Draft genome assembly of Passalora sequoiae a needle blight pathogen on Leyland cypress
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DATA NOTE
Draft genome assembly of Passalora sequoiae a needle blight pathogen on Leyland cypress Warren E. Copes1* , Jorge Ibarra Caballero2, Ebrahiem Babiker1, Jane E. Stewart2, Valerie A. Orner3, Alan S. Windham4 and Renee S. Arias3
Abstract Objective: Passalora sequoiae (family Mycosphaerellaceae) causes a twig blight on Leyland cypress that requires numerous fungicide applications annually to minimize economic losses for ornamental plant nursery and Christmas tree producers. The objective was to generate a high-quality draft assembly of the genome of P. sequoiae as a resource for primer development to investigate genotype diversity. Data description: We report here the genome sequence of P. sequoiae 9LC2 that was isolated from Leyland cypress ‘Leighton Green’ in 2017 in southern Mississippi, USA. The draft genome was obtained using Pacific Biosciences (PacBio) SMRT and Illumina HiSeq 2500 sequencing. Illumina reads were mapped to PacBio assembled contigs to determine base call consistency. Based on a total of 44 contigs with 722 kilobase (kb) average length (range 9.4 kb to 3.4 Mb), the whole genome size was estimated at 31,768,716 bp. Mapping of Illumina reads to PacBio contigs resulted in a 1000 × coverage and were used to confirm accuracy of the consensus sequences. Keywords: Cupressocyparis leylandii, Genome annotation, Illumina, Leyland cypress, Needle blight, PacBio Objective Passalora sequoiae (Ellis & Everh.) Y.L. Guo & W.H. Hsieh (syn. Cercosporidium sequoiae (Ellis and Everh.) Baker and Partridge) is a fungus that causes needle blight on genera in the Cupressaceae, mainly Leyland cypress (x Cupressocyparis leylandii) [1, 2]. Disease symptoms of brown to gray needles appear during the spring and progressively appear throughout the tree canopy to result in unmarketable trees (Fig. 1). Annual fungicide application and crop loss inflict significant costs on the ornamental tree and Christmas tree industries [3–5]. The objective of this work was to sequence the whole genome of P. sequoiae using PacBio and Illumina to *Correspondence: [email protected] 1 USDA ARS Thad Cochran Southern Horticultural Laboratory, Poplarville, MS 39470, USA Full list of author information is available at the end of the article
assemble contigs. A lack of genetic information for this fungus prevents utilization of genetic tools to determine genetic diversity of isolates, potential differences in virulence, and ultimately the development of control practices. Currently, only three entries are listed for Passalora spp. in GenBank (NCBI), corresponding to the 18S rDNA gene of this fungus, a total of 5476 base pairs (bp). A problem in sampling P. sequoiae populations is that numerous dematiaceous hyphomycetes with morphologically similar conidia and conidioma are found in many regions (Figs. 2 and 3). Proper identification of these organisms is further complicated by the numerous name revisions over the last two decades [1, 6–12]. A further constraining factor is that only a small number of
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