光照处理对菌丝生长的影响差异不同(表5)。从生长速度来看，在连续24 h光照下培养和在12 h/12 h光暗交替条件下培养，菌丝生长速度较慢；在连续黑暗条件下，菌丝生长速度快。从菌丝生长势来看，连续光照条件和12 h/12 h光暗交替条件下菌落生长势不佳、菌丝稀疏；在连续黑暗条件下，菌落生长势好，菌落菌丝浓密。显著性测试结果也表明，连续黑暗条件下菌丝的生长速度显著高于连续光照条件和12 h/12 h光暗交替条件下的菌丝生长速度。由此可见，光照抑制了菌丝的生长，亚弯柄灵芝的菌丝适宜在黑暗条件下培养。
Table 5 Effects of different light treatments on mycelial growth of Ganoderma subflexipes (x¯±SD, n=6)

表5 不同光照时间对亚弯柄灵芝菌丝生长的影响

光照时间
Illumination time		 生长速度
Mycelial growth (mm/d)		 差异显著性
Significance levels		 菌丝生长势
Mycelial growth vigor
0.05 0.01
24 h光照
24 h illumination		 14.87±1.31 b B ++
12 h/12 h光暗交替
Alternation of dark and illumination		 14.70±0.65 c C ++
24 h 黑暗
24 h dark		 17.44±0.52 a A +++

2.2.4 光质对菌丝生长的影响

亚弯柄灵芝菌丝在6种光质处理中均能生长(表6)。从生长速度来看，红光、黄光以及绿光均较黑暗条件下快，并具有显著性差异；从生长势来看，绿光和黑暗条件下生长势相当，此时菌丝浓密，生长势佳，而红光和黄光下的生长势则较黑暗条件下差。蓝光、白光和紫光下，其生长速度较黑暗条件下慢，且具有显著性差异，此外生长势也较黑暗条件下的差。由此可见，绿光为亚弯柄灵芝菌丝适宜培养的光质条件。
Table 6 Effects of different light quality on mycelial growth of Ganoderma subflexipes (x¯±SD, n=6)

表6 不同光质对亚弯柄灵芝菌丝生长的影响

光质
Light quality		 菌丝生长速度
Mycelial growth (mm/d)		 差异显著性
Significance levels		 菌丝生长势
Mycelial growth vigor
0.05 0.01
黑暗Dark 17.44±0.52 c BC +++
红Red light 18.60±0.38 b B ++
蓝Blue light 14.13±0.65 e E ++
绿Green light 20.33±0.26 a A +++
白White light 15.33±0.66 d D ++
黄Yellow light 18.50±0.40 b B ++
紫Purple light 11.58±1.03 f F +

2.3 不同营养源对菌丝生长的影响

2.3.1 碳源对菌丝生长的影响

亚弯柄灵芝菌丝在供试的12种碳源中均能生长(表7)。与碳源空白培养基相比，以核糖、甘露醇、乳糖为碳源时，菌丝生长速度慢，菌落稀疏，对菌丝生长具有抑制作用；葡萄糖、果糖、木糖、蔗糖、麦芽糖、糊精、可溶性淀粉、红糖、蜂蜜对菌丝生长则有促进作用。对菌丝生长有促进作用的9种碳源中，生长速度从快到慢依次是蔗糖、麦芽糖、葡萄糖、可溶性淀粉、红糖、果糖、蜂蜜、木糖、糊精；显著性测试结果表明，以蔗糖、麦芽糖、葡萄糖、可溶性淀粉作为碳源时，其菌丝生长速度与其他碳源间有差异或差异显著。在菌丝生长势方面观察，当葡萄糖、蔗糖、麦芽糖为碳源时，菌丝生长势佳，菌落菌丝浓密，其他碳源下的菌丝生长势则较差。综合来看，蔗糖、麦芽糖、葡萄糖是亚弯柄灵芝菌丝生长的适宜碳源。
Table 7 Impact of varied carbon sources on the mycelial growth of Ganoderma subflexipes (x¯±SD, n=6)

表7 碳源对亚弯柄灵芝菌丝生长的影响

碳源
Carbon source		 生长速度
Mycelial growth (mm/d)		 差异显著性
Significance levels		 菌丝生长势
Mycelial growth vigor
0.05 0.01
空白CK 15.50±0.45 e E ++
葡萄糖Glucose 21.25±0.27 a A +++
果糖Fructose 19.75±1.02 b BC ++
木糖Xylose 17.00±1.21 d D ++
蔗糖Sucrose 21.45±0.11 a A +++
麦芽糖Maltose 21.38±0.31 a A +++
乳糖Lactose 10.80±0.33 f F +
糊精Dextrin 16.35±0.89 d DE ++
甘露醇Mannitol 14.95±0.57 e E ++
可溶性淀粉Soluble starch 20.70±0.82 a AB ++
核糖Ribose 15.05±0.37 e E ++
红糖Brown sugar 19.92±0.34 b B ++
蜂蜜Honey 18.85±0.55 c C ++

