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

Abstract

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.