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- Title
新暗色柱节孢 H1 全基因组测序和注释.
- Authors
赵晓珍; 齐勇; 王红林; 马玉华; 郑乾明
- Abstract
[Objective] To provide foundation for understanding the genome composition, genetic variation, pathogenic mechanism and control method of Neoscytalidium dimidiatum H1 (one pathogen of pitaya canker disease), the genome sequence of N. dimidiatum H1 is sequenced and assembled. [Method] The genomic DNA of N. dimidiatum H1 that isolated from pitaya canker sample in Guizhou is extracted, and then the genome is sequenced, assembled and annotated by Illumina NovaSeq and Nanopole PromethION platforms. [Result] Based on the sequencing and assembly with Nanopore platform and the error correction with Illumina data, the N. dimidiatum H1 genome size was 43.78 Mb, and the number of Gap was 0. After sequence assembly, 14 contigs were obtained with a N50 length of 3.92 Mb, an average length of 3.13 Mb, and a longest length of 5.63 Mb. BUSCO was evaluated using eukaryotic and fungal lineal homologous gene sets, and the proportions of intact single-copy genes were 98.60% and 98.50%, respectively. There were 12 962 coding genes and 205 non-coding RNAs in N. dimidiatum H1. The content of repeat sequence was 1.62%, and simple repetition was the main type. Besides, the content of transposon was 1.59%, as the Gypsy subfamily belonging to LTR class and LINE class were the main type. Furthermore, a total of 12 703 (98%) coding genes were annotated, and showed high homology with that of Macrophomina phaseolina MS6 and Neofusicoccum parvum UCR-NP2, which both belonged to the Botryosphaeriaceae family. [Conclusion] In this study, a high quality genome sequence of N. dimidiatum H1 are obtained by using Nanopole and Illumina sequencing strategy, which provides a theoretical foundation for the study of pathogenic mechanism and prevention strategies.
- Subjects
GUIZHOU Sheng (China); GENETIC variation; GENOME size; MACROPHOMINA phaseolina; GENETIC code; NON-coding RNA
- Publication
Southwest China Journal of Agricultural Sciences, 2023, Vol 36, Issue 7, p1406
- ISSN
1001-4829
- Publication type
Article
- DOI
10.16213/j.cnki.scjas.2023.7.007