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

Science China(Life Sciences) 2012年第1期55卷 80-88页

作者： ZENG ZhaoQing ZHAO Peng LUO Jing ZHUANG WenYing YU ZhiHe State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Graduate University of Chinese Academy of Sciences Beijing 100049China College of Life Sciences Yangtze UniversityJingzhou 434025China

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.

关键词： barcoding gap expect value fungal genomes homologous sequence PCR and sequencing success rate sequence variation

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Infection mechanism of plant pathogenic Diaporthe actinidiae to kiwifruit deciphered by genome and transcriptome analysis

Infection mechanism of plant pathogenic Diaporthe actinidiae...

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中国植物病理学会2019年学术年会

作者：李黎 Deng Lei Chen Lianfu Pan Hui Wang Zupeng 钟彩虹 CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden Innovation Academy for Seed Design Chinese Academy of Sciences CAS Engineering Laboratory for Kiwifruit Industrial Technology Chinese Academy of Sciences

Diaporthe species are fungal pathogens that devastate crop plants and fruits *** actinidiae strain,the pathogens caused kiwifruit stem-end rot,has been regarded as one of the most serious threat to kiwifruit production in the *** the paper,we reported the whole genome and comparative transcriptome analyses of *** infecting *** genome size of *** strain was 58.30 Mb,17,176 protein-encoding genes were *** genomics with 30 other fungi showed 18.94% of the proteins were unique to ***,and the strain have highest level of CAZYme genes,especially Glycoside Hydrolases and Auxiliary activities enzymes.3140 pathogenicity-related genes were identified in *** genome,including 135 lethal genes,85 hyper-virulence genes and 9 genes resistance to ***-Seq analysis was conducted to compare the expression profiles among *** mycelium and infected flesh tissue of *** infecting three suspectable *** the differentially expressed genes（DEGs）,340 up-regulated and 1161 down-regulated genes could be assigned into functional categories of the gene ontology（GO）:biological process,molecular function,and cellular *** function of 23 significant DEGs genes involving in Pathogen Host Interactions（PHI） progress among *** and kiwifruit was *** study build the foundations for further characterize the underlying infecting mechanisms of this important fungal pathogen to kiwifruit.

关键词： Diaporthe spp. kiwifruit rot disease fungal genomes pathogenicity-related genes

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