2.3.2 氮源对菌丝生长的影响

亚弯柄灵芝菌丝在碳酸铵和尿素中不生长，在6-苄氨基嘌呤中微弱生长；与氮源空白组相比，(NH4)2HPO4、(NH₄)₂SO4、NH4Cl和KNO3为氮源时，生长速度慢，菌丝长势不佳，菌丝菌落稀疏，对菌丝的生长有抑制作用；牛肉蛋白胨、胰蛋白胨、NH₄H₂PO₄、柠檬酸铵、酵母浸膏、麦芽浸粉、酒石酸铵、酵母浸粉、牛肉浸膏、蛋白胨则能促进菌丝生长(表8)。对菌丝生长有促进作用的10种氮源中，生长速度从快到慢依次是麦芽浸粉、酵母浸粉、牛肉蛋白胨、酵母浸膏、蛋白胨、酒石酸铵、牛肉浸膏、柠檬酸铵、NH₄H₂PO₄、胰蛋白胨；显著性测试结果表明，以麦芽浸粉、酵母浸粉及牛肉蛋白胨作为氮源时，其菌丝生长速度与其他氮源间差异显著。从菌丝生长势来看，以麦芽浸粉、酵母浸粉及牛肉蛋白胨作为氮源时，菌丝长势佳，菌落菌丝也最浓密。综合来看，麦芽浸粉、酵母浸粉及牛肉蛋白胨是亚弯柄灵芝菌丝生长的适宜氮源。
Table 8 Impact of varied nitrogen sources on the mycelial growth of Ganoderma subflexipes (x¯±SD, n=6)

表8 氮源对亚弯柄灵芝菌丝生长的影响

氮源
Nitrogen source		 生长速度
Mycelial growth (mm/d)		 差异显著性
Significance levels		 菌丝生长势
Mycelial growth vigor
0.05 0.01
空白CK 9.90±0.30 f F +
牛肉蛋白胨Beef peptone 20.17±0.63 a A +++
胰蛋白胨Tryptone 11.45±0.33 e DE ++
NH4H2PO4 12.75±0.18 de DE ++
(NH4)2HPO4 8.10±0.38 f F +
(NH4)2CO3 - - - -
柠檬酸铵 Ammonium citrate 13.00±0.71 d D +
尿素Urea - - - -
酵母浸膏 Yeast extract ointment 17.10±0.29 b B ++
麦芽浸粉 Malt extract powder 20.70±0.57 a A +++
6-苄氨基嘌呤6-BA 2.87±0.32 g G +
酒石酸铵 Ammonium tartrate 15.30±0.42 c BC ++
酵母浸粉 Yeast extract powder 20.40±0.29 a A +++
牛肉浸膏 Beef extract ointment 15.00±0.71 c C ++
蛋白胨Peptone 15.87±1.29 bc BC ++
KNO3 10.33±0.26 e E +
(NH4)2SO4 11.50±0.22 e DE +
NH4Cl 11.08±1.22 e E +
-表示菌丝不生长，下同
- No mycelial growth. The same below.

2.3.3 无机盐对菌丝生长的影响

亚弯柄灵芝菌丝在以ZnSO4为无机盐时不生长；与无机盐空白组相比，MnSO4、FeSO4为无机盐时，菌丝生长速度慢，菌丝生长势不佳，菌落菌丝稀疏，对菌丝的生长有抑制作用；以MgSO4、CaSO4、K₂HPO4、KH2PO4、KCl为无机盐时，并不能加快菌丝的生长速度，但从菌丝长势来看，CaSO4、K₂HPO4以及KH2PO4为无机盐时，菌丝生长势佳，菌落菌丝浓密(表9)。所以CaSO4、K₂HPO4以及KH2PO4是适合亚弯柄灵芝菌丝生长的无机盐。
Table 9 Impact of varied inorganic salt on the mycelial growth of Ganoderma subflexipes (x¯±SD, n=6)

表9 无机盐对亚弯柄灵芝菌丝生长的影响

无机盐
Inorganic salt		 菌丝生长速度
Mycelial growth (mm/d)		 差异显著性
Significance levels		 菌丝生长势
Mycelial growth vigor
0.05 0.01
空白CK 15.56±0.83 a A ++
MgSO4 16.56±1.04 a A ++
CaSO4 16.96±2.68 a A +++
MnSO4 10.30±2.63 b B +
FeSO4 3.08±0.23 c C +
K₂HPO₄ 16.72±0.66 a A +++
KH2PO₄ 16.95±0.50 a A +++
KCl 15.72±1.60 a A ++
ZnSO4 - - - -

