PacBio Sequencing and Genome Assembly of Xanthomonas

Long read, SMRT sequencing (PacBio, Menlo Park, CA, United States) data were generated for five Xol strains and for the Xo strain X11-5A, to be used as an outgroup. DNA for SMRT sequencing was isolated by culturing strains on nutrient agar for 48 h then using the Genomic DNA buffer set and Genomic-tips according manufacturer instructions (Qiagen, Valencia, CA, United States). SMRT sequence was assembled using HGAP v4 (PacBio, Menlo Park, CA, United States). Genomes were circularized using circulator (Hunt et al., 2015 (link)). Assemblies and raw data have been deposited in NCBI (BioProject IDs PRJNA522807 and PRJNA522811; BioSample accessions SAMN03862116, SAMN02469650, SAMN10956066-68, SAMN10956070; raw sequencing files SRX5417793-98; Assembly accessions CP036251-56). Assembly CP036251 (X11-5A) replaces draft assembly GCF000212755.1 and assembly CP036253 (NCPPB4346) replaces draft assembly GCF001276975.1 (also in Bioproject PRJNA257008). Accessions for all genomes used in this study are listed in Supplementary Table S2.

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Lang J.M., Pérez-Quintero A.L., Koebnik R., DuCharme E., Sarra S., Doucoure H., Keita I., Ziegle J., Jacobs J.M., Oliva R., Koita O., Szurek B., Verdier V, & Leach J.E. (2019). A Pathovar of Xanthomonas oryzae Infecting Wild Grasses Provides Insight Into the Evolution of Pathogenicity in Rice Agroecosystems. Frontiers in Plant Science, 10, 507.

Publication 2019

SMRT sequencing Genomic DNA buffer set Genomic-tips

Agar Buffer Genomes Hgap Nutrient Smrt Strains

Corresponding Organization :

Other organizations : Laboratoire des Interactions Plantes Micro-Organismes, Institut de Recherche pour le Développement, Agropolis International, Colorado State University, Institut d'Économie Rurale, Université des Sciences, des Techniques et des Technologies de Bamako, Pacific Biosciences (United States), The Ohio State University, International Rice Research Institute

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Variable analysis

independent variables

SMRT sequencing (PacBio, Menlo Park, CA, United States) data
Five Xol strains
Xo strain X11-5A

dependent variables

Genome assemblies

control variables

Nutrient agar
Genomic DNA buffer set and Genomic-tips (Qiagen, Valencia, CA, United States)
HGAP v4 (PacBio, Menlo Park, CA, United States)
Circulator (Hunt et al., 2015)

controls

Xo strain X11-5A as an outgroup

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