Open access
Announcement
13 April 2017

Draft Whole-Genome Sequence of “Candidatus Liberibacter asiaticus” Strain TX2351 Isolated from Asian Citrus Psyllids in Texas, USA

ABSTRACT

We report here the draft genome sequence of “Candidatus Liberibacter asiaticus” strain TX2351, collected from Asian citrus psyllids in south Texas, USA. The TX2351 genome has a size of 1,252,043 bp, a G+C content of 36.5%, 1,184 predicted open reading frames, and 52 RNA genes.

GENOME ANNOUNCEMENT

Huanglongbing (HLB), or citrus greening disease, is a serious threat to citriculture worldwide (13). In the United States, HLB has been associated with a phloem-inhabiting alphaproteobacterium, “Candidatus Liberibacter asiaticus,” vectored by Asian citrus psyllid (ACP) (Diaphorina citri Kuwayama). In the Americas, “Ca. Liberibacter asiaticus” was first discovered in Brazil in 2004 (4) and later in Florida in 2005 (5) and in California in 2012 (6). HLB was first detected in a Valencia sweet orange tree in a commercial orchard in San Juan, Texas, USA, in 2012 (7, 8), and it has now spread to all citrus-growing regions in the Rio Grande Valley of south Texas. Because of its unculturable nature, the characterization of “Ca. Liberibacter asiaticus” relies heavily on genome sequence analyses. Whole-genome sequences of “Ca. Liberibacter asiaticus” have been reported from strains found in Florida (9, 10) and California (11, 12). Here, we report a draft whole-genome sequence of “Ca. Liberibacter asiaticus” strain TX2351, isolated directly from ACP in south Texas.
ACPs carrying “Ca. Liberibacter asiaticus” strain TX2351 were originally collected in May 2016, by USDA-APHIS-PPQ Citrus Health Response Program inspectors on a Mexican lime tree (Citrus aurantiifolia) showing typical HLB symptoms in McAllen, Texas. Total DNA from five field-collected ACPs was extracted using the BioSprint 96 DNA blood kit (Qiagen, Germantown, MD, USA) and tested positive for “Ca. Liberibacter asiaticus” (cycle threshold = 23.7) by the PCR method of Li et al. (13). A quantity of DNA was enlarged using Illustra GenomiPhi version 2 DNA amplification kits (GE Healthcare, Waukesha, WI, USA). Whole-genome sequencing was performed on an Illumina MiSeq platform (Illumina, Inc., San Diego, CA, USA). The MiSeq sequencing yielded a total of 4.27 × 107 reads with an average size of 251 bp. With the help of the whole-genome sequences of “Ca. Liberibacter asiaticus” strains Psy62 (9) and A4 (14) and 2 “Ca. Liberibacter asiaticus” phages/prophages (SC1 and SC2) (15), a total of 32,768 reads were identified and collected using Bowtie2 version 2.2.9 (16). Sequence assembly was performed using a combination of both Velvet 1.2.0 (17) and CLC Genomics Workbench version 7.5 software. The assembly contained 71 contigs, ranging from 1,139 bp to 121,132 bp in size with ~6.90×, comprising a total of 1,252,043 bp with a G+C content of 36.5%. Annotation was performed using the RAST server (http://rast.nmpdr.org ) (18), which predicted 1,184 open reading frames and 52 RNA genes.

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number MTIM00000000 . The version described here is the first version, MTIM01000000.

ACKNOWLEDGMENTS

We thank S. Vargas for technical assistance. This research was supported by the California Citrus Research Board. We sincerely thank the USDA-APHIS-PPQ CHRP field operation inspectors in Edinburg, Texas, for collection of the ACP-carrying “Ca. Liberibacter asiaticus” strain TX2351.
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.

REFERENCES

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Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 5Number 1513 April 2017
eLocator: 10.1128/genomea.00170-17

History

Received: 13 February 2017
Accepted: 16 February 2017
Published online: 13 April 2017

Contributors

Authors

Madhurababu Kunta
Texas A&M University–Kingsville Citrus Center, Weslaco, Texas, USA
Zheng Zheng
South China Agricultural University, Guangzhou, China
Fengnian Wu
South China Agricultural University, Guangzhou, China
John V. da Graca
Texas A&M University–Kingsville Citrus Center, Weslaco, Texas, USA
Jong-Won Park
Texas A&M University–Kingsville Citrus Center, Weslaco, Texas, USA
Xiaoling Deng
South China Agricultural University, Guangzhou, China
Jianchi Chen
USDA, ARS, San Joaquín Valley Agricultural Sciences Center, Parlier, California, USA

Notes

Address correspondence to Jianchi Chen, [email protected].

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