2.3.4 生长因子对菌丝生长的影响

亚弯柄灵芝菌丝在供试的13种生长因子中均能生长(表10)。椰子汁、平菇汁、VB1、VB3、VB6、叶酸为生长因子时，菌丝生长速度均较生长因子空白组慢，且具有显著性差异，可见，椰子汁、平菇汁、VB1、VB3、VB6、叶酸为生长因子时，对菌丝的生长多少都有抑制作用。以VC、VE、VB12、VB2、复合VB、烟酰胺、L-谷氨酸为生长因子时，其生长速度较生长因子空白组慢，但从菌丝长势来看，VB12、烟酰胺和L-谷氨酸为生长因子时，菌丝生长势佳，菌落菌丝浓密。综合来看，VB12、烟酰胺和L-谷氨酸是适合亚弯柄灵芝菌丝的生长因子。
Table 10 Impact of growth factors on the mycelial growth of Ganoderma subflexipes (x¯±SD, n=6)

表10 生长因子对亚弯柄灵芝菌丝生长的影响

生长因子
Growth factor		 菌丝生长速度
Mycelial growth (mm/d)		 差异显著性
Significance levels		 菌丝生长势
Mycelial growth vigor
0.05 0.01
空白CK 18.95±0.69 a A ++
VC 17.35±1.39 b AB ++
椰子汁 Coconut milk 16.04±0.58 bc B ++
平菇汁 Mushroom juice 16.37±1.74 bc B ++
VE 17.19±1.33 bc AB ++
VB1 16.29±1.80 bc B ++
VB12 17.56±0.97 ab AB +++
VB2 18.10±0.52 ab AB ++
复合VB VB complex 18.08±0.95 ab AB ++
VB3 16.69±1.01 bc BC ++
VB6 17.06±0.31 bc BC ++
烟酰胺 Nicotinamide 18.67±0.70 a A +++
叶酸 Folic acid 15.75±1.10 c B ++
L-谷氨酸L-glutamate 18.54±0.29 ab AB +++

2.3.5 培养基优化试验

通过4因素3水平的正交试验，对亚弯柄灵芝的碳源、氮源、无机盐以及生长因子进行优化，得出该灵芝的最佳营养源(表11)，培养基碳源为蔗糖，氮源为牛肉蛋白胨，无机盐为CaSO4，生长因子为VB12，菌丝生长迅速最快，且生长势最佳。正交试验方差分析结果表明(表12)，碳源的F值最高，其后依次是氮源、生长因子和无机盐；4个因素的P值从大到小依次为无机盐、生长因子、氮源、碳源，其中碳源的P值小于0.05，表现出显著性差异，这说明碳源对菌丝生长速度影响显著。
Table 11 L9(34) Results of orthogonal experiment (x¯±SD, n=6)

表11 L9(34)正交试验结果

实验号
No.		 碳源
Carbon source		 氮源
Nitrogen source		 无机盐
Inorganic salt		 生长因子
Growth factor		 生长速度
Mycelial growth
(mm/d)		 菌丝生长势
Mycelial growth
vigor
1 葡萄糖
Glucose		 麦芽浸粉
Malt extract powder		 CaSO4 VB12 15.44 ++
2 葡萄糖
Glucose		 酵母浸粉
Yeast extract powder		 K2HPO4 烟酰胺
Nicotinamide		 14.32 ++
3 葡萄糖
Glucose		 牛肉蛋白胨
Beef peptone		 KH2PO4 L-谷氨酸
L-glutamate		 15.44 ++
4 蔗糖
Sucrose		 麦芽浸粉
Malt extract powder		 K₂HPO4 L-谷氨酸
L-glutamate		 17.04 +++
5 蔗糖
Sucrose		 酵母浸粉
Yeast extract powder		 KH2PO4 VB12 17.16 +++
6 蔗糖
Sucrose		 牛肉蛋白胨
Beef peptone		 CaSO4 烟酰胺
Nicotinamide		 17.20 +++
7 麦芽糖
Maltose		 麦芽浸粉
Malt extract powder		 KH2PO4 烟酰胺
Nicotinamide		 16.92 +++
8 麦芽糖
Maltose		 酵母浸粉
Yeast extract powder		 CaSO4 L-谷氨酸
L-glutamate		 16.88 +++
9 麦芽糖
Maltose		 牛肉蛋白胨
Beef peptone		 K2HPO4 VB12 17.16 +++
K1 45.20 49.40 49.52 49.56
K2 51.20 48.16 49.32 48.44
K3 50.96 49.80 48.52 49.36
k1 15.07 16.47 16.51 16.52
k2 17.07 16.05 16.44 16.15
k3 16.99 16.6 16.17 16.45
R 2.00 0.55 0.34 0.37
Table 12 Variance analysis of orthogonal experiment

