Abstract
The draft genome sequence of “Candidatus Liberibacter asiaticus” strain YCPsy from an Asian citrus psyllid (Diaphorina citri) in Guangdong, China, is reported here. The YCPsy strain has a genome size of 1,233,647 bp, 36.5% G+C content, 1,171 open reading frames (ORFs), and 53 RNAs.
GENOME ANNOUNCEMENT
“Candidatus Liberibacter asiaticus,” an unculturable alphaproteobacterium, inhabits both Asian citrus psyllids (Diaphorina citri Kuwayama) and citrus plants. Infection of the bacterium is associated with citrus huanglongbing (HLB) (yellow shoot disease), a destructive disease in citrus production. D. citri transmits “Ca. Liberibacter asiaticus” (1). HLB was observed in Guangdong, China, >100 years ago (2). Transmission of the HLB pathogen by D. citri was reported in 1977 (3) before the detection of “Ca. Liberibacter asiaticus” in 1996 (4, 5). Because of the lack of in vitro culture, research on “Ca. Liberibacter asiaticus” has been challenging. Thanks to the development of next-generation sequencing technology, genomes of “Ca. Liberibacter asiaticus” strains can be sequenced directly from psyllid or plant hosts for biological study. Zheng et al. (6) sequenced the genome of “Ca. Liberibacter asiaticus” strain A4 from periwinkle in Guangdong. Here, we report a draft genome sequence of “Ca. Liberibacter asiaticus” from D. citri in the same geographical location.
A mandarin citrus tree (Citrus reticulata cv. Shatangju) infected with “Ca. Liberibacter asiaticus” was maintained in a growth chamber (RXZ-380A; Jiangnan Instrument, Inc., Ningbo, China) with the settings of 28 ± 1°C, 60% ± 5% rH, and 14:10 h light/dark (L:D) at South China Agricultural University in Guangzhou, China. The original source of “Ca. Liberibacter asiaticus” was from an HLB Shatangju tree in Boluo City of Guangdong (23°26′07″N, 114°29′56″E). Psyllids were fed on the infected citrus tree for 2 months. An individual psyllid adult was collected for DNA extraction using the DNeasy blood and tissue kit (Qiagen, Shanghai, China). Infection of “Ca. Liberibacter asiaticus” was monitored by the PCR method of Li et al. (7). DNA from a single psyllid sample (threshold cycle [CT], 18.1) was amplified using illustra GenomiPhi version 2 DNA amplification kits (GE Healthcare, Inc., Waukesha, WI, USA). The amplified DNA was sequenced using an Illumina MiSeq format (Illumina, Inc., San Diego, CA).
A total of 3.98 × 107 reads with a mean of 251 bp per read were generated from the psyllid DNA sample. Using the whole genomes of “Ca. Liberibacter asiaticus” strains psy62 (8) and A4 (6) as references, a total of 5,854,876 and 5,886,489 reads, respectively, were identified using the standalone BLAST software (version 2.2.30; e-value, <10-20) (9). The “Ca. Liberibacter asiaticus” reads were collected using a Perl script. The combination of de novo assembly using Velvet (version 1.2.10) (10) and reference assembly using Bowtie2 (version 2.2.6) (11) generated 9 contigs ranging from 1,587 bp to 755,458 bp, with an average coverage of 1,120×. The draft genome of “Ca. Liberibacter asiaticus” strain YCPsy comprises 1,233,647 bp, with a G+C content of 36.5%. Annotation was performed using the RAST server (http://rast.nmpdr.org/) (12), and the YCPsy genome was predicted to have 1,171 open reading frames (ORFs) and 53 RNAs.
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. LIIM00000000. The version described in this manuscript is the first version LIIM01000000.
ACKNOWLEDGMENTS
This research was supported by Chinese Modern Agricultural Technology Systems (CARS-27) and the Special Fund for Agro-Scientific Research in the Public Interest, China (grant 2010003067) and the California Citrus Research Board.
The mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.
Footnotes
Citation Wu F, Zheng Z, Deng X, Cen Y, Liang G, Chen J. 2015. Draft genome sequence of “Candidatus Liberibacter asiaticus” from Diaphorina citri in Guangdong, China. Genome Announc 3(6):e01316-15. doi:10.1128/genomeA.01316-15.
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