Comparative functional genomics of six Pectobacterium species reveals core and unique fitness determinants in potato tubers
- 1USDA-ARS
Abstract
Pectobacterium, a member of the soft rot Pectobacteriaceae (SRP), can cause highly destructive soft rot and blackleg diseases on many important crop and other host plants, particularly potato (Solanum tuberosum). Pectobacterium and its sister genus Dickeya have common virulence strategies, yet a highly diverse "open" pangenome containing many unique and hypothetical proteins. Here, we used randomly-barcoded transposon insertion-site sequencing (RB-TnSeq) on six Pectobacterium species to identify genes involved in bacterial survival and growth in potato tubers, as well as in minimal media conditions containing different single carbon sources. The strains evaluated varied broadly in genomic content as well as host plant and year of isolation. We focused on identifying conditionally essential genes across all strains tested, as well as genes that were important for growth in one or few of the tested strains. These results highlight the importance of many common genes involved in metabolism and maintaining cellular homeostasis, as well as shared and rare virulence traits including polygalacturonate catabolism, genes involved in polysaccharide biosynthesis, immunity proteins, and (for P. brasiliense) self-tolerance of the antibiotic carbapenem. This large dataset of conditionally essential genes, generated across Pectobacterium species during soft rot infection of the agriculturally important plant host potato, can serve as a rich dataset for further hypothesis generation and identification of important and/or novel in planta fitness factors.
Related
- Phylogeny and comparative chloroplast genomics reveal a rare new short-styled homostylous species of Primula (Primulaceae) from southwestern China
- Comparative genomics of Begonia chloroplasts: insights into molecular evolution, species identification, and phylogeny.
- Comparative Chloroplast Genomics Reveals Phylogenetic Relationships Among Korean Dioscorea Species
- Comparative population genomics reveals evolutionary potential and conservation priorities in three Procapra species.
- Complete Chloroplast Genome of Nepeta griffithii and Comparative Genomics of 10 Nepeta Species
BibTeX
@misc{helmann2026comparative,
title = {{Comparative functional genomics of six Pectobacterium species reveals core and unique fitness determinants in potato tubers}},
author = {T. C. Helmann and M. A. Karp and M. L. Daughtrey and L. E. Reid and P. V. Stodghill and M. J. Filiatrault},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.02.755747},
url = {https://www.biorxiv.org/content/10.64898/2026.10.02.755747v1},
note = {CC0},
}
RIS
TY - UNPB
TI - Comparative functional genomics of six Pectobacterium species reveals core and unique fitness determinants in potato tubers
AU - T. C. Helmann
AU - M. A. Karp
AU - M. L. Daughtrey
AU - L. E. Reid
AU - P. V. Stodghill
AU - M. J. Filiatrault
PY - 2026
DA - 2026/10/02
PB - bioRxiv
DO - 10.64898/2026.10.02.755747
UR - https://www.biorxiv.org/content/10.64898/2026.10.02.755747v1
AB - Pectobacterium, a member of the soft rot Pectobacteriaceae (SRP), can cause highly destructive soft rot and blackleg diseases on many important crop and other host plants, particularly potato (Solanum tuberosum). Pectobacterium and its sister genus Dickeya have common virulence strategies, yet a highly diverse "open" pangenome containing many unique and hypothetical proteins. Here, we used randomly-barcoded transposon insertion-site sequencing (RB-TnSeq) on six Pectobacterium species to identify genes involved in bacterial survival and growth in potato tubers, as well as in minimal media conditions containing different single carbon sources. The strains evaluated varied broadly in genomic content as well as host plant and year of isolation. We focused on identifying conditionally essential genes across all strains tested, as well as genes that were important for growth in one or few of the tested strains. These results highlight the importance of many common genes involved in metabolism and maintaining cellular homeostasis, as well as shared and rare virulence traits including polygalacturonate catabolism, genes involved in polysaccharide biosynthesis, immunity proteins, and (for P. brasiliense) self-tolerance of the antibiotic carbapenem. This large dataset of conditionally essential genes, generated across Pectobacterium species during soft rot infection of the agriculturally important plant host potato, can serve as a rich dataset for further hypothesis generation and identification of important and/or novel in planta fitness factors.
ER -