表12 正交试验方差分析

方差来源
Source		 偏差平方和
Sum of squares		 自由度
df		 均方
Mean square		 F P 显著性
Significance
碳源 Carbon source 7.69 2.00 3.85 3.85 0.030 P<0.05
氮源 Nitrogen source 0.49 2.00 0.24 2.05 0.33 P>0.05
无机盐 Inorganic salt 0.19 2.00 0.09 0.78 0.56 P>0.05
生长因子 Growth factor 0.24 2.00 0.12 1.00 0.50 P>0.05
误差 Error 0.24 2.00

2.4 驯化栽培

在平板固体培养基中，亚弯柄灵芝菌丝呈现绒毛状，颜色为白色，生长浓密。大约经过5 d的培养，菌丝长满约9 cm的培养皿。在制作亚弯柄灵芝液体种子的过程中，发酵菌液散发出浓郁的香气，菌球呈黄色，大小均匀，表面带有微小的刺状突起。经过摇床培养7 d后，菌丝的生物量达到最大值。在发菌阶段，亚弯柄灵芝菌丝约30 d长满培养袋，之后将长满菌丝的菌材埋入土中进行覆土栽培，浇水使土壤处于湿润状态；在出芝阶段，在土壤表面最先形成原基，原基形成约20 d；出原基后约15 d子实体成熟，并开始弹射孢子。
成熟的亚弯柄灵芝子实体具柄，柄长短不一，菌柄通常细长且背生，其菌盖肾形至近肾形，颜色红褐色，光滑，表面有环纹和放射状皱纹并具有似漆样光泽；菌肉和子实层体较薄，菌孔表面奶白色，触摸变褐色(图2)。人工栽培的亚弯柄灵芝子实体与野生子实体形态特征基本相同，但人工栽培的子实体有时候菌盖较大，可能是人工栽培模式下，亚弯柄灵芝具有更好的生长条件和更充分的营养，由此形成更大的子实体。
Fig. 2 Basidiomata of cultured Ganoderma subflexipes.

图2 人工栽培的亚弯柄灵芝子实体

Full size|PPT slide

3 讨论

本研究以菌丝生长速度以及菌落菌丝的生长势为指标，对亚弯柄灵芝菌丝的培养条件和培养基营养源进行了探究，结合单因素筛选和正交试验对其最佳的培养条件和培养基进行筛选，在此基础上，对其子实体进行诱导。
温度是影响真菌菌丝生长和发育的重要因素，前期研究发现温度过高或过低，菌丝或子实体的生长和发育均会受到抑制(徐锦堂等 1997；陈珣等 2023)。根据菌丝和温度的关系，可以把大型真菌分为3类，即低温型、中温型以及高温型真菌，中温型最适温度为24-30 ℃，高温型最适温度为28-34 ℃ (黄年来 1998)。研究表明，灵芝属真菌均为中温型和高温型真菌(表13)。本试验的结果显示亚弯柄灵芝菌丝适宜的生长温度为30-32 ℃，可初步判断其属于高温型真菌，这也与亚弯柄灵芝分布于亚热带、热带的地理气候特征相符(表2)。
Table 13 A comparison of the optimal conditions for the mycelial growth of Ganoderma subflexipes and other Ganoderma species

