Poster: Biology & Disease Mgmt: Bacteriology
Evaluation of assembling methods on determination of whole genome sequence of Xylella fastidiosa blueberry bacterial leaf scorch strain
J. CHEN (1), C. Wallis (1), C. Chang (2) (1) USDA-ARS, U.S.A.; (2) University of Georgia, U.S.A.
Blueberry bacterial leaf scorch (BBLS) disease, a threat to blueberry production in the Southern USA and elsewhere, is caused by Xylella fastidiosa. Efficient control of BBLS requires knowledge of the pathogen. Research is challenging because Xylella fastidiosa is difficult to culture. This study was to study BBLS strain based on whole genome sequence analyses. A total of 13,739,924 sequence paired reads (mean = 251 bp) were generated from a BBLS strain isolated from Georgia, USA. Draft whole genome sequences (minimum contig size = 1,000 bp) were generated by both de novo assembling (DA) and referenced assembling (RA) using CLC Genomic Workbench. The DA draft genome was 2,537K (95 contigs). Sizes (bp) of RAs varied depending on reference genome sequences: 2,449K (39 contigs) with NC_010513 (M12, subsp. multiplex), 2,461K (70 contigs) with NC_010577 (M23, subsp. fastidiosa), 2,467K (96 contigs) with NC_004556 (Temecula1, subsp. fastidiosa), and 2,457K (180 contigs) with NC_002488 (9a5c, subsp. pauca). Percentage coverages were 99.0% (M12), 97.1% (M23), 97.1% (Temecula1) and 91.7% (9a5c). ANI (average nucleotide identity) values were 99.9 (M12), 97.5 (M23), 97.6 (Temecula1) and 96.2 (9a5c). These data suggest that 1) DA alone was promising yet contig number remained high; 2) For RA, reference genome sequences had significant influence on the BBLS genome size; And 3) BBLS strain is a member of subsp. multiplex based on its similarity to strain M12.