Effective Identification and Annotation of Fungal Genomes

In the past few decades,the dangers of mycosis have caused widespread concern.With the development of the sequencing technology,the effective analysis of fungal sequencing data has become a hotspot.With the gradual increase of fungal sequencing data,there is now a lack of sufficient approaches for the identification and functional annotation of fungal chromosomal genomes.To overcome this challenge,this paper firstly deals with the approaches of the identification and annotation of fungal genomes based on short and long reads sequenced by using multiple platforms such as Illumina and Pacbio.Then this paper develops an automated bioinformatics pipeline called PFGI for the identification and annotation task.The experimental evaluation on a real-world dataset ENA(European Nucleotide Archive)shows that PFGI provides a user-friendly way to perform fungal identification and annotation based on the sequencing data analysis,and could provide accurate analyzing results,accurate to the species level(97%sequence identity).

Selection of a DNA barcode for Nectriaceae from fungal whole-genomes

A DNA barcode is a short segment of sequence that is able to distinguish species. A barcode must ideally contain enough variation to distinguish every individual species and be easily obtained. Fungi of Nectriaceae are economically important and show high species diversity. To establish a standard DNA barcode for this group of fungi, the genomes of Neurospora crassa and 30 other filamentous fungi were compared. The expect value was treated as a criterion to recognize homologous sequences. Four candidate markers, Hsp90, AAC, CDC48, and EF3, were tested for their feasibility as barcodes in the identification of 34 well-established species belonging to 13 genera of Nectriaceae. Two hundred and fifteen sequences were analyzed. Intraand inter-specific variations and the success rate of PCR amplification and sequencing were considered as important criteria for estimation of the candidate markers. Ultimately, the partial EF3 gene met the requirements for a good DNA barcode: No overlap was found between the intra-and inter-specific pairwise distances. The smallest inter-specific distance of EF3 gene was 3.19%, while the largest intra-specific distance was 1.79%. In addition, there was a high success rate in PCR and sequencing for this gene (96.3%). CDC48 showed sufficiently high sequence variation among species, but the PCR and sequencing success rate was 84% using a single pair of primers. Although the Hsp90 and AAC genes had higher PCR and sequencing success rates (96.3% and 97.5%, respectively), overlapping occurred between the intraand inter-specific variations, which could lead to misidentification. Therefore, we propose the EF3 gene as a possible DNA barcode for the nectriaceous fungi.