表13 亚弯柄灵芝与其他灵芝属真菌菌丝最适培养条件、营养源的对比

种类
Species		 碳源
Carbon
source		 氮源
Nitrogen
source		 无机盐
Inorganic
salt		 生长因子
Growth
factor		 光照时间
Illumination
time		 光质
Light
quality		 pH 温度
Temperature
(℃)		 参考文献
Reference
树舌灵芝
G. applanatum		 淀粉
Starch		 酵母提取物
Yeast extract		 MgSO4 VB6 - - 7.0 25-30 Jo et al. 2009
葡萄糖
Glucose		 酵母膏
Yeast ointment		 - - - - - 25-30 兰玉菲等 2016
Lan et al. 2016
南方灵芝
G. australe		 - - - - - - 6.0 30 胡真臻等 2021
Hu et al. 2021
滇中灵芝
G. dianzhongense		 葡萄糖
Glucose		 酵母粉
Yeast powder		 FeCl3 - - - 6.0 26 何俊等 2023
He et al. 2023
可食灵芝
G. esculentum		 麦芽糖
Maltose		 (NH4)2SO4 FeCl3 - - - 5.0 28 何俊等 2023
He et al. 2023
有柄灵芝
G. gibbosum		 果糖
Fructose		 酵母
Yeast		 - - - - 7.0 25 陈爽等 2023
Chen et al. 2023
葡萄糖、
麦芽糖
Glucose,
maltose		 胰蛋白胨、
大豆蛋白胨
Tryptone,
soya peptone		 MgSO4,
CaCl2,
MnSO4		 - - - 6.5 28-32 梁志群和
陈子武 2011
Liang & Chen 2011
白肉灵芝
G. leucocontextum		 蔗糖、
淀粉
Sucrose,
starch		 酵母粉、
牛肉膏
Yeast powder,
beef ointment		 - - - - 3.0 25 莫伟鹏等 2017
Mo et al. 2017
葡萄糖
Glucose		 蛋白胨
Peptone		 FeCl3
 - - - 5.5 26 牛开阳等 2022
Niu et al. 2022
- - - - 黑暗
Dark		 - - - 康晟菀等 2023
Kang et al. 2023
赤芝
G. lingzhi		 蔗糖
Sucrose		 酵母膏
Yeast ointment		 - - - - - 25 兰玉菲等 2016
Lan et al. 2016
淀粉
Starch		 酵母浸粉
Yeast extract
powder		 - - - - 5.0 30 吕艳聪等 2023
Lv et al. 2023
蔗糖、
葡萄糖
Sucrose, glucose		 酵母
Yeast		 - - - - 6.0 30 刘冬梅等 2022
Liu et al. 2022
- - - - - 蓝光
Blue light		 - - 梅锡玲 2013
Mei et al. 2013
葡萄糖、蔗糖
Glucose,
sucrose		 酵母膏
Yeast
ointment		 KH2PO4 - - - 7.0 28-32 雷萍等 2022
Lei et al. 2022
亚弯柄灵芝
G. subflexipes		 蔗糖、
麦芽糖、
葡萄糖
Sucrose,
maltose,
glucose		 麦芽浸粉、
酵母浸粉、
牛肉蛋白胨
Malt extract
powder, yeast
extract powder,
beef peptone		 CaSO4,
KH2PO4,
K2HPO4		 VB12、
L-谷氨酸、
烟酰胺
L-glutamate,
Nicotinamide
 黑暗
Dark		 绿光
Green light		 5.0-8.0 30-32 本研究
This study
韦伯灵芝
G. weberianum		 糊精
Dextrin		 酵母粉
Yeast powder		 - - - - 6.0 28-32 蒋帅等 2021
Jiang et al. 2021
山西灵芝
G. shanxiense		 葡萄糖
Glucose		 酵母粉
Yeast powder		 - - - - 4.0 30 杨杰和刘虹 2023
Yang & Liu 2023
四川灵芝
G. sichuanense		 麦芽糖
Maltose		 牛肉膏
Beef ointment		 KH2PO4 - - - 7.0 30 钱坤等 2022
Qian et al. 2022
紫芝
G. sinense		 麦芽糖
Maltose		 酵母膏
