Genome Sequence Resource for Spiroplasma citri, Strain CC-2, Associated with Citrus Stubborn Disease in California

Spiroplasma citri is a bacterium that causes stubborn disease of citrus and infects other crops, ornamentals, and weeds. It is transmitted by leafhoppers in a circulative manner. Due to limited sequence data on S. citri, the bacterium was isolated from naturally infected Chinese cabbage grown on a farm in Fresno County, CA. DNA from S. citri CC-2 was extracted from a pure culture in LD8 and subjected to PacBio sequencing. Four contigs were obtained with a single circular chromosome of 1,709,192 bp and three plasmids of 40,210, 39,313, and 2,921 bp in size. The genome developed herein extends the sequence database of S. citri and is the first whole-genome sequence record of S. citri from California.

Tempus et Locus: a tool for extracting precisely dated viral sequences from GenBank, and its application to the phylogenetics of primate erythroparvovirus 1 (B19V)

The presence of data in the “collection_date” field of a GenBank sequence record is of great assistance in the use of that sequence for Bayesian phylogenetics using “tip-dating”. We presentTempus et Locus(TeL), a tool for extracting such sequences from a GenBank-formatted sequence database. TeL shows that 60% of viral sequences in GenBank have collection date fields, but that this varies considerably between species. Primate erythroparvovirus 1 (human parvovirus B19 or B19V) has only 40% of its sequences dated, of which only 112 are of more than 4 kb. 100 of these are from B19V sub-genotype 1a and were collected from a mere 6 studies conducted in 5 countries between 2002 and 2013. Nevertheless, Bayesian phylogenetic analysis of this limited set gives a date for the common ancestor of sub-genotype 1a in 1990 (95% HPD 1981-1996) which is in reasonable agreement with estimates of previous studies where collection dates have been assembled by more laborious methods of literature search and direct enquiries to sequence submitters. We conclude that although collection dates should become standard for all future GenBank submissions of virus sequences, accurate dating of ancestors is possible with even a small number of sequences if sampling information is high quality.