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De novo Genome Assembly of the Acidovorax avenae subsp. cattleyae by Using the Nanopore-Based DNA Sequencing Technology
<i>De novo</i> assembly graph of (A) <i>Acidovorax avenae</i> subsp. <i>cattleyae</i> (AAC) starin 10001 and (B) strain 9906R genome.
De novo assembly graph of (A) Acidovorax avenae subsp. cattleyae (AAC) starin 10001 and (B) strain 9906R genome.

Author:Yuan-Kai Tu, Chia-Hsin Tsai, Yen-Chun Lin, Po-Chun Ou, and Han-Wei Chen*

Abstract:

In Taiwan, orchids takes the lead in floral exports, with the value reaching NTD 4 billion in 2020. However, the orchid bacterial brown spot disease caused by Acidovorax avenae subsp. cattleyae (AAC) is commonly observed in greenhouses. The combination of warm temperature and high humidity provides the optimum conditions for brown spot disease outbreak, resulting in the low-export quality of orchids. In this study, two AAC strains were sequenced using nanopore-based sequencing technology. Overall, the average read length and read quality of AAC_10001 and AAC_9906R were 1.49 Gb, 18.7 kb, 11.9 and 1.96 Gb, 17.29 kb, 12.3, respectively. The results showed high contiguity of DNA quality. After de novo genome assembly, 6 and 5 contigs were obtained for AAC_10001 and AAC_9906R, in which the largest contig was 5.7 Mb and 5.6 Mb with 67.4% and 67.5% guanine-cytosine (GC) content, and the average sequencing depths for both largest contigs were 230×. Genome structure comparison revealed 12 locally collinear blocks (LCBs) in AAC_10001 and AAC_9906R. We found a putative 132 kb genomic island (GEI) in LCB2 of AAC_10001, harboring a DNA repair protein, a cluster type IV secretory system proteins, an integrase and a transposase. GEI plays a critical role in the bacterial evolution of pathogenicity, symbiosis, metabolism, environmental adaptation, and antibiotics resistance. In this research, we first present a reliable long-read de novo assembly pipeline for AAC genome study by using nanopore sequencing data only. This could provide fundamental knowledge for strain detection, identification or long-term monitoring and give us a perspective disease prevention strategy to adopt.

Key words:Nanopore sequencing, Acidovorax avenae subsp. cattleyae, Genome assembly, Bacterial antibiotic resistance

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