Yeast ointment		 - - - - - 25-30 兰玉菲等 2016
Lan et al. 2016
果糖
Fructose		 酵母浸膏
Yeast extract
ointment		 - - - - 7.0 25-30 Nguyen et al.
2023
松杉灵芝
G. tsugae		 葡萄糖
Glucose		 蛋白胨
Peptone		 MgSO4
 - - - 6.0 25 李福强等 2017
Li et al. 2017
任何生命体的生长发育过程都需要适宜的pH值，大型真菌也不例外。当外环境的pH值过高或过低，酶的活力、细胞膜的通透性以及体内新陈代谢都会受到一定的影响，从而影响菌丝体正常的发育。因此，只有在最适宜的pH值下，菌丝内的各种生物酶才能参与正常的物质交换和新陈代谢，提供真菌菌丝发育所需的营养(徐锦堂等 1997)。灵芝属大多种类的菌丝都喜欢在中性和偏酸性的培养基中生长，尤其白肉灵芝更适合在酸性的条件下生长(表13)。亚弯柄灵芝则在偏酸、中性及偏碱的环境中都能生长。
在真菌菌丝发育过程中，光是一个不可忽略的重要因素，光质即不同波长的光谱成分能够刺激或抑制真菌菌丝的生长和发育(徐锦堂等 1997；洪沛等 2021)。研究表明，蓝光能促进赤芝菌丝的生长(表13)，本试验结果则表明紫光和蓝光会抑制亚弯柄灵芝菌丝的生长，绿光对菌丝的生长有显著的促进作用。光质对灵芝属真菌菌丝生长的影响研究较少，今后可加强对其进行研究。此外，光质是否会对灵芝属真菌子实体的生长及有效成分的积累产生影响，有待进一步研究。
碳源是大型真菌最重要的生命元素和营养成分之一。它不仅是糖类等碳水化合物和蛋白质以及核酸的基本组成部分，也是一种重要的能量原料(Tang et al. 2008)。灵芝属真菌可广泛利用各种碳源(表13)。与其他灵芝属真菌一样，亚弯柄灵芝菌丝可利用葡萄糖、果糖、木糖、蔗糖、麦芽糖、糊精、可溶性淀粉、红糖、蜂蜜等多种碳源，提示该灵芝在人工栽培过程中，可广泛利用各种含碳的废弃物。与此同时，本试验也发现核糖、甘露醇、乳糖抑制了亚弯柄灵芝菌丝的生长，可能是菌丝将核糖、甘露醇、乳糖转化为抑制其生长的物质。
氮是大型真菌体内合成蛋白质、核酸以及各种氮基物质和代谢物的重要来源，因此氮源的种类对真菌的生长和代谢有显著影响(徐锦堂等 1997)。在研究中，亚弯柄灵芝菌丝在供试的碳酸铵和尿素中不生长，在6-苄氨基嘌呤中微弱生长，可能的原因是菌丝将以上这些物质分解并转化为抑制其生长的物质(张松等 2002；谢放等 2014)。胡延如等(2022)则发现6-苄氨基嘌呤对平菇的菌丝生长具有促进作用。由此可以推断氮源对不同真菌菌丝生长的影响差异较大。此外，在氮源筛选结果中发现，亚弯柄灵芝菌丝在有机氮源的环境下比无机氮源生长得更好，这和其他灵芝属真菌有相同的特性(表13)。究其原因，可能是无机氮源只能提供氮源的供给，而有机氮源除了能提供氮源的支撑，还含有碳源、生长因子、无机盐以及其他微量元素，能给菌丝的生长提供更全面的营养支撑(陈斌等 2015；孙瑶等2021)。
在真菌的生长过程中，无机盐的需求量虽然很少，但它们所起的生理作用却非常重要，是生长发育所不可缺少的营养物质，其主要功能是：构成菌体细胞成分，促进菌体内生物酶的活性或作为酶的成分，调节菌体渗透压以及调控菌丝生长分化等(Jose & Jebakumar 2013；Chen et al. 2022)。灵芝属不同真菌所偏好的无机盐不尽相同(表13)，对于亚弯柄灵芝菌丝而言，CaSO4、KH2PO₄以及K2HPO4能促进亚弯柄灵芝菌丝生长，而ZnSO4、FeSO4以及MnSO4则会抑制菌丝的生长，究其原因，可能是3种无机盐中的金属离子干扰了亚弯柄灵芝菌丝体正常的生理功能从而导致其生长受到抑制(何俊等 2022)。
过去对生长因子促进灵芝属真菌菌丝生长的研究不多(表13)。对生长因子进行筛选后发现，本研究中选取的13种生长因子在对菌丝的生长速度与空白组相比无显著性促进作用，但生长因子却可以增加菌丝的生长势。因此亚弯柄灵芝菌丝生长的最适生长因子还需要在将来的试验中进行更大范围的筛选，以便筛选出能促进菌丝生长速度和增加其生长势的生长因子。
值得注意的是，通过对灵芝属其他真菌的最适培养条件、营养源进行对比(表13)，发现灵芝属不同物种的最适培养条件和营养源有所不同，即便是相同物种在不同研究中其最适培养条件和营养源也并不相同，推测原因可能是灵芝属不同物种或同一物种的不同菌株，其生物学特性不同。另外，也可能是研究者在设计实验方案时，所选因子的种类或范围不同，由此导致一些灵芝属物种或菌株对应的最佳培养条件和营养源不同。
本试验中，亚弯柄灵芝采用段木覆土栽培的方法，成功诱导出子实体。子实体培育生长周期较短，品质较好，子实体性状与野生的基本一致。在中国，赤芝、紫芝、白肉灵芝等灵芝属真菌已经有较大规模的人工栽培。亚弯柄灵芝经济价值高，目前所处市场前景良好。经过进一步的中试，相信亚弯柄灵芝也能够进行规模化人工栽培。

