Xylella fastidiosa comparative genomic database is an information resource to explore the annotation, genomic features, and biology of different strains

Abstract

The Xylella fastidiosa comparative genomic database is a scientific resource with the aim to provide a user-friendly interface for accessing high-quality manually curated genomic annotation and comparative sequence analysis, as well as for identifying and mapping prophage-like elements, a marked feature of Xylella genomes. Here we describe a database and tools for exploring the biology of this important plant pathogen. The hallmarks of this database are the high quality genomic annotation, the functional and comparative genomic analysis and the identification and mapping of prophage-like elements. It is available from web site http://www.xylella.lncc.br.

Draft Genome Sequence of the Xylella fastidiosa CoDiRO Strain

“…The draft genome of X. fastidiosa CoDiRO consisted of a total of 2,507,614 bp (with a GC content of 51.8%), likely representing >95% of the full genomic sequence since other X. fastidiosa strains have genomes ranging from 2.39 to 2.73 Mbp ( 9 ).…”

Comparative genomic analysis of coffee-infecting Xylella fastidiosa strains isolated from Brazil

“…Comparative genomic analyses have been performed with a great variety of strains of this phytopathogen, providing clues that are helping to unravel the basis of genomic evolution and adaptation of these bacteria to interact with such a broad range of hosts and induce the various diseases attributed to X. fastidiosa strains Doddapaneni et al, 2006Doddapaneni et al, , 2007Varani et al, 2012). The present study brings to this puzzle, for the first time, genomic information regarding strains responsible for CLS -a pathogeny that has been known to occur in South America since 1997 (Paradela-Filho et al, 1997).…”

“…As a consequence of these efforts, one X. fastidiosa strain (9a5c), associated with CVC in Brazil, was the first plant bacterium to have its complete genome elucidated (Simpson et al, 2000). Sequencing efforts have been extended to other X. fastidiosa strains and, currently, draft or complete genomic sequences have been obtained for a variety of strains, obtained from different hosts, including almond trees (strains M12, M23 and Dixon), oleander (strain Ann-1), grapevine (strains Temecula1 and GB514), elderberry (strain EB92-1), oak (strain Griffin-1), mulberry (strain Mul-MD), sycamore (strain Sy-VA) and pear trees (strain PLS229) (Zhang et al, 2011;Varani et al, 2012;Chen et al, 2013;Guan et al, 2014a, b;Su et al, 2014).…”

“…Genomic sequences from these X. fastidiosa strains have been submitted to extensive in silico evaluations, assisting researchers to identify and categorize genome-wide DNA variations, as well as their influence on strain functional divergence (Doddapaneni et al, 2006;Varani et al, 2012). Multiple alignment of chromosomal sequences identified single nucleotide polymorphisms and indels that can now be used to estimate the relative similarity between the strains and their rates of genomic evolution, which seem to be different for each of them (Doddapaneni et al, 2006).…”

Characterization of the Xylella fastidiosa PD1671 Gene Encoding Degenerate c-di-GMP GGDEF/EAL Domains, and Its Role in the Development of Pierce’s Disease

“…DNA sequences were submitted to the X . fastidiosa comparative genomic database [ 30 ] and submitted to BLAST program. Tn5 insertion was also confirmed by PCR (polymerase chain reaction) ( Table 1 ).…”