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International Journal of Medicinal Mushrooms
Factor de Impacto: 1.423 Factor de Impacto de 5 años: 1.525 SJR: 0.431 SNIP: 0.716 CiteScore™: 2.6

ISSN Imprimir: 1521-9437
ISSN En Línea: 1940-4344

Volumes:
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International Journal of Medicinal Mushrooms

DOI: 10.1615/IntJMedMushrooms.2019033232
pages 1223-1239

The Reliability of DNA Sequences in Public Databases Belonging to the Most Economically Important Shiitake Culinary-Medicinal Mushroom Lentinus edodes (Agaricomycetes) in Asia

Rui-Heng Yang
National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungal Resources and Utilization (South), Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
Ying-Ying Wu
National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungal Resources and Utilization (South), Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
Li-Hua Tang
National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungal Resources and Utilization (South), Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
Chuan-Hua Li
National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungal Resources and Utilization (South), Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
Jun-Jun Shang
National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungal Resources and Utilization (South), Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
Yan Li
National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungal Resources and Utilization (South), Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
Ying Song
Institute of Edible Fungi, Shenyang Academy of Agricultural Sciences, Shenyang 110161, China
Wei-Hua Huang
Mushroom Technological Innovation Service Platform, Edible Fungi Research Center, Qingyuan Zhejiang 323000, China
Xiang-Sheng Tao
Mushroom Technological Innovation Service Platform, Edible Fungi Research Center, Qingyuan Zhejiang 323000, China
Qi Tan
National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungal Resources and Utilization (South), Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
Da-Peng Bao
National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungal Resources and Utilization (South), Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China

SINOPSIS

Large numbers of DNA sequences deposited in the International Nucleotide Sequence Databases (INSD) are erroneously annotated. The erroneous information may lead to misleading conclusions or cause great economic losses to farmers. Lentinus edodes (= Lentinula edodes (Berk.) Pegler) is one of the most important and popular culinary-medicinal mushrooms with a high nutritional value. In this study, experimental and in silico methods were used to correct the sequences annotated as L. edodes in the INSD. A total of 3,426 nucleotide entries were retrieved from public databases, including 140 different types of genetic sequences. Excluding 1,893 genome sequences, the most abundant signatures represented by ITS (258) and IGS1 (259) sequences accounted for 33.23% of the total entries. A total of 3,058 sequences were annotated correctly, 350 were indeterminate, and 18 were annotated erroneously based on the two methods. Correction of sequences will be beneficial for species identification and annotation. Phylogenic analysis based on ITS sequences suggested that L. edodes segregate in four clades in the tree based on ITS sequences. The isolates from China were distributed into two clades. In L. edodes, the intraspecific variation of the ITS2 sequences was much higher than that of the ITS1 sequences. In addition, the genetic diversity of the L. edodes sequences from China was much higher than that of any other regions included in this study. The northwest and southwest regions of China were L. edodes diversity centers.

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