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Uliano-Silva M, Ferreira JGRN, Krasheninnikov K, Formenti G, Abueg L, Torrance J, Myers EW, Durbin R, Blaxter M, McCarthy SA, 2023. MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads. BMC Bioinformatics, 24: 288
https://doi.org/10.1186/s12859-023-05385-y
https://www.ncbi.nlm.nih.gov/pubmed/37464285
Cited in this article [1] Abstract
 PacBio high fidelity (HiFi) sequencing reads are both long (15-20 kb) and highly accurate (> Q20). Because of these properties, they have revolutionised genome assembly leading to more accurate and contiguous genomes. In eukaryotes the mitochondrial genome is sequenced alongside the nuclear genome often at very high coverage. A dedicated tool for mitochondrial genome assembly using HiFi reads is still missing. MitoHiFi was developed within the Darwin Tree of Life Project to assemble mitochondrial genomes from the HiFi reads generated for target species. The input for MitoHiFi is either the raw reads or the assembled contigs, and the tool outputs a mitochondrial genome sequence fasta file along with annotation of protein and RNA genes. Variants arising from heteroplasmy are assembled independently, and nuclear insertions of mitochondrial sequences are identified and not used in organellar genome assembly. MitoHiFi has been used to assemble 374 mitochondrial genomes (368 Metazoa and 6 Fungi species) for the Darwin Tree of Life Project, the Vertebrate Genomes Project and the Aquatic Symbiosis Genome Project. Inspection of 60 mitochondrial genomes assembled with MitoHiFi for species that already have reference sequences in public databases showed the widespread presence of previously unreported repeats. MitoHiFi is able to assemble mitochondrial genomes from a wide phylogenetic range of taxa from Pacbio HiFi data. MitoHiFi is written in python and is freely available on GitHub ( https://github.com/marcelauliano/MitoHiFi ). MitoHiFi is available with its dependencies as a Docker container on GitHub (ghcr.io/marcelauliano/mitohifi:master).© 2023. The Author(s).
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Vu D, Groenewald M, de Vries M, Gehrmann T, Stielow B, Eberhardt U, Al-Hatmi A, Groenewald JZ, Cardinali G, Houbraken J, Boekhout T, Crous PW, Robert V, Verkley GJM, 2019. Large-scale generation and analysis of filamentous fungal DNA barcodes boosts coverage for kingdom fungi and reveals thresholds for fungal species and higher taxon delimitation. Studies in Mycology, 92: 135-154
https://doi.org/10.1016/j.simyco.2018.05.001
https://www.ncbi.nlm.nih.gov/pubmed/29955203
Cited in this article [1] Abstract
Species identification lies at the heart of biodiversity studies that has in recent years favoured DNA-based approaches. Microbial Biological Resource Centres are a rich source for diverse and high-quality reference materials in microbiology, and yet the strains preserved in these biobanks have been exploited only on a limited scale to generate DNA barcodes. As part of a project funded in the Netherlands to barcode specimens of major national biobanks, sequences of two nuclear ribosomal genetic markers, the Internal Transcribed Spaces and 5.8S gene (ITS) and the D1/D2 domain of the 26S Large Subunit (LSU), were generated as DNA barcode data for ca. 100 000 fungal strains originally assigned to ca. 17 000 species in the CBS fungal biobank maintained at the Westerdijk Fungal Biodiversity Institute, Utrecht. Using more than 24 000 DNA barcode sequences of 12 000 ex-type and manually validated filamentous fungal strains of 7 300 accepted species, the optimal identity thresholds to discriminate filamentous fungal species were predicted as 99.6 % for ITS and 99.8 % for LSU. We showed that 17 % and 18 % of the species could not be discriminated by the ITS and LSU genetic markers, respectively. Among them, ∼8 % were indistinguishable using both genetic markers. ITS has been shown to outperform LSU in filamentous fungal species discrimination with a probability of correct identification of 82 % vs. 77.6 %, and a clustering quality value of 84 % vs. 77.7 %. At higher taxonomic classifications, LSU has been shown to have a better discriminatory power than ITS. With a clustering quality value of 80 %, LSU outperformed ITS in identifying filamentous fungi at the ordinal level. At the generic level, the clustering quality values produced by both genetic markers were low, indicating the necessity for taxonomic revisions at genus level and, likely, for applying more conserved genetic markers or even whole genomes. The taxonomic thresholds predicted for filamentous fungal identification at the genus, family, order and class levels were 94.3 %, 88.5 %, 81.2 % and 80.9 % based on ITS barcodes, and 98.2 %, 96.2 %, 94.7 % and 92.7 % based on LSU barcodes. The DNA barcodes used in this study have been deposited to GenBank and will also be publicly available at the Westerdijk Institute's website as reference sequences for fungal identification, marking an unprecedented data release event in global fungal barcoding efforts to date.
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https://doi.org/10.1038/s41598-020-69245-y
https://www.ncbi.nlm.nih.gov/pubmed/32724224
Cited in this article [1] Abstract
Sequence classification plays an important role in metagenomics studies. We assess the deep neural network approach for fungal sequence classification as it has emerged as a successful paradigm for big data classification and clustering. Two deep learning-based classifiers, a convolutional neural network (CNN) and a deep belief network (DBN) were trained using our recently released barcode datasets. Experimental results show that CNN outperformed the traditional BLAST classification and the most accurate machine learning based Ribosomal Database Project (RDP) classifier on datasets that had many of the labels present in the training datasets. When classifying an independent dataset namely the "Top 50 Most Wanted Fungi", CNN and DBN assigned less sequences than BLAST. However, they could assign much more sequences than the RDP classifier. In terms of efficiency, it took the machine learning classifiers up to two seconds to classify a test dataset while it was 53 s for BLAST. The result of the current study will enable us to speed up the taxonomic assignments for the fungal barcode sequences generated at our institute as ~ 70% of them still need to be validated for public release. In addition, it will help to quickly provide a taxonomic profile for metagenomics samples.
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https://doi.org/10.1093/bioinformatics/btx153
https://www.ncbi.nlm.nih.gov/pubmed/28369201
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GenomeScope is an open-source web tool to rapidly estimate the overall characteristics of a genome, including genome size, heterozygosity rate and repeat content from unprocessed short reads. These features are essential for studying genome evolution, and help to choose parameters for downstream analysis. We demonstrate its accuracy on 324 simulated and 16 real datasets with a wide range in genome sizes, heterozygosity levels and error rates.http://genomescope.org, https://github.com/schatzlab/genomescope.git.mschatz@jhu.edu.Supplementary data are available at Bioinformatics online.© The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com
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Wang K, Cai L, 2023. Overview of the historical and current status of fungal taxonomy and diversity in China. Mycosystema, 42(1): 50-62 (in Chinese)
https://doi.org/10.13346/j.mycosystema.220497
Abstract

