The Prokaryote type strain report provides information on type-strains for over 18,000 species. We revised and expanded the report to make it easier to identify cases where sequencing or establishing type material would have the biggest impact on improving prokaryote taxonomy and accurate identification. These cases include species with designated type strains but without a sequenced type strain assembly and species without designated type material. We hope that the community will prioritize sequencing type strains for the former set of species (Table 1) and establishing a neotype or reftype, where applicable (as defined in Cuifo et al 2018) for the latter set (Table 2).
Other changes from the old format file are detailed in a recent genomes announce post.
|Scientific Name||Type material/co-identical strains||Assemblies|
|Burkholderia ubonensis||CCUG:48852, CIP:1070, …||308|
|Escherichia albertii||Albert 19982, BCCM/LMG:20976, …||181|
|Xanthomonas perforans||AATCC:BAA-983, DSM:18975, …||153|
|Listeria innocua||ATCC:33090, BCCM/LMG:11387, …||106|
|Streptococcus iniae||ATCC:29178, BCCM/LMG:14520, …||94|
|Vibrio lentus||CECT:5110, CIP:107166, …||87|
|Vibrio cyclitrophicus||ATCC:700982, BCCM/LMG:21359, …||83|
|Pseudomonas coronafaciens||BCCM/LMG:5060, CFPB:2216, …||77|
|Aliivibrio fischeri||ATCC:7744, BCCM/LMG:4414, …||66|
|Xanthomonas fragariae||ATCC:33239, BCCM/LMG:708, …||61|
Table 1. The top 10 candidate species for sequencing type-strains sorted by the number of assemblies. These have designated type strains but no type strain assembly. We generated the list by sorting by “number of assemblies from type materials per species”, then by decreasing “number of assemblies per taxon”, then filtering out “type materials and coidentical strains” = “na”.
Table 2. The top 10 candidates for proposing a reftype assembly, or neotype where applicable sorted by the number of assemblies. These species have no designated type strain. We generated the list by selecting for “type materials and coidentical strains” = “na”, “number of assemblies from type materials per species” = 0, and sorting by decreasing “number of assemblies per taxon”, then filtering out Candidatus.
Please contact email@example.com if you want to provide information about missing type-strains.