Diseases of woody ornamentals and trees diseases. Cercosporidium blight of Leyland cypress and related conifers. Cercospora needle blight of Radiata pine in India. Species on other fungi, Pteridophyta and Gymnospermae. Cercosporoid fungi ( Mycosphaerellaceae) 1. The version described in this paper is the first version, WSQC01000000.īraun U, Nakashima C, Crous PW. This whole-genome project has been deposited in DDBJ/ENA/GenBank under the accession number WSQC00000000. Thirty-four proteins had blast hits to the phi-database. Of those 52, 9, 186, 3, 79 and 9 corresponded to auxiliary activity enzymes, carbohydrate esterases, glycoside hydrolases, polysaccharide lyases, glycosyl transferases and carbohydrate binding modules, respectively. Maker also identified 81 tRNA and 3.42% of the genome corresponded to short repetitive sequences.ĭbCAN2 identified 331 predicted proteins that had signatures as carbohydrate active enzymes (CAZymes). Of those, 10,576 genes were predicted to have proteins ≥ 50 amino acids. The total number of genes identified by Maker was 10,657. The MAKER pipeline included programs 1) RepeatMasker v.4.0.6 to mask interspersed repeats and low complexity DNA sequences 2) three gene predictors: GeneMark-ES SNAP, trained with Sordariomycetidae proteins from the Uniprot database and Augustus and 3) tRNAscan to identify tRNA genes in the genomic sequence. Structural annotation of the genome assembly was determined using MAKER v.2.31.8. A small percentage of gaps, 2–4 nt in length, approximately 2–3 gaps every 150,000 nt were observed using Illumina reads on the PacBio assembly, and they corresponded to microsatellites thus, in all cases, the PacBio assembly was chosen (Table 1). ![]() These reads were mapped to the PacBio assembled contigs resulting in 1011 x average coverage. A total of 244,368,646 reads with an average length of 148 nt after trimming were obtained from Illumina sequencing. The initial 19 contigs were manually split when necessary, rendering 44 contigs of 722,016 nt average and 44 x coverage. Subreads were corrected and de novo assembled. Bam files were processed using Finishing Module 20.0 of CLC_Bio Workbench v.12 (Qiagen LLC, Hilden, Germany). SMRTbell library was prepared, then sequenced on a PacBio Sequel sequencer at USDA-ARS, Stoneville, MS, USA. DNA was extracted and sheared to approximately 20 kb fragments. sequoiae 9LC2 was recovered from a Christmas tree near Hattiesburg, MS, USA. Mycosphaerellaceae was recently narrowed to 120 genera based on phylogenetic data. A further constraining factor is that only a small number of dematiaceous hyphomycetes have been included in genetic phylogenies using DNA loci, mRNA and proteins. ![]() ![]() Proper identification of these organisms is further complicated by the numerous name revisions over the last two decades. sequoiae populations is that numerous dematiaceous hyphomycetes with morphologically similar conidia and conidioma are found in many regions (Figs. in GenBank (NCBI), corresponding to the 18S rDNA gene of this fungus, a total of 5476 base pairs (bp).Ī problem in sampling P. Currently, only three entries are listed for Passalora spp. 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. sequoiae using PacBio and Illumina to assemble contigs. The objective of this work was to sequence the whole genome of P. Mapping of Illumina reads to PacBio contigs resulted in a 1000 × coverage and were used to confirm accuracy of the consensus sequences. 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. Illumina reads were mapped to PacBio assembled contigs to determine base call consistency. ![]() The draft genome was obtained using Pacific Biosciences (PacBio) SMRT and Illumina HiSeq 2500 sequencing. sequoiae 9LC2 that was isolated from Leyland cypress ‘Leighton Green’ in 2017 in southern Mississippi, USA. sequoiae as a resource for primer development to investigate genotype diversity. The objective was to generate a high-quality draft assembly of the genome of P. 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.
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