Fungal taxonomic study in China, originated at the beginning of 20th century, has achieved encouraging progress and gradually reached the forefront of the world after more than a hundred years’ exploration and development. In this study, the research progress of China’s fungal taxonomy is statistically summarized based on the data retrieved from Fungal Names database. The result shows that a total of 15 626 new fungal taxa, including 3 new classes, 27 new orders or suborders, 117 new families or subfamilies, 769 new genera or subgenera, 11 100 new species, 322 new intraspecific taxa and 3 288 new combinations were published by 2 214 Chinese scholars historically. Phytopathogenic fungi, wood-inhabiting fungi and agaricomycetes have received more attentions by Chinese scholars. Among all the known fungal species worldwide, 10 233 species, belonging to 3 kingdoms, 13 phyla, 44 classes, 174 orders, 572 families and 2 379 genera, were firstly discovered from China, ranking the 2nd worldwide and accounting for 6.84% of global known fungal diversity. Species discovered from southwest (Yunnan, Sichuan, Guizhou, Tibet) and low-latitude tropical and subtropical regions (Taiwan, China; Guangdong) accounted for highest proportion of China. According to the number of yearly published new taxa and the composition of scholars, the development history of China’s fungal taxonomy can be divided into five stages: foreigners collecting and studying fungi in China (1750s-1929), the start of mycology in China (1930-1949), the early development of fungal taxonomy in new China (1950-1977), national wide collection and study of fungi (1978-2010), being part of world forefront (2011-present). The status of species discovery and important historical events of each stage were also summarized and concluded. Through the above reviews, the development trend and research overview of China’s fungal taxonomy are systematically presented, which can provide reference for the current and future development of the subject.
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Wang Z, 2014. Research on the species resources of poisonous mushroom in Mount Tai. MS Thesis, Shandong Agricultural University, Tai’an. 1-65 (in Chinese)
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Zhang XB, Lin LN, Zhang GC, Yang J, Cheng HG, Zhang TT, 2019. Inhibitory effect and antimicrobial mechanism of Lysurus mokusin extracts on Botrytis cinerea. Journal of Jilin Agricultural University, 41: 161-167 (in Chinese)
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戴芳澜, 1979. 外人在华采集真菌考. 植物病理学报,1: 7-11
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王科, 蔡磊, 2023. 中国菌物分类学和多样性研究的历史与现状概况. 菌物学报, 42(1): 50-62
https://doi.org/10.13346/j.mycosystema.220497
Cited in this article [1] Abstract
我国菌物分类学研究始于20世纪初，经过百余年的不断探索和发展，取得了丰硕的成果，并逐渐走进世界前列。本研究通过对世界菌物名称信息库Fungal Names进行数据统计，对发现自中国的菌物新物种和中国学者发表菌物新分类单元等数据开展分析，从中揭示中国菌物分类学的历史和发展趋势。过去，一共有2 214位中国学者参与发表了15 626个菌物新分类单元，包括 3个新纲、27个新目及亚目、117个新科及亚科、769个新属及亚属、11 100个新种、322个新种下单元和3 288个新组合。在全球已知的菌物物种中，自中国发现的新物种有10 233种，隶属于 3界13门44纲174目572科2 379属，占全球已知物种多样性的6.84%，居世界第二位。地理分布上，我国西南地区(云南、四川、贵州、西藏)和低纬度的热带、亚热带地区(中国台湾、广东)发现的新物种最多。根据每年发现的新分类单元数量趋势和命名作者的构成，可将中国菌物分类学的发展历史分为五个阶段：外人在华采菌及研究(1750s-1929)、中国菌物分类学起步(1930-1949)、新中国菌物分类学早期发展(1950-1977)、全国性菌物标本采集与研究(1978-2010)、走进世界前列(2011至今)。本研究对每个发展时期的分类学概况和重要历史事件进行了总结和回顾，通过上述综述性研究，有助于系统地了解中国菌物分类学不同阶段的发展趋势和研究概况，为学科当下和未来的发展提供参考。
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王瑞琦, 张国财, 林连男, 杨璟, 邹传山, 2017. 基于ITS中华散尾鬼笔的分类及抑菌活性研究. 黑龙江畜牧兽医,12: 178-181, 299
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张晓波, 林连男, 张国财, 杨璟, 程红刚, 张婷婷, 2019. 中华散尾鬼笔提取物对灰葡萄孢霉菌的作用机制. 吉林农业大学学报,41: 161-167
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National Science and Technology Fundamental Resources Investigation Program of China(2021FY100900)
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